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we have 300 US-swine H3N2v segments from USA from this year at genbank,
but no human H3N2v from this summer.
But there are some good matches from this year swine and last year human H3N2v :
several swine from Indiana and Ohio match A/WV/06/2011/11/21 in segments 1,2,7
A/Sw/IO/A01203503/2012/05/09 matches A/IN/08_a/2011/97/27 in segment 4
A/Sw/IN/A01203541/2012/05/23 matches A/IN/08_a/2011/97/27 in segment 5
some Sw from IO,IN,OH match A/ME/06 and A/IO/08(m1) in segment 7
A/Sw/IL/A01203672/2012/07/21 matches multiple human viruses from 2011 in segments 4
but no human H3N2v from this summer.
But there are some good matches from this year swine and last year human H3N2v :
several swine from Indiana and Ohio match A/WV/06/2011/11/21 in segments 1,2,7
A/Sw/IO/A01203503/2012/05/09 matches A/IN/08_a/2011/97/27 in segment 4
A/Sw/IN/A01203541/2012/05/23 matches A/IN/08_a/2011/97/27 in segment 5
some Sw from IO,IN,OH match A/ME/06 and A/IO/08(m1) in segment 7
A/Sw/IL/A01203672/2012/07/21 matches multiple human viruses from 2011 in segments 4
Code:
000000000000000000000000000011111111111111111111222 0000000000000001111111111111 0000000000111111111111111
011122222344444555666677888901112224444555667999000 0023455677799991234444777799 1233334457001223444567899
414734688902447178166912789982678890223018572235034 1486779503901158622556001713 5502889918021055044929956
214795758926477012902473736668411464287254943026110 8520131485262812662781142083 0391452868539713736377602
-codon-position-------------------------------------- 22 1 1 21 112 1 2 1 2 2 11 1 1 2 1 1
---Index---------------------------------------------TAGAACGCACCACCACGGCGCCTAAAGGAAGGAGCCGAATGACAAGGTTAT TACTTAGAAGACGCGCGAAAGTATGAGG TATGCACGACAATCACCGGACGTCA
1 >Index ................................................... ............................ .........................
61 >A/WV/06/2011/11/21 C..GGAA...TG.T.T......CGCG...........G..A.T...ACCCC CG...G..G.GT...TA....A...... C.......G..........G..CTG
2 >A/Sw/Ohio/12TOSU450/2012,2012/08/09,H3N2 C..GGAA.G.TG.T.T.....TCGCG...G.......G..A.T.T.ACCCC ....C....AGTA....GGG..G..... C.C.....GA...A.....G..CTG
3 >A/Sw/Ohio/12TOSU447/2012,2012/08/09,H3N2 C..GGAA.G.TG.T.T.....TCGCG...G.......G..A.T.T.ACCCC ....C....AGTA....GGG..G..... C.C.....GA...A.....G..CTG
4 >A/Sw/Indiana/A00968380/2012,2012/07/18,H3N2 --------------------------------------------------- ---------------------------- -------------------------
5 >A/Sw/Indiana/A01104023/2012,2012/07/31,H3N2 C..GGAAAG.TG.T.T.....TCGCGA..G.......G.AA.T.T.ACCCC CG...GA.R.GT.T.TA....A.C.... C.C..T..GA...A...A.G..CTG
6 >A/Sw/Indiana/A01104016/2012,2012/07/31,H3N2 C..GGAAAG.TG.T.T.....TCGCGA..G.......G.AA.T.T.ACCCC ---------------------------- C.C..T..GA...A...A.G..CTG
7 >A/Sw/Ohio/12TOSU307/2012,2012/08/03,H3N2 C..GGAAAG.TG.T.T.....TCGCGA..G.......G.AA.T.T.ACCCC CG...GA.G.GT.T.TA....A.C.... C.C.....GA...A...A.G..CTG
8 >A/Sw/Ohio/12TOSU293/2012,2012/07/28,H3N2 C..GGAA...TG.T.TA.T..TCGCG...G.......GG.A.T.T.ACCCC CG...GA.G.GT.T.TA....A.C..A. C.C.....GA...A.....G..CTG
9 >A/Sw/Ohio/12TOSU268/2012,2012/07/28,H3N2 C..GGAA...TG.T.TA.T..TCGCG...G.......GG.A.T.T.ACCCC CG...GA.G.GT.T.TA....A.C..A. C.C.....GA...A.....G..CTG
10 >A/Sw/Indiana/A00968370/2012,2012/07/13,H3N2 --------------------------------------------------- ---------------------------- -------------------------
