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April 17th, 2011, 02:49 PM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,944
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Re: Sequences at Genbank!
390 ****** genomes from New York meanwhile
I removed the presumble sequencing errors near the start
or end of segments
you can see the 11 Cancun mutations in 90% of NY sequences
another 4% is pre-cancun with 5 of those 11 markers
another 3% is "northern/LaGloria" with the 2 markers in segments 3,5
you can see the 11 vertical black bars for the 11 Cancun mutations
the 7 vertical white bars separate the 8 flu-segments
the lower ~15% has viruses from the 2nd wave, 2009/10
with additional mutations:
A1500G(2),G1688A(2),G171A(3),C1594T(3),G340A(4),A4 53T(4),T852C(4),G1171A(4),G532T(8)
mutation G1171A(4) appears also in this year's strains on a different genetical background
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April 18th, 2011, 05:11 AM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,944
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Re: Sequences at Genbank!
Managua in Nicaragua had only ~30% cancun and
~70% airplane/Newberry-SC/cancun2/
7% from the England/195/2009/04/28 strain with a new PB2
1% original
Code:
000000000000000111111111111111111111222 00000000000000000111111111111112222222 000000000000000000011111111111111222 00000000000000000001111111111111 000000000000000011111111 000000000000000000011111 000000000000 0000000000000000000
001444455568999001111222334555577779001 00111123345677779011233346667790111222 000133456667777888900001244556789001 00111233445556688890000112233344 011223333677889901111222 001111123446678889901113 011134456688 0001111112233346666
699115646738258174556678233026745782476 39114700587712791508704720292408699357 058814052376799058702558668267094895 47448123361335657732339274800908 434692455399148990348459 241123651783743480313589 100958950605 1570358893936640446
263016064995474776891951906929732350613 53127150469873152855837588928195303071 871733521641589822297564348761798341 18255018506188526969162212125586 421087257938662627532843 642846176171524653974842 528243250353 8122976907866734233
-codon-position-------------------------2 12 1 1 12 1 2 1 2 1 1 21 1 1 11 11 2 111 221 11 112 2 11 2 112 2 1 112 21 1 11 2 21 1 1 1 1 221111221 11 1 2 11 11 1 1 121 1
---Index--------------------------------CAGATACGGCTGATCGGCAACGCAAGGGAAAGCGCGCCG TCATCAAAGGCGGCTGGACTTACACCGAAGAAGCGACA AGTGTACTTCGACCCTGCAGGAGGCAGTTGATTACG CGACGTTTGCAGATGTCTATGCAGGCACTGCG CCCAGCAGTAAGTGTAGGCGAGCG CTACAATCGCAAAAATCAGGCCGA CACCCTGGGTAT GTCTGGAAAGCAGAGGACA
1 >A/******/index/2009/02/01 ....................................... ...................................... .................................... ................................ ........................ ........................ ............ ................... 0 0 , 0 0 1:>A/******/index/2009/02/01
2 >A/Managua/4064.01/2009/08/08 ....................................... ...................................... .................................... ................................ ...........A............ ........................ ............ ................... 14 1 , 14 1 2:>A/Managua/4064.01/2009/08/08
3 >A/Managua/585.01/2009/07/12 ......................................A ...................................... .................................... .............A..............C.T. ..A.A..............AGA.. ........A....G.......... ......A.A... .............G..... 21 14 , 21 14 3:>A/Managua/585.01/2009/07/12
4 >A/Managua/3244.01/2009/08/18 ..................................T...A CTG................................G.. .....GT.......T............C...C.... .............A..........A...C.T. ..A.A..............AGA.. ........A....G.......... ......A.A... .........A...G..... 28 26 , 28 26 4:>A/Managua/3244.01/2009/08/18
5 >A/Managua/3013.01/2009/10/11 ..................................T...A CTG................................G.. .....GT.......T............C...C.... .............A..........A...C.T. ..A.A..............AGA.. ........A....G.......... ......A.A... .........A...G..... 26 26 , 26 26 5:>A/Managua/3013.01/2009/10/11
6 >A/Managua/554.01/2009/08/10 ..................................T...A CTG................................G.. .....GT.......T............C...C.... .............A..........A...C.T. ..A.A..............AGA.. ........A....G.......... ......A.A... .........A...G..... 26 26 , 26 26 6:>A/Managua/554.01/2009/08/10
7 >A/Managua/2093.01/2009/08/18 ..................................T...A CTG................................G.. .....GT.......T............C...C.... .............A..........A...C.T. ..A.A..............AGA.. ........A....G.......... ......A.A... .........A...G..... 26 26 , 26 26 7:>A/Managua/2093.01/2009/08/18
8 >A/Managua/432.01/2009/08/22 ..................................T...A .TG................................G.. .....GT............................. .............A..........A...C.T. ..A.A..............AGA.. ........A....G.......... ......A.A... .............G..... 28 21 , 28 21 8:>A/Managua/432.01/2009/08/22
9 >A/Managua/3014.02/2009/09/11 ......................................A .TG................................G.. .....GT............................. .............A..........A...C.T. ..A.A..............AGA.. ........A....G.......... ......A.A... .............G..... 23 20 , 23 20 9:>A/Managua/3014.02/2009/09/11
10 >A/Managua/466.01/2009/07/27 ......................................A .TG................................G.. .....GT.........................C... .............AA.T.......A...C.T. ..A.A..............AGA.. ........A....G.......... ......A.A... .............G..... 23 23 , 23 23 10:>A/Managua/466.01/2009/07/27
11 >A/Managua/4451.02/2009/08/04 ......................................A .TG................................G.. .....GT.........................C... .............AA.T.......A...C.T. ..A.A..............AGA.. ........A....G.......... ......A.A... .............G..... 25 23 , 25 23 11:>A/Managua/4451.02/2009/08/04
12 >A/Managua/3421.02/2009/08/24 ......................................A .TG................................G.. .....GT............................. .............A..........A...C.T. ..A.A..............AGA.. ........A....G.......... ......A.A... .............G..... 28 20 , 28 20 12:>A/Managua/3421.02/2009/08/24
13 >A/Managua/4218.01/2009/08/17 ......................................A .TG................................G.. .....GT............................. .............A..........A...C.T. ..A.A..............AGA.. ........A....G.......... ......A.A... .............G..... 23 20 , 23 20 13:>A/Managua/4218.01/2009/08/17
14 >A/Managua/5708.01/2009/03/19 A...............A..GA.................A .....G........C....C...G.T...........C ...A..........................G....A ............CA..........A....ATA ....A..............A.A.. ........AA...G.C.....A.. ..T.TCA.A... .....AGG..AG.G..... 40 39 , 40 39 14:>A/Managua/5708.01/2009/03/19
15 >A/Managua/3246.01/2009/03/25 A...............A..GA.................A .....G........C....C...G.T...........C ...A..........................G....A ............CA..........A....ATA ....A..............A.A.. ........AA...G.C.....A.. ..T.TCA.A... .....AGG..AG.G..... 39 39 , 39 39 15:>A/Managua/3246.01/2009/03/25
16 >A/Managua/07193_09/2010/02/03 ................A.....................A ...............A.....................C ..............................G....A .............A..........A.....T. ....A..............A.A.. ........AA...G.C........ ......A.A... ...........G.G..... 30 20 , 30 20 16:>A/Managua/07193_09/2010/02/03
17 >A/Managua/5295.02/2009/07/23 ......................................A ...................................... ...................................A .............A................T. ....A..............A.A.. ........A....G.......... ......A.A... ...........G.G..... 19 13 , 19 13 17:>A/Managua/5295.02/2009/07/23
18 >A/Managua/2323.02/2009/08/18 .....................A..........T.....A .....................G................ .................................... T............A............G...T. ....A..............A.A.. ........A....G.........G ......A.AC.. .............G..... 25 18 , 25 18 18:>A/Managua/2323.02/2009/08/18
19 >A/Managua/12.01/2009/09/14 .....................A...A......T...T.. .............T.......G.........G...... .............Y...................... T......A.....A............R...T. ....A..............A.A.. ........A....G....A....G ......A.AC.. .............G..... 25 24 , 25 24 19:>A/Managua/12.01/2009/09/14
20 >A/Managua/1909.02/2009/09/12 .....................A...A......T...T.. .............T.......G.........G...... ..........................A......... T......A.....A............G...T. ....A..............A.A.. ........A....G....A....G ......A.AC.. .............G..... 26 24 , 26 24 20:>A/Managua/1909.02/2009/09/12
21 >A/Managua/3359.01/2009/08/12 .....................A..........T.....A .....................G.........G...... ..........................A......... T............A............G...T. ....A..............A.A.. ........A....G.........G ......A.AC.. .............G..... 20 20 , 20 20 21:>A/Managua/3359.01/2009/08/12
22 >A/Managua/4570.01/2009/08/16 .....................A..........T.....A .....................G.........G...... ..........................A......... T............A............G...T. ....A..............A.A.. ........A....G.........G ......A.AC.. .............G..... 22 20 , 22 20 22:>A/Managua/4570.01/2009/08/16
23 >A/Managua/2339.03/2009/08/11 ......................................A ...C........A......................... ............T....................... ..G..........A................T. ....A..............A.A.. ....G...A....G.....A.... ......A.A..C .............G..... 21 18 , 21 18 23:>A/Managua/2339.03/2009/08/11
24 >A/Managua/4063.01/2009/08/31 ......................................A ...C........A......................... .................................... ..G..........A................T. ....A..............A.A.. ....G...A....G.....A.... ......A.A..C .............G..... 20 17 , 20 17 24:>A/Managua/4063.01/2009/08/31
25 >A/Managua/4972.02/2009/09/10 ......A...C....A......................A ...........................G....A..... ........C...............T........... .A..........GA......A.........T. ....A..............A.AT. T.....C.A....G.......... T.....AAA... A............G..... 28 27 , 28 27 25:>A/Managua/4972.02/2009/09/10
26 >A/Managua/1419.02/2009/09/12 ......A...C....A......................A ...........................G....A..... ........C...............T........... .A..........GA......A.........T. ....A..............A.AT. T.....C.A....G.......... T.....AAA... A............G..... 27 27 , 27 27 26:>A/Managua/1419.02/2009/09/12
27 >A/Managua/287.01/2009/08/20 ..................G...................A ...................................... .A.................................. .............A................T. ....A........A.....A.A.. ........A....G.......... ......A.A... .............G..... 17 14 , 17 14 27:>A/Managua/287.01/2009/08/20
28 >A/Managua/4147.01/2009/08/22 ......................................A ...................................... .................................... .............A................T. ....A........A.....A.A.. ........A....G.......... ......A.A... .............G..... 19 12 , 19 12 28:>A/Managua/4147.01/2009/08/22
29 >A/Managua/4407.02/2009/07/27 ......................................A ...................................... .................................... .............A................T. ....A........A.....A.A.. ........A....G...G...... ......A.A... .............G..... 14 13 , 14 13 29:>A/Managua/4407.02/2009/07/27
30 >A/Managua/5115.01/2009/09/11 ..............T.......................A ...........A............T............. .................................... .............A.......T........T. ....A.......CA.....A.A.. .....G..A....G...G...... ......A.A... .............G..... 21 19 , 21 19 30:>A/Managua/5115.01/2009/09/11
31 >A/Managua/5258.02/2009/09/29 ..............T.......................A ...........A............T............. ....................A............... .............A.......T........T. ....A.......CA.....A.A.. .....G..A....G...G...... ......A.A... .............G..... 26 20 , 26 20 31:>A/Managua/5258.02/2009/09/29
32 >A/Managua/164.01/2009/08/18 ......................................A ...................................... .................................... .............A................T. ....A........A.....A.A.. ........A....G...G...... ......A.A... .............G..... 15 13 , 15 13 32:>A/Managua/164.01/2009/08/18
33 >A/Managua/5401.01/2009/09/16 ......................................A ...............A...................... .................................... .............A................T. ....A........A.....A.A.. ........A....G...G...... ......A.A... .............G..... 16 14 , 16 14 33:>A/Managua/5401.01/2009/09/16
34 >A/Managua/1984.02/2009/08/30 ......................................A ........A............................. .............T...................... .............A................T. ....A........A.....A.A.. ........A....G...G...... ......A.A... .............G..... 21 15 , 21 15 34:>A/Managua/1984.02/2009/08/30
35 >A/Managua/5212.04/2009/08/11 ......................................A ........A............................. .............T...................... .............A................T. ....A........A.....A.A.. ........A....G...G...... ......A.A... ...C.........G.A... 23 17 , 23 17 35:>A/Managua/5212.04/2009/08/11
36 >A/Managua/4702.04/2009/08/19 ......................................A ........A............................. .............T......R............... .............A................T. ....A........A.....A.A.. ........A....G...G...... ......A.A... ...C.........G.A... 18 18 , 18 18 36:>A/Managua/4702.04/2009/08/19
37 >A/Managua/5036.01/2009/08/11 ......................................A ........A............................. .............T...................... .............A................T. ....A........A.....A.A.. ........A....G...G...... ......A.A... ...C.........G.A... 18 17 , 18 17 37:>A/Managua/5036.01/2009/08/11
38 >A/Managua/2155.01/2009/08/17 .......A................G.............. ........A............................. ...............CAT..AT.............. .............A................T. ....A........A.....A.A.. ........A....G...G...... ......A.A... ...C.........G..... 27 21 , 27 21 38:>A/Managua/2155.01/2009/08/17
39 >A/Managua/435.01/2009/07/02 .......A................G.............. .......G.........G..C........A...T.... ...............CAT..AT.............. ...A............................ ........................ .......T................ ............ ................... 18 14 , 18 14 39:>A/Managua/435.01/2009/07/02
40 >A/Managua/5590.02/2009/09/14 .......AA...............G.............. .......G.........G..C........A...Y.... ...............CA................... ...A............................ .......................A .......T......G......... ............ ................... 16 14 , 16 14 40:>A/Managua/5590.02/2009/09/14
41 >A/Managua/171.01/2009/06/07 .......A................G.............. .......G.........G..C........A...T.... ...............CA................... ...A............................ ........................ .......T......G......... ............ ................... 12 12 , 12 12 41:>A/Managua/171.01/2009/06/07
42 >A/Managua/5453.01/2009/06/15 .......A................G.............. .......G.........G..C........A...T.... ...............C.................... ...A......G..................... ........................ .......T................ ............ ..............A.... 13 12 , 13 12 42:>A/Managua/5453.01/2009/06/15
43 >A/Managua/5221.03/2009/06/13 .......A................G.............. .......G.........G..C........A...T.... ...............C.................... ...A.C....G..................... ........................ .......T................ ............ ..............A.... 13 13 , 13 13 43:>A/Managua/5221.03/2009/06/13
44 >A/Managua/2978.04/2009/07/29 .......A................G......A....... .......G.........G..C........A...T.... ...........C...C.................... ...A.C....G..................... ........................ .......T....G........... ............ ..............A.... 18 16 , 18 16 44:>A/Managua/2978.04/2009/07/29
45 >A/Managua/4960.01/2009/07/28 .......A................G......A....... .......G.........G..C........A...T.... ...........C...C.................... ...A.C....G..................... ........................ .......T....G........... ............ ..............A.... 17 16 , 17 16 45:>A/Managua/4960.01/2009/07/28
46 >A/Managua/3214.04/2009/07/16 .......A................G......A....... .......G.........G..C........A...T.... ...........C...C.........G.......... ...A.C....G..................... T....................... .......T................ ............ ..............A.... 17 17 , 17 17 46:>A/Managua/3214.04/2009/07/16
47 >A/Managua/3231.02/2009/07/24 .......A................G......A....... .......G.........G..C........A...T.... ...........C...C.........G.......... ...A.C....G..................... T....................... .......T................ ............ ..............A.... 18 17 , 18 17 47:>A/Managua/3231.02/2009/07/24
48 >A/Managua/2152.01/2009/06/13 .......A................G.............. .......G.........G..C........A...T.... ...............C.................... ...A.C....G..................... ........................ .......T................ ............ ..............A.... 13 13 , 13 13 48:>A/Managua/2152.01/2009/06/13
49 >A/Managua/4085.02/2009/06/13 .......A................G.............. .......G.........G..C........A...T.... ...............C.................... ...A.C....G..................... ........................ .......T................ ............ ..............A.... 13 13 , 13 13 49:>A/Managua/4085.02/2009/06/13
50 >A/Managua/1973.02/2009/07/22 .......A................G.............. .......G.........G..C........A...T.... ...............C.................... ...A......G..................... ........................ .......T................ ............ ..............A.... 14 12 , 14 12 50:>A/Managua/1973.02/2009/07/22
51 >A/Managua/2729.02/2009/07/07 .......A................G.............. .......G.........G..C........A...T.... ...............C.................... ...A.............C.............. ........................ .......T................ ............ ................... 20 11 , 20 11 51:>A/Managua/2729.02/2009/07/07
52 >A/Managua/792.01/2009/06/13 .......A................G.............. .......G.........G..C........A...T.... ...............C.................... ...A.............C.............. ........................ .......T..............A. ............ ................... 12 12 , 12 12 52:>A/Managua/792.01/2009/06/13
53 >A/Managua/578.01/2009/06/12 .......A................G.............. .......G.........G..C........A...T.... ...............C.................... ...A.............C.............. ........................ .......T................ ............ ................... 11 11 , 11 11 53:>A/Managua/578.01/2009/06/12
54 >A/Managua/5586.01/2009/06/30 .......A................G.............. .......G.........G..C........A...T.... ...............C.................... ...A.............C.............. ........................ .......T................ ............ ................... 14 11 , 14 11 54:>A/Managua/5586.01/2009/06/30
55 >A/Managua/1455.01/2009/06/06 .......A................G.............. .......G.........G..C........A...T.... ...............C.................... ...A............................ ........................ .......T................ ............ ................... 11 10 , 11 10 55:>A/Managua/1455.01/2009/06/06
56 >A/Managua/109.01/2009/06/13 .......A................G.............. .......G.........G..C........R......A. ...............C.................... ...A.............C.............. ........................ .......T................ ............ ................... 12 11 , 12 11 56:>A/Managua/109.01/2009/06/13
57 >A/Managua/2330.02/2009/06/16 .......A................G.............. .......G.........G..C...............A. ...............C.................... ...A.....T...................... ........................ .......T................ ............ ................... 11 10 , 11 10 57:>A/Managua/2330.02/2009/06/16
58 >A/Managua/5307.01/2009/08/15 ...G...A................G.............. .......G.........G..C...............A. ...............C.................... ...A.....T...................... ...............G........ .......T...............C ............ ................... 20 13 , 20 13 58:>A/Managua/5307.01/2009/08/15
59 >A/Managua/3490.03/2009/07/14 ...G...A................G.............. .......G.........G..C...............A. ...............C.................... ...A.....T...................... ...............G........ .......T................ ............ ................... 16 12 , 16 12 59:>A/Managua/3490.03/2009/07/14
60 >A/Managua/2750.01/2009/06/05 .......A................G.............. ......GG.........G..C...............A. ...............C.................... ...A.....T...................... ........................ .......T................ ............ ........C.......... 12 12 , 12 12 60:>A/Managua/2750.01/2009/06/05
61 >A/Managua/167.01/2009/06/11 .......A................G.............. ......GG.........G..C...............A. ...............C.................... ...A.....T...................... ........................ .......T................ ............ ........C.......... 14 12 , 14 12 61:>A/Managua/167.01/2009/06/11
62 >A/Managua/2652.01/2009/06/05 .......A................G.............. ......GG.........G..C...............A. ...............C.................... ...A.....T...................... ........................ .......T................ ............ ........C.......... 12 12 , 12 12 62:>A/Managua/2652.01/2009/06/05
63 >A/Managua/516.01/2009/06/08 .......A................G.............. ......GG.........G..C...............A. ...............C.................... ...A.....T...................... ........................ .......T................ ............ ........C.......... 12 12 , 12 12 63:>A/Managua/516.01/2009/06/08
64 >A/Managua/4467.05/2009/06/01 .......A................G.............. ......GG.........G..C...............A. ...............C.................... ...A.....T...................... ........................ .......T................ ............ ........C.......... 12 12 , 12 12 64:>A/Managua/4467.05/2009/06/01
65 >A/Managua/4016.02/2009/06/05 .......A................G.............. ......GG.........G..C...............A. ...............C.................... ...A.....T...................... ........................ .......T................ ............ ........C.......... 12 12 , 12 12 65:>A/Managua/4016.02/2009/06/05
66 >A/Managua/168.02/2009/06/09 .......A................G.............. ......GG.........G..C...............A. ...............C.................... ...A.....T...................... ........................ .......T................ ............ ........C.......... 12 12 , 12 12 66:>A/Managua/168.02/2009/06/09
67 >A/Managua/4905.02/2009/06/05 .......A................G.............. .......G.........G..C...............A. ...............C.................... ...A.....T...................... ........................ .......T................ ............ ........C.......... 14 11 , 14 11 67:>A/Managua/4905.02/2009/06/05
68 >A/Managua/3119.01/2009/06/01 ..A....A................G.............. .......G.........G..C...............A. ............T..C.................... ...A.....T...................... ........................ .......T................ ............ ................... 12 12 , 12 12 68:>A/Managua/3119.01/2009/06/01
69 >A/Managua/5339.04/2009/07/27 ..A....A................G.............. .......G.........G..C.......G.......A. ...............C.............T...... ...A.....T...................... ........................ .......T................ ............ .................T. 15 14 , 15 14 69:>A/Managua/5339.04/2009/07/27
70 >A/Managua/265.01/2009/07/16 ..A....A................G.............. .......G.........GT.C.......G.......A. ...............C.............T...... ...A.....T...................... ........................ .......T................ ............ .................T. 17 15 , 17 15 70:>A/Managua/265.01/2009/07/16
71 >A/Managua/3225.03/2009/07/27 ..A....A................G.............. .......G.........GT.C.......G.......A. ...............C.............T...... ...A.....T...................... ........................ .......T................ ............ .................T. 17 15 , 17 15 71:>A/Managua/3225.03/2009/07/27
72 >A/Managua/5273.02/2009/06/20 ..A....A................G.............. .......G.........G..C...............A. ...............C.................... ...A.....T...................... ........................ .C.T...T................ ............ ....A.............. 14 14 , 14 14 72:>A/Managua/5273.02/2009/06/20
73 >A/Managua/462.01/2009/06/26 ..A....A................G.............. .......G.........G..C...............A. ...............C.................... ...A.....T...................... ........................ .C.T...T................ ............ ....A.............. 16 14 , 16 14 73:>A/Managua/462.01/2009/06/26
74 >A/Managua/5364.01/2009/07/21 ..A....A................G.............. .......G.........G..C...............A. ...............C.................... ...A.....T...................... ........................ .......T................ ............ ................... 15 11 , 15 11 74:>A/Managua/5364.01/2009/07/21
75 >A/Managua/1637.01/2009/06/13 ..A....A................G.............. .......G.........G..C...............A. ...............C.................... ...A.....T...................... ........................ .......T................ ............ ................... 12 11 , 12 11 75:>A/Managua/1637.01/2009/06/13
76 >A/Managua/0536N/2009/06/26 ..................G.....G.............. .......G.........G..C................. ...............C.................... ...A............................ ........................ .......T................ ............ ..A................ 12 9 , 12 9 76:>A/Managua/0536N/2009/06/26
77 >A/Managua/1127.02/2009/06/29 .......A................G.............. .......G.........G..C................. ...............C.................... ...A....A....................... ........................ .......T................ ............ ..A................ 13 10 , 13 10 77:>A/Managua/1127.02/2009/06/29
78 >A/Managua/655.02/2009/06/12 .......A................G.............. .......G.........G..C................. ...............C.................... ...A....A....................... ........................ .......T................ ............ ..A................ 10 10 , 10 10 78:>A/Managua/655.02/2009/06/12
79 >A/Managua/4514.03/2009/06/21 .......A................G.............. .......G.........G..C................. ...............C.................... ...A............................ ...G.................... .......T................ ............ ..A................ 13 10 , 13 10 79:>A/Managua/4514.03/2009/06/21
80 >A/Managua/5665.01/2009/06/22 .......A................G.............. .......G.........G..C................. ...............C.................... ...A............................ ...G.................... .......T.....G.......... ............ ..A................ 12 11 , 12 11 80:>A/Managua/5665.01/2009/06/22
81 >A/Managua/611.01/2009/06/25 .......A................G.............. .......G.........G..C................. ...............C.................... ...A............................ ...G.................... .......T................ ............ ..A................ 13 10 , 13 10 81:>A/Managua/611.01/2009/06/25
82 >A/Managua/4197.01/2009/07/06 .......A................G....T......... .......G.........G..C................. ...............C.................... ...A............................ ........................ .......T................ ............ ..A................ 15 10 , 15 10 82:>A/Managua/4197.01/2009/07/06
83 >A/Managua/1244.01/2009/08/28 .......A................G....T......... .......G.........G..C................. ...............C.................... ...A............................ ........................ .......T..............A. ............ ..A................ 26 11 , 26 11 83:>A/Managua/1244.01/2009/08/28
84 >A/Managua/WRAIR8964F/2009/06/06 .G.....A................G.............. .......G............C................. ...............C..................T. ...A............................ ........................ .......T................ ............ ..A................ 14 10 , 14 10 84:>A/Managua/WRAIR8964F/2009/06/06
85 >A/Managua/WRAIR8997F/2009/06/13 .G.....A................G.............. .......G............C................. ...............C..................T. ...A............................ ........................ ........A............... ............ ................... 26 9 , 26 9 85:>A/Managua/WRAIR8997F/2009/06/13
86 >A/Managua/5230.01/2009/08/05 .......A.........T......G..A.........T. .......G..T......G..C.T............... ...............C..G................. ...A...........C................ ................A....... ........................ ............ ................... 16 15 , 16 15 86:>A/Managua/5230.01/2009/08/05
87 >A/Managua/1256.04/2009/08/04 .......A.........T......G..A.........T. .......G..T......G..C.T............... ...............C..G................. ...A...........C................ ................A....... ........................ ............ ................... 17 15 , 17 15 87:>A/Managua/1256.04/2009/08/04
88 >A/Managua/65.02/2009/08/25 .......A.........T......G..A.........T. .......G..T......G..C.T............... ...............C..G................. ...A...........C................ ................A....... ........................ ............ ................... 22 15 , 22 15 88:>A/Managua/65.02/2009/08/25
89 >A/Managua/4736.02/2009/09/01 .......A................G.............. .......G..T......G..C................. ...............C.................... ...A...........C................ .................A...... ........................ ............ ................... 20 10 , 20 10 89:>A/Managua/4736.02/2009/09/01
90 >A/Managua/3435.01/2009/08/18 .....G.A...A.C..........G..........A... .......G.........G.................... ..A....C.......C.................... ...A.......A.................... .................A...... ..........G.....T....... ............ ................... 16 16 , 16 16 90:>A/Managua/3435.01/2009/08/18
91 >A/Managua/3434.02/2009/08/27 .....G.A...A.C..........G..........A... .......G.........G.................... ..A....C.......C.................... ...A.......A.................... .................A...... ..........G.....T....... ............ ................... 18 16 , 18 16 91:>A/Managua/3434.02/2009/08/27
92 >A/Managua/4757.02/2009/08/18 .....G.A...A.C..........G..........A... .......G.........G.................... ..A....C.......C.................... ...A.......A.................... .................A...... ..........G.....T....... ............ ................... 19 16 , 19 16 92:>A/Managua/4757.02/2009/08/18
93 >A/Managua/4606.06/2009/07/12 .....G.A...A.C..........G..........A... .......G.........G.................... ..A....C.......C.................... ...A.......A.................... .......................A ..........G.....T....... ............ ................... 16 16 , 16 16 93:>A/Managua/4606.06/2009/07/12
94 >A/Managua/2999.03/2009/08/20 .....G.A...A.C..........G..........A... .......G.........G.................... ..A....C.......C.................... ...A.......A.................... .................A...... ..........G.....T....... ............ ................... 16 16 , 16 16 94:>A/Managua/2999.03/2009/08/20
95 >A/Managua/989.01/2009/08/18 .....G.A...A.C..........G..........A... .......G.........G.................... ..A....C.......C.................... ...A.......A.................... .................A...... ..........G.....T....... ............ ................... 18 16 , 18 16 95:>A/Managua/989.01/2009/08/18
96 >A/Managua/5119.06/2009/08/11 .....G.A...A.C..........G..........A... .......G.........G.................... ..A....C.......C.................... ...A.......A.................... .................A...... ..........G.....T....... ............ ................... 18 16 , 18 16 96:>A/Managua/5119.06/2009/08/11
97 >A/Managua/209.01/2009/08/03 .......A...A.C..........G..........A... .......G.........G.................... ..A....C.......C.................... ...A............................ .................A...... ..........G............. ............ ................... 21 13 , 21 13 97:>A/Managua/209.01/2009/08/03
98 >A/Managua/4943.09/2009/07/06 .......A................G.............. .......G.A.......G.................... ...............C.................... ...A..............T...G....T.... ........................ ........................ ............ ................... 12 10 , 12 10 98:>A/Managua/4943.09/2009/07/06
99 >A/Managua/5248.03/2009/08/31 .......AA..............GG.............. .......G.A.......G.................... ...............C.................... ...A..............T...G....T.... ........................ .........T.............. .G.......... ................G.. 20 15 , 20 15 99:>A/Managua/5248.03/2009/08/31
100 >A/Managua/1356.03/2009/08/11 .......AA..............GG.............. .......G.A.......G.................... ...............C.................... ...A..............T...G....T.... ........................ .........T.............. .G.......... ................G.. 17 15 , 17 15 100:>A/Managua/1356.03/2009/08/11
101 >A/Managua/3438.02/2009/07/21 .......A.............A..G.............. .......G.A.......G.................... ...............C.................... ...A..............T...G....T.... ........................ ........................ .G.......... ................... 14 12 , 14 12 101:>A/Managua/3438.02/2009/07/21
102 >A/Managua/1836.02/2009/07/30 .......A.A...........A..G.............. .......G.A.......G.................... .........T.....C.................... ...A..............T...G....T.... ..............C......... ........................ .G.T........ .C................. 19 17 , 19 17 102:>A/Managua/1836.02/2009/07/30
103 >A/Managua/3083.01/2009/08/10 .......A.A...........A..G.............. .......G.A.......G.................... .........T.....C.................... ...A..............T...G....T.... ..............C......... ........................ .G.T........ .C................. 18 17 , 18 17 103:>A/Managua/3083.01/2009/08/10
104 >A/Managua/5227.04/2009/08/22 ....C..A.............A..G.............. .......G.A.......G........A........... ..........A....C.................... ...A..............TC..G....T.... ..............C......... ........................ .G.T......G. ................... 19 19 , 19 19 104:>A/Managua/5227.04/2009/08/22
105 >A/Managua/3507.01/2009/08/31 ....C..A.............A..G.............. .......G.A.......G........A..A........ ..........A....C.................... ...A..............TC..G....T.... ..............C......... ........................ .G.T......G. ................... 21 20 , 21 20 105:>A/Managua/3507.01/2009/08/31
106 >A/Managua/5399.04/2009/08/07 ....C..A.............A..G.............. .......G.A.......G........A........... ..........A....C.................... ...A..............TC..G....T.... ..............C......... ........................ .G.T......G. ................... 19 19 , 19 19 106:>A/Managua/5399.04/2009/08/07
107 >A/Managua/3642.04/2009/08/13 ....C..A.............A..G.............. .......G.A.......G........A........... ..........A....C.................... ...A..............TC..G....T.... ..............C......... ........................ .G.T......G. ................... 20 19 , 20 19 107:>A/Managua/3642.04/2009/08/13
108 >A/Managua/1264.03/2009/07/25 .......A................G.............. .......G.A.......G.................... ...............C.................... ...A..............T...G....T.... ........C............... ........................ ............ ................... 13 11 , 13 11 108:>A/Managua/1264.03/2009/07/25
109 >A/Managua/451.01/2009/08/03 .......A................G.............. .......G.A.......G.................... ...............C.................... ...A..............T...G....T.... ........................ ........................ ............ ................... 16 10 , 16 10 109:>A/Managua/451.01/2009/08/03
110 >A/Managua/4590.03/2009/07/22 ......................T...A...G..A..... ....T..G........AG.................... G......................A.........G.. ...A..C......................... .T................T..... ..................A..... ............ ................... 16 16 , 16 16 110:>A/Managua/4590.03/2009/07/22
111 >A/Managua/2275.01/2009/08/11 ......................T...A...G..A..... ....T..G........AG.................... G..................A...A.........G.. ...A..C......................... .T.......G........T..... ..................A..... ............ ................... 18 18 , 18 18 111:>A/Managua/2275.01/2009/08/11
112 >A/Managua/5747.02/2009/08/15 ......................T...A...G..A..... ....T..G........AG.................... G..................A...A.........G.. ...A..C......................... .T.......G........T..... ..G...............A..... ............ ................... 19 19 , 19 19 112:>A/Managua/5747.02/2009/08/15
113 >A/Managua/473.02/2009/08/15 ......................T...A...G..A..... ....T..G........AG.................... G..................A...A.........G.. ...A..C......................... .T.......G........T..... ..G...............A..... ............ ................... 19 19 , 19 19 113:>A/Managua/473.02/2009/08/15
114 >A/Managua/4012.01/2009/08/11 ......................T...A...G..A..... ....T..G........AG.................... G..................A...A.........G.. ...A..C......................... .T.......G........T..... ..................A..... ............ ................... 18 18 , 18 18 114:>A/Managua/4012.01/2009/08/11
115 >A/Managua/921.02/2009/08/13 ......................T...A...G..A..... ....T..G........AG.................... G..................A...A....C....G.. ...A..C......................... .T.......G........T..... ..................A..... ............ ................... 19 19 , 19 19 115:>A/Managua/921.02/2009/08/13
116 >A/Managua/527.04/2009/08/13 ......................T...A...G..A..... ....T..G........AG.................... G..................A...A....C....G.. ...A..C......................... .T.......G........T..... ..................A..... ............ ................... 19 19 , 19 19 116:>A/Managua/527.04/2009/08/13
117 >A/Managua/4747.01/2009/07/22 ......................T...A...G..A..... ....T..G........AG.................... G......................A.........G.. ...A..C......................... .T................T..... ..................A..... ............ ................... 16 16 , 16 16 117:>A/Managua/4747.01/2009/07/22
118 >A/Managua/4951.02/2009/07/24 .......A....G.......................... .......G.........G................A... .A..C............................... ...AA.........A..........T...... .....T..C.G............. ...........G............ ............ ................... 20 15 , 20 15 118:>A/Managua/4951.02/2009/07/24
119 >A/Managua/572.02/2009/09/05 .......A....G.......................... .......G.........G................A... ....C............................... ...AA.........A..........T...... .....T..C.G............. ...........G............ ............ ................... 22 14 , 22 14 119:>A/Managua/572.02/2009/09/05
120 >A/Managua/4935.03/2009/06/15 .......A....G.......................... .......G.........G................A... ....C.....................A......... ...AA.........A..........T...... .....T..C.G............. ...........G............ ............ ................... 17 15 , 17 15 120:>A/Managua/4935.03/2009/06/15
121 >A/Managua/1077.04/2009/08/05 .......A....................C.......... .......G.........G............G....... ........................T........... ...AA.........A................. .....T.....A............ ...........G............ ............ ............A.....C 15 14 , 15 14 121:>A/Managua/1077.04/2009/08/05
122 >A/Managua/3189.01/2009/06/29 .......A....................C.......... .......G.........G............G....... ........................T........... ...AA.........A................. .....T.....A............ ...........G............ ............ ............A.....C 15 14 , 15 14 122:>A/Managua/3189.01/2009/06/29
123 >A/Managua/5363.02/2009/06/13 .......A....................C.......... .......G.........G............G....... ........................T........... ...AA.........A................. .....T.....A............ ...........G............ ............ ............A.....C 14 14 , 14 14 123:>A/Managua/5363.02/2009/06/13
124 >A/Managua/1054.02/2009/08/16 .......A....................C.......... .......G.........G............G....... ........................T........... ...AA.........A................. .....T.....A............ ...Y.......G............ ............ ............A.....C 19 15 , 19 15 124:>A/Managua/1054.02/2009/08/16
125 >A/Managua/791.03/2009/06/25 .......A....................C.......... .......G.........G............G....... ........................T........... ...AA.........A................. .....T.....A............ ...........G............ ............ ............A.....C 14 14 , 14 14 125:>A/Managua/791.03/2009/06/25
126 >A/Managua/2604.02/2009/08/07 .......A....................C.......... .......G.........G............G....... ........................T........... ...AA.........A........A........ .....T.....A............ ...........G............ ............ ............A.....C 21 15 , 21 15 126:>A/Managua/2604.02/2009/08/07
127 >A/Managua/3467.01/2009/07/24 .......A....................C.......... .......G.........G............G....... ........................T........... ...AA.........A........A........ .....T.....A............ ...........G............ ............ ............A.....C 17 15 , 17 15 127:>A/Managua/3467.01/2009/07/24
128 >A/Managua/4209.04/2009/08/28 .......A....................C.......... .......G.........G............G....... ........................T........... ...AA.........A................. .....T.....A............ ...........G............ ............ ............A.....C 20 14 , 20 14 128:>A/Managua/4209.04/2009/08/28
129 >A/Managua/3275.01/2009/08/15 .......A....................C.......... .......G.........G............G....... ........................T........... ...AA.........A................. .....T.....A............ ...........G............ ............ ............A.....C 21 14 , 21 14 129:>A/Managua/3275.01/2009/08/15
130 >A/Managua/2958.01/2009/09/02 .......A....................C.......... .......G.........G............G....... ........................T........... ...AA.........A................. .....T.....A............ ...........G............ ............ ............A.....C 17 14 , 17 14 130:>A/Managua/2958.01/2009/09/02
131 >A/Managua/5235.03/2009/07/02 .......A....................C.......... .......G.........G............G....... ........................T........... ...AA.........A................. .....TC....A............ ...........G............ ............ ............A.....C 17 15 , 17 15 131:>A/Managua/5235.03/2009/07/02
132 >A/Managua/5953.01/2009/09/08 .......A....................C.......... .......G.........G............G....... ........................T........... ...AA.........A................. .....TC....A............ ...........G............ ............ ............A.....C 16 15 , 16 15 132:>A/Managua/5953.01/2009/09/08
133 >A/Managua/4186.02/2009/08/12 .......A....................C.......... .......G.........G............G....... ......................A.T........... ...AA.........A................. .....T.A...A............ ...........G........T... ............ ............A.....C 21 17 , 21 17 133:>A/Managua/4186.02/2009/08/12
134 >A/Managua/5595.03/2009/08/08 .......A....................C.......... .......G.........G............G....... ......................A.T........... ...AA.........A................. .....T.A...A............ ...........G........T... ............ ............A.....C 21 17 , 21 17 134:>A/Managua/5595.03/2009/08/08
---Index--------------------------------CAGATACGGCTGATCGGCAACGCAAGGGAAAGCGCGCCG TCATCAAAGGCGGCTGGACTTACACCGAAGAAGCGACA AGTGTACTTCGACCCTGCAGGAGGCAGTTGATTACG CGACGTTTGCAGATGTCTATGCAGGCACTGCG CCCAGCAGTAAGTGTAGGCGAGCG CTACAATCGCAAAAATCAGGCCGA CACCCTGGGTAT GTCTGGAAAGCAGAGGACA
-codon-position-------------------------2 12 1 1 12 1 2 1 2 1 1 21 1 1 11 11 2 111 221 11 112 2 11 2 112 2 1 112 21 1 11 2 21 1 1 1 1 221111221 11 1 2 11 11 1 1 121 1
000000000000000111111111111111111111222 00000000000000000111111111111112222222 000000000000000000011111111111111222 00000000000000000001111111111111 000000000000000011111111 000000000000000000011111 000000000000 0000000000000000000
001444455568999001111222334555577779001 00111123345677779011233346667790111222 000133456667777888900001244556789001 00111233445556688890000112233344 011223333677889901111222 001111123446678889901113 011134456688 0001111112233346666
699115646738258174556678233026745782476 39114700587712791508704720292408699357 058814052376799058702558668267094895 47448123361335657732339274800908 434692455399148990348459 241123651783743480313589 100958950605 1570358893936640446
263016064995474776891951906929732350613 53127150469873152855837588928195303071 871733521641589822297564348761798341 18255018506188526969162212125586 421087257938662627532843 642846176171524653974842 528243250353 8122976907866734233
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April 18th, 2011, 08:43 AM
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Senior User
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Join Date: Jun 2007
Posts: 2,963
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Re: Sequences at Genbank!