11 >A/Sw/Indiana/A00968379/2012,2012/07/13,H3N2 C..GGAA.G.TG.T.T..T..TCGCG...G.......G..A.T.T.ACCCC CG...GA.G.GT.T.TA...AA.C.... C.C.....GA...A.....G..CTG
12 >A/Sw/Indiana/A00968373/2012,2012/07/13,H3N2 C..GGAA.G.TG.T.T..T..TCGCG...G.......G..A.T.T.ACCCC CG...GA.G.GT.T.TA...AA.C.... C.C.....GA...A.....G..CTG
13 >A/Sw/Indiana/A00968376/2012,2012/07/13,H3N2 C..GGAA.G.TG.T.T..T..TCGCG...G.......G..A.T.T.ACCCC CG...GA.G.GT.T.TA...AA.C.... C.C.....GA...A.....G..CTG
14 >A/Sw/Indiana/A00968386/2012,2012/07/26,H3N2 C..GGAA.G.TG.T.T..T..TCGCG...G.......G..A.T.T.ACCCC CG...GA.G.GT.T.TA...AA.C.... C.C.....GA...A.....G..CTG
15 >A/Sw/Ohio/12TOSU420/2012,2012/08/06,H3N2 C..GGAA.G.TGTT.T.....TCGCG..GG.....A.G..A.T.T.ACCCC CG.C.GA.G.GT.T.TA....A.C.... C.C....AGA...A.....G..CTG
16 >A/Sw/Ohio/12TOSU467/2012,2012/08/09,H3N2 C..GGAA.G.TG.T.T.....TCGCG..GG.A.....G..A.T.T.ACCCC CGTC.GA.G.GT.T.TA....A.C.G.. C.C....AGAG..A.....G.ACTG
17 >A/Sw/Ohio/12TOSU464/2012,2012/08/09,H3N2 C..GGAA.G.TG.T.T.....TCGCG..GG.A.....G..A.T.T.ACCCC CGTC.GA.G.GT.T.TA....A.C.G.. C.C....AGAG..A.....G.ACTG
18 >A/Sw/Indiana/A01203509/2012,2012/05/09,H3N2 --------------------------------------------------- ---------------------------- -------------------------
19 >A/Sw/Indiana/A01104030/2012,2012/08/01,H3N2 C..GGAA.G.TGTT.T.....TCGCG..GG.....A.G..A.T.T.ACCCC ....C..G.AGTA.A..GG...G.A..A C.C....AGA..CA.....GA.CTG
20 >A/Sw/Indiana/A01104029/2012,2012/08/01,H3N2 C..GGAA.G.TGTT.T.....TCGCG..GG.....A.G..A.T.T.ACCCC ....C..G.AGTA.A..GG...G.A..A C.C....AGA..CA.....GA.CTG
23 >A/Sw/Michigan/A01203498/2012,2012/05/07,H3N2 --------------------------------------------------- ---------------------------- -------------------------
27 >A/Sw/Minnesota/2/2012,2012/06/05,H3N2 --------------------------------------------------- ---------------------------- -------------------------
28 >A/Sw/Minnesota/14/2012,2012/07/06,H3N2 --------------------------------------------------- ---------------------------- -------------------------
21 >A/Sw/Minnesota/17/2012,2012/08/10,H3N2 --------------------------------------------------- ---------------------------- -------------------------
22 >A/Sw/Nebraska/A01300032/2012,2012/06/12,H3N2 --------------------------------------------------- ---------------------------- -------------------------
24 >A/Sw/South Dakota/3/2012,2012/06/,H3N2 --------------------------------------------------- ---------------------------- -------------------------
25 >A/Sw/Minnesota/4/2012,2012/06/06,H3N2 --------------------------------------------------- ---------------------------- -------------------------
26 >A/Sw/Iowa/A01203612/2012,2012/06/30,H3N2 --------------------------------------------------- ---------------------------- -------------------------
51 >A/Sw/South Dakota/13/2012,2012/07/03,H1N1 --------------------------------------------------- ---------------------------- -------------------------
44 >A/Sw/Nebraska/A01203626/2012,2012/07/12,H1N2 --------------------------------------------------- ---------------------------- -------------------------
53 >A/Sw/Iowa/A01203534/2012,2012/05/23,H1N1 --------------------------------------------------- ---------------------------- -------------------------
38 >A/Sw/Ohio/A01203624/2012,2012/07/12,H3N2 --------------------------------------------------- ---------------------------- -------------------------
39 >A/Sw/Iowa/A01203675/2012,2012/07/19,H1N2 --------------------------------------------------- ---------------------------- -------------------------