Looking at the Genbank InDRe/Chihuahua and the GISAID CDC/US sequences, I aligned the last large submission from the CDC and found a very distinct group of 12 sequences. I deleted the mutations they all shared and what I'm seeing is one-loosely defined clade and one very well-defined clade.
After the alignment, I wanted to see if the Chihuahua sequences were similar, so I took out all the commonly shared mutations from those, too.
For discussion purposes, I'll consider the loosely-defined group chi1 and the well-defined group chi2.
Chi1 only appears in the US and shares these mutations: G16A, C473A, G1400A, G1546A
Chi2 appears in the US and Mexico. The 3 full InDRE/1945,46,47 sequences and 5 from the US share mutations: C135T, G207A, T462A, A489C, A1215G.
I'm currently searching for any sequences collected before Jan. 2011 that share any 2 or more of these mutations.
Since I have no scientific background, I welcome anyone to double checking my findings.
__________________
The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918
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April 19th, 2011, 11:33 PM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,944
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Re: Sequences at Genbank!
Thailand pH1N1 HA , all mutations
Code:
00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000011111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
00000000000000000000000000000000000000011111111111111111111111111111111111111111111222222222222222222222222333333333333333333333333333444444444444444444444444444445555555555555555555555555555555566666666666666666666666666666666667777777777777777777777777888888888888888888888888888888888888899999999999999999999999999900000000000000000000000000111111111111111111111111122222222222222222222222233333333333333333333334444444444444444444444555555555555555555555666666666666666666666666677
00111222222333334444444566677777888999900001111222222244444455556666777788888889999122344455566666667788999000001123334445556667788999001111222333445566777788899990001111122334444555556666677899900000112222344555666677778889999990001111122233334555556779000001112222333344555556677777888899900012233344445567778889999900011111223344455566788899001111224446677777889999901113344445666667788999900112245566666788889990012233444566677888899001111223344566677789122355667778888899999999900
46136124689246790234578834923478124068925693679013458901245804892358124701356890239058203927913456892325078012385840280581240375815039890378346235071913457838902352470356957016789235890137837814803578290147502578156914783470567895781467912635688034697373013470362359024769125890503469045817803681403423684532483571346835823467695814736958104628170389250567801269581345762480945896013692512346923130912902358502342453802507039547813256846690258482956703467845004036585782568912345678901
-codon-position---------------------------------1 211 1 21221 1 1 12 2 1 1 122 1 2 1122 2 1 122 2 1 11 12 1 1 1 2 2 1 11 1 21 2 12122 2 1 12 2 221 1 1 1 122 1 1 1 2 1 21 1 1 2 1 1 1 2 22 12 1 12 2 1 1 1 212 12 21 1 112 222 2 2 12 2 2 212 1 1 1 1 22 12 2 1 121 2 121 1 12 1 1 11 1 2 21 1 1 21 12 2 1 2 2 1 12 2 1 2 2 12 1 1 1 1 2 2 1 1 1 2 1 2 21 2 11 1 2 1 12 1 112 22 11 1 122 2 2 12 12 12
---Index----------------------------------------AGTCGTCGTTACTTGAACGCAATTTATTCACGCATATTACAGCAAGATGAACTATTACCCAGAGTACGACACACAGAGGGAGTTTCAATGTCCCCCACGCGCCCTATTAGTAAGCAATGTGGCAGAAGAAGGTAGACGATCATCTGAAGTCCAAAACAAATTACATAAGATCCAGCATTTGTAGGGAAGCCTCTTTTGGCCAGTCTCGAGGTTGACGAAGAGGACAATACAAGGATAGAGACTTCAAGGGACCCTACGATACGGAAAGTATCTTATACGCTTCTACTTGCAGTTCCAGTAGAAAAAAAACATGCGGCCTGGGTCCGATCATGCCTCAGGGGAACTCTAAGGGCTGTGCGATTAATCTGTGTCGAGACCCAAAAGTATAGTTCGCATACGACCTCCCTGGACTAAGGCACGTCCCACCTAAGATGCTGCCCAACGGACAGGAGCAGGCCTAGGTCCTTTCAGTGATATGTATTTAA
1 >A/******/index/2009/02/01 ..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... 0 0 , 0 0 1:>A/******/index/2009/02/01
2 >A/Thailand/CU-H122/2009,2009/07/04 -.............................................................................................................................................................................................................................................................................................................................................------------------------------------------------------------------------------------------------------------------------------------------------------- 152 152 , 0 0 2:>A/Thailand/CU-H122/2009,2009/07/04
3 >A/Thailand/CU-H429/2009,2009/08/20 ................................................................................................................................................................................................................................................................................................................................................................................................................................T.................................................................... 1 1 , 1 1 3:>A/Thailand/CU-H429/2009,2009/08/20
4 >A/Thailand/CU-H128/2009,2009/07/06 .........................................................................................................................................................................................................................................................................................................T......................................................................................................................T.................................................................... 2 2 , 2 2 4:>A/Thailand/CU-H128/2009,2009/07/06
5 >A/Thailand/CU-H132/2009,2009/07/06 .........................................................................................................................................................................................................................................................................................................T......................................................................................................................T.................................................................... 2 2 , 2 2 5:>A/Thailand/CU-H132/2009,2009/07/06
6 >A/Thailand/CU-H133/2009,2009/07/06 .........................................................................................................................................................................................................................................................................................................T......................................................................................................................T.................................................................... 2 2 , 2 2 6:>A/Thailand/CU-H133/2009,2009/07/06
7 >A/Thailand/CU-H134/2009,2009/07/07 .........................................................................................................................................................................................................................................................................................................T......................................................................................................................T.................................................................... 2 2 , 2 2 7:>A/Thailand/CU-H134/2009,2009/07/07
8 >A/Thailand/CU-H139/2009,2009/07/07 .........................................................................................................................................................................................................................................................................................................T......................................................................................................................T.................................................................... 2 2 , 2 2 8:>A/Thailand/CU-H139/2009,2009/07/07
9 >A/Thailand/CU-H203/2009,2009/07/13 .........................................................................................................................................................................................................................................................................................................T......................................................................................................................T.................................................................... 2 2 , 2 2 9:>A/Thailand/CU-H203/2009,2009/07/13
10 >A/Thailand/CU-H216/2009,2009/07/15 --------------...........................................................................................................................................................................................................................................................................................T......................................................................................................................T.................--------------------------------------------------- 67 67 , 2 2 10:>A/Thailand/CU-H216/2009,2009/07/15
11 >A/Thailand/CU-H300/2009,2009/07/26 .........................................................................................................................................................................................................................................................................................................T......................................................................................................................T.................................................................... 2 2 , 2 2 11:>A/Thailand/CU-H300/2009,2009/07/26
12 >A/Thailand/CU-H302/2009,2009/07/27 .........................................................................................................................................................................................................................................................................................................T......................................................................................................................T.................................................................... 2 2 , 2 2 12:>A/Thailand/CU-H302/2009,2009/07/27
13 >A/Thailand/CU-H393/2009,2009/08/14 .........................................................................................................................................................................................................................................................................................................T......................................................................................................................T.................................................................... 2 2 , 2 2 13:>A/Thailand/CU-H393/2009,2009/08/14
14 >A/Thailand/CU-H427/2009,2009/08/19 .........................................................................................................................................................................................................................................................................................................T......................................................................................................................T.................................................................... 2 2 , 2 2 14:>A/Thailand/CU-H427/2009,2009/08/19
15 >A/Thailand/CU-H874/2009,2009/11/02 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------...................................................................................................................................T...............................------------------------------------------------------------------------------------------------------------------------------------------------------------ 323 323 , 1 1 15:>A/Thailand/CU-H874/2009,2009/11/02
16 >A/Thailand/CU-H243/2009,2009/07/17 ...................................................................................................................................................................................................................A.....................................................................................T......................................................................................................................T.................................................................... 3 3 , 3 3 16:>A/Thailand/CU-H243/2009,2009/07/17
17 >A/Thailand/CU-H109/2009,2009/07/03 -..................................................................................................................................................................................................................A.....................................................................................T....................................------------------------------------------------------------------------------------------------------------------------------------------------------- 154 154 , 2 2 17:>A/Thailand/CU-H109/2009,2009/07/03
18 >A/Thailand/CU-H119/2009,2009/07/04 ...................................................................................................................................................................................................................A.....................................................................................T...................................-------------------------------------------------------------------------------------------------------------------------------------------------------- 154 154 , 2 2 18:>A/Thailand/CU-H119/2009,2009/07/04
19 >A/Thailand/CU-H130/2009,2009/07/06 ...................................................................................................................................................................................................................A............................................................................................................................................................................................................T.................................................................... 2 2 , 2 2 19:>A/Thailand/CU-H130/2009,2009/07/06
20 >A/Thailand/CU-H491/2009,2009/08/01 ...................................................................................................................................................................................................................A............................................................................................................................................................................................................T.................................................................... 2 2 , 2 2 20:>A/Thailand/CU-H491/2009,2009/08/01
21 >A/Thailand/CU-H952/2009,2009/11/17 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------.............................................A.....................................................................................................................------------------------------------------------------------------------------------------------------------------------------------------------------------ 323 323 , 1 1 21:>A/Thailand/CU-H952/2009,2009/11/17
22 >A/Thailand/CU-H1039/2009,2009/12/01 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A.....................................................................................................................------------------------------------------------------------------------------------------------------------------------------------------------------------ 368 368 , 1 1 22:>A/Thailand/CU-H1039/2009,2009/12/01
23 >A/Thailand/CU-H1065/2009,2009/12/04 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------....................................A.....................................................................................................................------------------------------------------------------------------------------------------------------------------------------------------------------------ 332 332 , 1 1 23:>A/Thailand/CU-H1065/2009,2009/12/04
24 >A/Thailand/CU-H1224/2010,2010/01/13 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------.............................................A.....................................................................................................................------------------------------------------------------------------------------------------------------------------------------------------------------------ 323 323 , 1 1 24:>A/Thailand/CU-H1224/2010,2010/01/13
25 >A/Thailand/CU-H1256/2010,2010/01/18 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------.............................................A.....................................................................................................................------------------------------------------------------------------------------------------------------------------------------------------------------------ 323 323 , 1 1 25:>A/Thailand/CU-H1256/2010,2010/01/18
26 >A/Thailand/CU-H1301/2010,2010/01/23 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------.............................................A.....................................................................................................................------------------------------------------------------------------------------------------------------------------------------------------------------------ 323 323 , 1 1 26:>A/Thailand/CU-H1301/2010,2010/01/23
27 >A/Thailand/CU-H1310/2010,2010/01/25 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------.............................................A.....................................................................................................................------------------------------------------------------------------------------------------------------------------------------------------------------------ 323 323 , 1 1 27:>A/Thailand/CU-H1310/2010,2010/01/25
28 >A/Thailand/CU-H1313/2010,2010/01/25 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------.............................................A.....................................................................................................................------------------------------------------------------------------------------------------------------------------------------------------------------------ 323 323 , 1 1 28:>A/Thailand/CU-H1313/2010,2010/01/25
29 >A/Thailand/CU-H1351/2010,2010/01/28 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------.............................................A.....................................................................................................................------------------------------------------------------------------------------------------------------------------------------------------------------------ 323 323 , 1 1 29:>A/Thailand/CU-H1351/2010,2010/01/28
30 >A/Thailand/CU-H104/2009,2009/07/02 ...................................................................................................................................................................................................................A.....................................................G......................................................................................................................................................T.................................................................... 3 3 , 3 3 30:>A/Thailand/CU-H104/2009,2009/07/02
31 >A/Thailand/CU-H75/2009,2009/06/30 ...................................................................................................................................................................................................................A.....................................................G....................................................................------------------------------------------------------------------------------------------------------------------------------------------------------- 153 153 , 2 2 31:>A/Thailand/CU-H75/2009,2009/06/30
32 >A/Thailand/CU-H88/2009,2009/07/01 ...................................................................................................................................................................................................................A.....................................................G...................................................................-------------------------------------------------------------------------------------------------------------------------------------------------------- 154 154 , 2 2 32:>A/Thailand/CU-H88/2009,2009/07/01
33 >A/Thailand/CU-H126/2009,2009/07/06 ...................................................................................................................................................................................................................A.....................................................G...................................................................-------------------------------------------------------------------------------------------------------------------------------------------------------- 154 154 , 2 2 33:>A/Thailand/CU-H126/2009,2009/07/06
34 >A/Thailand/CU-H140/2009,2009/07/07 ...................................................................................................................................................................................................................A.....................................................G......................................................................................................................................................T.................................................................... 3 3 , 3 3 34:>A/Thailand/CU-H140/2009,2009/07/07
35 >A/Thailand/CU-H143/2009,2009/07/07 ...................................................................................................................................................................................................................A.....................................................G......................................................................................................................................................T................................------------------------------------ 39 39 , 3 3 35:>A/Thailand/CU-H143/2009,2009/07/07
36 >A/Thailand/CU-H199/2009,2009/07/13 ...................................................................................................................................................................................................................A.....................................................G......................................................................................................................................................T.................................................................... 3 3 , 3 3 36:>A/Thailand/CU-H199/2009,2009/07/13
37 >A/Thailand/CU-H313/2009,2009/07/29 ...................................................................................................................................................................................................................A.....................................................G......................................................................................................................................................T.................................................................... 3 3 , 3 3 37:>A/Thailand/CU-H313/2009,2009/07/29
38 >A/Thailand/CU-H88/2009,2009/08/ ...................................................................................................................................................................................................................A.....................................................G......................................................................................................................................................T.................................................................... 3 3 , 3 3 38:>A/Thailand/CU-H88/2009,2009/08/
39 >A/Thailand/CU-H137/2009,2009/07/07 ...................................................................................................................................................................................................................A.....................................................G.............................................................C........................................................................................T.................................................................... 4 4 , 4 4 39:>A/Thailand/CU-H137/2009,2009/07/07
40 >A/Thailand/THB0389/2009,2009/07/13 ...................................................................................................................................................................................................................A.....................................................G..........................................................................................................................A...........................T.................................................................... 4 4 , 4 4 40:>A/Thailand/THB0389/2009,2009/07/13
41 >A/Thailand/THB0411/2009,2009/07/16 ...................................................................................................................................................................................................................A.....................................................G..........................................................................................................................A...........................T.................................................................... 4 4 , 4 4 41:>A/Thailand/THB0411/2009,2009/07/16
42 >A/Thailand/THB0421/2009,2009/07/20 ...................................................................................................................................................................................................................A.....................................................G..........................................................................................................................A...........................T.................................................................... 4 4 , 4 4 42:>A/Thailand/THB0421/2009,2009/07/20
43 >A/Thailand/CU-B938/2009,2009/08/ G..................................................................................................................................................................................................................A.....................................................G..........................................................................................................................A...........................T...............................................................----- 10 10 , 5 5 43:>A/Thailand/CU-B938/2009,2009/08/
44 >A/swine/Thailand/CU-RA9/2009,2009/11/ ...................................................................................................................................................................................................................A.....................................................G.....................................................................................................................A....A...........................T.................................................................... 5 5 , 5 5 44:>A/swine/Thailand/CU-RA9/2009,2009/11/
45 >A/Thailand/THB0408/2009,2009/07/15 .........................................................................................A.........................................................................................................................A..................G..................................G..........................................................................................................................A...........................T.................................................................... 6 6 , 6 6 45:>A/Thailand/THB0408/2009,2009/07/15
46 >A/Thailand/THB0405/2009,2009/07/15 ..C......................................................................................A.........................................................................................................................A..................G..................................G..........................................................................................................................A...........................T.................................................................... 7 7 , 7 7 46:>A/Thailand/THB0405/2009,2009/07/15
47 >A/Thailand/CU-H276/2009,2009/07/ ----.....................................................................................A...............................A.........................................................................................A.....................................................G.................................................................................................................C....................................T.................................................................... 10 10 , 6 6 47:>A/Thailand/CU-H276/2009,2009/07/
48 >A/Thailand/34-9943/2010,2010/07/14 -------------------------------------------------------------------------------------------------------------------------------....................................................................................A.............................G..............------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 358 358 , 2 2 48:>A/Thailand/34-9943/2010,2010/07/14
49 >A/Nonthaburi/102/2009,2009// -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.G...............................................................................------------------------------------------------------------------------------------------------------------------------------------- 405 405 , 1 1 49:>A/Nonthaburi/102/2009,2009//
50 >A/Thailand/PMKE0009/2009,2009/08/28 ...................................................................................................................................................................................................................A............................................................................................................................................................................................................T.............................................C...................... 3 3 , 3 3 50:>A/Thailand/PMKE0009/2009,2009/08/28
51 >A/Thailand/C602/2010,2010/01/26 ...................................................................................................................................................................................................................A..................................................................................................................................................A.........................................................T.................................................................... 3 3 , 3 3 51:>A/Thailand/C602/2010,2010/01/26
52 >A/Bangkok/INS428/2010,2010/03/04 .............................................................................................................................................G.................................T...................................A..................................................................................................................................................A.........................................................T.................................................................... 5 5 , 5 5 52:>A/Bangkok/INS428/2010,2010/03/04
53 >A/Thailand/CU-H2293/2010,2010/09/02 ----------------------------------------------------------------------......................................................A................G.....................................................................A.........................................................................................................................-------------------------------------------------------------------------------------------------------------------------------------------------------- 225 225 , 3 3 53:>A/Thailand/CU-H2293/2010,2010/09/02
54 >A/Thailand/CU-H2079/2010,2010/07/07 ---------------------------------------------------------------------------------------------------------...................A................G.....................................................................A.........................................................................................................................-------------------------------------------------------------------------------------------------------------------------------------------------------- 260 260 , 3 3 54:>A/Thailand/CU-H2079/2010,2010/07/07
55 >A/Thailand/CU-H2085/2010,2010/07/07 ------------------------------------------------------------------------------------........................................A................G.....................................................................A...........................................G.............................................................................-------------------------------------------------------------------------------------------------------------------------------------------------------- 240 240 , 4 4 55:>A/Thailand/CU-H2085/2010,2010/07/07
56 >A/Thailand/CU-H1786/2010,2010/03/20 ................................................................................................................................................................................................T..................A..................................................................................................................................................A..........................G..............................T.................................................................... 5 5 , 5 5 56:>A/Thailand/CU-H1786/2010,2010/03/20
57 >A/Thailand/CU-B2357/2010,2010/04/20 ................................................................................................................................................................................................T..................A..................................................................................................................................................A..........................G..............................T.................................................................... 5 5 , 5 5 57:>A/Thailand/CU-B2357/2010,2010/04/20
58 >A/Thailand/CU-H354/2009,2009/08/08 ...................................................................................................................................................................................................................A..............................................................................................C..................T..........................................................................................T.................................................................... 4 4 , 4 4 58:>A/Thailand/CU-H354/2009,2009/08/08
59 >A/Thailand/CU-C161/2009,2009/08/26 .........................................................T.........................................................................................................................................................A...............................................................................................................................................................................G............................T.................................................................... 4 4 , 4 4 59:>A/Thailand/CU-C161/2009,2009/08/26
60 >A/Thailand/CU-H910/2009,2009/11/09 .........................................................T.........................................................................................................................................................A...............................................................................................................................................................................G............................T.................................................................... 4 4 , 4 4 60:>A/Thailand/CU-H910/2009,2009/11/09
61 >A/Thailand/CU-H1222/2010,2010/01/13 .........................................................T.........................................................................................................................................................A...............................................................................................................................................................................G............................T.................................................................... 4 4 , 4 4 61:>A/Thailand/CU-H1222/2010,2010/01/13
62 >A/Thailand/CU-H847/2009,2009/10/26 .........................................................T.........................................................................................................................................................A...............................................................................................................................................................................G.........A..................T.................................................................... 5 5 , 5 5 62:>A/Thailand/CU-H847/2009,2009/10/26
63 >A/Thailand/CU-H982/2009,2009/11/23 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------.............................................A...............................................................................................................A.....------------------------------------------------------------------------------------------------------------------------------------------------------------ 324 324 , 2 2 63:>A/Thailand/CU-H982/2009,2009/11/23
64 >A/Thailand/H1255/2010,2010/01/18 ...................................................................................................................................................................................................................A.........................................T...............................................................A.....................................................................G............................T.................................................................... 5 5 , 5 5 64:>A/Thailand/H1255/2010,2010/01/18
65 >A/Nonthaburi/102/2009,2009/05/ .................................................................................................................................G............................................................................................................................................................................................................................................................G.................................T.................................................................... 3 3 , 3 3 65:>A/Nonthaburi/102/2009,2009/05/
66 >A/Thailand/104/2009,2009/05/06 .................................................................................................................................G............................................................................................................................................................................................................................................................G.................................T.................................................................... 3 3 , 3 3 66:>A/Thailand/104/2009,2009/05/06
67 >A/Nonthaburi/102/2009,2009// .................................................................................................................................G............................................................................................................................................................................................................................................................G...................................................................................................... 2 2 , 2 2 67:>A/Nonthaburi/102/2009,2009//
68 >A/Nonthaburi/104/2009,2009/05/10 ------------------------------------------------------------------------------------------------------....C......................G................................................................................................................................................................................................................................................------------------------------------------------------------------------------------------------------------------- 219 219 , 2 2 68:>A/Nonthaburi/104/2009,2009/05/10
69 >A/Thailand/CU-H1002/2009,2009/11/26 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------.............................................A.................................G...................................................................................------------------------------------------------------------------------------------------------------------------------------------------------------------ 324 324 , 2 2 69:>A/Thailand/CU-H1002/2009,2009/11/26
70 >A/Thailand/CU-H1127/2009,2009/12/19 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------.............................................A...................................A.................................................................................------------------------------------------------------------------------------------------------------------------------------------------------------------ 324 324 , 2 2 70:>A/Thailand/CU-H1127/2009,2009/12/19
71 >A/Thailand/CU-H1167/2009,2009/12/30 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------...................................G.........A...................................A.................................................................................------------------------------------------------------------------------------------------------------------------------------------------------------------ 325 325 , 3 3 71:>A/Thailand/CU-H1167/2009,2009/12/30
72 >A/Thailand/CU-H106/2009,2009/07/ ......................................................................G............................................................................................................................................A.................................................................................G.A........................................................................................................................T.................................................................... 5 5 , 5 5 72:>A/Thailand/CU-H106/2009,2009/07/
73 >A/Thailand/0404-00-N0/2009,2009/07/17 ...................................................................................................................................................................................................................A.................................................................................G.A........................................................................................................................T.........T.......................................................... 5 5 , 5 5 73:>A/Thailand/0404-00-N0/2009,2009/07/17
74 >A/Thailand/PMKD0028/2009,2009/09/24 ........................................................................................................C..........................................................................................................A.................................................................................G.A........................................................................................................................T.........TC......................................................... 7 7 , 7 7 74:>A/Thailand/PMKD0028/2009,2009/09/24
75 >A/Thailand/0419-00-N0/2009,2009/06/23 ...A...............................................................A...............................................................................................................................................A.................................................................................G.A........................................................................................................................T.................................................................... 6 6 , 6 6 75:>A/Thailand/0419-00-N0/2009,2009/06/23
76 >A/Thailand/34-9913/2010,2010/07/14 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.............................A....................A.......................------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 413 413 , 2 2 76:>A/Thailand/34-9913/2010,2010/07/14
77 >A/Thailand/THB0390/2009,2009/07/13 .........................................A.........................................................................................................................................................................A....................A.......................................................................................................................................................................A...............T.................................................................... 5 5 , 5 5 77:>A/Thailand/THB0390/2009,2009/07/13
78 >A/Thailand/CU-C1192/2010,2010/09/15 -------------------------------------------.........................................................................T................................................................................C.............A.........................................................................................................................-------------------------------------------------------------------------------------------------------------------------------------------------------- 198 198 , 3 3 78:>A/Thailand/CU-C1192/2010,2010/09/15
79 >A/Thailand/CU-C1151/2010,2010/09/07 --------------------------------------------------------------------------------....................................T................................................................................C.............A..........................................................................................................................------------------------------------------------------------------------------------------------------------------------------------------------------- 234 234 , 3 3 79:>A/Thailand/CU-C1151/2010,2010/09/07
80 >A/Thailand/34-9912/2010,2010/07/14 ----------------------------------------------------------------------------------------------------------------------------------...................................................................C.........A...A............................................------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 362 362 , 3 3 80:>A/Thailand/34-9912/2010,2010/07/14
81 >A/Thailand/CU-H2364/2010,2010/09/09 ------------------------------------------------------------------------------------------------------------------------------------.......................G.........................................C.........A...A.........................................................................................................................-------------------------------------------------------------------------------------------------------------------------------------------------------- 288 288 , 4 4 81:>A/Thailand/CU-H2364/2010,2010/09/09
82 >A/Thailand/CU-C1070/2010,2010/08/18 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------................C.........A...A.......................A.................................................................................................-------------------------------------------------------------------------------------------------------------------------------------------------------- 337 337 , 4 4 82:>A/Thailand/CU-C1070/2010,2010/08/18
83 >A/Thailand/CU-C1006/2010,2010/07/22 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.....A.......................A................................................G..................................................------------------------------------------------------------------------------------------------------------------------------------------------------ 359 359 , 3 3 83:>A/Thailand/CU-C1006/2010,2010/07/22
84 >A/Thailand/CU-C1025/2010,2010/07/29 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------....................A.......................A................................................G................................................-------------------------------------------------------------------------------------------------------------------------------------------------------- 346 346 , 3 3 84:>A/Thailand/CU-C1025/2010,2010/07/29
85 >A/Thailand/CU-H567/2009,2009/09/02 ...............................................................................................................G...................................................................................................A..........................................................C.................................................................................................................................................T...............................................T.................... 5 5 , 5 5 85:>A/Thailand/CU-H567/2009,2009/09/02
86 >A/Bangkok/INS424/2010,2010/02/23 .........................................................................................................................................................................................C..................T......A.............................................................................................................A..............................................................................................T.................................................................... 5 5 , 5 5 86:>A/Bangkok/INS424/2010,2010/02/23
87 >A/Thailand/CU-B5/2009,2009/06/13 G........................................................................................................................................................................................................................................................................................................T...........................................G..........................................................................T.................................................................... 4 4 , 4 4 87:>A/Thailand/CU-B5/2009,2009/06/13
88 >A/Thailand/0316-00-N0/2009,2009/06/23 G........................................................................................................................................................................................................................................................................................................T...........................................G..........................................................................T.................................................................... 4 4 , 4 4 88:>A/Thailand/0316-00-N0/2009,2009/06/23
89 >A/Thailand/CU-H85/2009,2009/07/01 G........................................................................................................................................................................................................................................................................................................T...................................-------------------------------------------------------------------------------------------------------------------------------------------------------- 154 154 , 2 2 89:>A/Thailand/CU-H85/2009,2009/07/01
90 >A/Thailand/THB0402/2009,2009/07/15 G........................................................................................................................................................................................................................................................................................................T...........................................G..........................................................................T.................................................................... 4 4 , 4 4 90:>A/Thailand/THB0402/2009,2009/07/15
91 >A/Thailand/THB0415/2009,2009/07/16 G........................................................................................................................................................................................................................................................................................................T...........................................G..........................................................................T.................................................................... 4 4 , 4 4 91:>A/Thailand/THB0415/2009,2009/07/16
92 >A/Thailand/THB0420/2009,2009/07/20 G........................................................................................................................................................................................................................................................................................................T...........................................G..........................................................................T.................................................................... 4 4 , 4 4 92:>A/Thailand/THB0420/2009,2009/07/20