54 >A/Sw/Iowa/A01203491/2012,2012/05/02,H1N1 --------------------------------------------------- ---------------------------- -------------------------
30 >A/Sw/Indiana/A01203521/2012,2012/05/15,H3N2 --------------------------------------------------- ---------------------------- -------------------------
31 >A/Sw/Indiana/A01203522/2012,2012/05/15,H3N2 --------------------------------------------------- ---------------------------- -------------------------
29 >A/Sw/Iowa/A01203503/2012,2012/05/09,H3N2 --------------------------------------------------- ---------------------------- -------------------------
40 >A/Sw/Indiana/A01203541/2012,2012/05/23,H1N2 --------------------------------------------------- ---------------------------- -------------------------
41 >A/Sw/Virginia/A01203711/2012,2012/08/01,H1N2 --------------------------------------------------- ---------------------------- -------------------------
42 >A/Sw/Iowa/A01203575/2012,2012/06/02,H1N2 --------------------------------------------------- ---------------------------- -------------------------
43 >A/Sw/Minnesota/12/2012,2012/06/28,H1N2 --------------------------------------------------- ---------------------------- -------------------------
49 >A/Sw/South Dakota/11/2012,2012/06/26,H1N1 --------------------------------------------------- ---------------------------- -------------------------
46 >A/Sw/Iowa/A01203577/2012,2012/06/04,H1N1 --------------------------------------------------- ---------------------------- -------------------------
47 >A/Sw/Iowa/A01203658/2012,2012/07/19,H1N1 --------------------------------------------------- ---------------------------- -------------------------
48 >A/Sw/South Dakota/8/2012,2012/06/,H1N1 --------------------------------------------------- ---------------------------- -------------------------
45 >A/Sw/Minnesota/5/2012,2012/06/,H1N1 --------------------------------------------------- ---------------------------- -------------------------
50 >A/Sw/Illinois/A01328406/2012,2012/05/15,H1N1 --------------------------------------------------- ---------------------------- -------------------------
52 >A/Sw/Nebraska/10/2012,2012/06/20,H1N1 --------------------------------------------------- ---------------------------- -------------------------
55 >A/Sw/Iowa/A01203544/2012,2012/05/23,H1N1 --------------------------------------------------- ---------------------------- -------------------------
33 >A/Sw/Ohio/9/2012,2012/06/,H3N2 --------------------------------------------------- ---------------------------- -------------------------
34 >A/Sw/Ohio/7/2012,2012/06/,H3N2 .G.......T.......T.A.......A..A.GTT.A....C...A..C.. ---------------------------- .G.AT..........T..AG....G
35 >A/Sw/Ohio/1/2012,2012/06/,H3N2 .G.......T.......T.A.......A..A.GTT.A....C...A..... ---------------------------- .G.AT..........T..AG....G
36 >A/Sw/Ohio/6/2012,2012/06/,H3N2 .G.......T.......T.A.......A..A.GTT.A....C...A..... ---------------------------- .G.AT.............AG....G
32 >A/Sw/Illinois/A01203672/2012,2012/07/21,H3N2 --------------------------------------------------- ---------------------------- -------------------------
37 >A/Sw/Michigan/A01259000/2012,2012/06/19,H3N2 ..A..........TCT....T.C....................G...C... ---------------------------- ......T..A.G..G.T........
62 >A/Sw/IN/A01049653/2011/03/08,H3N2 .............TCT....T.C....................G...C... ---------------------------- ......T..A.G..G.T........