93 >A/Thailand/THB0434/2009,2009/07/27 G........................................................................................................................................................................................................................................................................................................T...........................................G..........................................................................T.................................................................... 4 4 , 4 4 93:>A/Thailand/THB0434/2009,2009/07/27
94 >A/Thailand/THB0444/2009,2009/07/29 G........................................................................................................................................................................................................................................................................................................T...........................................G..........................................................................T.................................................................... 4 4 , 4 4 94:>A/Thailand/THB0444/2009,2009/07/29
95 >A/Thailand/THB0472/2009,2009/08/07 G........................................................................................................................................................................................................................................................................................................T...........................................G..........................................................................T.................................................................... 4 4 , 4 4 95:>A/Thailand/THB0472/2009,2009/08/07
96 >A/Thailand/THB0419/2009,2009/07/20 G..................................................................................................................................................................................................................................................................................................A.....T...........................................G..........................................................................T.................................................................... 5 5 , 5 5 96:>A/Thailand/THB0419/2009,2009/07/20
97 >A/Thailand/THB0427/2009,2009/07/22 G..................................................................................................................................................................................................................................................................................................A.....T...........................................G..........................................................................T.................................................................... 5 5 , 5 5 97:>A/Thailand/THB0427/2009,2009/07/22
98 >A/Thailand/THB0428/2009,2009/07/22 G..................................................................................................................................................................................................................................................................................................A.....T...........................................G..........................................................................T.................................................................... 5 5 , 5 5 98:>A/Thailand/THB0428/2009,2009/07/22
99 >A/Thailand/THB0454/2009,2009/08/03 G..................................................................................................................................................................................................................................................................................................A.....T...........................................G..........................................................................T.................................................................... 5 5 , 5 5 99:>A/Thailand/THB0454/2009,2009/08/03
100 >A/Thailand/THB0433/2009,2009/07/27 G..................................................................................................................................................................................................................................................................................................A.....T...........................................G..........................................................A...............T.................................................................... 6 6 , 6 6 100:>A/Thailand/THB0433/2009,2009/07/27
101 >A/Thailand/THB0435/2009,2009/07/28 G........................................................................................................................................................................G...............................................................................................................................T...........................................G..........................................................................T.................................................................... 5 5 , 5 5 101:>A/Thailand/THB0435/2009,2009/07/28
102 >A/Thailand/0445-00-N0/2009,2009/07/30 G........................................................................................................................................................................G...............................................................................................................................T...........................................G..........................................................................T.................................................................... 5 5 , 5 5 102:>A/Thailand/0445-00-N0/2009,2009/07/30
103 >A/Thailand/THB0438/2009,2009/07/28 G........................................................................................................................................................................................................................................................................................................T...........................................G..........................................................................T...............................A.................................... 5 5 , 5 5 103:>A/Thailand/THB0438/2009,2009/07/28
104 >A/Thailand/THB0474/2009,2009/08/10 G........................................................................................................................................................................................................................................................................................................T...........................................G............................................................C.............T.................................................................... 5 5 , 5 5 104:>A/Thailand/THB0474/2009,2009/08/10
105 >A/Thailand/THA0364/2009,2009/07/22 G............................................................A..........................................................................................................................................................................................A................................................T...........................................G..........................................................................T.................................................................... 6 6 , 6 6 105:>A/Thailand/THA0364/2009,2009/07/22
106 >A/Thailand/THB0437/2009,2009/07/28 G............C...........................................................................................................................................................................................................................................................................................T...........................................G..............................................A...........................T.................................................................... 6 6 , 6 6 106:>A/Thailand/THB0437/2009,2009/07/28
107 >A/Thailand/THB0442/2009,2009/07/29 G...A.......................................................................................................................................................T............................................................................................................................................T...........................................G..........................................................................T.................................................................... 6 6 , 6 6 107:>A/Thailand/THB0442/2009,2009/07/29
108 >A/Thailand/CU-H572/2009,2009/09/03 G......A.................................................................................................................................................................................................................................................................................................T........................................T..G..........................................................................T.................................................................... 6 6 , 6 6 108:>A/Thailand/CU-H572/2009,2009/09/03
109 >A/Thailand/PMKD0030/2009,2009/09/25 G.............................................................................................................................................................................................T..........................................................................................................T...........................................G..........................................................................T..................................................................G. 6 6 , 6 6 109:>A/Thailand/PMKD0030/2009,2009/09/25
110 >A/Thailand/CU-H340/2009,2009/08/ --.......................................................................................A...........................................................................................................................................................G...................................................T...........................................G..........................................................................T.............................................----------------------- 30 30 , 5 5 110:>A/Thailand/CU-H340/2009,2009/08/
111 >A/swine/Thailand/CU-SA43/2010,2010/02/ G........................................................................................................................................................................................................................................................................................................T........................................A..G..........................................................................T...........................................A................A------- 14 14 , 7 7 111:>A/swine/Thailand/CU-SA43/2010,2010/02/
112 >A/swine/Thailand/CU-SA412/2010,2010/04/ -----....................................................................................................................................................................................................................................................................................................T........................................A..G..C....................................................................G..T..........................................CA.....------------------- 32 32 , 8 8 112:>A/swine/Thailand/CU-SA412/2010,2010/04/
113 >A/swine/Thailand/CU-SA432/2010,2010/04/ -------....................................................................A.............................................................................................................................................................................................................................T........................................A..G.......................................................................G..T..........................................CA..........-------------- 29 29 , 8 8 113:>A/swine/Thailand/CU-SA432/2010,2010/04/
114 >A/Thailand/CU-H94/2009,2009/07/02 ...................................................................................................................................................................................................................A.................................................................................C...T.............................C......------------------------------------------------------------------------------------------------------------------------------------------------------- 155 155 , 4 4 114:>A/Thailand/CU-H94/2009,2009/07/02
115 >A/Thailand/34-9936/2010,2010/07/14 ----------------------------------------------------------------------------------------------------------------------------------...........G.....................................................................AC...........................................------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 362 362 , 3 3 115:>A/Thailand/34-9936/2010,2010/07/14
116 >A/Thailand/PMKSV0305/2009,2009/08/02 ......................................................C..............................................................................................................................................................A...................................................................................T...........................................G..........................................................................T.................................................................... 5 5 , 5 5 116:>A/Thailand/PMKSV0305/2009,2009/08/02
117 >A/Thailand/THB0423/2009,2009/07/21 G............................................................................................................................................................................................................................................................................................A.....T.....T......................................................................................................................T.......................C............................................ 6 6 , 6 6 117:>A/Thailand/THB0423/2009,2009/07/21
118 >A/Thailand/0440-00-N0/2009,2009/07/29 G................................................G........A...................................................................................................................................................................A.......................................A..................................T......................A....................G..........................................................................T.................................................................... 9 9 , 9 9 118:>A/Thailand/0440-00-N0/2009,2009/07/29
119 >A/swine/Thailand/CU-RA15/2010,2010/01/ ------.............................................................................................................................................................................................................A.....................................................G............................................................................G.............................................A...........................T..................C.............................................---- 16 16 , 6 6 119:>A/swine/Thailand/CU-RA15/2010,2010/01/
120 >A/swine/Thailand/CU-RA114/2010,2010/01/ -----..............................................................................................................................................................................................................A.....................................................G............................................................................G.............................................A.C.........................T..................C............................................----- 17 17 , 7 7 120:>A/swine/Thailand/CU-RA114/2010,2010/01/
121 >A/swine/Thailand/CU-RA75/2010,2010/01/ --...................................................................................................................................................................................................C.............A.....................................................G............................................................................G.............................................A...........................T..................C..............................................--- 12 12 , 7 7 121:>A/swine/Thailand/CU-RA75/2010,2010/01/
122 >A/Thailand/34-9937/2010,2010/07/14 -----------------------------------------------------------------------------------------------------------------------------------.........................................A........................C.............A............................................------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 363 363 , 3 3 122:>A/Thailand/34-9937/2010,2010/07/14
123 >A/Thailand/CU-C1119/2010,2010/09/01 ---------------------------------------------------------------------------------------------------------............................................................................................C.............A......................................................................................................A..................-------------------------------------------------------------------------------------------------------------------------------------------------------- 260 260 , 3 3 123:>A/Thailand/CU-C1119/2010,2010/09/01
124 >A/Thailand/CU-C1099/2010,2010/08/25 --------------------------...............................T...........................................................................................................................................C.........A...A.........................................................................................................................-------------------------------------------------------------------------------------------------------------------------------------------------------- 182 182 , 4 4 124:>A/Thailand/CU-C1099/2010,2010/08/25
125 >A/Thailand/CU-H2216/2010,2010/08/21 ---------------------....................................T...................T.............................................................................G.........................................C.........A...A...............C.........................................................................................................-------------------------------------------------------------------------------------------------------------------------------------------------------- 180 180 , 7 7 125:>A/Thailand/CU-H2216/2010,2010/08/21
126 >A/Thailand/CU-H2359/2010,2010/09/09 -------------------------------------------------------------------------------------------------------------------------------------................................................................C.........A...A.....................................................G...........................................................T.......-------------------------------------------------------------------------------------------------------------------------------------------------------- 290 290 , 5 5 126:>A/Thailand/CU-H2359/2010,2010/09/09
127 >A/Thailand/THB0441/2009,2009/07/28 ....................................................................................................A..............................................................................................................A.....................................................G..........................................................................................................................A...........................T.............A...................................................... 6 6 , 6 6 127:>A/Thailand/THB0441/2009,2009/07/28
128 >A/swine/Thailand/CU-RA29/2009,2009/12/ ............................................................................................................................A......................................................................................A.....................................................G...............................A..........................................................................................A...........................T..................C.............A................................... 8 8 , 8 8 128:>A/swine/Thailand/CU-RA29/2009,2009/12/
129 >A/swine/Thailand/CU-RA4/2009,2009/11/ ...................................................................................................................................................................................................................A........................G............................G................................................AA..........................G.............................T...............A...........................T..................C................................................. 10 10 , 10 10 129:>A/swine/Thailand/CU-RA4/2009,2009/11/
130 >A/Thailand/ST_0112_1/2010,2010/10/ ---------------------------------------------------------------------------------------------------------------------------------...................A.............................................C................A.....................------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ 384 384 , 3 3 130:>A/Thailand/ST_0112_1/2010,2010/10/
131 >A/Thailand/ST_0111/2010,2010/10/ ---------------------------------------------------------------------------------------------------------------------------------------------.......A.............................................C................A.-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 416 416 , 3 3 131:>A/Thailand/ST_0111/2010,2010/10/
132 >A/Thailand/ST_0153/2010,2010/10/ -----------------------------------------------------------------------------------------------------------------------------------------...........A.............................................C................A............--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 401 401 , 3 3 132:>A/Thailand/ST_0153/2010,2010/10/
133 >A/Thailand/ST_0113/2010,2010/10/ --------------------------------------------------------------------------------------------------------------------------------------..............A.............................................C................A..................................................................................----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 328 328 , 3 3 133:>A/Thailand/ST_0113/2010,2010/10/
134 >A/Thailand/CU-H2301/2010,2010/09/02 -----------------------------------------------------------------------------------------...........................................................A.............................................C................A.........................................................................................................................-------------------------------------------------------------------------------------------------------------------------------------------------------- 244 244 , 3 3 134:>A/Thailand/CU-H2301/2010,2010/09/02
135 >A/Thailand/CU-H2295/2010,2010/09/02 -----------------------------------------------------------------------------------.................................................................A.........................A...................C................A.................................................................................................T.......................-------------------------------------------------------------------------------------------------------------------------------------------------------- 240 240 , 5 5 135:>A/Thailand/CU-H2295/2010,2010/09/02
136 >A/Thailand/SN_0112_2/2010,2010/10/ ---------------------------------------------------------------------------------------------------------------------------------...................A.............................................C................A..............................C.......------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 368 368 , 4 4 136:>A/Thailand/SN_0112_2/2010,2010/10/
137 >A/Thailand/CU-H1782/2010,2010/03/14 -----------------------------------------------------------------------------------...............................................................................................................................AA...................................................................A.....................................................-------------------------------------------------------------------------------------------------------------------------------------------------------- 238 238 , 3 3 137:>A/Thailand/CU-H1782/2010,2010/03/14
138 >A/Thailand/CU-H1774/2010,2010/03/18 -----------------------------------------------------------------------------------------------------.............................A...............................................................................AA...................................................................A.....................................................-------------------------------------------------------------------------------------------------------------------------------------------------------- 257 257 , 4 4 138:>A/Thailand/CU-H1774/2010,2010/03/18
139 >A/Thailand/CU-H1379/2010,2010/01/01 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------.............................................A......................................................................................C..............................------------------------------------------------------------------------------------------------------------------------------------------------------------ 324 324 , 2 2 139:>A/Thailand/CU-H1379/2010,2010/01/01
140 >A/Thailand/CU-H1340/2010,2010/01/27 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------.............................................A......................................................................................C..............................------------------------------------------------------------------------------------------------------------------------------------------------------------ 324 324 , 2 2 140:>A/Thailand/CU-H1340/2010,2010/01/27
141 >A/Thailand/CU-H1392/2010,2010/01/30 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------.............................................A......................................................................................C..............................------------------------------------------------------------------------------------------------------------------------------------------------------------ 324 324 , 2 2 141:>A/Thailand/CU-H1392/2010,2010/01/30
142 >A/Thailand/CU-H1210/2010,2010/01/09 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------.....................G.......................A.....................................................................................................................------------------------------------------------------------------------------------------------------------------------------------------------------------ 324 324 , 2 2 142:>A/Thailand/CU-H1210/2010,2010/01/09
143 >A/Thailand/CU-C1005/2010,2010/07/22 --------------------------.......................................G......................................................A...................................................................A......................A........................................................................G...................................................----------------------------------------------------------------------------------------------------------------------------------------------------- 180 180 , 5 5 143:>A/Thailand/CU-C1005/2010,2010/07/22
144 >A/Thailand/CU-C1028/2010,2010/08/05 --------------------------.......................................G......................................................A...................................................................A......................A........................................................................G................................................-------------------------------------------------------------------------------------------------------------------------------------------------------- 183 183 , 5 5 144:>A/Thailand/CU-C1028/2010,2010/08/05
145 >A/Thailand/CU-H2417/2010,2010/09/13 .............A...................................................G......................................................A...................................................................A......................A........................................................................G.........................................................................A.........................................................T.................................................................... 8 8 , 8 8 145:>A/Thailand/CU-H2417/2010,2010/09/13
146 >A/Bangkok/INS427/2010,2010/03/04 .................A.................................................................................................................................................................................................A...T...........................C..................................................................................................................A.........................................................T.......................C.........G.................................. 8 8 , 8 8 146:>A/Bangkok/INS427/2010,2010/03/04
147 >A/Thailand/H1818/2010,2010/03/29 ..................A.....................................................................C................................................A...............................................................G.........A...T...........................C..............................................G...................................................................A......A..................................................T.......................C.........G.................................. 13 13 , 13 13 147:>A/Thailand/H1818/2010,2010/03/29
148 >A/Thailand/CU-H2389/2010,2010/09/10 ....................................................................................................................T................................................................................C.............A..........................................................................................................................C.......................A........................................................AT........T........................................................... 8 8 , 8 8 148:>A/Thailand/CU-H2389/2010,2010/09/10
149 >A/Thailand/CU-H2283/2010,2010/08/31 ...............................................................A....................................................T................................................................................C.........A...A..........................................................................................................................C.......................A........................................................AT.................................................................... 9 9 , 9 9 149:>A/Thailand/CU-H2283/2010,2010/08/31
150 >A/Thailand/CU-C1157/2010,2010/09/07 .........................................................T...........................................................................................................................................C.........A...A..........................................................................................................................C.......................A........................................................AT....T.........................................T..................... 10 10 , 10 10 150:>A/Thailand/CU-C1157/2010,2010/09/07
151 >A/Thailand/CU-H2358/2010,2010/09/08 .........................................................T...........................................................................................................................................C.........A...A..........................................................................................................................C.......................A........................................................AT....T.........................................T..................... 10 10 , 10 10 151:>A/Thailand/CU-H2358/2010,2010/09/08
152 >A/Thailand/CU-H2543/2010,2010/09/25 .........................................................T...........................................................................................................................................C.........A...A..........................................................................................................................C.......................A........................................................AT....T.........................................T..................... 10 10 , 10 10 152:>A/Thailand/CU-H2543/2010,2010/09/25
153 >A/Thailand/CU-B4148/2010,2010/10/09 .........................................................................................................................................................................G...........................C.........A...A..........................................................................................................................C.......................A........................................................AT....T.........................................T..................... 10 10 , 10 10 153:>A/Thailand/CU-B4148/2010,2010/10/09
154 >A/Thailand/CU-H2548/2010,2010/09/27 .....................................................................................................................................................................................................C.........A...A...................................................................T......................................................C....A..................A........................................................AT....T.........................................T..................... 11 11 , 11 11 154:>A/Thailand/CU-H2548/2010,2010/09/27
155 >A/Thailand/CU-H2698/2010,2010/11/03 ...........................C.............................T.................................................................................................G.........................................C.........A...A..........................................................................................................................C.......................A........................................................AT....T.........................................T..................... 12 12 , 12 12 155:>A/Thailand/CU-H2698/2010,2010/11/03
156 >A/Thailand/CU-B4339/2010,2010/11/04 .........................................................T.................................................................................................G.........................................C.........A...A..........................................................................................................................C.......................A....................................................C...AT....T.........................................T..................... 12 12 , 12 12 156:>A/Thailand/CU-B4339/2010,2010/11/04
157 >A/Thailand/CU-H2911/2011,2011/01/20 ......A..................................................T............................................................................A....................G.........................................C.........A...A..........................................................................................................................C.......................A........................................................AT....T.........................................T..................... 13 13 , 13 13 157:>A/Thailand/CU-H2911/2011,2011/01/20
158 >A/Thailand/CU-H2176/2010,2010/08/17 ...................................................................................................................................................................................................................A...............C........................T.................................................................................C................................................................................AT....T.........................................T..................... 8 8 , 8 8 158:>A/Thailand/CU-H2176/2010,2010/08/17
159 >A/Thailand/CU-H9/2009,2009/06/17 .....................................A.........................................A.........A.........................................................................................................................A.......................................T.............G............................T.............................................................................................A...........................T.................................................................... 9 9 , 9 9 159:>A/Thailand/CU-H9/2009,2009/06/17
160 >A/Bangkok/INS426/2010,2010/02/25 .........................................A...................A...................T.................................................................................................................................A..............................................................................................................................AT...............................................G............................T.........................................C.......................... 9 9 , 9 9 160:>A/Bangkok/INS426/2010,2010/02/25
161 >A/Thailand/CU-H1140/2009,2009/12/23 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------.......................A.....................A.............................................................................................................A....G..------------------------------------------------------------------------------------------------------------------------------------------------------------ 326 326 , 4 4 161:>A/Thailand/CU-H1140/2009,2009/12/23
162 >A/Bangkok/INS425/2010,2010/02/25 .........................................A..............................................................................................................................A............C........................T....A.................................................T.............................................................................................................................G......................T.....T.............................T.....................T................ 11 11 , 11 11 162:>A/Bangkok/INS425/2010,2010/02/25
163 >A/Thailand/CU-H1821/2010,2010/03/31 .....................................................................T......................................................A.............................................................................A........A............................................T.....................................................................................................A.............................................T...........T........................................T........................... 9 9 , 9 9 163:>A/Thailand/CU-H1821/2010,2010/03/31
164 >A/swine/Thailand/CU-M8_2/2009,2009/11/ .............................................A.................A.......................................T................................................G..........................................................A.................................................................................G..C.....................C.........................................................T..............................A........T.................................................................... 11 11 , 11 11 164:>A/swine/Thailand/CU-M8_2/2009,2009/11/
165 >A/Nonthaburi/102/2009,2009/05/06 ------------------------------------------------------------------------------------------------------...........................G..................................................................................................................................................................................................................................A..G.A--------------------------------------------------------------------------------------------------------------------------- 229 229 , 4 4 165:>A/Nonthaburi/102/2009,2009/05/06
166 >A/Thailand/CU-H935/2009,2009/11/13 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------.............................................A........G..............A.....................................................................................AA.G....------------------------------------------------------------------------------------------------------------------------------------------------------------ 328 328 , 6 6 166:>A/Thailand/CU-H935/2009,2009/11/13
167 >A/swine/Thailand/CU-RP3/2010,2010/09/ .........C...............................................................T.........C.............................................................................................G................A................A...........G............................................................................................T..A.A....................................A...............................................C.........T...C.........................................----------------------- 37 37 , 14 14 167:>A/swine/Thailand/CU-RP3/2010,2010/09/
168 >A/swine/Thailand/CU-DP83/2010,2010/12/ G........................................................T...........................................................................................................................................C.........A...A........................G.............................G..............................T.........................................A.G.........................................................................AT....T..G......................................T..------------------- 34 34 , 15 15 168:>A/swine/Thailand/CU-DP83/2010,2010/12/
169 >A/Thailand/SN_0116/2010,2010/10/ -----------------------------------------------------------------------------------------------------------------------------------------....................................C...............T.......C.........A...A...................................---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 380 380 , 5 5 169:>A/Thailand/SN_0116/2010,2010/10/
170 >A/swine/Thailand/CU-PL63/2010,2010/11/ --------------------------.........................................A...............................................................................G.....................G................G................C..............................................................G..............................T.........................................A.G........................................................A.................T.................................................CC....TCA.ATC.C.C.. 47 47 , 21 21 170:>A/swine/Thailand/CU-PL63/2010,2010/11/
171 >A/swine/Thailand/CU-PL65/2010,2010/11/ ...................................................................A......................................................................TG.......G.....G.....T..TT......................G................C................................G..........................................................T.........G..G.......................A.C........T..............A.......................................A.................T.................................................................... 20 20 , 20 20 171:>A/swine/Thailand/CU-PL65/2010,2010/11/
172 >A/swine/Thailand/CU-SA433/2010,2010/06/ ............................TC.........................................................................................................................................................................G.................................................................................................T........................................A..G.........................................A.............................G..T....................G.....................CA........TAGAT.G.A.T.AA-- 24 24 , 22 22 172:>A/swine/Thailand/CU-SA433/2010,2010/06/
173 >A/swine/Thailand/CU-RP1/2010,2010/09/ ...............G.T.TGGG.......GA.G...GG.CT.G..CCAGCTGC.CT..A.............T.........C..............................................................................................................A................A...........G......................................................................................................................................A...............................................C.........T...C................................................................ 34 34 , 34 34 173:>A/swine/Thailand/CU-RP1/2010,2010/09/
174 >A/swine/Thailand/CU-PS73/2010,2010/09/ --..TCT.A.GTC.ATG....G.....C...AT..TA.TT....G..........G....G.GAC....T.TG.GA...A.....ACGCA.T.AT..A..ATT....ATAC.GATG.CACA.TG.G..T....GAG.A..T..AAA.G.CAT..C..G..C...GA.G...T..ATG.CCA.GAAA.G.....C....A......C..CAC..C....GA..A.G..C.A.G.A...TC..T..A....TC.T.C..ATC...A.G.T.....G.C..A.AATC....AT.A.....A.GAG..GG.C....AA..T.CA.A.....CT..A.TCT...AA......T..AATAA....GC..GC.AACACTA.AG.T..GG....C....TATG....G.T.T.TC.AC.CG.A..G.A.TAT..T.GTAGCAT.A.TTGGTATG.GA.GATCAAT....T...C..T..C............G 223 223 , 221 221 174:>A/swine/Thailand/CU-PS73/2010,2010/09/
175 >A/swine/Thailand/CU-ST3/2009,2009/11/ .A..TCT...G....CGA.....CCGC....AT.CT..TTCAT......C.........T..GAC.T.G..TC..TG.AAG.CCCAC.C.CTTATTG.ATA.T..G.A.AC.GA...CA.A...A.GA...AC.AGA.....CGAAG..C.T..C..GG..CG..AGG.GCT...TG...A.GAA....TTC..CCCAA.T....C..C....AGTAG.A.AA..TGAG..G..G...CAG...T.G..TC.T.C..A..TT.ATGGCCGCGCAG.GT.T....G.CCA...GC.T....A.TT.G.C..GCAA..T.C..A.A.T..TGCA.TCTGAAAA.G.CTCGGAAAGAAC.TAGC.G......ACT.GA...T.....CGCG.C.T.T.AT---------------------A------------------------------------------------------------------ 299 299 , 212 212 175:>A/swine/Thailand/CU-ST3/2009,2009/11/
---Index----------------------------------------AGTCGTCGTTACTTGAACGCAATTTATTCACGCATATTACAGCAAGATGAACTATTACCCAGAGTACGACACACAGAGGGAGTTTCAATGTCCCCCACGCGCCCTATTAGTAAGCAATGTGGCAGAAGAAGGTAGACGATCATCTGAAGTCCAAAACAAATTACATAAGATCCAGCATTTGTAGGGAAGCCTCTTTTGGCCAGTCTCGAGGTTGACGAAGAGGACAATACAAGGATAGAGACTTCAAGGGACCCTACGATACGGAAAGTATCTTATACGCTTCTACTTGCAGTTCCAGTAGAAAAAAAACATGCGGCCTGGGTCCGATCATGCCTCAGGGGAACTCTAAGGGCTGTGCGATTAATCTGTGTCGAGACCCAAAAGTATAGTTCGCATACGACCTCCCTGGACTAAGGCACGTCCCACCTAAGATGCTGCCCAACGGACAGGAGCAGGCCTAGGTCCTTTCAGTGATATGTATTTAA
-codon-position---------------------------------1 211 1 21221 1 1 12 2 1 1 122 1 2 1122 2 1 122 2 1 11 12 1 1 1 2 2 1 11 1 21 2 12122 2 1 12 2 221 1 1 1 122 1 1 1 2 1 21 1 1 2 1 1 1 2 22 12 1 12 2 1 1 1 212 12 21 1 112 222 2 2 12 2 2 212 1 1 1 1 22 12 2 1 121 2 121 1 12 1 1 11 1 2 21 1 1 21 12 2 1 2 2 1 12 2 1 2 2 12 1 1 1 1 2 2 1 1 1 2 1 2 21 2 11 1 2 1 12 1 112 22 11 1 122 2 2 12 12 12
00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000011111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
00000000000000000000000000000000000000011111111111111111111111111111111111111111111222222222222222222222222333333333333333333333333333444444444444444444444444444445555555555555555555555555555555566666666666666666666666666666666667777777777777777777777777888888888888888888888888888888888888899999999999999999999999999900000000000000000000000000111111111111111111111111122222222222222222222222233333333333333333333334444444444444444444444555555555555555555555666666666666666666666666677
00111222222333334444444566677777888999900001111222222244444455556666777788888889999122344455566666667788999000001123334445556667788999001111222333445566777788899990001111122334444555556666677899900000112222344555666677778889999990001111122233334555556779000001112222333344555556677777888899900012233344445567778889999900011111223344455566788899001111224446677777889999901113344445666667788999900112245566666788889990012233444566677888899001111223344566677789122355667778888899999999900
46136124689246790234578834923478124068925693679013458901245804892358124701356890239058203927913456892325078012385840280581240375815039890378346235071913457838902352470356957016789235890137837814803578290147502578156914783470567895781467912635688034697373013470362359024769125890503469045817803681403423684532483571346835823467695814736958104628170389250567801269581345762480945896013692512346923130912902358502342453802507039547813256846690258482956703467845004036585782568912345678901
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April 25th, 2011, 06:11 AM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,944
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Re: Sequences at Genbank!
Milan, Italy this season:
Code:
000000000000000000000000000000000000011111111111
011122223333344444455555566666679999900113344466
947812482344602567703567904569990233615178800725
142382981302084152821279850857863134326810638693
-codon-position-------------------1 1 2 1 11 111 12112121 1 1 21 21
---Index--------------------------GCCAATGTTTGTGGAGTGACGTAATGGTGATGTCTAAGTAGGAGCCGT
1 >A/******/index/2009/02/01 ................................................
2 >A/Milan/186,2011/01/26 ...............A........C..A......C...----------
3 >A/Milan/170,2011/01/20 ...............A........C..A......C...----------
4 >A/Milan/121,2011/02/02 ...............A.T..A...C..A....GT.G..----------
5 >A/Milan/210,2011/02/08 ...............A.T..A...C..A....GT.G........T...
6 >A/Milan/15,2011/01/11 .....C........G............A............A...T...
7 >A/Milan/01,2011/01/04 .....C........G.......C....A..........----------
8 >A/Milan/04,2010/11/29 ..T......A..A.G.......C....A............A...T...
9 >A/Milan/05,2010/12/01 ..T......A..A.G.......C....A............A...T...
10 >A/Milan/10,2010/12/27 ..T......A..A.G.......C....A............A...T...
11 >A/Milan/26,2011/01/18 ..T......A..A.G......C.....A............A...T...
12 >A/Milan/03,2010/11/24 ..T......A..A.G.......C....A............A...T.--
13 >A/Milan/10,2011/01/03 ...G...CC...A.G.......C....A..........----------
14 >A/Milan/55,2011/01/17 ...G...CC.A.....A....C.....AAG.T....C..CAA..T...
15 >A/Milan/162,2011/01/14 ...G...CC.A.....A....C.....AAG.T....C.----------
16 >A/Milan/40,2011/01/18 ...G...CC.A.....A....C.....AAG.T....C..CAA..T...
17 >A/Milan/220,2011/01/20 ...G...CC.A.....A....C.....AAG.T....C.----------
18 >A/Milan/98,2011/01/21 ...G...CC.A.....A....C.....AAG.T....C.----------
19 >A/Milan/124,2011/02/04 ...G...CC.A.....A....C.....AAG.T----------------
20 >A/Milan/35,2011/01/13 ...G...CC.A.....A....C.....AAG.T....C..CAA..T...
21 >A/Milan/166,2011/01/17 ...G...CC.A.....A....C.....AAG.T....C.----------
22 >A/Milan/80,2011/01/24 ...G...CC.A.....A....C.....AAG.T....C..CAA..T...
23 >A/Milan/99,2011/01/21 ...G...CC.A.....A....C.....AAG.T......----------
24 >A/Milan/84,2011/01/25 ...G...CC.A.....A....C.....AAG.T....C..CAA..T...
25 >A/Milan/90,2011/01/26 ...G...CC.A.....A....C.....AAG.T....C..CAA..T.A.
26 >A/Milan/75,2011/01/26 ...G...CC.A.....A....C.....AAG.T....C.----------
27 >A/Milan/188,2011/01/27 A..G...CC.A.....A....C.....AAG.T....C..CAA..T...
28 >A/Milan/230,2011/02/03 C..G...CC.A.....A....C.....AAG.T....C..CAA..T..-
29 >A/Milan/194,2011/01/31 ...G...CC.A.....A....C.....AAG.T....C..CAA..T...
30 >A/Milan/213,2011/02/10 ...G...CC.A.....A....C.....AAG.T....C..CAA..T...
31 >A/Milan/236,2011/02/19 ...G...CC.A.....A....C.....AAG.T....C..CAA..T...
32 >A/Milan/122,2011/01/31 ...G...CC.A.....A....C.....AAG.T....C.----------
33 >A/Milan/237,2011/02/20 ...G...CC.A.....A....C.....AAG.T....C..CAA..T...
34 >A/Milan/197,2011/01/31 ...G...CC.A.....A....C.....AAG.T....C.----------
35 >A/Milan/206,2011/02/08 ...G...CC.A.....A....C.....AAG.T....C..---------
36 >A/Milan/88,2011/01/24 ...G...CC.AA....A....C.....AAG.T....C..CAA..T...
37 >A/Milan/24,2011/01/14 ...G...CC.AA....A..T.C.....AAG.T....C..CAA..TT..
38 >A/Milan/72,2011/01/21 ...G...CC.AA....A..T.C.....AAG.T....C..CAA..TT..
39 >A/Milan/181,2011/01/28 A..G...CC.A.....A....C.....AAG.T....C...AA..T...
40 >A/Milan/184,2011/01/25 .......CC.A.....A....C.....AAG.T....CA----------
41 >A/Milan/235,2011/02/22 ...G...CC.A.....A....C.....AAG.T....C..CAA..T.A.
42 >A/Milan/64,2011/01/20 ...G......A..........C.....AAG.T----------------
43 >A/Milan/160,2011/01/11 ...G......A..........C.....AAG.T.....A----------
44 >A/Milan/18,2011/01/11 ....G.A...A..............C.A..........C.A..AT..C
45 >A/Milan/163,2011/01/14 ....G.A...A..............C.A..........----------
46 >A/Milan/219,2011/02/13 .T........A..............C.A..........C.A..AT..C
47 >A/Milan/198,2011/02/01 ..........A..............C.A....----------------
48 >A/Milan/199,2011/02/01 ..........A......A.....G.C.A..........C.A.GAT...
49 >A/Milan/231,2011/02/03 ..........A......A.....G.C.A..........C.A.GAT...
50 >A/Milan/209,2011/02/08 ..........A......A.....G.C.A....----------------
51 >A/Milan/159,2011/01/07 ..........A......A.....G.C.A..........----------
52 >A/Milan/218,2011/02/12 ..........A............G.C.A..C.......C.A.GAT...
53 >A/Milan/196,2011/02/01 ..........A............G.C.A..C.......C.A.GAT...
54 >A/Milan/224,2011/01/31 ..........A............G.C.A..........----------
55 >A/Milan/229,2011/02/03 .T....A......A....G......CAA....----------------
56 >A/Milan/94,2011/01/25 .T...........A....G......CAA..........----------
---Index--------------------------GCCAATGTTTGTGGAGTGACGTAATGGTGATGTCTAAGTAGGAGCCGT
-codon-position-------------------1 1 2 1 11 111 12112121 1 1 21 21
000000000000000000000000000000000000011111111111
011122223333344444455555566666679999900113344466
947812482344602567703567904569990233615178800725
142382981302084152821279850857863134326810638693
I'd assume there were at least 5 introductions into Milan
the dominant strain (31/55 = 56%) has 15 mutations = 7.5 per year
(11/55=20%) from the India/UK - strain with markers 605,1056,1171,1403
none of the Russ,Chi-mutations
Milan/10 looks recombined
--------------------------------------
2,>A/Milan/186,2011/01/26,23-1041,
G451A,T598C,T933C
2,>A/Milan/210,2011/02/08,23-1671,
G451A,G472T,G531A,T598C,A795G,T903G,C921T,A934G,A1 131G,C1464T,G1486A
--------------------------------------------------------
2,>A/Milan/15,2011/01/11,22-1701,
T222C,A424G,G1171A,A1449G
5-6,>A/Milan/04,2010/11/29,22-1701,
C172T,T333A,G360A,A424G,A567C,G1171A
-----------------------------------------------------
30-31,>A/Milan/55,2011/01/17,22-1701,
A183G,T288C,T321C,G340A,T465A,T552C,G665A,A697G,G7 96T,A963C,
A1118C,G1171A,G1380A
--------------------------------------------------------
("India/UK"-strain)
4,>A/Milan/219,2011/02/13,23-1671,C144T,G836A,
G340A,G605C,T1056C,G1171A,G1403A,T1653C
7,>A/Milan/199,2011/02/01,23-1671,G472A
G340A,A579G,G605C,T1056C,G1171A,A1386G,G1403A
---------------------------------------------------------
2,>A/Milan/94,2011/01/25,22-1023,
C144T,G408A,A447G,A478G,G605C,G640A
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April 28th, 2011, 03:24 AM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,944
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Re: Sequences at Genbank!
pH1 HAs at genbank since July 2010
Code:
00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000111111111111111111111111111111111111111
00000000011111111111222222222223333333333333344444444444444555555555555555556666666666666777777777778888888889999999999000000001111111122222233333344444445666
01246667934444666788011124588990022334445669902334555667789012333455666677990012445678999011112455790033467890023334569011225881345677901223725678800334676255
66270342152478368213702829628182314230287060684237013252892267169625357839285701078581078856799849761406950090310345735227036068108512465273597840638079463936
-codon-position----------------------------------- 112 1 1 1 111 11 22 1 12 2 1 1 1 1 11 1 2 22 21 1 11211 1212 12 12 2 11 1 22 1 12 1 2 1 2 112 1 1 212
---Index------------------------------------------GGCAATATGCACTCAGGCCAGTAATGTCTGTGTTCATGTGAGGGGGACTAGGATTGAATCACGGACTTAGAGCACTGGGTGTTGGCAATAGATAACGGCGAGAGCGCAAGTCGTACAACAGGTTTGAAACGAGATGAAATTGGTTGAGCTCACCGGTC
1 >A/******/index/2009/02/01 .............................................................................................................................................................. 0 0 , 0 0 1:>A/******/index/2009/02/01
2 >A/THA/CU-C1192,2010/09/15 ---------..........................T........................................C.....A.........................................---------------------------------- 120 46 , 3 3 2:>A/THA/CU-C1192,2010/09/15
3 >A/THA/CU-C1151,2010/09/07 --------------------...............T........................................C.....A.........................................---------------------------------- 152 57 , 3 3 3:>A/THA/CU-C1151,2010/09/07
4 >A/THA/34-9912,2010/07/14 -------------------------------------------.................................C...A.A..................--------------------------------------------------------- 248 103 , 3 3 4:>A/THA/34-9912,2010/07/14
5 >A/THA/CU-H2364,2010/09/09 --------------------------------------------............G...................C...A.A.........................................---------------------------------- 195 82 , 4 4 5:>A/THA/CU-H2364,2010/09/09
6 >A/THA/CU-C1070,2010/08/18 -------------------------------------------------------------------.........C...A.A.........A...............................---------------------------------- 239 105 , 4 4 6:>A/THA/CU-C1070,2010/08/18
7 >A/THA/CU-C1099,2010/08/25 -------....T................................................................C...A.A.........................................---------------------------------- 110 45 , 4 4 7:>A/THA/CU-C1099,2010/08/25
8 >A/North Carolina/AF21794,2010/12/20 ...........T............................................G...................C...A.A.........................................C.......A..----------------------- 73 30 , 7 7 8:>A/North Carolina/AF21794,2010/12/20
9 >A/North Carolina/AF21795,2011/01/12 ...........T............................................G...................C...A.A.........................................C.......A..----------------------- 73 30 , 7 7 9:>A/North Carolina/AF21795,2011/01/12
10 >A/Korea/AF21787,2011/01/04 ...........T............................................G...................C...A.A.........................................C.......A..----------------------- 75 30 , 9 7 10:>A/Korea/AF21787,2011/01/04
11 >A/Mexico/InDRE2409,2011/04/01 -------------------------------------........A..........G...................C...A.A...............------------------------------------------------------------ 246 102 , 5 5 11:>A/Mexico/InDRE2409,2011/04/01
12 >A/Milan/94,2011/01/25 --------...T.................................A...G......G...................C...A.A.........................................---------------------------------- 118 49 , 7 7 12:>A/Milan/94,2011/01/25
13 >A/Milan/229,2011/02/03 ----.......T.............A...................A..........G...................C...A.A........................--------------------------------------------------- 152 62 , 7 7 13:>A/Milan/229,2011/02/03
14 >A/Mexico/InDRE4274,2011/04/06 -------------------------------------........A..........G...................C...A.A.............A.------------------------------------------------------------ 247 103 , 6 6 14:>A/Mexico/InDRE4274,2011/04/06
15 >A/Karaj/5607,2010/12/19 ...........T............................................G...................C...A.A.........................................C.......A..............AT.T....... 10 10 , 10 10 15:>A/Karaj/5607,2010/12/19
16 >A/Karaj/5327,2010/12/06 ...........T............................................G...................C...A.A.........................................C.......A..............AT.T......T 11 11 , 11 11 16:>A/Karaj/5327,2010/12/06
17 >A/Beijing/3848,2010/11/ ---------------------------------------------------------------------------------------------------.........................C.......A..............AT.T......T 206 105 , 6 6 17:>A/Beijing/3848,2010/11/
18 >A/Beijing/3856,2010/11/ ----------------------------------------------------------------------------------------------..............................C.......A..............AT.T......T 196 100 , 6 6 18:>A/Beijing/3856,2010/11/
19 >A/Karaj/5985,2010/12/27 ...........T............................................G...................C...A.A.........................................C.......A..............AT.T......T 11 11 , 11 11 19:>A/Karaj/5985,2010/12/27
20 >A/Karaj/5987,2010/12/27 ...........T............................................G...................C...A.A.........................................C.......A..............AT.T......T 11 11 , 11 11 20:>A/Karaj/5987,2010/12/27
21 >A/Tehran/5958,2010/12/27 ...........T............................................G...................C...A.A.........................................C.......A..............AT.T......T 11 11 , 11 11 21:>A/Tehran/5958,2010/12/27
22 >A/Tehran/5963,2010/12/27 ...........T............................................G...................C...A.A.........................................C.......A..............AT.T......T 11 11 , 11 11 22:>A/Tehran/5963,2010/12/27
23 >A/Karaj/6072,2010/12/29 ...........T............................................G...................C...A.A.........................................C.......A..............AT.T......T 11 11 , 11 11 23:>A/Karaj/6072,2010/12/29
24 >A/Ghom/215,2010/12/30 ...........T............................................G...................C...A.A.........................................C.......A..............AT.T......T 11 11 , 11 11 24:>A/Ghom/215,2010/12/30
25 >A/THA/CU-C1157,2010/09/07 ...........T................................................................C...A.A.........................................C.......A..............AT.T......T 10 10 , 10 10 25:>A/THA/CU-C1157,2010/09/07
26 >A/THA/CU-H2358,2010/09/08 ...........T................................................................C...A.A.........................................C.......A..............AT.T......T 10 10 , 10 10 26:>A/THA/CU-H2358,2010/09/08
27 >A/THA/CU-H2543,2010/09/25 ...........T................................................................C...A.A.........................................C.......A..............AT.T......T 10 10 , 10 10 27:>A/THA/CU-H2543,2010/09/25
28 >A/Tehran/5675,2010/12/18 ...........T................................................................C...A.A.........................................C.......A..............AT.T......T 10 10 , 10 10 28:>A/Tehran/5675,2010/12/18
29 >A/Karaj/6076,2010/12/29 ...........T................................................................C...A.A.........................................C.......A..............AT.T......T 10 10 , 10 10 29:>A/Karaj/6076,2010/12/29
30 >A/Moscow/IIV-33,2010/10/13 ............................................................................C...A.A.........................................C.......A..............AT.T......T 9 9 , 9 9 30:>A/Moscow/IIV-33,2010/10/13
31 >A/THA/CU-B4148,2010/10/09 ............................................................G...............C...A.A.........................................C.......A..............AT.T......T 10 10 , 10 10 31:>A/THA/CU-B4148,2010/10/09
32 >A/THA/CU-H2548,2010/09/27 ............................................................................C...A.A.......................T.................CA......A..............AT.T......T 11 11 , 11 11 32:>A/THA/CU-H2548,2010/09/27
33 >A/Ontario/720545,2010/11/17 ...........T................................................................C...A.A....................................G....C.......A..............AT.T......T 11 11 , 11 11 33:>A/Ontario/720545,2010/11/17
34 >A/THA/CU-H2698,2010/11/03 .......C...T............................................G...................C...A.A.........................................C.......A..............AT.T......T 12 12 , 12 12 34:>A/THA/CU-H2698,2010/11/03
35 >A/Beijing/3907,2010/11/ .......C...T..............................A.............G...................C...A.A.........................................C.......A..............AT.T......T 13 13 , 13 13 35:>A/Beijing/3907,2010/11/
36 >A/Beijing/3884,2010/11/ .......C...T..............................A.............G...................C...A.A....................................G....C.......A..............AT.T......T 15 14 , 15 14 36:>A/Beijing/3884,2010/11/
37 >A/THA/CU-B4339,2010/11/04 ...........T............................................G...................C...A.A.........................................C.......A..............AT.T......T 12 11 , 12 11 37:>A/THA/CU-B4339,2010/11/04
38 >A/Karaj/5921,2010/12/27 ...........T............................................G............A......C...A.A.........................................C.......A..............AT.T......T 12 12 , 12 12 38:>A/Karaj/5921,2010/12/27
39 >A/Karaj/5924,2010/12/27 ...........T............................................G...................C...A.A.........................................C.......A..............AT.T......T 12 11 , 12 11 39:>A/Karaj/5924,2010/12/27
40 >A/Karaj/5718,2010/12/14 ...........T........................C...................G...................C...A.A.........................................C.......A..............AT.T....... 11 11 , 11 11 40:>A/Karaj/5718,2010/12/14
41 >A/Karaj/5685,2010/12/21 ...........T............................................G...................C...A.A.........................................C.......A..............AT.T....... 11 10 , 11 10 41:>A/Karaj/5685,2010/12/21
42 >A/Hangzhou/1,2011/01/04 ..A........T.................................A..........G...................C...A.A.........................................C.......A..............AT.T....--- 28 15 , 12 12 42:>A/Hangzhou/1,2011/01/04
43 >A/THA/CU-H2911,2011/01/20 ..A........T.................................A..........G...................C...A.A.........................................C.......A..............AT.T......T 13 13 , 13 13 43:>A/THA/CU-H2911,2011/01/20
44 >A/Korea/AF21790,2011/01/09 ..A........T.................................A..........G..................CC...A.A.........................................C.......A..----------------------- 76 33 , 10 10 44:>A/Korea/AF21790,2011/01/09
45 >A/Karaj/5795,2010/12/23 ...........T............................................G...................C...A.A.........................................C.......A..............AT.T......T 13 11 , 13 11 45:>A/Karaj/5795,2010/12/23
46 >A/Vladivistok/7,2010/12/03 ...........T............................................G...................C...A.A............A............................C.......A..............AT.T......T 14 12 , 14 12 46:>A/Vladivistok/7,2010/12/03
47 >A/Ulaanbaatar/190,2011/01/11 .......C...T...................................T........G...................C...A.A.........................................C.......A..............AT.T......T 14 13 , 14 13 47:>A/Ulaanbaatar/190,2011/01/11
48 >A/Japane/AF21777,2011/01/13 .......C...T............................................G...................C...A.A.........................................C.......A..----------------------- 75 31 , 9 8 48:>A/Japane/AF21777,2011/01/13
49 >A/Korea/AF21785,2011/01/10 .......C...T.................................A..........G...................C...A.A.........................................C.......A..----------------------- 76 32 , 10 9 49:>A/Korea/AF21785,2011/01/10
50 >A/Florida/AF21772,2011/01/20 ...........T.................................A..........G......A............C...A.A.........................................C.......A..----------------------- 76 32 , 10 9 50:>A/Florida/AF21772,2011/01/20
51 >A/THA/CU-H2216,2010/08/21 ---........T............................................G...................C...A.A.....C...................................---------------------------------- 108 43 , 7 6 51:>A/THA/CU-H2216,2010/08/21
52 >A/Denmark/107,2010/12/10 ----.......T............................................G...................C...A.A.........................................C.......A..............AT.T....... 41 14 , 13 10 52:>A/Denmark/107,2010/12/10
53 >A/Florida/AF21770,2010/12/30 ...........TC.G...................................T.....G...................C...A.A.........................................C.......A..----------------------- 76 33 , 10 10 53:>A/Florida/AF21770,2010/12/30
54 >A/New Mexico/AF21792,2011/01/14 ...........TC.G...................................T.....G...................C...A.A.........................................C.......A..----------------------- 76 33 , 10 10 54:>A/New Mexico/AF21792,2011/01/14
55 >A/Korea/AF21784,2011/01/04 A..........T............................................G...................C...A.A................................A........C.......A.A----------------------- 76 33 , 10 10 55:>A/Korea/AF21784,2011/01/04
56 >A/Korea/AF21788,2011/01/05 A...G......T............................................G...................C...A.A................................A........C.......A.A----------------------- 77 34 , 11 11 56:>A/Korea/AF21788,2011/01/05
57 >A/Korea/AF21789,2011/01/07 A...G......T............................................G...................C...A.A................................A........C.......A.A----------------------- 77 34 , 11 11 57:>A/Korea/AF21789,2011/01/07
58 >A/THA/CU-C1119,2010/09/01 ------------------------------..............................................C.....A.........................................---------------------------------- 170 66 , 3 2 58:>A/THA/CU-C1119,2010/09/01
59 >A/THA/34-9937,2010/07/14 -------------------------------------------..................A..............C.....A..................--------------------------------------------------------- 249 103 , 3 3 59:>A/THA/34-9937,2010/07/14
60 >A/Denmark/125,2010/12/21 ---.................A.......................................................C.....A.........................................C.......A..............AT.......-- 32 12 , 7 7 60:>A/Denmark/125,2010/12/21
61 >A/Denmark/132,2010/12/27 ---.................A.......A...............................................C.....A.........................................C.......A..............AT.......-- 33 13 , 8 8 61:>A/Denmark/132,2010/12/27
62 >A/THA/CU-H2389,2010/09/10 ...................................T........................................C.....A.........................................C.......A..............AT......... 8 7 , 8 7 62:>A/THA/CU-H2389,2010/09/10
63 >A/THA/CU-H2283,2010/08/31 ...................................T........................................C...A.A.........................................C.......A..............AT......... 9 8 , 9 8 63:>A/THA/CU-H2283,2010/08/31
64 >A/THA/CU-H2359,2010/09/09 --------------------------------------------................................C...A.A......................................T..---------------------------------- 196 82 , 5 4 64:>A/THA/CU-H2359,2010/09/09
65 >A/Czech Republic/1,2011/01/25 .....................................A......................................C.....A.........................................C.......A..............AT.......C. 9 8 , 9 8 65:>A/Czech Republic/1,2011/01/25
66 >A/Milan/198,2011/02/01 ----.................................A......................................C.....A...............T...........------------------------------------------------ 141 56 , 4 4 66:>A/Milan/198,2011/02/01
67 >A/Denmark/118,2010/12/22 ----.................................A......................................C.....A...............T.........................C.......A..............AT.......C. 37 13 , 9 9 67:>A/Denmark/118,2010/12/22
68 >A/North Carolina/AF21793,2010/12/14 .....................................A......................................CA....A...............T.........................C.......A..----------------------- 73 30 , 7 7 68:>A/North Carolina/AF21793,2010/12/14
69 >A/Denmark/109,2010/12/10 ----.C...............................A......................................C.....A.........................................C.......A..............AT.......C. 37 13 , 9 9 69:>A/Denmark/109,2010/12/10
70 >A/Denmark/131,2010/12/27 ---..C......C........................A......................................C.....A.........................................C.......A..............AT.......C. 31 13 , 10 10 70:>A/Denmark/131,2010/12/27
71 >A/Denmark/130,2010/12/21 ----.C...............................A......................................C.....A.........................................C....T..A..............AT.......C. 37 14 , 11 10 71:>A/Denmark/130,2010/12/21
72 >A/Milan/163,2011/01/14 --------...............G.A...........A......................................C.....A.........................................---------------------------------- 116 47 , 5 5 72:>A/Milan/163,2011/01/14
73 >A/Milan/18,2011/01/11 --------...............G.A...........A......................................C.....A.........................................C.......A..............AT.......C. 30 18 , 10 10 73:>A/Milan/18,2011/01/11
74 >A/Denmark/129,2010/12/26 ---....................G.A...........A......................................C.....A.........................................C.......A..............AT.......C. 32 13 , 11 10 74:>A/Denmark/129,2010/12/26
75 >A/Mexico/InDRE2202,2011/03/22 -------------------------------------A...................................G..C.....A...............------------------------------------------------------------ 245 101 , 4 4 75:>A/Mexico/InDRE2202,2011/03/22
76 >A/Illinois/AF21776,2011/01/03 .....................................A...................................G..C.....A.........................................C.......A..----------------------- 73 29 , 7 6 76:>A/Illinois/AF21776,2011/01/03
77 >A/Milan/209,2011/02/08 ----.................................A.................A.................G..C.....A...........................------------------------------------------------ 142 57 , 5 5 77:>A/Milan/209,2011/02/08
78 >A/Milan/199,2011/02/01 ----.................................A.................A.................G..C.....A.........................................C.......A.............GAT......... 36 14 , 10 10 78:>A/Milan/199,2011/02/01
79 >A/Milan/231,2011/02/03 ----.................................A.................A.................G..C.....A.........................................C.......A.............GAT......... 36 14 , 10 10 79:>A/Milan/231,2011/02/03
80 >A/Milan/159,2011/01/07 --------.............................A.................A.................G..C.....A.........................................---------------------------------- 117 47 , 6 5 80:>A/Milan/159,2011/01/07
81 >A/Denmark/115,2010/12/14 ---..................................A...................................G..C.....A................................T........C.......A.............GAT......... 31 13 , 10 10 81:>A/Denmark/115,2010/12/14
82 >A/Denmark/113,2010/12/15 ----.................................A...................................G..C.....A................................T........C.......A.............GAT......... 38 14 , 10 10 82:>A/Denmark/113,2010/12/15
83 >A/Denmark/133,2010/12/25 ----.................................A...................................G..C.....A................................T........C.......A.............GAT......... 38 14 , 10 10 83:>A/Denmark/133,2010/12/25
84 >A/Denmark/137,2010/12/26 ----.................................A...................................G..C.....A................................T........C.......A.............GAT......... 36 14 , 10 10 84:>A/Denmark/137,2010/12/26
85 >A/Denmark/134,2010/12/27 ----.................................A...................................G..C.....A................................T........C.......A.............GAT......... 38 14 , 10 10 85:>A/Denmark/134,2010/12/27
86 >A/Denmark/26,2011/01/13 .....................................A...................................G..C.....A................................T........C.......A.............GAT......... 24 10 , 11 10 86:>A/Denmark/26,2011/01/13
87 >A/Ohio/AF21801,2011/01/20 .....................................A...................................G..C.....A.............................A...........C.......A..----------------------- 73 30 , 7 7 87:>A/Ohio/AF21801,2011/01/20
88 >A/Ohio/AF21802,2011/01/20 .....................................A...................................G..C.....A.........................................C.......A..----------------------- 73 29 , 7 6 88:>A/Ohio/AF21802,2011/01/20
89 >A/Hawaii/AF21775,2010/11/16 .....................................A...................................G..C.....A.........................................C..------------------------------- 89 36 , 6 5 89:>A/Hawaii/AF21775,2010/11/16
90 >A/Denmark/120,2010/12/20 ---..................................A...................................G..C.....A........R................................C.......A.............GAT......... 31 13 , 10 10 90:>A/Denmark/120,2010/12/20
91 >A/Denmark/24,2011/01/15 ---..................................A...................................G..C.....A........R................................C.......A.............GAT......... 32 13 , 11 10 91:>A/Denmark/24,2011/01/15
92 >A/Milan/218,2011/02/12 ----.................................A...................................G..C.....A.....C...................................C.......A.............GAT......... 36 14 , 10 10 92:>A/Milan/218,2011/02/12
93 >A/Milan/196,2011/02/01 ----.................................A...................................G..C.....A.....C...................................C.......A.............GAT......... 37 14 , 11 10 93:>A/Milan/196,2011/02/01
94 >A/Milan/224,2011/01/31 --------.............................A...................................G..C.....A.........................................---------------------------------- 116 46 , 5 4 94:>A/Milan/224,2011/01/31
95 >A/Ohio/AF21798,2011/01/18 ...............A.....................A...................................G..C.....A.........................................C.......A..----------------------- 74 30 , 8 7 95:>A/Ohio/AF21798,2011/01/18
96 >A/Ohio/AF21799,2011/01/18 .....................................A...................................G..C.....A.........................................C.......A..----------------------- 74 29 , 8 6 96:>A/Ohio/AF21799,2011/01/18
97 >A/Delaware/AF21764,2010/12/07 ...............................T.....A......................................C.....A.................................................A..----------------------- 71 28 , 5 5 97:>A/Delaware/AF21764,2010/12/07
98 >A/Hawaii/AF21773,2010/10/15 ........................C.....................G...................................A.................................................A..----------------------- 70 27 , 4 4 98:>A/Hawaii/AF21773,2010/10/15
99 >A/THA/CU-H2079,2010/07/07 ------------------------------...........A....G...................................A.........................................---------------------------------- 171 67 , 3 3 99:>A/THA/CU-H2079,2010/07/07
100 >A/THA/CU-H2293,2010/09/02 ------------------.......................A....G...................................A.........................................---------------------------------- 145 55 , 3 3 100:>A/THA/CU-H2293,2010/09/02
101 >A/THA/CU-H2085,2010/07/07 -----------------------..................A....G...................................A.................G.......................---------------------------------- 158 61 , 4 4 101:>A/THA/CU-H2085,2010/07/07
102 >A/Milan/04,2010/11/29 --------.........T..................A....A....G.......................C...........A.................................................A...............T......... 28 16 , 8 8 102:>A/Milan/04,2010/11/29
103 >A/Milan/05,2010/12/01 --------.........T..................A....A....G.......................C...........A.................................................A...............T......... 28 16 , 8 8 103:>A/Milan/05,2010/12/01
104 >A/Milan/10,2010/12/27 --------.........T..................A....A....G.......................C...........A.................................................A...............T......... 28 16 , 8 8 104:>A/Milan/10,2010/12/27
105 >A/Milan/26,2011/01/18 --------.........T..................A....A....G...................C...............A.................................................A...............T......... 28 16 , 8 8 105:>A/Milan/26,2011/01/18
106 >A/Milan/03,2010/11/24 --------.........T..................A....A....G.......................C...........A.................................................A...............T......--- 52 19 , 11 8 106:>A/Milan/03,2010/11/24
107 >A/THA/CU-C1025,2010/07/29 -------------------------------------------------------------------------.........A.........A..............G................---------------------------------- 245 110 , 3 3 107:>A/THA/CU-C1025,2010/07/29
108 >A/THA/CU-C1006,2010/07/22 --------------------------------------------------------------------------------..A.........A..............G.................--------------------------------- 258 116 , 3 3 108:>A/THA/CU-C1006,2010/07/22
109 >A/Milan/15,2011/01/11 --------................C.....................G...................................A.................................................A...............T..G...... 26 14 , 6 6 109:>A/Milan/15,2011/01/11
110 >A/Denmark/116,2010/12/14 ----....................C.....................G...................................A.................................................A...............T..G...... 35 10 , 7 6 110:>A/Denmark/116,2010/12/14
111 >A/Denmark/108,2010/12/10 ---.....................C.....................G...................................A.................................................A...............T..G...... 29 9 , 8 6 111:>A/Denmark/108,2010/12/10
112 >A/Milan/01,2011/01/04 --------................C.....................G.......................C...........A.........................................---------------------------------- 116 46 , 5 4 112:>A/Milan/01,2011/01/04
113 >A/THA/34-9936,2010/07/14 -------------------------------------------...G...................................A..................--------------------------------------------------------- 248 102 , 3 2 113:>A/THA/34-9936,2010/07/14
114 >A/THA/CU-H2301,2010/09/02 -------------------------..........................A.......................C......A.........................................---------------------------------- 161 62 , 3 3 114:>A/THA/CU-H2301,2010/09/02
115 >A/THA/ST_0111,2010/10/ ----------------------------------------------.....A.......................C......A--------------------------------------------------------------------------- 288 124 , 3 3 115:>A/THA/ST_0111,2010/10/
116 >A/THA/ST_0112_1,2010/10/ -------------------------------------------........A.......................C......A.......-------------------------------------------------------------------- 268 114 , 3 3 116:>A/THA/ST_0112_1,2010/10/
117 >A/THA/ST_0113,2010/10/ ---------------------------------------------......A.......................C......A............................----------------------------------------------- 227 95 , 3 3 117:>A/THA/ST_0113,2010/10/
118 >A/THA/ST_0153,2010/10/ ----------------------------------------------.....A.......................C......A....----------------------------------------------------------------------- 280 120 , 3 3 118:>A/THA/ST_0153,2010/10/
119 >A/Milan/186,2011/01/26 --------...........................................A.......................C......A..............................C..........---------------------------------- 114 46 , 4 4 119:>A/Milan/186,2011/01/26
120 >A/Milan/170,2011/01/20 --------...........................................A.......................C......A..............................C..........---------------------------------- 117 46 , 6 4 120:>A/Milan/170,2011/01/20
121 >A/THA/SN_0112_2,2010/10/ -------------------------------------------........A.......................C......A...............------------------------------------------------------------ 255 106 , 4 3 121:>A/THA/SN_0112_2,2010/10/
122 >A/THA/CU-H2295,2010/09/02 ---------------------..............................A..........A............C......A.........................................---------------------------------- 157 59 , 5 4 122:>A/THA/CU-H2295,2010/09/02
123 >A/Korea/AF21781,2010/12/21 ...................................................A..........A............C......A............................T................G......----------------------- 72 29 , 6 6 123:>A/Korea/AF21781,2010/12/21
124 >A/Korea/AF21779,2010/12/24 ...................................................A..........A............C......A............................T................G......----------------------- 72 29 , 6 6 124:>A/Korea/AF21779,2010/12/24
125 >A/Korea/AF21782,2010/12/29 ...................................................A..........A............C......A............................T................G......----------------------- 73 29 , 7 6 125:>A/Korea/AF21782,2010/12/29
126 >A/Ontario/804635,2010/12/14 ...................................................A..........A............C......A............................T................G...................T...T..... 9 8 , 9 8 126:>A/Ontario/804635,2010/12/14
127 >A/Tunisia/422,2011/01/07 ...................................................A..........A............C......A............................T................G...................T...T..... 9 8 , 9 8 127:>A/Tunisia/422,2011/01/07
128 >A/Milan/210,2011/02/08 ----...............................................A...T......A............C......A...........................GT..G.............G...................T...T..... 39 15 , 13 11 128:>A/Milan/210,2011/02/08
129 >A/Milan/121,2011/02/02 --------...........................................A...T......A............C......A...........................GT..G.........---------------------------------- 119 50 , 8 8 129:>A/Milan/121,2011/02/02
130 >A/Bandar Abbas/5096,2010/10/02 ..........................C........................A.......................C......A..................................................G..............T...T..... 9 7 , 9 7 130:>A/Bandar Abbas/5096,2010/10/02
131 >A/North Carolina/AF21797,2011/01/20 ...................................................A.......................C......A.A................................................G.----------------------- 72 28 , 6 5 131:>A/North Carolina/AF21797,2011/01/20
132 >A/Shahriar/5336,2010/12/06 ...................................................A.......................C......A..............................C........C............A....C...G...T...T..... 11 10 , 11 10 132:>A/Shahriar/5336,2010/12/06
133 >A/Karaj/5660,2010/12/13 ...................................................A.......................C......A..............................C........C............A........G...T...T..... 15 9 , 15 9 133:>A/Karaj/5660,2010/12/13
134 >A/THA/34-9913,2010/07/14 --------------------------------------------------------------------..............A..................--------------------------------------------------------- 294 126 , 2 1 134:>A/THA/34-9913,2010/07/14
135 >A/THA/34-9943,2010/07/14 -------------------------------------------.......................................A..................--------------------------------------------------------- 247 101 , 2 1 135:>A/THA/34-9943,2010/07/14
136 >A/THA/CU-H2176,2010/08/17 ..................................................................................A.....C.........T.........................C......................AT.T......T 8 8 , 8 8 136:>A/THA/CU-H2176,2010/08/17
137 >A/Denmark/104,2010/11/17 ----..............................................................................A.........................................C.......A..............AT......T.. 35 10 , 7 6 137:>A/Denmark/104,2010/11/17
138 >A/Korea/AF21778,2010/12/23 ............................................................................C.....A.A.......................................C.......A..----------------------- 73 28 , 7 5 138:>A/Korea/AF21778,2010/12/23
139 >A/Denmark/114,2010/12/14 ---..................................A......................................C.....A.........................................C.......A..............AT.......C. 31 11 , 10 8 139:>A/Denmark/114,2010/12/14
140 >A/Milan/219,2011/02/13 ----.......T.........................A......................................C.....A....................A....................C.......A..............AT.......C. 36 14 , 10 10 140:>A/Milan/219,2011/02/13
141 >A/Ontario/130741,2010/10/13 ............................................................................C.....AA........................................C.......A..............AT......... 11 7 , 11 7 141:>A/Ontario/130741,2010/10/13
142 >A/Denmark/20,2011/01/04 ---.................A.......................................................C.....A....................A....................C.......A..............AT......T.. 33 12 , 12 9 142:>A/Denmark/20,2011/01/04
143 >A/District of Columbia/AF21769,2011/01/10 ...............A...............................................A............C.....A..............T.......................A..C.......A..----------------------- 75 31 , 9 8 143:>A/District of Columbia/AF21769,2011/01/10
144 >A/Ohio/AF21800,2011/01/18 .......................................A.......................A............C.....A..............T.......................A..C.......A..----------------------- 75 31 , 9 8 144:>A/Ohio/AF21800,2011/01/18
145 >A/THA/CU-C1028,2010/08/05 -------.......G........................A...............................A..........A........................G................---------------------------------- 111 46 , 5 5 145:>A/THA/CU-C1028,2010/08/05
146 >A/THA/CU-C1005,2010/07/22 -------.......G........................A...............................A..........A........................G.................--------------------------------- 110 45 , 5 5 146:>A/THA/CU-C1005,2010/07/22
147 >A/THA/CU-H2417,2010/09/13 ..............G........................A...............................A..........A........................G........................A...............T......... 8 7 , 8 7 147:>A/THA/CU-H2417,2010/09/13
148 >A/Ghom/169,2010/12/29 ...................G.................A.A..........................C...............AA...G...........T................................A............A..T......... 11 11 , 11 11 148:>A/Ghom/169,2010/12/29
149 >A/Ghom/198,2010/12/29 ...................G.................A.A..........................C...............AA...G...........T................................A............A..T......... 11 11 , 11 11 149:>A/Ghom/198,2010/12/29
150 >A/Ghom/167,2010/12/30 ...................G.................A.A..........................C...............AA...G...........T................................A............A..T......... 11 11 , 11 11 150:>A/Ghom/167,2010/12/30
151 >A/Denmark/127,2010/12/22 ----.........T.....G.................A.A..........................C...............AA...G...........T...........................G....A............A..T......... 39 17 , 13 13 151:>A/Denmark/127,2010/12/22
152 >A/Milan/64,2011/01/20 ----.........T.....G.................A.A..........................C...............AA...G...........T.......--------------------------------------------------- 155 64 , 9 9 152:>A/Milan/64,2011/01/20
153 >A/Denmark/27,2011/01/13 ----.........T.....G.................A.A..........................C...............AA...G...........T...........................G....A............A..T......... 42 17 , 14 13 153:>A/Denmark/27,2011/01/13
154 >A/Washington/AF21804,2011/01/02 ...................G.................A.A..........................C...............AA...G...........T......T.........................A..----------------------- 77 33 , 11 10 154:>A/Washington/AF21804,2011/01/02
155 >A/Milan/55,2011/01/17 --------...........G........C....C...A................A...........C...............AA...G...........T.................C.........C....A............A..T......... 35 23 , 15 15 155:>A/Milan/55,2011/01/17
156 >A/Milan/162,2011/01/14 --------...........G........C....C...A................A...........C...............AA...G...........T.................C......---------------------------------- 122 53 , 11 11 156:>A/Milan/162,2011/01/14
157 >A/Milan/40,2011/01/18 --------...........G........C....C...A................A...........C...............AA...G...........T.................C.........C....A............A..T......... 35 23 , 15 15 157:>A/Milan/40,2011/01/18
158 >A/Milan/220,2011/01/20 --------...........G........C....C...A................A...........C...............AA...G...........T.................C......---------------------------------- 122 53 , 11 11 158:>A/Milan/220,2011/01/20
159 >A/Milan/98,2011/01/21 --------...........G........C....C...A................A...........C...............AA...G...........T.................C......---------------------------------- 122 53 , 11 11 159:>A/Milan/98,2011/01/21
160 >A/Milan/124,2011/02/04 ----...............G........C....C...A................A...........C...............AA...G...........T.......--------------------------------------------------- 156 65 , 10 10 160:>A/Milan/124,2011/02/04
161 >A/Milan/35,2011/01/13 --------...........G........C....C...A................A...........C...............AA...G...........T.................C.........C..A.A............A..T......... 36 24 , 16 16 161:>A/Milan/35,2011/01/13
162 >A/Milan/166,2011/01/17 --------...........G........C....C...A................A...........C...............AA...G...........T.................C......---------------------------------- 120 53 , 12 11 162:>A/Milan/166,2011/01/17
163 >A/Milan/80,2011/01/24 --------...........G........C....C...A................A...........C...............AA...G...........T.................C.........C....A............A..T......... 36 23 , 16 15 163:>A/Milan/80,2011/01/24
164 >A/Milan/99,2011/01/21 --------...........G........C....C...A................A...........C...............AA...G...........T........................---------------------------------- 120 52 , 10 10 164:>A/Milan/99,2011/01/21
165 >A/Milan/84,2011/01/25 --------...........G........C.C..C...A................A...........C...............AA...G...........T.................C.........C....A............A..T......... 36 24 , 16 16 165:>A/Milan/84,2011/01/25
166 >A/Milan/90,2011/01/26 --------...........G........C....C...A................A...........C...............AA...G...........T.................C.........C....A............A..T......A.. 36 24 , 16 16 166:>A/Milan/90,2011/01/26
167 >A/Milan/75,2011/01/26 --------...........G........C....C...A................A...........C...............AA...G...........T.................C......---------------------------------- 122 53 , 12 11 167:>A/Milan/75,2011/01/26
168 >A/Milan/188,2011/01/27 ----....A..........G........C....C...A................A...........C...............AA...G...........T.................C.........C....A............A..T......... 42 20 , 16 16 168:>A/Milan/188,2011/01/27
169 >A/Milan/230,2011/02/03 ----....C..........G........C....C...A................A...........C...............AA...G...........T.................C.........C....A............A..T.......-- 46 22 , 16 16 169:>A/Milan/230,2011/02/03
170 >A/Milan/194,2011/01/31 ----...............G........C....C...A................A.....G.....C...............AA...G...........T.................C.........C....A............A..T......... 42 20 , 16 16 170:>A/Milan/194,2011/01/31
171 >A/Milan/213,2011/02/10 ----...........T...G........C....C...A................A...........C...............AA...G...........T.................C.........C....A............A..T......... 42 20 , 16 16 171:>A/Milan/213,2011/02/10
172 >A/Milan/236,2011/02/19 ----...............G........C....C...A................A...........C...............AA...G...........T.................C.........C....A............A..T......... 42 19 , 16 15 172:>A/Milan/236,2011/02/19
173 >A/Milan/122,2011/01/31 --------...........G........C....C...A................A...........C...............AA...G...........T.................C......---------------------------------- 123 53 , 12 11 173:>A/Milan/122,2011/01/31
174 >A/Milan/237,2011/02/20 ----...............G........C....C...A................A...........C...............AA...G...........T.................C.........C....A............A..T......... 42 19 , 16 15 174:>A/Milan/237,2011/02/20
175 >A/Milan/197,2011/01/31 --------...........G........C....C...A............A...A...........C...............AA...G...........T.................C......---------------------------------- 121 54 , 12 12 175:>A/Milan/197,2011/01/31
176 >A/Milan/206,2011/02/08 --------...........G........C....C...A................A...........C...............AA...G...........T.................C.......--------------------------------- 119 52 , 12 11 176:>A/Milan/206,2011/02/08
177 >A/Milan/88,2011/01/24 --------...........G........C....C...AA...............A...........C...............AA...G...........T.................C.........C....A............A..T.T....... 37 25 , 17 17 177:>A/Milan/88,2011/01/24
178 >A/Milan/24,2011/01/14 --------...........G........C....C...AA...............A....T......C...............AA...G...........T.................C.........C....A............A..T....T.... 49 26 , 18 18 178:>A/Milan/24,2011/01/14
179 >A/Milan/72,2011/01/21 --------...........G........C....C...AA...............A....T......C...............AA...G...........T.................C.........C....A............A..T....T.... 38 26 , 18 18 179:>A/Milan/72,2011/01/21
180 >A/Milan/181,2011/01/28 ----....A..........G........C....C...A................A...........C...............AA...G...........T.................C..............A............A..T......... 42 19 , 16 15 180:>A/Milan/181,2011/01/28
181 >A/Milan/184,2011/01/25 --------....................C....C...A................A...........C...............AA...G..A........T.................C..A...---------------------------------- 123 54 , 12 12 181:>A/Milan/184,2011/01/25
182 >A/Milan/235,2011/02/22 ----...............G........C....C...A.........T......A.........G.C...............AA...G...........T................GC.........C....A............A..T......A.. 47 23 , 21 19 182:>A/Milan/235,2011/02/22
183 >A/Milan/160,2011/01/11 --------...........G......C..........A....A.......................C...............AA...G...........T....................A...---------------------------------- 122 52 , 11 10 183:>A/Milan/160,2011/01/11
184 >A/Sw/THA/CU-RP3,2010/09/ ..................T..C.....................................................A......A...G.................................A...........A..........C....TC......-- 29 12 , 14 10 184:>A/Sw/THA/CU-RP3,2010/09/
185 >A/Sw/Taiwan/TD-2542,2010/09/01 ...............................................T..................................A.........................................................C.......T......... 11 4 , 11 4 185:>A/Sw/Taiwan/TD-2542,2010/09/01
186 >A/Yamagata/165,2010/08/03 ............................A..A................................................A.A......................................T.....------------------------------- 91 36 , 7 5 186:>A/Yamagata/165,2010/08/03
187 >A/Beijing/3872,2010/11/ .......C...T..............................A.............G...................C...A.A.....................................................G..........AT.T......T 13 12 , 13 12 187:>A/Beijing/3872,2010/11/
188 >A/Korea/AF21780,2010/12/24 .......C...T............................................G...........G.......C...A.A.........................................C.......A..----------------------- 77 32 , 11 9 188:>A/Korea/AF21780,2010/12/24
189 >A/Korea/AF21783,2010/12/29 .......C...T............................................G..........C........C...A.A.........................................C.......A..----------------------- 78 32 , 12 9 189:>A/Korea/AF21783,2010/12/29
190 >A/Fuzhou/02,2010/12/19 ..A........T...................A.............A......G...G...................C..AA.A.........................................C.......A..............AT.T......T 19 16 , 19 16 190:>A/Fuzhou/02,2010/12/19
191 >A/Sw/THA/CU-DP83,2010/12/ ...........T................................................................C...A.A..........G........G.........T............AG....................AT.TG.....T 26 14 , 15 14 191:>A/Sw/THA/CU-DP83,2010/12/
192 >A/THA/SN_0116,2010/10/ ----------------------------------------------..........................T...C...A.A.............-------------------------------------------------------------- 266 112 , 5 4 192:>A/THA/SN_0116,2010/10/
193 >A/Denmark/111,2010/12/07 ----......G.....................C...........A..................A.............A....A..T...................A....G.....G........A.............C........T..G....-- 44 20 , 14 14 193:>A/Denmark/111,2010/12/07
194 >A/New Jersey/AF21791,2011/01/13 ..........G.....................C...........A..................A.............A....A..T...................A....G.....G........A.........----------------------- 79 34 , 13 11 194:>A/New Jersey/AF21791,2011/01/13
195 >A/Florida/AF21771,2011/01/12 .A......A.G.................................A..................A.............A....A..T...................A....G.....G........A.........----------------------- 78 35 , 12 12 195:>A/Florida/AF21771,2011/01/12
196 >A/North Carolina/AF21796,2011/01/18 .A....G...G.......................T.........A..................A.............A....A..T..................TA....G.....G........A.........----------------------- 80 37 , 14 14 196:>A/North Carolina/AF21796,2011/01/18
197 >A/South Carolina/AF21803,2011/01/14 .A....G...G.......................T.........A..................A.............A....A..T..................TA....G.....G........A....A....----------------------- 81 38 , 15 15 197:>A/South Carolina/AF21803,2011/01/14
198 >A/Arizona/AF21768,2011/01/07 .A....G...G.......................T.........A...............G..A.............A....A..T..................TA....G.....G........A.........----------------------- 82 38 , 16 15 198:>A/Arizona/AF21768,2011/01/07
199 >A/Mexico/InDRE1946,2011/03/22 .........TG.........A......T................A........A...C.....A.............A....A..T...................A....G.....G........A..........G..C........T......... 18 18 , 18 18 199:>A/Mexico/InDRE1946,2011/03/22
200 >A/Mexico/InDRE2192,2011/03/28 -------------------------------------.......A........A...C.....A.............A....A..T............------------------------------------------------------------ 248 104 , 7 7 200:>A/Mexico/InDRE2192,2011/03/28
201 >A/Mexico/InDRE2197,2011/03/28 -------------------------------------.......A........A...C.....A.............A....A..T............------------------------------------------------------------ 248 104 , 7 7 201:>A/Mexico/InDRE2197,2011/03/28
202 >A/Mexico/InDRE2200,2011/03/29 -------------------------------------.......A........A...C.....A.............A....A..T............------------------------------------------------------------ 248 104 , 7 7 202:>A/Mexico/InDRE2200,2011/03/29
203 >A/Mexico/InDRE2222,2011/03/31 -------------------------------------.......A........A...C.....A.............A....A..T............------------------------------------------------------------ 248 104 , 7 7 203:>A/Mexico/InDRE2222,2011/03/31
204 >A/Mexico/InDRE2415,2011/03/31 -------------------------------------.......A........A...C.....A.............A....A..T............------------------------------------------------------------ 248 104 , 7 7 204:>A/Mexico/InDRE2415,2011/03/31
205 >A/Mexico/InDRE2407,2011/04/01 -------------------------------------.......A........A...C.....A.............A....A..T............------------------------------------------------------------ 248 104 , 7 7 205:>A/Mexico/InDRE2407,2011/04/01
206 >A/Mexico/InDRE2408,2011/04/02 -------------------------------------.......A........A...C.....A.............A....A..T............------------------------------------------------------------ 248 104 , 7 7 206:>A/Mexico/InDRE2408,2011/04/02
207 >A/Mexico/InDRE1945,2011/03/ .........TG.........A......T................A........A...C.....A.............A....A..T....A..............A....G.....G........A..........G..C........T......... 19 19 , 19 19 207:>A/Mexico/InDRE1945,2011/03/
208 >A/Mexico/InDRE1947,2011/03/23 .........TG.........A.......................A........A...C.....A.............A....A..T..............G....A....G.....G........A..........G..C........T......... 18 18 , 18 18 208:>A/Mexico/InDRE1947,2011/03/23
209 >A/Mexico/InDRE2413,2011/03/27 -------------------------------------.......A........A...C.....A.............A....A..T...........A------------------------------------------------------------ 250 105 , 9 8 209:>A/Mexico/InDRE2413,2011/03/27
210 >A/Mexico/InDRE2195,2011/03/28 -------------------------------------.......A........A...C.....A.............A....A..T....RR......------------------------------------------------------------ 250 106 , 9 9 210:>A/Mexico/InDRE2195,2011/03/28
211 >A/Ontario/741328,2010/11/23 ...G...............................................A......C...A....C.......C......A...........G..............T..................G...................T...T.A... 13 13 , 13 13 211:>A/Ontario/741328,2010/11/23
212 >A/Ontario/3620,2010/11/24 ...G...............................................A......C...A....C.......C......A...........G..............T..................G...................T...T.A... 13 13 , 13 13 212:>A/Ontario/3620,2010/11/24
213 >A/Milan/10,2011/01/03 --------...........G........C....C.......A....G.......................C...........A.........................................---------------------------------- 118 49 , 7 7 213:>A/Milan/10,2011/01/03
214 >A/Hawaii/AF21774,2010/11/07 .................T.......................A....G...................................AA................................................A..----------------------- 76 29 , 10 6 214:>A/Hawaii/AF21774,2010/11/07
215 >A/Tunisia/197,2011/01/04 ..............................C......................................A............A..........................................A......A...............T......... 15 6 , 15 6 215:>A/Tunisia/197,2011/01/04
216 >A/HuZhou/01,2010/12/ ........................A..................A....C...............CT...............CA.................G.............G................TA...............T......... 16 12 , 16 12 216:>A/HuZhou/01,2010/12/
217 >A/Mexico/InDRE2194,2011/03/28 -------------------------------------...G..A....C...............CT...............CA...............------------------------------------------------------------ 248 104 , 7 7 217:>A/Mexico/InDRE2194,2011/03/28
218 >A/Mexico/InDRE2214,2011/03/31 -------------------------------------...G..A....C...............CT...............CA...............------------------------------------------------------------ 248 104 , 7 7 218:>A/Mexico/InDRE2214,2011/03/31
219 >A/Mexico/InDRE2419,2011/04/02 -------------------------------------...G..A....C...............CT...............CA...............------------------------------------------------------------ 248 104 , 7 7 219:>A/Mexico/InDRE2419,2011/04/02
220 >A/Mexico/InDRE2425,2011/04/05 -------------------------------------...G..A....C...............CT...............CA...............------------------------------------------------------------ 248 104 , 7 7 220:>A/Mexico/InDRE2425,2011/04/05
221 >A/Mexico/InDRE2424,2011/04/04 -------------------------------------...G..A....C...............CT...A...........CA...............------------------------------------------------------------ 250 105 , 9 8 221:>A/Mexico/InDRE2424,2011/04/04
222 >A/Sw/Minnesota/54354,2010/10/27 .T.........................A........C.............................................A................................................C..G.............T......... 17 7 , 17 7 222:>A/Sw/Minnesota/54354,2010/10/27
223 >A/Sw/Costa Rica/000125-14,2010/11/01 ..........G...........G......A...............T......T...................T................G.....TA....A......G.........T....C.....T.G.......................... 15 15 , 15 15 223:>A/Sw/Costa Rica/000125-14,2010/11/01
224 >A/Sw/Costa Rica/000125-19,2010/11/01 ..........G...........G......A...............T......T...................T................G.....TA....A......G.........T....C.....T.G.....G.................... 17 16 , 17 16 224:>A/Sw/Costa Rica/000125-19,2010/11/01
225 >A/Sw/Costa Rica/000125-20,2010/11/01 ..........G...........G......A...............T......T....................................G.....TA....A......G.........T....C.....T.G..........A............... 15 15 , 15 15 225:>A/Sw/Costa Rica/000125-20,2010/11/01
226 >A/Sw/Costa Rica/000125-3,2010/11/01 ..........G...........G......A...............T......T........T............G...T..........G.....TA....A......G.........T....C.....T.G.....GT...A............... 20 20 , 20 20 226:>A/Sw/Costa Rica/000125-3,2010/11/01
227 >A/Sw/Costa Rica/000125-15,2010/11/01 ..........G...........G......A...............T......T.....................G...T..........G.....TA....A......G.........T....C.....T.G.......................... 19 16 , 19 16 227:>A/Sw/Costa Rica/000125-15,2010/11/01
228 >A/Sw/Costa Rica/000125-16,2010/11/01 ..........G...........G......A...............T......T........T.T........T................G.....TA....A......G.........T....C.....T.G......T................... 19 18 , 19 18 228:>A/Sw/Costa Rica/000125-16,2010/11/01
229 >A/Korea/AF21786,2011/01/04 .........T...........................A.......T..............................C.....A.........................................C.......A..----------------------- 78 30 , 12 7 229:>A/Korea/AF21786,2011/01/04
230 >A/Sw/THA/CU-PL65,2010/11/ ................A................................G.........T........G..........C.............G.................T............C.......A........A......T......... 20 11 , 20 11 230:>A/Sw/THA/CU-PL65,2010/11/
231 >A/Sw/THA/CU-PL63,2010/11/ -------.........A................................G..........G.......G..........C......................G.........T............AG..............A......T......... 39 18 , 21 11 231:>A/Sw/THA/CU-PL63,2010/11/
232 >A/Sw/THA/CU-RP1,2010/09/ ...G......T..A....T..C.....................................................A......A...G.............................................A..........C....TC........ 34 12 , 34 12 232:>A/Sw/THA/CU-RP1,2010/09/
---Index------------------------------------------GGCAATATGCACTCAGGCCAGTAATGTCTGTGTTCATGTGAGGGGGACTAGGATTGAATCACGGACTTAGAGCACTGGGTGTTGGCAATAGATAACGGCGAGAGCGCAAGTCGTACAACAGGTTTGAAACGAGATGAAATTGGTTGAGCTCACCGGTC
-codon-position----------------------------------- 112 1 1 1 111 11 22 1 12 2 1 1 1 1 11 1 2 22 21 1 11211 1212 12 12 2 11 1 22 1 12 1 2 1 2 112 1 1 212
00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000111111111111111111111111111111111111111
00000000011111111111222222222223333333333333344444444444444555555555555555556666666666666777777777778888888889999999999000000001111111122222233333344444445666
01246667934444666788011124588990022334445669902334555667789012333455666677990012445678999011112455790033467890023334569011225881345677901223725678800334676255
66270342152478368213702829628182314230287060684237013252892267169625357839285701078581078856799849761406950090310345735227036068108512465273597840638079463936
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April 28th, 2011, 07:59 AM
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Senior User
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Join Date: Jun 2007
Posts: 2,963
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Re: Sequences at Genbank!
Here's a different look at the new InDRE/Chihuahua sequences from Genbank, including the first 3 full length and 8 partials from the last submission. I shortened the 3 full ones for comparison purposes.
We are seeing 2 well-defined groups and a 3rd odd one from just the partials. I underlined the changes at position D225N/X (G715A and G715R, A716R) from the first group; there are no changes in that position in the new group.
A357G,G390A,T433C,A539C,C546T,G565A,C570A,T647C,T6 58A InDRE2424
A357G,G390A,T433C,A539C,C546T,T647C,T658A InDRE2419
A357G,G390A,T433C,A539C,C546T,T647C,T658A InDRE2425
A357G,G390A,T433C,A539C,C546T,T647C,T658A InDRE/2194
A357G,G390A,T433C,A539C,C546T,T647C,T658A InDRE/2214
***************
A354G,G396A,T462A,A489C,G536A,G607A,T658A,C681T,G7 59A InDRE2413
G396A,T462A,A489C,G536A,G607A,T658A,C681T InDRE2407
G396A,T462A,A489C,G536A,G607A,T658A,C681T InDRE2408
G396A,T462A,A489C,G536A,G607A,T658A,C681T InDRE2415
G396A,T462A,A489C,G536A,G607A,T658A,C681T,G715R,A716R InDRE/2195
G396A,T462A,A489C,G536A,G607A,T658A,C681T,G715A, InDRE/1945
G396A,T462A,A489C,G536A,G607A,T658A,C681T InDre/2192
G396A,T462A,A489C,G536A,G607A,T658A,C681T InDRE/1946
G396A,T462A,A489C,G536A,G607A,T658A,C681T InDRE/1947
G396A,T462A,A489C,G536A,G607A,T658A,C681T InDRE/2197
G396A,T462A,A489C,G536A,G607A,T658A,C681T InDRE/2200
G396A,T462A,A489C,G536A,G607A,T658A,C681T InDRE/2222
****************
G408A,A478G,G605C,G640A,T658A,G754A InDRE4274
G408A,A478G,G605C,G640A,T658A InDRE2409
G340A,A579G,G605C,T658A InDRE/2202
******************************
Here are the 3 full length HA sequences (tails cut off), INDRE/1945,46,47
InDRE/1945
C135T,A142G,G207A,C282T,G396A,T462A,A489C,G536A,G6 07A,T658A,C681T,G715A,
G865A,T903G,A957G,G1080A,A1215G,T1233C,C1408T,A173 0C,
InDRE/1946
C135T,A142G,G207A,C282T,G396A,T462A,A489C,G536A,G6 07A,T658A,C681T,G865A,
T903G,A957G,G1080A,A1215G,T1233C,C1408T,A1730C,
InDRE/1947
C135T,A142G,G207A,G396A,T462A,A489C,G536A,G607A,T6 58A,C681T,A801G,G865A,
T903G,A957G, G1080A,A1215G,T1233C,C1408T,A1730C
__________________
The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918
Last edited by mixin; April 30th, 2011 at 07:27 AM.
Reason: Added the 3 full length sequences
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April 30th, 2011, 03:37 AM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,944
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Re: Sequences at Genbank!
did we have Chile already ?
remember, they had a bad wave in mid 2009, together
with Argentina and we were wondering whether the
virus had mutated
well, I see I had mxsa5 from Jan.2011, 238 viruses from South America,
54 of them from Chile
Anyway, Chile sequences at genbank, maybe old ones and I'm running
them through my program, 61 viruses, results in ~10min
A/Santiago/3221/2009/06/30(H1N1) has a different NP (segment 5)
Chile1(46=90%) markers: C68T(1),G1485A(5),G89A(7),G339A(7)
Chile2(5=10%) markers: C1263T(2),T414C(8)
Code:
00000001111122 00112 0001112 000011111 000111111 00000011 000000 00000
01123490367911 46350 0592370 069911344 123122445 34457801 003456 03334
61227869527456 60746 8586737 953848403 090456890 12794965 683990 72681
87368995893733 13421 4103520 584308187 083618890 66192435 999290 30774
-codon-position----------------------------2 1 2 2 2 22 11 2112 1 11 2 2 1 21 1 2 2 121
---Index-----------------------------------CAGAATCGCGGAAG GGAGG GGACAGC CTAACAACC GGCGGGGGA GCCAACAT GGGGCG ACAAT
1 >A/******/index/2009/02/01 .............. ..... ....... ......... ......... ........ ...... .....
2 >A/Chile/95/2009/05/27 T........A...A ..... ....... .A.....T. .A.AAAA.. A...G... .AAA.A ..G.. 1
3 >A/Chile/1624/2009/06/15 T........A...A ..... ....... .A.....T. .A.AAAA.. A...G... .AAA.A ..G.. 1
4 >A/Chile/1603/2009/06/15 T........A...A ..... ....... .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 1
5 >A/Chile/158/2009/05/28 T........A...A ..... ....... .A.....T. .A.AA.A.. A.T.G.G. .AAA.A ..G.. 1
6 >A/Chile/2009/2009/06/18 T........A...A ..... ....... .A.....T. .A.AA.A.. A.T.G.G. .AAA.A ..G.. 1
7 >A/Chile/88/2009/05/27 T........A...A ..... ....... .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 1
8 >A/Chile/3819/2009/07/06 TG.......A...A ..... ......T .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 2
9 >A/Chile/1586/2009/06/13 TG.......A...A ..... ......T .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 2
10 >A/Chile/3019/2009/06/26 TG.......A...A ..... ......T .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 2
11 >A/Chile/3361/2009/07/01 TG.......A...A ..... ....... .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 1
12 >A/Chile/4438/2009/07/20 T........A...A ..... ....... .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 1
13 >A/Chile/28/2009/05/23 T............A ..... ....... .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 1
14 >A/Chile/3349/2009/07/01 T............A ..... .....A. .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 1
15 >A/Chile/4064/2009/07/09 T............A ..... .....A. .A.....T. .A.AA.A.. AT..G... .AAA.A ..G.. 2
16 >A/Chile/31/2009/05/25 T............A ..... ....TA. .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 1
17 >A/Chile/32/2009/05/25 T............A ..... ....TA. .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 2
18 >A/Chile/3295/2009/06/30 T............A ..... .....A. .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 2
19 >A/Chile/3935/2009/07/07 T............A ..... .....A. .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 2
20 >A/Chile/3244/2009/06/30 T............A ..... .....A. .A.....T. .A.AA.A.. A...G... AAAA.A ..G.. 1
21 >A/Chile/4257/2009/07/13 T............A ..... .....A. .A.....T. .A.AA.A.. A...G... AAAA.A ..G.. 2
22 >A/Chile/36/2009/05/25 T.......TA...A ..... .....A. .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 1
23 >A/Chile/56/2009/05/26 T.......TA...A ..... ....... .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 1
24 >A/Chile/3056/2009/06/26 T........A...A ..... ....... .AG....T. .A.AA.A.. A...G... .AAATA ..G.. 1
25 >A/Chile/3123/2009/06/26 T.A..........A ..... ....... .AG....T. .A.AA.A.. A...G... .AAATA ..G.. 1
26 >A/Chile/1598/2009/06/15 T.A..........A ...A. ....... .A.....T. .A.AA.A.. A...G... .AAA.A ..GG. 1
27 >A/Chile/3242/2009/06/30 T.A..........A ...A. ....... .A.....T. .A.AA.A.. A...G... .AAA.A ..GG. 2
28 >A/Chile/1600/2009/06/15 T............A ..... ....... .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 1
29 >A/Chile/40/2009/05/25 T............A ..... ..G.... .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 1
30 >A/Chile/2362/2009/06/22 T............A ..... ..G.... .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 2
31 >A/Chile/1599/2009/06/15 T............A ..... ..G.... .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 2
32 >A/Chile/42/2009/05/25 T............A ..... ..G.... .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 1
33 >A/Chile/19/2009/05/22 T............A A.... ....... .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 1
34 >A/Chile/3553/2009/07/02 T............A A.... ....... .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 2
35 >A/Chile/3905/2009/07/07 T............A A...A ....... .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 1
36 >A/Chile/4406/2009/07/17 T............A A...A ....... .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 2
37 >A/Chile/3760/2009/07/06 T............A A...A ....... .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 2
38 >A/Chile/3467/2009/07/02 T............A A...A ....... .A.....T. .A.AA.A.. A...G... .AAA.A ..G.. 1
39 >A/Chile/4182/2009/07/10 T............A A.G.A ....... TA.....T. .A.AA.A.. A..GG... .AAA.A T.G.. 2
40 >A/Chile/4181/2009/07/09 T............A A.G.A ....... TA.....T. .A.AA.A.. A..GG... .AAA.A T.G.. 2
41 >A/Chile/2994/2009/06/26 T............A ..... ....... .A.....T. AA.AA.... A...G..C ..AA.A ..G.. 1
42 >A/Chile/2239/2009/06/19 T............A ..... ....... .A....GT. AA.AA.... A...G..C ..AA.A ..G.. 1
43 >A/Chile/180/2009/05/29 T............A ..... ....... .A....GT. AA.AA.... A...G..C ..AA.A ..G.. 1
44 >A/Chile/3220/2009/06/30 T............A ..... ....... .A.....T. .A.AA.... A...G... ..AA.A ..G.. 2
45 >A/Chile/2911/2009/06/25 T.....TA...G.A ..... ....... .A..TG.T. .AAAA.... A...G... ..AA.A ..G.. 1
46 >A/Chile/2851/2009/06/20 T.....TA...G.A ..... ....... .A..TG.T. .AAAA.... A...G... ..AA.A ..G.. 2
47 >A/Chile/2909/2009/06/25 T............A ..... ....... .A.....T. .A.AA.... A...G... ..AA.A ..G.. 1
48 >A/Chile/3586/2009/07/03 .............A ..... ...T... .A.....T. .A.AA.... A...G... ...A.A ..G.. 2
49 >A/Chile/3766/2009/07/06 ...CGC....A.GA .T... AA.T... .A.G...TT .A.AA.... A...GT.. ...A.A .TG.C 2
50 >A/Chile/3375/2009/07/01 ...CGC....A.GA .T... AA.T... .A.G...TT .A.AA.... A...GT.. ...A.A .TG.C 2
51 >A/Chile/3369/2009/07/01 .............A ..... ...T... .A.....T. .A.AA.... A...G... ...A.A ..G.C 1
52 >A/Tk/Chile/28317-6504-3/2009/08/17 .............A ..... ...T... .A.....T. .A.AA.... AT..G... ...A.A ..G.C 2
53 >A/Castro/JXP/2009/06/11 -------------- ..... ------- .A.....T. -------AT -------- ------ ----- 19
54 >A/Chile/8947/2009/05/17 -------------- ----- ------- .A..----- -------AT A...G... ------ ----- 20
55 >A/Chile/8949/2009/05/18 -------------- ----- ------- .A..----- -------AT A...G... ------ ----- 20
56 >A/Santiago/3827/2009/07/07 -------------- ----- ------- -A..----- -------AT ------.. ------ ----- 23
57 >A/Puerto Montt/Bio87/2009/06/19 -------------- ----- ------- .A..T..T. -------AT -------- ------ ----- 22
58 >A/Santiago/21579/2009/07/05 -------------- ----- ------- .A..----- -------AT A...G... ------ ----- 21
59 >A/Santiago/3221/2009/06/30 -------------- ----- ------- .A..----- .A.------ ------.. ------ ----- 22
60 >A/Chile/8886/2009/05/18 -------------- ----- ------- .A..----- -------AT A...G... ------ ----- 20
61 >A/Santiago/2009/2009/06/18 -------------- ----- ------- .A..----- -------AT ------.. ------ ----- 23
62 >A/Chile/9113/2009/05/19 -------------- ----- ------- ....----- -------AT ........ ------ ----- 21
---Index-----------------------------------CAGAATCGCGGAAG GGAGG GGACAGC CTAACAACC GGCGGGGGA GCCAACAT GGGGCG ACAAT
-codon-position----------------------------2 1 2 2 2 22 11 2112 1 11 2 2 1 21 1 2 2 121
00000001111122 00112 0001112 000011111 000111111 00000011 000000 00000
01123490367911 46350 0592370 069911344 123122445 34457801 003456 03334
61227869527456 60746 8586737 953848403 090456890 12794965 683990 72681
87368995893733 13421 4103520 584308187 083618890 66192435 999290 30774
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May 2nd, 2011, 08:49 AM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,944
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Re: Sequences at Genbank!
Quote:
Originally Posted by gsgs
no reassortments in humans reported AFAIK between
***(pH1N1) and other flu, e.g. H3N2.
Both strains circulated in USA this season simultaneously,
so there was ample opportunity.
But
in swine we have lots of reassortments.
Triple reassortment,classical swine, H1N2(2003),
H1N1,H3N2 all mixing with pH1N1
These may then jump to humans ...("mixing vessel")
with possible increased virulence or transmission.
It's just a great enhancement of virus evolution,
do we want that ?
****** segments reassorting into swine:
Code:
-----+--:HK/201/2010
+++++-++:THA/CU-SA43/2010
+++---++:IN/240218
-------+:Korea/4779
+++++-++:Korea/4940
++++--++:Korea/4941
+++++-++:THA/CU-SA412
+++++-++:THA/CU-SA432
+++-+-++:England/1382
-++---+-:NC/239108
+++-+-++:Argentina/CIP051-StaFeN2
------++:Korea/5008
+-+-+-++:MN/239106
+++++-++:Italy/116114
--+-+-++:MN/226128
----+-++:NC/226124
----+-++:NC/226125
----+-++:NC/226126
...-.-+.:SD/2
...-.-+.:SD/3
+++-+-.+:MN/A01047604
...-..++:Quebec/1259260
+++-+-++:Quebec/1265553
...-.-+.:SD/4
...-.-+.:SD/5
...-.-+.:SD/6
...-.-+.:SD/7
+:pH1N1
-:other
.: not available |
updated list, reassorted swine with ****** and other segments
updated list, reassorted Sw with ****** and other segments
Code:
308 >A/******/index/2009-02-01
ommmmmmm
325:501, 0, 0, 4, 2, 2, 3, 2 A/Sw/QLD/09-02865-07/2009(H1N1/08/24
mmmmmomm
226: 3, 3, 6, 16, 0,462, 0, 3 A/Sw/Korea/4940/2010(H1N2/04/
328: 4, 2, 2, 5, 6,479, 6, 7 A/Sw/Italy/116114/2010(H1N2/06/01
340: 2, 3, 1, 4, 4, 99, 6, 3 A/Sw/Thailand/CU-SA412/2010(H1N1/04/
341: 2, 1, 4, 12, 6, 99, 6, 6 A/Sw/Thailand/CU-SA433/2010(H1N1/06/
342: 2, 2, 0, 4, 4,101, 3, 3 A/Sw/Thailand/CU-SA43/2010(H1N1/02/
343: 2, 3, 3, 4, 5,100, 5, 3 A/Sw/Thailand/CU-SA432/2010(H1N1/04/
mmmomomm
6: 4, 3, 8,471, 4,468, 6, 5 A/Sw/Quebec/1265553/2010(H3N2/12/22
158: 3, 1, 4,248, 6,482, 3, 2 A/Sw/Argentina/CIP051-StaFeN2/2010(H1N2/05/
159: 4, 1, 1,236, 3,485, 7, 4 A/Sw/England/1382/2010(H1N2/04/13
227: 1, 0, 3,138, 0,469, 0, 3 A/Sw/Korea/4382/2009(H1N2/11/
306: 3, 1, 2,239, 3,220, 4, 1 A/Sw/Argentina/CIP051-BsAs76/2009(H1N1/10/
momomomm
128: 5, 58, 3,241, 4,466, 3, 4 A/Sw/Minnesota/239106/2010(H1N2/05/05
mmmooomm
224: 2, 3, 2, 99, 50,474, 3, 3 A/Sw/Indiana/240218/2010(H1N2/02/21
225: 3, 0, 3, 12, 52,472, 0, 3 A/Sw/Korea/4941/2010(H1N2/04/
oomomomm
76: 69, 38, 11, 69, 19,201, 3, 4 A/Sw/Minnesota/226128/2010(H1N1/09/08
ommooomo
157: 58, 3, 1,239, 50,474, 3, 51 A/Sw/North Carolina/239108/2010(H1N2/04/21
oomomomo
8: 57, 63, 1,469, 2,474, 3, 54 A/Sw/Minnesota/239105/2009(H3N2/11/24
oooomomm
233: 55, 60, 96,244, 8,473, 4, 7 A/Sw/North Carolina/226125/2010(H1N2/09/08
234: 55, 59, 65,244, 8,474, 4, 7 A/Sw/North Carolina/226126/2010(H1N2/09/08
235: 55, 60, 65,244, 8,474, 4, 7 A/Sw/North Carolina/226124/2010(H1N2/09/08
oooomoom
228: 68, 58, 62,109, 4,462,100, 3 A/Sw/Korea/4456/2009(H1N2/11/
oooooomm
230: 68, 58, 62,109, 52,462, 0, 3 A/Sw/Korea/5008/2010(H1N2/05/
ooooomoo
168: 53, 55, 56,258, 48, 2,127, 63 A/Sw/Hong Kong/201/2010(H1N1/01/07
ooooooom
231: 68, 58, 62,109, 52,462,100, 3 A/Sw/Korea/4383/2009(H1N2/11/
232: 68, 54, 62,134, 73,462,118, 3 A/Sw/Korea/4779/2010(H1N2/03/
omoooooo
216: 66, 3, 68,134, 73,469,100, 70 A/Sw/Korea/4381/2009(H1N2/11/
???o?om?
9:---,---,---,469,---,473, 6,--- A/Sw/Iowa/A0109034/2010(H3N2/11/16
10:---,---,---,469,---,473, 6,--- A/Sw/Iowa/A0109035/2010(H3N2/11/16
74:---,---,---, 68,---,205, 5,--- A/Sw/South Dakota/7/2011(H1N1/02/28
75:---,---,---, 65,---,201, 5,--- A/Sw/Minnesota/A0109101/2010(H1N1/11/17
129:---,---,---,240,---,469, 5,--- A/Sw/South Dakota/2/2010(H1N2/11/23
130:---,---,---,242,---,469, 5,--- A/Sw/Iowa/A0109071/2010(H1N2/11/16
132:---,---,---,242,---,471, 3,--- A/Sw/South Dakota/4/2010(H1N2/12/28
134:---,---,---,240,---,469, 5,--- A/Sw/South Dakota/3/2010(H1N2/11/23
135:---,---,---,247,---,467, 5,--- A/Sw/South Dakota/5/2011(H1N2/02/25
136:---,---,---,243,---,466, 3,--- A/Sw/South Dakota/6/2011(H1N2/02/25
???o??mm
5:---,---,---,465,---,---, 7, 5 A/Sw/Quebec/1259260/2010(H3N2/12/20
mmmomo?m
131: 5, 7, 5,242, 14,469,---, 9 A/Sw/Minnesota/A01047604/2010(H1N2/12/07
???o?mm?
315:---,---,---, 73,---, 2, 3,--- A/Sw/Iowa/44837-1/2009(H1N1/11/08
40 viruses now, 18 reassortment-variants
one virus with European swine HA and also a ****** segment:
A/Sw/HK/201/2010/01/07(H1N1)
other segments are triple-reassortant (1998,USA)
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May 5th, 2011, 04:25 AM
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Senior User
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Join Date: Jun 2007
Posts: 2,963
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Re: Sequences at Genbank!
On May 3, the CDC released another group of 35 US isolates at GISAID. There are 3 from the Chihuahua clade that includes T462A and A489C.
Almost all were characterised and all of those were California/07-like; none were designated as low reactors.
I didn't see any that were oseltamivir resistant.
__________________
The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918
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May 11th, 2011, 11:41 AM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,944
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Re: Sequences at Genbank!
below the mutation table of Mexico genomes plus genomes
from a substrain (call it pre-chi) that
appeared in Sept.2009 and which seems to be the precursor
of the current "Chi" (Chihuahua,Ecuador,USA-2011) strain.
At least in segments 1,2,3,8.
This substrain is specified by the 11 Cancun mutations plus
A1381G(1),A1674G(1)
T1760G(2),C1955T(2),T2241C(2)
T1305C(3)
C1434T(5)
G724A(8)
it seems that segments 4,5,6,7 may come from another virus
by reassortment.
I.e. segment 4 was first seen in A/Germany/AF2207/2010/01/19
with markers A142C,G536A,G607A,C681T,A957G,G1080A
you see another obvious reassortment in the Canada viruses #95-#100
1,3,7,8:original,2:pre-chi,4,5,6:Cancun
the blocks in segment 1(#59-60),4(#73-75,56),7(sevral CAGT)
could be sequencing errors
Code:
000000000000000000000000000000000000001111111111111111111222222 00000000000000000000001111111111111111111111111112222222 000000000000000000000011111111111111111111111111122222 000000000000000000000000000000000000000011111111111111111111 0000000000000000000011111111111111 0000000000000000000000001111111111 00000000000000 00000000000000000000000
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678991133466771469335568801123488956781702371568117778197581368 35526656895747103458585557912511560103624026700597289045 348467928991846812688602691590120405278349236444457044 403461455569569033346044569911313668914918577812222337888057 3490377263509445945701345664895573 2003334444581910145245255967937224 00010333910596 73892246614833445902341
351690458412679590340950676921623478958730738131097456399595231 41624746496128777452743897572828465460308120911556443217 704713630282112933758924880945921307681714406468950336 565576347968209956690907855649986278885940512226789018123853 6981325654452395433598435478936744 6232012789736644561129540769408398 68906956200560 55997307957624391834884
-codon-position------------------------- 2 2 2 2 12 1 1 21 1 2 1 2 1 2 1 1 1 2 1 11 1 2 122 1 11 1 1 11 22 11 1 212 11 1 12 221211 1 12 2 12122 21221 1 12 2 12 1 2 1 11 12 22 2 1 2 1 2 212 211 1 1111 22 1 2 1 1 1 1 12211 1 1111 211 11
---Index--------------------------------TGTAGGGCAGGACAAAACGTCTTGGAGGAGGGGTACGGAGGCGGATCACGAAATATAGTCAGG ACGTTAGATAGGGGGTGCTAGTAAATACAGTGCGATGCTATATTTAACCCGCGGTC AGGGCGAGCCGAACCGTCAGTCCCGGCGGTGTGGGCTCAGACCAATTTAGCGCA AGCCGTTACCCTCGAAGAGTGTGTTGCAGATCGCCTACCACGAGACTCAGTAGAAACCCG ACGGTCTCTCTGCTTAGCCGACCGCAGGGGGCCC CTATGATGTGCAGCCTGAGGAGACAGTCGAACAA TTTCGGTCGTGACT TAATCGCACATAGCCGGAGGCTA
1 >A/******/index/2009/02/01 ............................................................... ........................................................ ...................................................... ............................................................ .................................. .................................. .............. ....................... 2 0 , 0 0 1:>A/******/index/2009/02/01
2 >A/swine/4/Mx/2009/04/ ............................................................... ..........................................C............. ...................................................... ......................A......R.......................G...... ............T..................... .NG............................... .............C ....................... 48 8 , 43 8 2:>A/swine/4/Mx/2009/04/
3 >A/Mx/InDRE4114/2009// ............................................................... .........................................G.............. ...................................................... ............................................................ .................................. .................................. .............. ....................... 9 1 , 7 1 3:>A/Mx/InDRE4114/2009//
4 >A/MxCity/018/2009/05/10 ...................................T........G.................. ....................................................A... .A.................................................... ............................................................ .................................. .................................. .............. ....................... 13 4 , 11 4 4:>A/MxCity/018/2009/05/10
5 >A/MxCity/009/2009/05/12 ..............................A.........A...................... ........................................................ ...................................................... .............................................T.............. .................................. ..........................C....... .............. ....................... 8 4 , 6 4 5:>A/MxCity/009/2009/05/12
6 >A/MxCity/017/2009/05/09 ..............................A................................ .......................G................................ ...................................................... ............................................................ .................................. .................................. .............. ....................... 16 2 , 14 2 6:>A/MxCity/017/2009/05/09
7 >A/Mx/InDRE13495/2009/04/29 ..............................A..........T..................... ........................................................ ...................................................... ............................................................ .................................. .................................. .............. ....................... 12 2 , 10 2 7:>A/Mx/InDRE13495/2009/04/29
8 >A/Mx/InDRE4115/2009// ...............G............................................... ........................................................ .................A.................................... ............................................................ .................................. .................................. .............. ....................... 4 2 , 2 2 8:>A/Mx/InDRE4115/2009//
9 >A/Mx/4115/2009/04/07 ...............G............................................... ........................................................ .................A.......................T............ ............................................................ .................................. .................................. .............. ....................... 5 3 , 3 3 9:>A/Mx/4115/2009/04/07
10 >A/Mx/InDRE4487/2009/04/14 ...............G............................................... ........................................................ .................A.................................... .............................G.............................. .................................. .................................. .............. ....................... 5 3 , 3 3 10:>A/Mx/InDRE4487/2009/04/14
11 >A/Mx/InDRE13494/2009/04/29 ............................................................... ........................................................ .................................A................T... ............................................................ .................................. .................................. .............. ....................... 14 2 , 12 2 11:>A/Mx/InDRE13494/2009/04/29
12 >A/Mx/InDRE13547/2009/04/27 ............................................................... ........................................................ ...................................................... .........................A.................................. ..A.....C......................... ..........T....................... .............. ....................... 13 4 , 11 4 12:>A/Mx/InDRE13547/2009/04/27
13 >A/MxCity/013/2009/05/09 ............................................................... ........................................................ ...................................................... .........................................................T.. ..A....................A.......... ............A.......G............. .............. ....................... 9 5 , 7 5 13:>A/MxCity/013/2009/05/09
14 >A/MxCity/007/2009/05/09 ............................................................... ...................GA.........C......................... ...................................................... .........................................................T.. ..A....................A.......... ............A.......G............. .............. ............A.......... 16 9 , 14 9 14:>A/MxCity/007/2009/05/09
15 >A/Mx/InDRE13555/2009/04/29 ............................................................... ...................GA.........C......................... ...................................................... .........................................................T.. ..A....................A.......... ............A.......G............. .............. ....................... 13 8 , 11 8 15:>A/Mx/InDRE13555/2009/04/29
16 >A/Mx/InDRE13551/2009/04/28 ............................................................... ....................................A................... ................................A..................... .........................................................T.. ..A....................A.......... ............A.......G............. .............. ....................... 13 7 , 11 7 16:>A/Mx/InDRE13551/2009/04/28
17 >A/MxCity/023/2009/05/01 ............................................................... ........................................................ ...................................................... .........................................................T.. ..A....................A.......... ............A.......G............. ............T. ....................... 11 6 , 9 6 17:>A/MxCity/023/2009/05/01
18 >A/MxCity/001/2009/05/07 ............................................................... ........................................................ ...................................................... ................................A........................T.. ..A....................A.......... ............A.......G..T.......... ............T. ....................... 12 8 , 10 8 18:>A/MxCity/001/2009/05/07
19 >A/MxCity/021/2009/05/01 ............................................................... ........................................................ ...................................................... .........................................................T.. ..A....................A.......... ............A.......G..T.......... ............T. ....................... 11 7 , 9 7 19:>A/MxCity/021/2009/05/01
20 >A/MxCity/022/2009/05/02 ............................................................... ........................................................ ...................................................... .........................................................T.. ..A....................A....R..... ............A.......G..T.......... ............T. ....................... 11 8 , 9 8 20:>A/MxCity/022/2009/05/02
21 >A/MxCity/006/2009/05/09 ............................................................G.. ........................................................ ...................................................... .........................................................T.. ..A....................A....A..... ............A.......G..T.......... ............T. ....................... 14 9 , 12 9 21:>A/MxCity/006/2009/05/09
22 >A/MxCity/003/2009/05/08 .......................................................Y....G.. ........................................................ ...................................................... .........................................................T.. ..A....................A....A..... ............A.......G..T.......... ............T. ....................... 15 10 , 13 10 22:>A/MxCity/003/2009/05/08
23 >A/MxCity/020/2009/04/30 ............................................................G.. ........................................................ ...................................................... .........................................................T.. ..A....................A....A..... ............A.......G..T.......... ............T. ....................... 12 9 , 10 9 23:>A/MxCity/020/2009/04/30
24 >A/MxCity/008/2009/05/10 .....................C......................................... ........................................................ ...................................................... .........................A...............................T.. ..A....T...............A.......... ............A.......G............. .............. ....................... 15 8 , 13 8 24:>A/MxCity/008/2009/05/10
25 >A/MxCity/002/2009/05/08 ......................................................G........ ........................................................ ...................................................... .........................................................T.. ..A....................A.......... ............A.......G............. .............. ....................... 12 6 , 10 6 25:>A/MxCity/002/2009/05/08
26 >A/Mx/4604/2009/04/19 ............................................................... ........................................................ ...................................................... .........................................................T.. ..A....................A.......... ............A.......G............. .............. ....................... 11 5 , 9 5 26:>A/Mx/4604/2009/04/19
27 >A/Mxcity/CIA9/2009/05/16 .............................................................A. ........................................................ ........................................C............. ............................................................ ..A....................A...A...... ............A.......G............. .............. ............A.......... 15 8 , 13 8 27:>A/Mxcity/CIA9/2009/05/16
28 >A/MxCity/011/2009/05/09 ............................................................... ........................................................ ...................................................... .........................................................T.. ..A....................A.......... ..........T.A.......G...........C. .............. ....................... 15 7 , 13 7 28:>A/MxCity/011/2009/05/09
29 >A/MxCity/024/2009/04/30 ............................................................... ....................................................A... ...................................................... ........................................T................T.. ..A....................A.......... ............A.......G...........C. .............. ....................... 16 8 , 14 8 29:>A/MxCity/024/2009/04/30
30 >A/Mx/4603/2009/04/19 ............................................................... ........................................................ ...................................................... .........................................................T.. ..A....................A.......... ............R.......G...........C. .............. ....................... 9 6 , 7 6 30:>A/Mx/4603/2009/04/19
31 >A/MxCity/014/2009/05/09 ............................................................... ........................................................ ...................................................... ..................A......................................T.. ..A....................A.......... ............A.......G...........C. .............. ....................... 12 7 , 10 7 31:>A/MxCity/014/2009/05/09
32 >A/MxCity/019/2009/04/30 ............................................................... ........................................................ ...................................................... .........................................................T.. ..A....................A.......... ............A.......G...........C. .............. ....................... 11 6 , 9 6 32:>A/MxCity/019/2009/04/30
33 >A/Mx/4635/2009/04/20 ............................................................... ........................................................ ...................................................... .........................................................T.. ..A....................A.......... ............A.......R...........C. .............. ----------------------- 82 29 , 9 6 33:>A/Mx/4635/2009/04/20
34 >A/MxCity/012/2009/05/09 .................................................A............. ........................................................ ...................................................... .........................................................T.. ..A....................A.......... ............A.......G...........C. .............. .............T.......C. 17 9 , 15 9 34:>A/MxCity/012/2009/05/09
35 >A/MxCity/010/2009/05/09 ............................................................... ........................................................ ...................................................... .........................................................T.. ..A....................A.......... ............A.......G...........C. .............. ....................... 12 6 , 10 6 35:>A/MxCity/010/2009/05/09
36 >A/MxCity/WR1087T/2009/06/19 .....CA...........................G...........................A ........................................................ ...................................................... ..T......................................................... G.A..................T.A.......... ............A.......G...........C. .............. ....................... 25 12 , 23 12 36:>A/MxCity/WR1087T/2009/06/19
37 >A/Mx/48N/2009/04/25 ............................................................... ...........A............................................ ........................................C............. ...A.C...................................................... .....................T............ .......A...G.................G.... .............. ....................... 11 8 , 9 8 37:>A/Mx/48N/2009/04/25
38 >A/Mx/47N/2009/04/25 ............................................................... ...........A............................................ ........................................C............. ...A.C...................................................... .....................T............ .AG....A...G.................G.... .............. ....................... 15 10 , 13 10 38:>A/Mx/47N/2009/04/25
39 >A/MxCity/015/2009/05/09 ............................................................... ...........A............................................ ...........................A............C............. ...A........................................................ .....................T............ ...........G...................... .............. ....................... 14 6 , 12 6 39:>A/MxCity/015/2009/05/09
40 >A/MxCity/025/2009/05/01 ...........................................................T... ...........A............................................ ........................................C............. ...A........................................................ .....................T............ ...........G...................... .............. ....................... 14 6 , 12 6 40:>A/MxCity/025/2009/05/01
41 >A/Mx/4108/2009/04/03 ............................................................... ........................................................ ........................................C............. ............................................................ .....................T............ .................................. .............. ....................... 8 2 , 6 2 41:>A/Mx/4108/2009/04/03
42 >A/MxCity/026/2009/05/02 ..................................................G............ .................................A...................... ..........................T.............C............. .........A.................................................. .....................T............ .................................. .............. ....................... 11 6 , 9 6 42:>A/MxCity/026/2009/05/02
43 >A/Mx/4269/2009/04/15 ..................................................G............ ........................................................ ........................................C............. ............................................................ .....................T............ .................................. .............. ....................... 11 3 , 9 3 43:>A/Mx/4269/2009/04/15
44 >A/MxCity/004/2009/05/08 ..................................................G............ ...........................................C............ ........................................C............. ............................................................ .....................T............ .............................G.... .............. ....................... 10 5 , 8 5 44:>A/MxCity/004/2009/05/08
45 >A/Mx/4486/2009/04/14 ..................................................G............ ........................................................ ........................................C............. ........................................TA...............T.. .....................TT........... .............T.................... .............. ....................... 11 8 , 9 8 45:>A/Mx/4486/2009/04/14
46 >A/MxCity/005/2009/05/08 ..............G................................................ ................................................T....... ........................................C............. ............................................................ .....................T............ .................................. .............. ....................... 14 4 , 12 4 46:>A/MxCity/005/2009/05/08
47 >A/Mx/LaGloria-3/2009/04/03 ....R.........G................................................ ................................................T....... .....................T.........C........C............. .............................G.............................. ...R.................T..Y.R....... .AG............................... .............. ..........C............ 16 14 , 14 14 47:>A/Mx/LaGloria-3/2009/04/03
48 >A/Mx/LaGloria-4/2009/03/24 ....R.........G................................................ ................................................T....... .....................T.........C........C............. .............................G.............................. ...R.................T..Y.R....... .N................................ .............. ..........C............ 21 13 , 17 13 48:>A/Mx/LaGloria-4/2009/03/24
49 >A/Mx/LaGloria-8/2009/03/25 ....R.........G................................................ ................................................T....... .....................T.........C........C............. .............................G.............................. .....................T............ .CG............................... .............. ..........C............ 14 11 , 12 11 49:>A/Mx/LaGloria-8/2009/03/25
50 >A/MxCity/WR1306N/2009/09/02 .....C.................................A....G................A. ........................................................ ..........A..............................T..........T. .................G....A.A..............................G.T.. ..A....................A...A...... ............A.......G............. ........A.A... .......G.............C. 34 21 , 32 21 50:>A/MxCity/WR1306N/2009/09/02
51 >A/MxCity/WR1100N/2009/06/29 .....CA......................................................A. ........................................................ ...................................................... ........................A................................T.. ..A....................A...A...... ............A.......G............. .....A..A.A... .......G............... 19 14 , 17 14 51:>A/MxCity/WR1100N/2009/06/29
52 >A/MxCity/WR1765N/2009/11/19 .....C.....G.................................................A. ........................................C........A...... .A........A..........................................C .....C..................A..................A.............T.. ..A..T.................A...A....T. ............A.......G.......A..... ........A.A... .......G............... 36 23 , 34 23 52:>A/MxCity/WR1765N/2009/11/19
53 >A/MxCity/WR1668T/2009/09/23 .....CA.....................................G................A. ........................................C........A...... .A.A......................A..................GCGT....C ........................A...A..............A.............T.. ..A..T.................A...A....T. ............A.......G.......A..... ........A.A... .......G............... 46 29 , 44 29 53:>A/MxCity/WR1668T/2009/09/23
54 >A/MxCity/WR1695N/2009/10/01 .....CA.......................A.............G................A. .................................................A...... ...................................................... .........................................................T.A ..A....................A...A....T. ............A.......G............. ........A.A... C......G............... 33 18 , 31 18 54:>A/MxCity/WR1695N/2009/10/01
55 >A/MxCity/WR1301N/2009/09/12 .....C............AG................A.......G.........G........ .................TG..................................... G............A...........A......T.....T............... TA..A.....A..............................................TT. ..A....T.........T.....A.....A.G.. ............A.T.....G..........T.. .............C ....................... 36 30 , 34 30 55:>A/MxCity/WR1301N/2009/09/12
56 >A/MxCity/WR1307N/2009/09/14 .....C..............................A.......G.........G........ .................T............................G......... G............A...........A......T.....T............... TA..A.....A....................................GCCAGT....TT. ..A....T.........T.....A.....A.G.. ............A.T.....G..........T.. .............C ....................... 39 34 , 37 34 56:>A/MxCity/WR1307N/2009/09/14
57 >A/MxCity/WR1747N/2009/11/09 .....C.....G...........A..............G...A.G..........C.....A. ..A...............................G..............A...... ..A..A..............C.....................TG.......... ........................A..TA.......G.....G..............T.. ..A........A......A....A...A...... ............A..C....GA...........G CAGT....A.A... ...C...G.G........A.... 46 42 , 44 42 57:>A/MxCity/WR1747N/2009/11/09
58 >A/MxCity/WRAIR1781T/2009/11/10 .....C.................A..................A............C.....A. ..A.CG..........ATG...............G..............A...... ..A..A..............C.....................TG.......... ........................A..TA.......G.....G..............T.. ..A........A......A....A...A...... ............A..C....GA...........G ........A.A... ...C...G.G........A.... 42 40 , 40 40 58:>A/MxCity/WRAIR1781T/2009/11/10
59 >A/MxCity/WRAIR1691N/2009/09/23 CACGA..TGAA.........TCC.ATAACA..............G................A. ........................................................ ...................................................... ........................A................................T.. ..A....................A...A...... ............A.......G............. ........A.A... .......G............... 35 30 , 33 30 59:>A/MxCity/WRAIR1691N/2009/09/23
60 >A/MxCity/WRAIR1679N/2009/09/23 CACGA.ATGAA.........TCC.ATAACA.....T...AA...G..G...G.........A. ......................................A................. ..............................T...................T.T. ........T...............A................................T.. ..A.....C...........G..A...A...... ............A.......G............. ........A.A... .......G...........A... 102 44 , 100 44 60:>A/MxCity/WRAIR1679N/2009/09/23
61 >A/MxCity/WR1706T/2009/09/18 .....C.....G....................A.............................. .............................A...................A....C. ......................................C..........A.... ....................A...A.T............G................AT.. ..A....................A.......... ............A.......G...........C. CAGT.......... ....................... 43 23 , 41 23 61:>A/MxCity/WR1706T/2009/09/18
62 >A/MxCity/WR1701T/2009/09/24 .....CA..........................C...........C...............A. ........................................................ ....T.................TT..A......................A.... ................A...A...A................................T.. ..A....................A...A...... ............A.......G.....C....... CAGT.......... ....................A.. 32 25 , 30 25 62:>A/MxCity/WR1701T/2009/09/24
63 >A/MxCity/WR1692T/2009/09/22 .....CA..........................C..........GC...............A. ................ATG...G......A.................T.A...... ....T.G...............TT..A..................GCGTA.... ................A...A...A................................T.. ..A....................A...A...... ............A.......G.....C....... ........A.A... .......G...........A... 42 37 , 40 37 63:>A/MxCity/WR1692T/2009/09/22
64 >A/MxCity/WR1696T/2009/09/17 .....C............AG.............C.T........GC...............A. .......G..............G......A.................T.A....C. ......G...............TT..A......................A.... ................A...A...A.......A........................T.. ..A....................A...A..A..T ............A.......G.....C....... CAGT....A.A... ..G...........T....A... 50 41 , 47 41 64:>A/MxCity/WR1696T/2009/09/17
65 >A/MxCity/WR1697T/2009/09/15 .....CA.....................................G..G...G.....A...A. ...........................................G...T.A....C. ......................TT..A........................... .................G......A................................T.. ..A....................A...A.....T ............A.......G....A........ CAGT....A.A... .......G...........A... 41 32 , 39 32 65:>A/MxCity/WR1697T/2009/09/15
66 >A/MxCity/WR1708T/2009/10/09 ................G....................A.........G...G.........A. C.....A...A...A............................G..GT.A...AC. ......................TT..A..CT....T.T................ ......C.....T...........A..................A.............T.. ..A...................TA...A.....T ............A.......G............. CAGT....A.A... .G.....G...........AT.. 56 44 , 54 44 66:>A/MxCity/WR1708T/2009/10/09
67 >A/MxCity/WR1090N/2009/10/22 ............G..................................G...G.C.......A. ................................A..........G..GT.A....C. .............................C........................ .A......................A........T.......A...............T.. ..A....................A.C.A.....T ............A.......G............. CAGT....A.A... .......GA.......A..A... 44 34 , 42 34 67:>A/MxCity/WR1090N/2009/10/22
68 >A/MxCity/WR1673N/2009/10/05 .....C.....G....................A..............G.A.G.........A. ...............................................T.A...... .......................-.....C...A.................A.. ...................C....A................................T.. ..A....................A...A.....T .....T......A.....A.G............. ........A.A... .......G...........A... 46 28 , 40 27 68:>A/MxCity/WR1673N/2009/10/05
69 >A/MxCity/WR1704T/2009/09/25 .....C......................................G.AG...G.........A. ...........................................G...T.A....C. .............................C.........T.............. ........T...........A...A.T.....A.......................AT.A ..A...C.............G..A...A.....T ............A.......G............. ........A.A... .......G...........A... 37 32 , 35 32 69:>A/MxCity/WR1704T/2009/09/25
70 >A/MxCity/WR1687T/2009/09/23 .....CA.....................................G.AG...G.........A. ..............A............................G...T.A...... .............................C.........T.......GT..... ........T...............A.......A.......................AT.. ..A...C.............G..A...A.....T ............A.......G............. ........A.A... .......G...........A... 36 32 , 34 32 70:>A/MxCity/WR1687T/2009/09/23
71 >A/MxCity/WR1683T/2009/09/25 .....C......G.....AG.............C..........G.AG...G.........A. ..............A.AT.....G.....A.................T.A...... ......................TT..A........................A.. ................A.......A.......A....T..................AT.. ..A...C.............G..A...A.....T ............A.......G............. ........A.A... .......G...........A... 46 39 , 44 39 71:>A/MxCity/WR1683T/2009/09/25
72 >A/MxCity/WR1675T/2009/09/23 .....C........................................AG...G.........A. ......................G......A................GT......C. ......................TT..A......................A.... ...........C............A.......A.......................AT.. ..A...C.............G..A...A.....T ............A.......G............. ........A.A... .......G...........A... 34 31 , 32 31 72:>A/MxCity/WR1675T/2009/09/23
73 >A/MxCity/WR1297N/2009/09/03 .....CA.....................................G..G...G.........A. .T.....G........ATG........................G...T......C. ........T....................C........................ ........................A......................GCCAGT....T.. ..A....................A...A.....T ............A.......G....A........ ........A.A... ..G....G......T....A... 40 37 , 38 37 73:>A/MxCity/WR1297N/2009/09/03
74 >A/MxCity/WR1310N/2009/09/09 .....C.........................................G...G.........A. .......G...................................G...T......C. ........T....................C........................ ........................A......................GCCAGT....T.. ..A....................A...A..A..T ........C...A.......G....A........ ........A.A... ..G....G......T....A... 35 33 , 33 33 74:>A/MxCity/WR1310N/2009/09/09
75 >A/MxCity/WR1311T/2009/09/10 .....C.........................................G...G.........A. .......G.........TG........................G...T......C. ........T....................C........................ ........................A......................GCCAGT....T.. ..A....................A...A..A..T ........C...A.......G....A........ ........A.A... ..G....G......T....A... 38 35 , 36 35 75:>A/MxCity/WR1311T/2009/09/10
76 >A/MxCity/WR1308T/2009/09/04 .....C......................................G..G...G.........A. .......G........AT.........................G..........C. ........T....................C........................ ........................A................................T.. ..A....................A...A.....T ............A.......G....A........ ........A.A... ..G....G......T....A... 29 27 , 27 27 76:>A/MxCity/WR1308T/2009/09/04
77 >A/MxCity/WR1312N/2009/09/10 .....C.........................................G...G.........A. .......G.........T.........................G...T......C. ........T....................C........................ ........................A................................T.. ..A....................A...A..A..T ........C...A.......G....A........ ........A.A... ..G....G......T....A... 30 28 , 28 28 77:>A/MxCity/WR1312N/2009/09/10
78 >A/MxCity/WRAIR1752N/2010/01/26 ...............................................G...G........... ...........................................G...T......C. ...........................A.C........................ ..T.....................A..................A.............T.. ..A....................A.C.A.....T ............A.......G....A........ ........A.A... .......G...........A... 42 23 , 40 23 78:>A/MxCity/WRAIR1752N/2010/01/26
79 >A/MxCity/WRAIR1773T/2010/01/25 .....C.........................T...............G.............A. ....CG....A.A..............................G...T......C. .......A...G.................C........................ ..................A.....A................................TT. ..A....................A...A...... ............A.......G............. ........A.A... .......G...........A... 45 27 , 43 27 79:>A/MxCity/WRAIR1773T/2010/01/25
80 >A/MxCity/WRAIR1786T/2009/12/01 .....C...................................T.A...G...G.........A. ....CG........A............................G...T..TT..C. ............G.T.C..T.........C....A.C.......G......... .............A..........A.............T..................T.. ..A....................A...A.....T ............A.......G...G......... ........A.A... .......G...........A... 39 37 , 37 37 80:>A/MxCity/WRAIR1786T/2009/12/01
81 >A/MxCity/WRAIR1779T/2009/12/01 .....C...................................T.A...G...G.........A. ....CG........A............................G...T..TT..C. ............G.T.C..T.........C....A.C.......G......... .............A.......C..A.............T..................T.. ..A....................A...A.....T ............A.......G...G......... ........A.A... .......G...........A... 40 38 , 38 38 81:>A/MxCity/WRAIR1779T/2009/12/01
82 >A/MxCity/WR1762T/2009/11/03 .....C.................A..............G.....G..G...G.........A. .........G....A..................................AT...C. ............G.T.C..T..............A.C.......G......... .............A.......C..A................................T.. ..A....................A...A.....T ............A.......G...G......... CAGT....A.A... .......G...........A... 40 38 , 38 38 82:>A/MxCity/WR1762T/2009/11/03
83 >A/CA/VRDL129/2009/12/30 ...............................................G...GG......T.A. ......A........C......................C....G...T......C. ..................G................................... .......................CA..............................G.T.. ..A....................A...A.....T ............A.......G............. ........A.A... .......G...........A... 34 26 , 34 26 83:>A/CA/VRDL129/2009/12/30
84 >A/CA/VRDL120/2009/12/15 ...............................................G...GG........A. ........C......C......................C....G...T......C. .......A....G.....G..........C........................ .......................CA................................T.. ..A....................A...A.....T ............A.......G............. ........A.A... .......G.........G.A... 36 28 , 36 28 84:>A/CA/VRDL120/2009/12/15
85 >A/CA/VRDL92/2009/10/17 ...............................................G...G.........A. .....................A.....................G...T......C. .A...........................C........................ ........................A...................G............T.. ..A....................A...A.....T ............A.......G............. ........A.A... .......G...........A... 35 22 , 35 22 85:>A/CA/VRDL92/2009/10/17
86 >A/CA/VRDL98/2009/10/29 ...............................................G...G......CT.A. .....................A...C.................G...T......C. .............................C........................ .......G................A...................G.........G..T.. ..A......A.............A...A.....T ............A.......G............. ........A.AG.. .......G...........A... 30 28 , 30 28 86:>A/CA/VRDL98/2009/10/29
87 >A/CA/VRDL128/2009/12/22 ...............................................G...G.........A. ..A........................................G...T......C. .............................C........................ ........................A.........T..........T...........T.. ..A....................A.C.A.....T ............A.......G............. ........A.A... ....A..GA..........A... 35 25 , 35 25 87:>A/CA/VRDL128/2009/12/22
88 >A/CA/VRDL110/2009/11/24 ...............................................G...G.........A. ..A..............................A.......G.G...T......C. .............................C........................ ........................A.........T..........T...........T.. ..A................A...A.C.A.....T ............A.......G............. ........A.A... ....A..GA..........A... 35 28 , 35 28 88:>A/CA/VRDL110/2009/11/24
89 >A/CA/VRDL7/2010/02/01 ...............................................G...G....G....A. ...........................................GC..T......C. .........T...................C........................ ........................A................................T.. ..A............G.......A...A.....T ............A.......G....A........ ........A.A... .......G...........A... 36 24 , 36 24 89:>A/CA/VRDL7/2010/02/01
90 >A/CA/VRDL6/2010/02/02 ...............................T...............G.............A. .T........A.AA.............T...............G...T......C. ...........G................AC........................ ......C.......G...A.....A..........C.....................T.. ..A.C..................A...A...... ......A.....A...A...G............. ........A.A... .......G.....T.....A... 39 33 , 39 33 90:>A/CA/VRDL6/2010/02/02
91 >A/CA/VRDL4/2010/02/08 ...............................T...............G.....C.......A. ..........A..A.............T...............G...T......C. ...........G.................C........................ ......C.......G...A.....A..........C.....................T.. ..A.C..................A...A...... ......A.....A...A...G............. ........A.A... C......G...........A... 46 31 , 46 31 91:>A/CA/VRDL4/2010/02/08
92 >A/Taipei/WR1472T/2009/10/21 .....C..............................A..........G...G.........A. ......................G........A.......G..CG...T.A....C. .............................C........................ ...........C............A................................T.. ..A....................A...A.....T .....T......A.......G............. CAGT....A.A... .......G...........A... 55 32 , 49 32 92:>A/Taipei/WR1472T/2009/10/21
93 >A/Ontario/26184/2009/09/29 ...............................................G...G.........A. ...........................................G...T......C. .............................C........................ ........................A................................T.. G.A....................A.C.A.....T ....A.......A.......G............. ........A.A... .......GA..G.......A... 28 24 , 28 24 93:>A/Ontario/26184/2009/09/29
94 >A/Ontario/29801/2009/10/19 ...............................................G...G.........A. .....................................T.....G...T......C. ........................A....C........................ ........................A................................T.. ..A....................A...A...... .........A..A.......G.G........... ........A.A... .......G...........A... 28 22 , 28 22 94:>A/Ontario/29801/2009/10/19
95 >A/CanadaON/RV2890/2009/09/24 ............................................................... .......G...................................G...T......C. ...................................................... ........................A................................T.. ..A....................A...A...... ............A.......G....A........ .............. ....................... 20 12 , 15 12 95:>A/CanadaON/RV2890/2009/09/24
96 >A/CanadaAB/RV2854/2009/09/06 ............................................................... ...C........................C..............G...T......C. ...................................................... ........................A.....C..........................T.. ..A........A.C.........A...A...... ...C........A.......G............. .............. ....................... 21 16 , 16 16 96:>A/CanadaAB/RV2854/2009/09/06
97 >A/CanadaON/RV2887/2009/10/15 ............................................................... ...C........................C..............G...T......C. ...................................................... ........................A.....C..........................T.. ..A........A.C.........A...A...... ...C........A.......G............. .............. ....................... 21 16 , 16 16 97:>A/CanadaON/RV2887/2009/10/15
98 >A/CanadaSK/RV2926/2009/10/07 ............................................................... .....................................T.....G...T......C. ...................................................... ........................A............................G...T.. ..A....................A...A.....T .........A..A.......G.G........... .............. ....................... 20 15 , 15 15 98:>A/CanadaSK/RV2926/2009/10/07
99 >A/CanadaON/RV2964/2009/10/14 ............................................................... .....................................T.....G...T......C. ...................................................... ........................A............................G...T.. ..A....................A...A.....T .........A..A.......G.G........... .............. ....................... 21 15 , 16 15 99:>A/CanadaON/RV2964/2009/10/14
100 >A/CanadaNFL/RV3019/2009/10/25 ............................................................... .....................................T.....G...T......C. ...................................................... ........................A............................G...T.. ..A....................A...A.....T ............A.......G.G........... .............. ....................... 21 14 , 16 14 100:>A/CanadaNFL/RV3019/2009/10/25
101 >A/******/index/2009/02/01 ............................................................... ........................................................ ...................................................... ............................................................ .................................. .................................. .............. ....................... 0 0 , 0 0 101:>A/******/index/2009/02/01
102 >A/WI/629-D00908,2009/11/22 ..................................G............G...G.........A. ..........................G................G...T......C. .............................C........................ ...............G........A......A.........................T.. ..A......TC............A...A.....T ............A....G..G......A...... ......C.A.A... .......G.......A...A... 31 29 , 31 29 102:>A/WI/629-D00908,2009/11/22
103 >A/WI/629-D00888,2009/11/02 ..................................G............G...G.........A. ..........................G................G...T......C. .............................C........................ ...............G........A......A.........................T.. ..A......TC............A...A.....T ............A....G..G......A...... ......C.A.A... .......G.......A...A... 29 29 , 29 29 103:>A/WI/629-D00888,2009/11/02
104 >A/WI/629-D02317,2009/11/05 ...............................................G...G.........A. ..........................G................G...T......C. .............................C........................ ...............G........A......A.........................T.. ..A......TC............A...A.....T ............A....G..G......A...... ......C.A.A... .......G.......A...A... 32 28 , 32 28 104:>A/WI/629-D02317,2009/11/05
105 >A/WI/629-D01190,2009/11/24 ...............................................G...G.........A. ..........................G................G...T......C. .............................C........................ .........A.....G........A......A.........................T.. ..A......TC............A...A.....T ............A....G..G......A...... ......C.A.A... .......G.......A...A... 34 29 , 34 29 105:>A/WI/629-D01190,2009/11/24
106 >A/WI/629-D02073,2009/12/16 ...............................................G...G.........A. ..........................G................G...T......C. ............................AC........................ ...............G........A......A.........................T.. ..A......TC............A...A.....T ............A....G..G......A...... ......C.A.A... .......G.......A...A... 35 29 , 35 29 106:>A/WI/629-D02073,2009/12/16
107 >A/Texas/JMS366,2009/11/08 ...............................................G...G....G....A. ...........................................GC..T......C. .............................C........................ ........................A................................T.. ..A............G.......A...A.....T ............A.......G....A........ ........A.A... .......G...........A... 32 23 , 32 23 107:>A/Texas/JMS366,2009/11/08
108 >A/Texas/46182018,2009/10/18 ...............................................G...G....G....A. ...........................................GCG.T......C. .............................C........................ ........................A..................A.............T.. ..A............GA......A...A.....T ............A......AG....A........ ........A.A... .......G...........A... 29 27 , 29 27 108:>A/Texas/46182018,2009/10/18
109 >A/Texas/JMS392,2009/12/25 ...............................................G...G....G....A. .................................T.........GCG.T......C. .............................C........................ ........................A..................A.............T.. ..A............GA......A...A.....T ............AT.....AG....A........ ........A.A... .......G...........A... 34 29 , 34 29 109:>A/Texas/JMS392,2009/12/25
110 >A/NY/5620,2009/11/02 ................G..............................G...G..G......A. C.....A...A...A.................A..........G...T.....AC. ...............T...................................... ............T.......A...A..................A.............T.. ..A...................TA...A.....T ............A.......G............. ........A.A... .G.....G...........AT.. 39 33 , 39 33 110:>A/NY/5620,2009/11/02
111 >A/NY/5173,2009/10/17 ................G..............................G...G..G......A. C.....A...A...A.................A..........G...T.....AC. .............................C.....T.T................ ............T...........A..................A.............T.. ..A...................TA...A.....T ............A.......G............. ........A.A... .G.....G...........AT.. 35 34 , 35 34 111:>A/NY/5173,2009/10/17
112 >A/Madrid/INS222,2009/11/03 ................G..............................G...G.........A. C.....A...A...A............................G...T.....AC. .............................C.....T.T................ ............T...........A..................A.............T.. ..A...................TA...A.....T ............A.......G............. ........A.A... .G.....G...........AT.. 35 32 , 35 32 112:>A/Madrid/INS222,2009/11/03
113 >A/San Diego/INS214,2009/11/09 ...............................................G...GG........A. ........C......C......................C....G...T......C. ..................G..........C........................ .......................CA................................T.. ..A....................A...A.....T ............A.......G............. ........A.A... .......G.........G.A... 31 26 , 31 26 113:>A/San Diego/INS214,2009/11/09
114 >A/Pensacola/INS212,2009/11/10 ...............................................G...G.......T.A. .....................A.....................G...T......C. .............................C........................ ........................A...................G............T.. ..A....................A...A.....T ............A.......G............. ........A.AG.. ......TG...........A... 33 24 , 33 24 114:>A/Pensacola/INS212,2009/11/10
115 >A/Athens/INS392,2010/01/06 ...............................................G...G......CT.A. .....................A...C.................G...T......C. .............................C........................ .......G................A...................G.........G..T.. ..A......A.........A...A...A.....T ............A.....A.G............. .......TA.AG.. .......G...........A... 35 31 , 35 31 115:>A/Athens/INS392,2010/01/06
116 >A/WI/629-D02082,2009/10/19 ...............................................G...G......CT.A. .....................A.....................G...T......C. .........T...................C........................ ........................A...................G............T.. ..A....................A...A.....T ............A.......G............. ........A.AG.. .......G...........A... 31 25 , 31 25 116:>A/WI/629-D02082,2009/10/19
117 >A/San Diego/INS105,2009/11/04 ............................................................... ...........................................G...T......C. .........T............................................ .........................................................T.. ..A.........T..........A...A.....T ............A.......G............. ........A.A... .......G...........A... 37 16 , 37 16 117:>A/San Diego/INS105,2009/11/04
118 >A/Texas/JMS360,2009/11/07 .............T...T...............C..............T............A. .......................................G...G...T........ ...........G.......................................... ...A....................A............Y................R..T.. .AA....................A...A...... ............A.......G............. ........ACA... .......G........A..A..G 38 27 , 38 27 118:>A/Texas/JMS360,2009/11/07
119 >A/Texas/JMS359,2009/11/07 .............T...T...............C..............T............A. ...................................C...G...G...T......C. ........................A....C........................ ........................A............T...................T.. .AA....................A...A...... ............A.......G............. ........ACA... .......G........A..A..G 31 28 , 31 28 119:>A/Texas/JMS359,2009/11/07
120 >A/Texas/JMS404,2010/01/08 ...............................................G.............A. ...................................C...G...G...T......C. .............................C.........T.............. ........................A................................T.. ..A....................A..AA...... ............A.......G............. ....A...A.A... .......G...........A... 34 22 , 34 22 120:>A/Texas/JMS404,2010/01/08
121 >A/NY/6663,2009/11/23 ...............................................G.............A. ...C....C...................C..............G...T......C. .............................C........................ ...A....................A.....C..........................T.. ..A........A.C.........A...A...... ...C........A.......G............. ....A...A.A... .......G...........A... 37 26 , 37 26 121:>A/NY/6663,2009/11/23
122 >A/NY/7480,2010/03/01 ..............................A................G...G.........A. .........G..............G....A.............G...T......C. ...............A.............C........................ ........................A.....................C..........T.. ..A..T.................A...A....T. ............A.......G............. ........A.A... .....A.GA..G.......A... 44 29 , 44 29 122:>A/NY/7480,2010/03/01
123 >A/NY/6937,2009/12/11 ..............................A................G...G.....A.T.A. ........................G....A.............G...T......C. ...............A.............C........................ ........................A.....................C..........T.. ..A...........C........A.C.A.....T ............A.......G............G ........A.A... .....A.GA..G.......A... 40 32 , 40 32 123:>A/NY/6937,2009/12/11
124 >A/NY/5196,2009/10/20 ..............................A................G...G.........A. ........................G....A.............G...T......C. ...............A.............C........................ ........................A.....................C..........T.. ..A...........C........A.C.A.....T ............A.......G............. ........A.A... .....A.GA..G.......A... 29 29 , 29 29 124:>A/NY/5196,2009/10/20
125 >A/Chicago/WRAIR1691P,2009/10/14 ...G.CA..............................A.........G...G........... ...........................................G...T........ .............................C........................ ........................A................................T.. ..A....................A.C.A.....T ............A.......G............. ........A.A... .......GA..G.......A... 32 24 , 32 24 125:>A/Chicago/WRAIR1691P,2009/10/14
126 >A/Boston/658,2009/11/13 .....................................A.........G...G.........A. ...........................................G...T......CA .............................C........C............... ........................A................................T.. ..A....................A.C.A.....T ............A.......G............. ........A.A... ......TGA..G.......A... 36 26 , 36 26 126:>A/Boston/658,2009/11/13
127 >A/Aarhus/INS237,2009/11/23 ..........A..........................A.........G...G.........A. ....................................A......G...T......C. .............................C........................ ........................A...............................AT.. ..A....................A.C.A.....T ............A.......G............. ........A.A... ..G....GA..G.......A... 38 27 , 38 27 127:>A/Aarhus/INS237,2009/11/23
128 >A/Texas/JMS371,2009/11/14 ...........G...................................G...G.......T.A. ..A........................................G...T......C. .............................C........................ ........................A........TT..........T...........T.. ..A....................A.C.A.....T ............A.......G............. ........A.A... ....A..GA..........A... 32 28 , 32 28 128:>A/Texas/JMS371,2009/11/14
129 >A/Athens/INS125,2009/12/13 ...........G...................................G...G.........A. ..A.................A......................G...T......C. .............................C........................ ........................A.........T..........T...........T.. ..A....................A.C.A.....T ....A.......A.......G............. .......TA.A... ....A..GA..........A... 33 29 , 33 29 129:>A/Athens/INS125,2009/12/13
130 >A/Athens/INS275,2009/12/15 ...........G...................................G...G.........A. ..A.................A......................G...T......CA .............................C........................ ........................A.........T..........T...........T.. ..A....................A.C.A.....T ....A.......A.......G.........G... ........A.A... ....A..GA..........A... 32 30 , 32 30 130:>A/Athens/INS275,2009/12/15
131 >A/Athens/INS261,2009/12/13 ...........G...................................G...G.........AA ..A.................A......................G...T......C. .............................C........................ ........................A.........T..........T...........T.. ..A....................A.C.A.....T ....A.......A.......G.........G... ........A.A... ....A..GA..........A... 33 30 , 33 30 131:>A/Athens/INS261,2009/12/13
132 >A/WI/629-D02489,2009/11/18 ...........G...................................G...G.........A. ..A........................................G...T......C. .............................C........................ ...A....................A.........T..........T...........T.. ..A....................A.C.A.....T ............A.......G............. ........A.A... ....A..GA..........A... 32 27 , 32 27 132:>A/WI/629-D02489,2009/11/18
133 >A/WI/629-D00636,2009/12/10 .......................A.....................................A. ..A............................A...........G...T......C. ...................................................... ...A............A.......A.........T..........T...........T.. ..A....................A...A...... T...........A.......G............. ........A.A... .......G............... 33 22 , 33 22 133:>A/WI/629-D00636,2009/12/10
134 >A/Aarhus/INS238,2009/11/24 .......................A.....................................A. ....................................A......G...Y......Y. ...A.................................................. ...................C..T.A...........G....................T.. ..A....................A...A...... T...........A.......G............. .....A..A.A... .......G............... 30 22 , 30 22 134:>A/Aarhus/INS238,2009/11/24
135 >A/Ankara/WRAIR1428T,2009/10/21 .....C......................................G................A. ....CG...........T.........................G...T.A...... ....................................C................. ........................AA.............G....G............T.. ..A....................A...A...... ............A.......G............. ........A.A... .......G............... 43 23 , 43 23 135:>A/Ankara/WRAIR1428T,2009/10/21
---Index--------------------------------TGTAGGGCAGGACAAAACGTCTTGGAGGAGGGGTACGGAGGCGGATCACGAAATATAGTCAGG ACGTTAGATAGGGGGTGCTAGTAAATACAGTGCGATGCTATATTTAACCCGCGGTC AGGGCGAGCCGAACCGTCAGTCCCGGCGGTGTGGGCTCAGACCAATTTAGCGCA AGCCGTTACCCTCGAAGAGTGTGTTGCAGATCGCCTACCACGAGACTCAGTAGAAACCCG ACGGTCTCTCTGCTTAGCCGACCGCAGGGGGCCC CTATGATGTGCAGCCTGAGGAGACAGTCGAACAA TTTCGGTCGTGACT TAATCGCACATAGCCGGAGGCTA
-codon-position------------------------- 2 2 2 2 12 1 1 21 1 2 1 2 1 2 1 1 1 2 1 11 1 2 122 1 11 1 1 11 22 11 1 212 11 1 12 221211 1 12 2 12122 21221 1 12 2 12 1 2 1 11 12 22 2 1 2 1 2 212 211 1 1111 22 1 2 1 1 1 1 12211 1 1111 211 11
000000000000000000000000000000000000001111111111111111111222222 00000000000000000000001111111111111111111111111112222222 000000000000000000000011111111111111111111111111122222 000000000000000000000000000000000000000011111111111111111111 0000000000000000000011111111111111 0000000000000000000000001111111111 00000000000000 00000000000000000000000
000001111111112233444444455555555567880011112223445666789001111 00122233334566788888990000011122224455566777789990111222 000122344446677788888900001123334455666777888999900111 011112222222333444555666666677788888899900111122222222233444 0223333445677888899911111112223334 0111222222223345666778990011122333 00003344456667 01112333344456666677778
678991133466771469335568801123488956781702371568117778197581368 35526656895747103458585557912511560103624026700597289045 348467928991846812688602691590120405278349236444457044 403461455569569033346044569911313668914918577812222337888057 3490377263509445945701345664895573 2003334444581910145245255967937224 00010333910596 73892246614833445902341
351690458412679590340950676921623478958730738131097456399595231 41624746496128777452743897572828465460308120911556443217 704713630282112933758924880945921307681714406468950336 565576347968209956690907855649986278885940512226789018123853 6981325654452395433598435478936744 6232012789736644561129540769408398 68906956200560 55997307957624391834884
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May 11th, 2011, 12:49 PM
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Senior User
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Join Date: Jun 2007
Posts: 2,963
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Re: Sequences at Genbank!
Thanks for posting that.
Do we have a list somewhere of the possible causes of sequencing errors?
I know samples can get contaminated, etc. There must be other things?
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May 21st, 2011, 02:10 PM
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Re: Sequences at Genbank!
26 full genomes from this season at genbank
22 of them are the India/UK strain
I count
25=7+3+5+4+1+2+1+2 markers for the India/UK strain
with 2 substrains
1.) Beijing,Czech,Denmark,Ontario with
earliest THA/09/10
2.) Thailand,Ontario,Sibiria with additional 20=2+4+6+3+3+1+0+1 markers
(earliest THA/2010/09/07
1.)
C666T,T957C,G1030A,A1060T,G1149A,A1446G,G2091A
C1186T,C1896A,C2190T
C99T,G663A,T873C,C963A,G1986A
G605C,T1056C,G1171A,C1403T
A1329G
C1107A,G1131A
G238A
C264T,T414C
plus the 11 Cancun markers
2.)
C1044T,G1665A
A366G,A630G,C999T,A1191G,T1304C,A1905G
C336T,A507G,G1027A,C1428T,T1776C,T2115C
C144T,G640A,C1437T,C1656T
C930T,C963T,G987A,T1059C
A131G
.
C268A
plus the 36 from 1.)
60 mutations --> created in mid 2010
_________________
no patents on genes, publish the GISAID sequences !
Code:
00000000000001111111111111111111122 00000000000001111111111111111122222 0000000000000000000000011111111111111122 0000000000000000001111111111 000000000111111 00000000011111111 00000000 0000000000
11244667777890000112223455667889901 01134666699990011223333346899911112 0012233445566677778889900134456778999911 0013344455556667990113444456 223459999011223 01337778911112223 23466788 1222333477
14726361169953466476686436369052696 31361033513992989010037926905704895 8950923560068903781276822442345171078801 4743457935790452045378003665 797613468546492 53182242300384690 33906222 6166346134
74982361735670402936927613957640813 01561302226393861653454858655733407 8934676224737155599233879938789362870665 7242018215985089056116387436 688890237931839 61600123817108602 89203757 3748907495
-codon-position----------------------- 2 1 2 1 1 12 1 1 21 1 12 2 1 1 1 2 2 1 1 11 2 2 2111 1211 1 21 1 2212 1112 1 1 1 2 11 1 11 11
---Index------------------------------AGTGCGCGCGCGTGCAAGGTGCAAGGGGGATGCGG AAAAAGAGCGTGCCACAATATCACCACACCTGCCC ACCGGGCCGGAGTGAGCGGTTCAGACCCCTGCTGGGTGTT ATCAGGATGTATGGTAGCTAGAGCCCGC AGCCCCCCGTGCGGA TAGTTGACAACGGTCAC GGGGTCTT GTCCCCATGG
1 >A/******/index/2009/02/01 ................................... ................................... ........................................ ............................ ............... ................. ........ ..........
2 >A/THA/CU-H2417/2010/09/13 ..................................A ................................... ....A................................... ..............A.....A..T.... .A........A.A.. ..A...G.......... ..AA.... ......G...
3 >A/Cancun-NY/Index/2009/04/15 ..................................A ................................... ........................................ ..............A........T.... .A........A.A.. ..A...G.......... ..AA.... ......G...
4 >A/Ontario/3620/2010/11/24 G....A.A.A.A......A.....AAA..G..T.A G...GA.AT..A.....G.G..G.T...T.AAT.T G....A...........AAC.....TA.A..T.A.AC.C. G....A.CAC.C..AGT..G...T.TA. .A..T.T...A.A.. ..A...G.GG..A.TGT .AAA.A.. CA..T.G...
5 >A/Ontario/741328/2010/11/23 G....A.A.A.A......A.....AAA..G..T.A ---.GA.AT..A.....G.G..G.T...T.AAT.T G....A...........AAC.....TA.A..T.A.AC.C. G....A.CAC.C..AGT..G...T.TA. .A..T.T...A.A.. ..A...G.GG..A.TGT .AAA.A.. CA..T.G...
6 >A/Ontario/804635/2010/12/14 G....A...A........A.....A.A..G..T.A G...G..A...A.......G....T...T...T.. G..........T......A.......A.A......AC.C. .....A..A..C..A....G...T.T.. .A....T...A.A.. ..A...G.G...A..G. .AAA.... CA....G...
7 >A/THA/CU-H2176/2010/08/17 ......T.....CATTGA.....G...A.....AA ...G..G..A.........G.............T. .T....T...GA.........A.A...T....C....A.C ..............A...C...ATT..T .A...T.TACA.A.G .GA.CAG.......... A.AA.... ..TA..GC..
8 >A/THA/CU-B4148/2010/10/09 ......T.....CATT.A.....G...A.....AA ...G..G.....T..T..........AG.....T. .T....T...GA........CA.A...T..A.C....A.C ............CAA...C.A.ATT..T .A...T.TA.A.A.G .GA.CAG...AA..... A.AA.... ..TA..GC..
9 >A/Moscow/IIV-33/2010/10/13 ......T.....CATT.A.....G...A..C..AA ...G..G.....T..TG.........AG.....T. .T....T...GA...A....CA.A...T....C....A.C ............CAA...C.A.ATT..T .A...T.TA.A.A.G .GA.CAG...AA..... A.AA.... ..TA..GC..
10 >A/THA/CU-H2548/2010/09/27 ..C...T.....CATT.A.....G...A..C..AA ...G..G.....T..TG.........AG.....T. .T....T...GA...A....CA.A...T....C....A.C ............CAA...C.A.ATT..T .A...T.TA.A.A.G .GA.CAG...AA..... A.AA.... ..TA..GC..
11 >A/Vladivistok/7/2010/12/03 ..C...T.....CATT.A.....G...A.....AA ...G..G.....T..TG...CT....AG.....T. .T....T.A.GA........CA.A...T....C....A.C ..T...G.....CAA...C.A.ATT..T .A...T.TACA.A.G .GA.CAG...AA..... A.AA.... ..TA..GC..
12 >A/THA/CU-H2911/2011/01/20 ......T.....CATT.A.....G...A.....AA ...G..G.....T..TG...C.....AG.....T. .T....T.A.GA........CA.A...T....C....A.C ..T...G.....CAA...C.A.ATT..T .A...T.TACA.A.. .GA.CAG...AA..... A.AA.... ..TA..GC..
13 >A/THA/CU-H2698/2010/11/03 ...A..T.....CATT.A.....G...A...A.AA ..GG..G.....T..TG...C....GAG.....T. .T....T.A.GA....T...CA.AC..T....C....A.C .CT...G.....CAA...C.A.ATT..T .A...T.TAC..A.G .GACCAG...AA..... A.AA.... ..TA..GCA.
14 >A/Ulaanbaatar/190/2011/01/11 ...A..T.....CATT.A.....G...A...A.AA ..GG..G.....T..TG...C....GAG.....T. .T....T.A.GA....T...CA.AC..T....C....A.C .CT...G.....CAA...C.A.ATT..T .A...T.TACA.A.G .GACCAG...AA..... A.AA.... ..TA..GCA.
15 >A/THA/CU-B4339/2010/11/04 ......T.....CATT.A.....G...A.....AA ...G..G....AT..TG...C.....AG.T..... .T....T.A.GA........CA.A...T....C.A..A.C ..T...G.....CAA...C.A.ATT..T .A...T.TACA.A.G .GA.CAG...AA..... A.AA.... ..TA.AGC..
16 >A/Ontario/720545/2010/11/17 ......T.....CAT..A.....G...A.....AA ...G..G.....T..TG...C.....AG.....T. .T....T..AGA........CA.A...T....C....A.C ..T.........CAA...C.A.ATT..T .A...T.TACA.A.G .GA.CAG...AA..... A.AA.... ..TA..GC..
17 >A/THA/CU-C1157/2010/09/07 ......T.....CATT.A.....G...A.....AA ...G..G........TG...C.....AG.....T. .T....T...GA........CA.A...T..A.C....A.C ..T.........CAA...C.A.ATT..T .A...T.TACA.A.G .GA.CAG...AA..... A.AA..C. ..TA..GC..
18 >A/THA/CU-H2543/2010/09/25 ......T.....CATT.A.....G...A.....AA ......G..A..........C.....AG.....T. .T....T...GA........CA.A...T....C....A.C ..T.........CAA...C.A.ATT..T .A...T.TAC.AA.. .GA...G.......... ..AAC.CC ..TG..G...
19 >A/THA/CU-H2358/2010/09/08 ......T.T...CATT....A..G...A.....AA .........A.........G.............T. ....A......A........C......T.........A.C ..T.........CAA...C.A.ATT..T .A...T.TAC.AA.. .GA.CAGT..AA..... ..AAC.CC ..TA..GC..
20 >A/THA/CU-H2283/2010/08/31 .A....T.....CA.T.A..A............AA .............T.T..A.......A......T. .TT........A..G.....C................A.. ...T........CAA...C.A.AT.... .AT.......AAA.. ..A...GT..AA..... A.AA.... ..T...GC.A
21 >A/THA/CU-H2389/2010/09/10 .A....T.....CA.T.A.....G.........AA .............T.T..A.......A......T. .TT........A..G.....C................A.. ...T........C.A...C.A.AT.... .AT.......A.A.. ..A.CAGT..AA..... A.AA.... ..T...GC.A
22 >A/Beijing/HZ01/2011/01/14 ......T.T...CA.TGA.....G.........AA ......G........T..........A......T. .T....T....A..G.....CA...............A.. ............C.A...C.A.AT.... .A........A.A.G ..A.CAG...AAA.... A.AA.... ..T...GC..
23 >A/Denmark/72/2011/02/07 ....A.T...TACA.T.A.C.TGG....A....AA .G........C...GT.......T..A......T- .T.A...Y...ACA......CAG......C.......A-- ....A.....G.C.A..TC.AGAT.... CA.A......A.AAG C.A.CAGT..AA.C... A.AA.... ..T...GC..
24 >A/Denmark/71/2011/02/08 ....A.T...TACA.T.A.C.TGG....A....AA .G........C...GT.......T..A......T- .T.A...Y...ACA......CAG......C.......A-- ....A.....G.C.A..TC.AGAT.... CA.A......A.AAG C.A.CAGY..AA.C... A.AA.... ..T...GC..
25 >A/Denmark/36/2011/02/01 ....A.T...TACA.T.A.C.TGG....A....AA .G........C...GT.......T..A......T- .T.A.......ACA......CAG......C.......A-- ....A.....G.C.A..TC.AGAT.... CA.A......A.AAG C.A.CAGY..AA.C... A.AA.... ..T...GC..
26 >A/Denmark/73/2011/01/29 ....A.T...TACA.T.A.C.TGG....A....AA .G........C...GT.......T..A......T- .T.A.......ACA......CAG......C.......A-- ....A.....G.C.A..TC.AGAT.... CA.A......A.AAG C.A.CAG...AA.C... A.AA.... ..T...GC..
27 >A/Czech Republic/1/2011/01/25 ......T...T.CA.T.A.....G.........AA ...............T..........A..T...T. .T.......A.A........CA...............A.. ....A.......C.A...C.A.AT.... .A........A.A.G ..A.CAG...AA.C... A.AA.... ..T..AGC..
28 >A/Ontario/130741/2010/10/13 ......T.....CA.T.A.....G.........AA ...............T.....T....A......T. .T.........A........CA............A..A.. ............C.A...C.A.AT.... .A........A.A.G ..A...G...A...... A.AA.... ..T...GC..
---Index------------------------------AGTGCGCGCGCGTGCAAGGTGCAAGGGGGATGCGG AAAAAGAGCGTGCCACAATATCACCACACCTGCCC ACCGGGCCGGAGTGAGCGGTTCAGACCCCTGCTGGGTGTT ATCAGGATGTATGGTAGCTAGAGCCCGC AGCCCCCCGTGCGGA TAGTTGACAACGGTCAC GGGGTCTT GTCCCCATGG
-codon-position----------------------- 2 1 2 1 1 12 1 1 21 1 12 2 1 1 1 2 2 1 1 11 2 2 2111 1211 1 21 1 2212 1112 1 1 1 2 11 1 11 11
00000000000001111111111111111111122 00000000000001111111111111111122222 0000000000000000000000011111111111111122 0000000000000000001111111111 000000000111111 00000000011111111 00000000 0000000000
11244667777890000112223455667889901 01134666699990011223333346899911112 0012233445566677778889900134456778999911 0013344455556667990113444456 223459999011223 01337778911112223 23466788 1222333477
14726361169953466476686436369052696 31361033513992989010037926905704895 8950923560068903781276822442345171078801 4743457935790452045378003665 797613468546492 53182242300384690 33906222 6166346134
74982361735670402936927613957640813 01561302226393861653454858655733407 8934676224737155599233879938789362870665 7242018215985089056116387436 688890237931839 61600123817108602 89203757 3748907495
seem that A/THA/CU-H2417/2010/09/13 is from 2009
rather than 2010
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May 24th, 2011, 06:35 AM
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Registered User
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Re: Sequences at Genbank!
2506 full ****** genomes from genbank
number of mutations over time
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June 6th, 2011, 09:47 AM
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Re: Sequences at Genbank!
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June 13th, 2011, 02:21 AM
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Re: Sequences at Genbank!
Singapore HA sorted by submission date
no Chi in SGP until Feb.2011
19 from the India/UK - strain , earliest 2010/10/20
the other 11 from this season (since summer 2010)
have markers T552C,A183G,G340A,G796T,A963C,A1118C,G1380A,T1467C ,
not in England
http://www.flutrackers.com/forum/showpost.php?p=386228
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June 20th, 2011, 12:42 PM
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Registered User
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Re: Sequences at Genbank!
Genomic Polymorphism of the Pandemic A (H1N1) Influenza Viruses Correlates with Viral Replication, Virulence, and Pathogenicity In Vitro and In Vivo
http://www.plosone.org/article/info%...e-0020698-t001
these were in Russia (also Ukraine ?) in 2009 with reassortments,
presumably severe cases
Sichuan/1/2009(H1N1)
included in my russ8 table :
Code:
011222 00000111 00001 00000001 00111 0000011 000 0
504011 11134046 00140 12456784 12123 2337823 468 3
411369 55606529 58998 45315120 39448 3144123 909 6
632037 69205856 14853 52368698 28386 8662312 202 7
-codon-position------------------------ 222 1 2 1 1 1 1211 1 1111 1 1
---Index-------------------------------GTCAGT GAGAAACA GGTAG CTTATAAC CGGGA GGGACTC GGG A
1 >A/******/index/2009/02/01 ...... ........ ..... ........ ..... ....... ... .
2 >A/Kaluga/01/2009/05/22 ------ -------- ----- A....... ----- ....... ... -
3 >A/Norway/1177/2009/05/08 AC.G.. AGAG.G.. A.... A....... T.... ....... ..A .
4 >A/Norway/1168/2009/05/07 AC.G.. AGAG.G.. A.... A....... T.... ....... ..A .
5 >A/Vladivostok/01/2009// A.T..C ...GGG.G ...GA .....G.. ..... A.A.T.. ... .
6 >A/Vladivostok/IIV18/2009/07/24 A.T..C ...GGG.G .ACGA A....... ..... A.A.T.T ... .
7 >A/Vladivostok/IIV17/2009/07/22 A.T..C ...GGG.G .ACGA A....... ..... A.A.T.T ... .
8 >A/Moscow/226/2009// ------ -------- ----- ........ .AAA. ------- ... .
9 >A/Sichuan/1/2009/05/10 A.T... ...G.G.G ..CG. A....... ..... A...T.T ... .
10 >A/Tomsk/01/2009// A.T..C ...GGG.G ..... ....A.GT .AAA. ....... AA. .
11 >A/Chita/01/2009// A.T..C ....GG.G ..... ..C.A..T .AAAG ...G... .A. G
12 >A/Ekaterinburg/01/2009// A.T..C ...GGG.G ..... ....A..T .AAA. .A...C. AA. G
13 >A/Tomsk/02/2009// A.T..C ........ ..... .C.GA..T .AAA. .....C. AA. G
14 >A/Tomsk/03/2009/07/19 A.T... ......T. ..... .C.GA.GT .AAA. .A.G.C. AA. .
15 >A/Karasuk/01/2010/01/04 A.T... ........ ..... ..C.AG.T .AAA. .A.G.C. AA. .
16 >A/Moscow/IIV05/2009/06/20 ....A. ......T. ..... ....A..T .AAAG .A.G... AA. G
17 >A/Finland/554/2009/05/26 ...... -------- ..... .......T .AA.. .A.G... ..A .
18 >A/Cancun-NY/Index/2009/04/15 ....A. ........ ..... ....A..T .AAA. .A.G... AA. G
---Index-------------------------------GTCAGT GAGAAACA GGTAG CTTATAAC CGGGA GGGACTC GGG A
-codon-position------------------------ 222 1 2 1 1 1 1211 1 1111 1 1
011222 00000111 00001 00000001 00111 0000011 000 0
504011 11134046 00140 12456784 12123 2337823 468 3
411369 55606529 58998 45315120 39448 3144123 909 6
Last edited by gsgs; June 20th, 2011 at 03:52 PM.
Reason: table-format
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June 20th, 2011, 01:28 PM
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Re: Sequences at Genbank!
gs: Not exactly.. 2 had mild strains but were either severe/deceased and the one that had the severe A/Sichuan/1/2009 strain had a mild case. [edited to add:] A/California/04/2009, A/California/07/2009, A/Sichuan/1/2009, A/Shandong/1/2009, A/Beijing/3/2009, A/Fujian/1/2009, A/Shanghai/1/2009, and A/Jiangsu/1/2009 viruses were all collected from patients with mild symptoms.
Quote:
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Our results also suggested that the virulence of the 2009 pandemic A (H1N1) viruses were not associated with the clinical phenotypes of the corresponding patients; A/Sichuan-Wenjiang/SWL456/2009 and A/Guangdong/SWL28/2009, viruses collected from a deceased and severely ill patient respectively, showed much lower replication ability, virulence, and pathogenicity than A/Sichuan/1/2009, a virus from a patient with mild symptoms.
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The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918
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June 20th, 2011, 03:57 PM
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Re: Sequences at Genbank!
I meant the Russian cases. I remember that many of them were severe or
deadly, but don't know which exactly.
Well, this strain was complete only in Vladivostok,
Tomsk,Chita,Ekaterinburg were already reassorted with a Cancun-virus.
Since long I didn't see even a non-cancun segment
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June 21st, 2011, 04:30 PM
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Senior User
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Re: Sequences at Genbank!
Fifty isolates were submitted at GISAID today.
There are 4 from New Mexico that grouped together, sharing changes at positions 222A, 357G, 390G, 433C, 546T, 647T, 801G, 891A, 934G, 1030C (plus some others). I don't recognize that strain; gs will be able to tell us which one it is.
These share the Chihuahua mutations:
A/Alaska/12/2011,2011/04/05,
A/Arizona/02/2011,2011/03/08,
A/Maryland/04/2011,2011/02/02,
A/Massachusetts/09/2011,2011/03/07,
A/New_York/04/2011,2011/02/21,
A/Pennsylvania/02/2011,2011/02/22,
A/Pennsylvania/08/2011,2011/02/23,
A/Vermont/04/2011,2011/01/14,
Four of the 50 have D225N and one has D225G:
A/Kansas/02/2011,2011/01/19
A/Mexico/1658/2011,2011/02/22
A/Mississippi/07/2011,2011/02/23
A/New_York/03/2011,2011/03/20
A/Alaska/02/2011, 2011/01/14, D225G, California/07-like
__________________
The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918
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June 23rd, 2011, 11:41 AM
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Re: Sequences at Genbank!
In response to our recent discussion regarding D225 mutations and egg passage, I pulled up all the GISAID 2011 HAs (386 total).
I sorted by passage methods and it showed 27 used various types of egg passaging. I'm going to discount Jiangsu/1/2011 because it has so many mutations...(did that one have an error or was it reassorted?)
So, out of 26 egg passages, 14 had changes at D225 (715-716) and/or Q226 (719):
A/Voronezh/1/2011,2011/03/14
A/Voronezh/1/2011,2011/03/14 = 719R
A/St._Petersburg/27/2011,2011/02/14
A/Thessaloniki/1078/2011,2011/03/08
A/Kavala/19/2011,2011/02/10
A/South_Dakota/01/2011,2011/01/12
A/Thessaloniki/1099/2011,2011/03/08 = 716R, 719R
A/Thessaloniki/1151/2011,2011/03/08
A/Tennessee/01/2011,2011/02/23= 719R
A/Colorado/05/2011,2011/03/08
A/Czech_Republic/4/2011,2011/01/18
A/Texas/01/2011,2011/01/05
A/Alaska/02/2011,2011/01/14 = 716G,719A
A/Minnesota/03/2011,2011/02/18 = 719R
A/Kaluga/1/2011,2011/03/14
A/St._Petersburg/25/2011,2011/02/14 = 715R, 716R, 719A
A/Malta/MV000235/2011,2011/02/01 = 719A
A/Thessaloniki/1376/2011,2011/03/08= 716G, 719A
A/Minnesota/03/2011,2011/02/18 = 716R, 719A
A/St._Petersburg/100/2011,2011/03/14
A/St._Petersburg/100/2011,2011/03/14
A/Kansas/02/2011,2011/01/19 = 715A, 719A
A/Vermont/04/2011,2011/01/14 = 719A
A/Maryland/04/2011,2011/02/02 = 719A
A/Pennsylvania/02/2011,2011/02/22 = 719R
A/Mississippi/07/2011,2011/02/23 = 715A, 719A
Here are some of our links regarding D225 mutations and egg passaging:
The WHO: Preliminary review of D222G amino acid substitution in the haemagglutinin of pandemic influenza A (H1N1) 2009 viruses FluTrackers
Egg Passaged Sequences with D225 and Q226 Mutations PanFlu Stats discussion
Alterations in receptor-binding properties of swine influenza viruses of the H1 subtype after isolation in embryonated chicken eggs Journal of General Virology
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The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918
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June 23rd, 2011, 01:27 PM
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Senior User
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Re: Sequences at Genbank!
Another look at all the D225 mutations from 2011:
D225N = 715A/R
A/St._Petersburg/25/2011,2011/02/14= R E1/E2
A/Milan/184/2011,2011/01/25= A
A/Netherlands/219/2011,2011/01/02= A
A/Kansas/02/2011,2011/01/19= A E3
A/Mexico/1658/2011,2011/02/22= A
A/Mississippi/07/2011,2011/02/23= A E2
A/New_York/03/2011,2011/03/20= A
D225G = 716G/R
A/CastillaLaMancha/RR7050/2011,2011/01/07= G
A/Iraq/21-SAK/2011,2011/01/10= R
A/Athens/351/2011,2011/01/20= G
A/Minnesota/03/2011,2011/02/18= R E2
A/Denmark/24/2011,2011/01/15= R
A/California/17/2011,2011/02/15= G
A/St._Petersburg/25/2011,2011/02/14=R E1/E2
A/Thessaloniki/1376/2011,2011/03/08=G E1/E1
A/Thessaloniki/1099/2011,2011/03/08=R E2/E1
A/Alaska/02/2011,2011/01/14=G E3
My usual disclaimer:
Please keep in mind that I have no background in virology or science in general; if anyone sees any errors in my findings, please feel free to point them out. 
__________________
The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918
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June 24th, 2011, 02:52 AM
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Re: Sequences at Genbank!
14 out of 26 is 54%
comparing with mxhah :
715: G:6136,A:22,R:32
716: A:6041,G:90,R:54
719: A:6131,G:37,R:18
~3%
mxhai:
715:750,8,1
716:734,19,8
719:755,5,1
~6%
increasing in 2010
------------------------------
If (only) the egg-passage "creates" (selects) D225G, then the person might not have "felt" it.
Amount of D225G could be small and egg-passage increases it
they may prefer egg-passage in lung samples
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July 14th, 2011, 06:00 AM
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Re: Sequences at Genbank!
new genomes from Chile, summer 2010
went to Sydney ? seen there one month later
pH1,HA since May,2010
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August 24th, 2011, 05:57 AM
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Re: Sequences at Genbank!
update of early sequences
Mexico 4115,4487 are still the most original ones with only 3 mutations in the whole genome
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August 31st, 2011, 01:05 AM
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Re: Sequences at Genbank!
tropical India or Thailand could be the place where flu survives summer
and yearly sends new survivers to nontropical regions where it had
died in summer.
However the Chi-strain was not found in Thailand 2010, see below.
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August 31st, 2011, 01:09 AM
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Re: Sequences at Genbank!
lots of sements 8 today from H1N1 2009
why ? special mutation ? new paper ?
what was with the new reading frame in segment 8,
we didn't hear about it since 2009
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September 22nd, 2011, 06:30 AM
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Re: Sequences at Genbank!
more sequences (partial HA) from 1918
Iowa,May,June
Washington DC,June
SC,July
had the same HA as the 2nd wave that started in ~Sept. in USA
Sept.15 = first death in NY
A716G is D239G=D222G=D225G
Code:
000000000000
233566677777
138701100112
904647869568
-codon-position----------------------------- 12 11122
---Index------------------------------------TACAGAGAGGAG
1 >A/Brevig_Mission/1/18(H1N1),1918// ............
2 >A/London/1,1918// .G.GA.......
3 >A/New_York/1/18(H1N1),1918// ..T.......G.
4 >A/South Carolina/1/18 (H1N1),1918// ..T.........
5 >A/Iowa/1,1918/05/11 ---G......G.
6 >A/Iowa/2,1918/06/02 ---G......G.
7 >A/Washington DC/1,1918/06/24 ---G........
8 >A/South Carolina/2,1918/07/22 ---G......G.
9 >A/New York/2,1918/09/21 ---G..A.....
10 >A/New York/3a,1918/09/24 ---G......G.
11 >A/New York/3b,1918/09/24 ---G.....A..
12 >A/New York/4,1918/09/26 ---G.......A
13 >A/Virginia/1,1918/09/27 ---G.G......
14 >A/Virginia/2,1918/09/30 ---G........
15 >A/Virginia/3,1918/10/01 ---G...G....
16 >A/AFIP/1,1918/10/08 ---G........
17 >A/London/1,1919// C..G....A.G.
---Index------------------------------------TACAGAGAGGAG
-codon-position----------------------------- 12 11122
000000000000
233566677777
138701100112
904647869568
Camp Dodge, Johnston, IA,11-May-1918
Camp Dodge, Johnston, IA,02-Jun-1918
Walter Reed Hospital, Washington, DC,24-Jun-1918
Camp Jackson, Columbia, SC,22-Jul-1918
Autopsy Series of 68 Cases Dying Before and During the 1918 Influenza Pandemic Peak
http://www.pnas.org/content/early/2011/09/12/1111179108
------------------------------------------------------------
The 1918 pandemic virus was circulating for at least 4 months in the United States
before it was recognized epidemiologically in September 1918.
A/SC/1(H1N1),1918/09/21
A/Brevig mission(H1N1),1918/11/17
http://www.pnas.org/content/suppl/20...01111179SI.pdf
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December 16th, 2011, 06:46 AM
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Re: Sequences at Genbank!
early ****** genomes from the UK now at genbank, after 3.6 years !
2 original
8 northern,LaGloria
27 NovaScotia, special English variant
23 Airplane,airmany,England
12 Pre-Cancun
46 Cancun
so, at least 6 independent introductions in April-June
(more likely at least ~13 introductions)
551 and 430 look reassorted, getting a non-Cancun HA
Code:
0000000000001111111222 0000000001111111122 00000000000000111111 000000000000000011111 00000011111 000001111111 0000 0000000
1224556778991444555011 0012355670003567901 00012334467889235789 011345556666788901456 11223700112 123770112233 3346 1133346
6138484798185189779369 3888099051550796075 05899092927014504400 004861330258599327041 38699359144 331481373323 0690 3913628
1610608598513241786036 5759014301083860965 87484036525698422142 485116265787618053881 23787878838 786269100492 6620 8526767
-codon-position-------------------2 1 11 122 2 2 2 21 21 121 1 2 112 11 1 1 2 122 1 1 2 1 11 1 2 2111 2 1 1
---Index--------------------------GACGGCGTGCAGACTTAGGAGG TAGGAGGGTGAAAAATACG AGGTAACGAACGGCTGTAGG AACACACGGTTGGGAGAGCAC CATGCAATCGG TGGAGCGGACAC GTGG AGGAAGA
1 >A/******/index/2009/02/01 ...................... ................... .................... ..................... ........... ............ .... .......
original
2 >A/EN/431/2009/06/05 ...................... ................... .................... ..................... ........... ............ .... .......
3 >A/EN/201/2009/05/02 ...................... ................... .................... .............A....... ........... ............ .... .......
"nordisch",LaGloria,Canada
6 >A/EN/365/2009/05/31 ...................... ................... .................C.. ..................... ........T.. ............ .... .......
10 >A/EN/350/2009/05/27 ...................... ....G.............. .................C.. .............A....... ........T.. ............ .... .......
11 >A/EN/401/2009/06/03 ................G..... ................... ...........A.....C.. .............A....... ........T.. C........... .... .......
4 >A/EN/197/2009/04/27 ................G..... ................... .................C.. ..................... ..C.A...T.. ....A....... .... .......
5 >A/EN/247/2009/05/03 ................G..... ................... .................C.. ..................... ..C.A...T.. ....A....... .... .......
7 >A/EN/217/2009/04/30 ........A......C...... ................... .................C.. ...........TA....A..T ........T.. ............ .... .......
8 >A/EN/XFL00311/2009/05/07 ........A......C...... ................... .................C.. ...........TA....A..T ........T.. ............ .... ......G
9 >A/EN/256/2009/05/08 ........A......C...... ................... .................C.. ...........TA....A..T ........T.. ............ .... ......G
Nova Scotia, special English variant
38 >A/EN/433/2009/06/05 ..........G.....G..... ...............C... ....G..A........CC.. ..................... .G.....CT.. .....T..GT.. .... .A...A.
23 >A/EN/384/2009/06/01 ..........G.....G..... ...............C... ....G..A........CC.. ..................... .G.....CT.. .....T..GT.. .C.. .A...A.
15 >A/EN/386/2009/06/01 ..........G.....G..... ...............C... ....G..A........CC.. ..................... .G.....CT.. .....T..GT.. .C.. .A...A.
16 >A/EN/360/2009/06/01 ..........G.....G..... ...............C... ....G..A........CC.. ..................... .G.....CT.. .....T..GT.. .C.. .A...A.
18 >A/EN/345/2009/05/30 ..........G.....G..... ...............C... ....G..A........CC.. ..................... .G.....CT.. .....T..GT.. .C.. .A...A.
20 >A/EN/445/2009/06/09 ..........G.....G..... ...............C... ....G..A........CC.. ..................... .G.....CT.. .....T..GT.. .C.. .A...A.
21 >A/EN/349/2009/05/30 ..........G.....G..... ...............C... ....G..A........CC.T ..................... .G.....CT.. .....T..GT.. .C.. .A...A.
17 >A/EN/364/2009/05/31 ..........G.....G..... ...............C... ....G..A........CC.T ..................... .G.....CT.. .....T..GT.. .C.. .A...A.
19 >A/EN/382/2009/06/01 ..........G.....G..... ...............C... ....G..A........CC.. ..................... .G.....CT.. .....T..GT.. .C.. .AA..A.
22 >A/EN/348/2009/05/30 ..........G.....G..... ...............C... ....G..A........CC.. ..................... .G.....CT.. .....T..GT.. .C.. .AA..A.
28 >A/EN/347/2009/05/30 ..........G.....G..... ...............C... ....G..A........CC.. ....T................ .G.....CT.. .....T..GT.. A... GA...A.
29 >A/EN/337/2009/05/30 ..........G.....G..... ...............C... ....G..A........CC.. ....T................ .G.....CT.. .....T..GT.. A... GA...A.
30 >A/EN/423/2009/06/04 ..........G.....G..... ...............C... ....G..A........CC.. ....T................ .G.....CT.. .....T..GT.. A... GA...A.
31 >A/EN/381/2009/06/01 ..........G.....G..... ...............C... ....G..A........CC.. ....T................ .G.....CT.. .....T..GT.. A... GA...A.
32 >A/EN/383/2009/06/01 ..........G.....G..... ...............C... ....G..A........CC.. ....T................ .G.....CT.. .....T..GT.. A... GA...A.
33 >A/EN/394/2009/06/02 ..........G.....G..... ...............C... ....G..A........CC.. ....T.............T.. .G.....CT.. .....T..GT.. A... GA...A.
34 >A/EN/395/2009/06/01 ..........G.....G..... ...............C... ....G..A........CC.. ....T................ .G.....CT.. .....T..GT.. A... GA...A.
35 >A/EN/428/2009/06/04 ..........G.....G..... ...............C... ....G..A........CC.. ..................... .G.....CT.. .....T..GT.. A... GA...A.
36 >A/EN/342/2009/05/29 ..........G.....G..... ...............C... ....G..A........CC.. ..................... .G.....CT.. .....T..GT.. A... .A...A.
37 >A/EN/374/2009/06/01 ..........G.....G..... ...............C... ....G..A........CC.. ..................... .G.....CT.. .....T..GT.. A... .A...A.
26 >A/EN/328/2009/05/28 ..........G.....G..... ..A............C... ....G..A........CC.. ..................... .G.....CT.. .....T.AGT.. .... .A...A.
27 >A/EN/456/2009/06/05 ..........G.....G..... ..A............C... ....G..A........CC.. ..................... .G.....CT.. ..A..T.AGT.. .... .A...A.
12 >A/EN/361/2009/06/01 ..........G.....G..... ...............CG.. ....G..A........CC.. ..................... .G.....CT.. .....T..GT.. .... .A...A.
13 >A/EN/400/2009/06/05 ..........G.....G..... ...............CG.. ....G..A........CC.. ..................... .G.....CT.. .....T..GT.. .... .A...A.
14 >A/EN/359/2009/05/31 ..........G.....G..... ...............CG.. ....G..A........CC.. ..................... .G.....CT.. .....T..GT.. .... .A...A.
24 >A/EN/377/2009/06/02 A.........G.....G..... .....A...A.....C... .A..G..A........CC.. ..................... .G.....CT.. .....T..GT.. .... .A...A.
25 >A/EN/399/2009/06/03 A.........G.....G..... .....A...A.....C... .A..G..A........CC.. ..................... .G.....CT.. .....T..GT.. .... .A...A.
airplane,airmany
60 >A/EN/388/2009/06/02 ....A........T........ ....G......G..G.... ...C....G........... ..A.................. ........... .A.........T .... .......
61 >A/EN/414/2009/06/04 ....A........T........ ....G......G..G.... ...C....G........... ..A................G. ........... .A.........T .... .......
39 >A/EN/246/2009/05/02 ....A................. ....G......G....... G................... ..................... T.......... ............ .... .......
42 >A/EN/211/2009/04/28 ....A................. ...AG.A....G....... G................... ..A.............T.... T.......... ............ .... .......
43 >A/EN/216/2009/04/30 ....A................. ...AG.A....G....... G................... ..A.............T.... T.......... ............ .... .......
44 >A/EN/215/2009/04/30 ....A................. ...AG.A....G....... G................... ..A.............T.... T.......... ............ .... .......
45 >A/SC/4/2009/05/03 ....A..............G.. ....G......G....... G................... ..A.................. T.......... ............ .... .......
46 >A/EN/195/2009/04/28 ....A..............G.. ....G......G....... G................... ..A.................. T.......... ............ .... .......
47 >A/EN/218/2009/05/02 ....A..............G.. ....G......G....... G................... ..A.................. T.......... ............ .... .......
40 >A/EN/219/2009/05/02 ....A................. ....G.....GG....... G................... ..................... T.......... ............ .... .......
41 >A/EN/266/2009/05/15 ....A................. ....G.....GG....... G................... ..A.................. T.......... ............ .... .......
48 >A/EN/249/2009/05/05 ....A................. ....G.....RR....... G................... ..A.................. TR.....YY.. ............ .... .......
49 >A/EN/XFL00200/2009/05/04 ....A................. ....G.....GG....... G................... ..A.................. T.......... ............ .... .......
50 >A/EN/221/2009/05/02 ....A................. ....G.....GG....... G................... ..A.................. T.......... ............ .... .......
52 >A/EN/XFL00304/2009/05/05 ....A................. ....G.....GG....... G................... ..A.................. T.......... ............ .... .......
53 >A/EN/253/2009/05/07 ....A................. ....G.....GG....... G................... ..A.................. T.......... ............ .... .......
54 >A/EN/XFL00419/2009/05/12 ....A................. ....G.....GG....... G................... ..A.................. T.......... ............ .... .......
55 >A/EN/XFL00275/2009/05/05 ....A................. ....G.....GG....... G................... ..A.................. T.......... ............ .... .......
57 >A/EN/254/2009/05/05 ....A................. ....G.....GG....... G................... ..A.................. T.......... ............ .... .......
58 >A/EN/220/2009/05/02 ....A................. ....G.....GG....... G................... ..A.................. T.......... ............ .... .......
59 >A/EN/252/2009/05/08 ....A................. ....G.....GG....... G................... ..A.................. T.......... ............ .... .......
51 >A/EN/XFL00300/2009/05/07 ....A................. ....G.....GG....... G................... ..A.................. T.......... ......A..... .... .......
56 >A/EN/257/2009/05/09 ....A................. ....G.....GG....... G................... ..A.................. T.......... ......A..... .... .......
pre-Cancun
73 >A/EN/XFL00354/2009/05/10 ...................... ................... .................... ..................T.. ...A.....A. ..AG........ .... .......
62 >A/EN/205/2009/04/27 ...................... ................... ...............A.... ..................T.. ...A.....A. ..AG......C. .... .......
63 >A/EN/XFL00071/2009/04/27 ...................... ................... ...............A.... ..................T.. ...A.....A. ..AG......C. .... .......
64 >A/EN/213/2009/04/29 ............G......... ..........R.G.....A ..........T......... .G.T...A..........T.. ...A.....A. ..AG......C. .... .......
65 >A/EN/XFL00137/2009/04/29 ............G......... ............G.....A ..........T......... .G.T...A..........T.. ...A.....A. ..AG......C. .... .......
66 >A/EN/204/2009/04/28 ...................... ............G...... ..........T......... .G.T...A..........T.. ...A.....A. ..AG......C. .... .......
67 >A/EN/351/2009/05/31 .........T............ .......A.........T. .................... G..............T..T.. ...A.....A. ..AG........ .... .......
68 >A/EN/391/2009/06/02 .........T............ .......A.........T. .................... G..............T..T.. ...A.....A. ..AG........ .... .......
71 >A/EN/313/2009/05/26 .........T...........A .......AC........T. ..A................. G..............T..T.. ...A.....A. ..AG........ .... .......
69 >A/EN/436/2009/06/05 .........T...........A .......AC....G...T. ..A................. G..............T..T.. ...A.....A. ..AG........ .... .......
70 >A/EN/443/2009/06/05 .........T...........A .......AC....G...T. ..A................. G..............T..T.. ...A.....A. ..AG........ .... .......
72 >A/EN/432/2009/06/05 .........T...........A .......AC....G...T. ..A................. G..............T..T.. ...A.....A. ..AG........ .... .......
Cancun
74 >A/EN/551/2009/04/27 ....................A. ................... .................... ..................... ...A.....AA ..AG........ ..AA ....G..
95 >A/EN/366/2009/05/31 ....................A. ................... .................... ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
114 >A/EN/XFL00482/2009/05/13 ....................A. ................... .................... ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
115 >A/SC/10/2009/06/11 ....................A. ................... .................... ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
90 >A/EN/421/2009/06/06 ....................A. ................... .................... ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
91 >A/SC/91800799/2009/04/24 ....................A. ................... .................... ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
110 >A/EN/200/2009/04/28 ....................A. ................... .................... ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
118 >A/EN/214/2009/04/30 ....................A. ................... .................... ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
119 >A/EN/541/2009/06/23 ....................A. ................... .................... ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
96 >A/EN/380/2009/06/02 ....................A. ................... .................... ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
97 >A/EN/398/2009/06/03 ....................A. ................... .................... ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
98 >A/EN/202/2009/04/27 ....................A. ................... .................... ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
79 >A/EN/207/2009/04/27 ....................A. ................... .................... ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
80 >A/EN/393/2009/06/02 ....................A. ................... .................... ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
86 >A/EN/223/2009/04/29 ....................A. ................... .................... ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
81 >A/SC/91800797/2009/04/25 ....................A. ................... .................... ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
82 >A/EN/385/2009/06/01 ....................A. ................... .................... ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
75 >A/EN/430/2009/06/05 .G..................A. ................... .................... ..................... ...A.G...AA ..AG........ ..AA ....G..
76 >A/EN/343/2009/05/30 .G..................A. ................... .................... .........CA.......T.. ...A.G...AA ..AG........ ..AA ....G..
77 >A/EN/411/2009/06/04 .G..................A. ................... .................... .........CA.......T.. ...A.G...AA ..AG........ ..AA ....G..
78 >A/EN/303/2009/05/26 .G..................A. ................... .................... ..........A.......T.. ...A.G...AA ..AG........ ..AA ....G..
83 >A/EN/424/2009/06/04 ..T....C............A. Y.................. .........G.......... ......T.T.A.......T.. ...A.....AA ..AG........ ..AA ....G..
84 >A/EN/429/2009/06/08 ..T....C............A. Y.................. .........G.......... ......T.T.A.......T.. ...A.....AA ..AG........ ..AA ....G..
85 >A/EN/435/2009/06/06 ..T....C............A. ................... .........G.......... ......T.T.A.......T.. ...A.....AA ..AG........ ..AA ....G..
87 >A/SC/8/2009/05/31 ....................A. ................... ...........A........ ..........A.......T.. ...A.....AA C.AG........ ..AA ...GG..
88 >A/EN/341/2009/05/30 ...........A........A. .G................. ...........A........ ..........A.......T.. ...A.....AA ..AG........ ..AA ...GG..
89 >A/EN/346/2009/05/30 ...........A........A. .G................. ...........A........ ..........A.......T.. ...A.....AA ..AG........ ..AA ...GG..
93 >A/EN/419/2009/06/05 .....A..............A. ................... .....G.............. ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
94 >A/EN/418/2009/06/05 .....A..............A. ................... .....G.............. ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
92 >A/EN/XFL00418/2009/05/11 ..................T.A. ................... .................... ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
99 >A/EN/263/2009/05/12 ..................T.A. ................... .................... ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
100 >A/EN/259/2009/05/11 ..................T.A. ................... .................... ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
103 >A/EN/264/2009/05/12 ..................T.A. ................... .................... ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
104 >A/EN/265/2009/05/12 ..................T.A. ................... .................... ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
105 >A/EN/XFL00481/2009/05/13 ..................T.A. ................... .................... ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
101 >A/EN/XFL00473/2009/05/12 ..................T.A. ................... ......T............. ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
102 >A/EN/XFL00532/2009/05/15 ..................T.A. ................... ......T............. ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
106 >A/EN/446/2009/06/09 ...A..........C.....A. ................... ..................A. ..........A...G...T.. ...A.....AA ..AG........ ..AA ....G..
107 >A/EN/451/2009/06/07 ...A..........C.....A. ................... ..................A. ..........A...G...T.. ...A.....AA ..AG........ ..AA ....G..
108 >A/EN/450/2009/06/07 ...A..........C.....A. ................... ..................A. ..........A...G...T.. ...A.....AA ..AG........ ..AA ....G..
109 >A/EN/416/2009/06/02 ...A..........C.....A. ................... ..................A. ..........A...G...T.. ...A.....AA ..AG........ ..AA ....G..
116 >A/EN/434/2009/06/06 ....................A. ................... ............A....... ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
117 >A/EN/402/2009/06/01 ....................A. ................... ............A....... ..........A.......T.. ...A.....AA ..AG........ ..AA ....G..
111 >A/EN/415/2009/06/04 ......A..........A..A. ................... .................... .....G....A.......TG. ...A..G..AA ..AG........ ..AA ....G..
112 >A/EN/389/2009/06/03 ......A..........A..A. ................... .............AG..... .....G....A.......T.. ...A..G..AA ..AG........ ..AA ....G..
113 >A/EN/392/2009/06/03 ......A..........A..A. ................... .............AG..... .....G....A.......T.. ...A..G..AA ..AG........ ..AA ....G..
---Index--------------------------GACGGCGTGCAGACTTAGGAGG TAGGAGGGTGAAAAATACG AGGTAACGAACGGCTGTAGG AACACACGGTTGGGAGAGCAC CATGCAATCGG TGGAGCGGACAC GTGG AGGAAGA
-codon-position-------------------2 1 11 122 2 2 2 21 21 121 1 2 112 11 1 1 2 122 1 1 2 1 11 1 2 2111 2 1 1
0000000000001111111222 0000000001111111122 00000000000000111111 000000000000000011111 00000011111 000001111111 0000 0000000
1224556778991444555011 0012355670003567901 00012334467889235789 011345556666788901456 11223700112 123770112233 3346 1133346
6138484798185189779369 3888099051550796075 05899092927014504400 004861330258599327041 38699359144 331481373323 0690 3913628
1610608598513241786036 5759014301083860965 87484036525698422142 485116265787618053881 23787878838 786269100492 6620 8526767
these viruses have all subsequently died
In 2010/2011 new viruses came to the UK, the main strain of them
was first seen in India, May 2010
here again my old list of substrains from Nov.2009
none of these seem to have survived , from the sub-sub strains
(created after April 2009)
Code:
28
early Mex,0
Northern,2,A1741C,3,C1118T,5
Houston,5,A1741C,3,C1118T,5,G0571A,2,C0145A,4,A0283G,6
Sask,11,A1741C,3,C1118T,5,A0541G,2,C1332T,2,A1603G,2,G0797A,3,C1945T,3,T1354C,4,T0480C,5,C1389A,5,T0711C,6
swine,6,A0588G,3,A1741C,3,C0022A,4,C1118T,5,A0283G,6,C0738A,8
Jersey,6,G0799A,1,A1741C,3,G0687T,4,A0877G,4,G1173A,4,C1118T,5
Nova Scotia,3,A1577G,1,A1741C,3,C1118T,5
Hamburg,7,A1577G,1,A1741C,3,C1118T,5,G0786A,6,C0397A,5,T0267C,5,G0037A,4
Texas,7,G1308A,1,T0450C,2,A0561C,3,G1173A,4,G1563A,4,G0522A,7,A0775G,8
early US,3,A1218G,1,G1986T,3,A1044G,6
CAFuk,8,A1218G,1,G1986T,3,A1044G,6,T1872C,1,T0670C,3,T0298C,4,G0891A,4,G1012A,4
airplane,1,G0546A,1
Wisconsin3,5,G0546A,1,C0547A,1,G0037A,4,A0723G,4,C0896T,4
airmany,4,G0546A,1,A1058G,2,A0300G,2,C0145A,4
StoDomingo,13,G0546A,1,A1058G,2,A0300G,2,C0145A,4,A0273G,1,T1854C,1,T1275C,2,T0435A,3,A0456G,3,C0870T,4,A1429G,4,G0165A,7,C0717A,7
England,7,G0546A,1,A2030G,1,A0300G,2,A1058G,2,A0008G,3,C0145A,4,C0132T,5
Korea,3,G0298A,5,G1143A,5,G0316A,6
Japan,9,T1711C,1,G1945A,1,G0636A,2,T2000C,2,G0936A,3,G0298A,5,G1143A,5,G0316A,6,G0659A,8
pre-Cancun,5,C1408T,4,G0298A,5,G1143A,5,G0316A,6,A0742G,6
Wisconsin1,8,C1408T,4,G0298A,5,G1143A,5,G0316A,6,A0742G,6,C0696T,7,G0892A,7,C0954T,6
Wisconsin2,13,C1408T,4,G0298A,5,G1143A,5,G0316A,6,A0742G,6,C0696T,7,G0892A,7,C0954T,6,A1051G,1,T1150C,2,G1680A,2,G0576A,4,C0148T,4
Manitoba,10,C1408T,4,G0298A,5,G1143A,5,G0316A,6,A0742G,6,C0888T,1,G0603A,2,C2076T,2,A0004G,4,G0930T,4
Cancun,11,G2163A,1,T0658A,4,C1408T,4,G0298A,5,G1143A,5,G1248A,5,G0316A,6,A0742G,6,G0492A,7,G0600A,7,A0367G,8
TexDen,15,G2163A,1,T0658A,4,C1408T,4,G0298A,5,G1143A,5,G1248A,5,G0316A,6,A0742G,6,G0492A,7,G0600A,7,A0367G,8,A0177T,1,T2189C,2,G0624A,5,G0279A,8
Singapore,14,G2163A,1,T0658A,4,C1408T,4,G0298A,5,G1143A,5,G1248A,5,G0316A,6,A0742G,6,G0492A,7,G0600A,7,A0367G,8,T1899C,1,A1979G,1,G0477A,3
NY47,28,G2163A,1,T0658A,4,C1408T,4,G0298A,5,G1143A,5,G1248A,5,G0316A,6,A0742G,6,G0492A,7,G0600A,7,A0367G,8,C0334T,1,G0480A,1,T0774C,1,T1626C,1,C1332T,2,A1467T,2,A1920G,2,G2091A,2,T1335C,3,T1527C,3,T0717C,4,A0898G,4,C1140T,4,G0201A,5,A0923G,6,C0163A,8,A0208G,8
Zhejiang,24,G2163A,1,T0658A,4,C1408T,4,G0298A,5,G1143A,5,G1248A,5,G0316A,6,A0742G,6,G0492A,7,G0600A,7,A0367G,8,G0282A,1,G1438A,1,G0705A,2,T1857C,2,G1163A,3,C1263T,3,A1845G,3,G2019A,3,G1968A,3,G0268T,4,C0259T,4,A0716G,4,T0933C,4
MexWR,24,G2163A,1,T0658A,4,C1408T,4,G0298A,5,G1143A,5,G1248A,5,G0316A,6,A0742G,6,G0492A,7,G0600A,7,A0367G,8,G0110C,1,A1381G,1,A1674G,1,A0366G,2,T1760G,2,T2241C,2,C0480T,3,T1305C,3,C1434T,5,G1097A,6,A0189G,8,C0643T,8,G0724A,8
Chiba  +3)
San Salvador +5)
NY2 M+11)
Mex2 M+14)
Zhej M+13)
WI2 WI+3)
---------------edit----------
paper:
http://jvi.asm.org/content/86/1/11.full.pdf+html
more info on the viruses:
http://jvi.asm.org/content/suppl/201...C1/TableS1.pdf
they also have 13 "culsters" (~13 introductions into UK)
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August 24th, 2012, 07:24 AM
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Registered User
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Join Date: Feb 2006
Location: germany
Posts: 9,944
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Re: Sequences at Genbank!
33 HAs from Freiburg-city, SW-Germany early 2011
6 different introductions
Code:
HK/2213 : A357G,G390A,T433C,A539C,C546T
Tunisia : G451A,T598C
Bangkok : A183G,G340A,G348A,T552C,G665A,A697G,G796T,G1171A
DC : G605C,T1056C,G1171A
Korea : C144T,A478G,G605C,G640A,T1056C,G1171A
Ohio : G340A,A579G,G605C,T1056C,G1171A
CHI1 : G607A,C681T,G398A...
CHI2 : G607A,C681T,G398A...
o o
k k k k k .
b bb x b t. b b b . b
000000000000000000000000000000000000000000000000000000000111111111111111111111111111
111111122222233333334444445555555666666666777777888999999000011111123333334444444455
223447801478802446690234672356799001456899015679468556789158811147793366880000123577
040342348921821080968430586621918579085478534576316013959760168990163525063678357217
-codon-position---------------------- 112 1 2 22 2 1 112 112 1211112 12 21 1 12 11 1 2 1 1 22 1 22
---Index-----------------------------TAAACCATAGGCTGTGGGCGGATATACGTGACTGGAGTGGATCGGCCGTATTTAATAGTGATAGGCGCCACCGAGAGCAGCTCG
1 >A/******/index/2009/02/01 ....................................................................................
2 >A/Freiburg/729366/2011(H1N1) ....T..............A....AG.......C..AA....................C..C...TAT......A..T..T...
3 >A/Freiburg/727273/2011(H1N1) ....T..............A....AG.......C..AA....................C..C...TAT......A..T..T...
4 >A/Freiburg/728006/2011(H1N1) .......C...........A....AG.......C..AA....................C..C...TAT......A..T..T...
13 >A/Freiburg/727507/2011(H1N1) .GTT...........A.................C...A....................C.......A.......A..T......
14 >A/Freiburg/722791/2010(H1N1) ...............A.................C...A........T...........C.......A.......A..T.A.C..
15 >A/Freiburg/728080/2011(H1N1) ......G........A.................C...A.A......T...........C.......A.......ATAT......
16 >A/Freiburg/726522/2011(H1N1) ........GA.....A.................C...A...................TC....A..A.......A..T......
17 >A/Freiburg/726872/2011(H1N1) ........GA.....A....T............C...A...A...............TC....A..A.......A..T......
18 >A/Freiburg/725733/2011(H1N1) .............T.A...............A.C...A................T...........A....T..A..T......
19 >A/Freiburg/726304/2011(H1N1) .............T.A...............A.C...A................T...........A....T..A..T......
20 >A/Freiburg/730207/2011(H1N1) .............T.A.................C.G.A............................A....T..A..TG.....
5 >A/Freiburg/727291/2011(H1N1) ...............A..............G..C...A....................C.......A......GA..T......
6 >A/Freiburg/729306/2011(H1N1) ...............A..............G..C...A....................C.......A......GA..T......
7 >A/Freiburg/727269/2011(H1N1) ...............A..............G..C...A....................C.......A...T..GA..T......
8 >A/Freiburg/729584/2011(H1N1) ...............A..............G..C...A............C.......C.......A......GA..T......
9 >A/Freiburg/724875/2011(H1N1) ...............A...........A..G..C...A....................C.......A......GA..T......
10 >A/Freiburg/725724/2011(H1N1) ...............A..............G..C...A.............C...C..C.......A......GA..T......
11 >A/Freiburg/728232/2011(H1N1) ...............A..........T...G..C...A....................C.......A.G....GA..T..T...
12 >A/Freiburg/732430/2011(H1N1) .......C.......A......C.......G..CA..A....................C.......A......GA..T......
21 >A/Freiburg/729297/2011(H1N1) ......G........AA...........C........AA.G.T....T........G.........A.....A....T......
22 >A/Freiburg/728839/2011(H1N1) ......G...A....AA...........C........AA.G.T....T........G.........A.....A....T......
23 >A/Freiburg/729731/2011(H1N1) ......G........AA...........C...C....AA.G.T....T........G.........A.....A....T......
24 >A/Freiburg/727875/2011(H1N1) ......G........AA...........C........AA.G.TA...T........G.......A.A.....A....T......
25 >A/Freiburg/728880/2011(H1N1) ......G........AA...........C........AA.G.TA...T........G.......A.A.....A....T......
26 >A/Freiburg/730442/2011(H1N1) ......G........AA...........CA.......AA.G.T..T.T..................A.....A....T......
27 >A/Freiburg/729028/2011(H1N1) ......G........AA...........CA.......AA.G.T..T.T..................A.....A....T....T.
28 >A/Freiburg/726097/2011(H1N1) ......G.....C.CA........A...C........AA.G......T.....C........C...A.....A....T......
29 >A/Freiburg/731503/2011(H1N1) ......G.....C.CA........A...C........AA.G......T.....C........C...A.....A....T......
30 >A/Freiburg/730282/2011(H1N1) ......G.....C.CA........A...C........AA.G...A..T.....C........C...A.....A....T......
31 >A/Freiburg/723886/2011(H1N1) .....T.....T.....A...G.......A.......A..........CG..C.............A..G.......T.....A
32 >A/Freiburg/723154/2011(H1N1) .....T.....T.....A...G.......A.......A..........CG..C.............A..G.......T.....A
34 >A/Freiburg/725296/2011(H1N1) .....T.....T.....A...G.G.....A.......A..........CG..C......TT.....A..G.......T.....A
33 >A/Freiburg/725001/2011(H1N1) C....T...........AT..G.......A.......A..........CG..C.............A..G.......T.....A
---Index-----------------------------TAAACCATAGGCTGTGGGCGGATATACGTGACTGGAGTGGATCGGCCGTATTTAATAGTGATAGGCGCCACCGAGAGCAGCTCG
-codon-position---------------------- 112 1 2 22 2 1 112 112 1211112 12 21 1 12 11 1 2 1 1 22 1 22
000000000000000000000000000000000000000000000000000000000111111111111111111111111111
111111122222233333334444445555555666666666777777888999999000011111123333334444444455
223447801478802446690234672356799001456899015679468556789158811147793366880000123577
040342348921821080968430586621918579085478534576316013959760168990163525063678357217
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