58 >A/Sw/NY/A01104005/2011/09/13 .........T....................A.G...A....C...A..... .....G..G.GT....A........... ...A...............G....G
56 >A/IN/08_a/2011/07/27 ..A...........................A.G...A....C...A..... .........AGT..........G..... .........A.........G....G
58 >A/Sw/NY/A01104005/2011/09/13 .........T....................A.G...A....C...A..... .....G..G.GT....A........... ...A...............G....G
59 >A/IO/08(m1)/2011/11/14(H3N2) .........T....................A.G...A....C...A..... -G...G..G.GT...TA.G..A...... C.......G..........G..C.G
61 >A/WV/06/2011/11/21 C..GGAA...TG.T.T......CGCG...........G..A.T...ACCCC CG...G..G.GT...TA....A...... C.......G..........G..CTG
57 >A/IN/10/2011/10/22 .........T..................G.A.G...A....C...A..... .........AGT..........G..... C.......G..........G..C.G
60 >A/ME/06/2011/10/10 C....A.....G.T.T......CG..................T....CC.. .G...G..G.GT...TA....A...... ...A...............G....G
---Index---------------------------------------------TAGAACGCACCACCACGGCGCCTAAAGGAAGGAGCCGAATGACAAGGTTAT TACTTAGAAGACGCGCGAAAGTATGAGG TATGCACGACAATCACCGGACGTCA
-codon-position-------------------------------------- 22 1 1 21 112 1 2 1 2 2 11 1 1 2 1 1
000000000000000000000000000011111111111111111111222 0000000000000001111111111111 0000000000111111111111111
011122222344444555666677888901112224444555667999000 0023455677799991234444777799 1233334457001223444567899
414734688902447178166912789982678890223018572235034 1486779503901158622556001713 5502889918021055044929956
214795758926477012902473736668411464287254943026110 8520131485262812662781142083 0391452868539713736377602
000000000000000000000000001111111111 0000000000011111111 00000000000000000000000000000111111111111 0000000000000000000000000000000000000000000000 000000000000
002233333344455556667788990012234555 1123333578901222344 00011112222333445555667888999000111111222 0111111222222333444445555556666677777778888899 011233333446
331855779923401346890238134551681067 1460069102949349644 16900230111116683488293457008129134569047 4001788225789236037890256880367800136671233817 157515579168
156517593966614730732641307012020642 1173669685971393659 59325156023899837902732360697208912114086 5254439122051463854321851580969104156825389396 861511790687
12 1 12 1 21 2 2 1 1 12 1 2 2 1 1 1 1 22 1 2 1 12 1 12112111 2 1 2
TGCCTGGCCCTGAGAGCCAGGCTACTCAAAGGATCG GCTCAATTGCCGTAAGTGT ATTAAGCCCCCTCAATCTAAGCGTGCCACCTCTCACCTACT CGGTAAGTGAGATACTATGTATAGGGTAATGTCAGACTTATTAGAA GCCTTGGAGACA
.................................... ................... ......................................... .............................................. ............
C....A..T......A........T....G...... ..CT......TA....... ----------------------------------------- AA.......GA..G......G.G....G..A......C........ ........A...
C.T..A..T......A.....A..T....G.....A .......C..........C ----------------------------------------- AA.......GA..G......GAG....G..A......C........ ..T...AGA...
C.T..A..T......A.....A..T....G.....A .......C..........C ----------------------------------------- AA.......GA..G......GAG....G..A......C........ ..T...AGA...
C....A..T......A.....A..T....G.....A ------------------- ----------------------------------------- AA.......GA..G......GAG....G..A......C........ ------------
C....A..T......A.....A..T.T..G.....A .......C.T........C ----------------------------------------- AA.......GA..G......GAG....G..A......C......G. ..T...AGA..G
C....A..T......A.....A..T.T..G.....A .......C.T........C ----------------------------------------- AA.......GA..G......GAG....G..A......C......G. ..T...AGA..G
C....A..T......A.....A..T....G.....A .......C..........C ----------------------------------------- AA.......GA..G......GAG....G..A......C......G. ..T...AGA..G
CA.T.A..TT.....A.T...A..T...GG.....A .......C.........AC ----------------------------------------- AA.......GA..G......GAG....G..A......C........ ..T...AGA...
CA.T.A..TT.....A.T...A..T...GG.....A .......C.........AC ----------------------------------------- AA.....C.GA..G......GAG....G..A......C........ ..T...AGA...
C..T.A..T......A.....A..T...GG.....A .......C..........C ----------------------------------------- AA.....C.GA..G......GAG....G..A......C........ ..T...AGA...
C..T.A..T......A.....A..T...GG.....A .......C....C.....C ----------------------------------------- AA.....C.GA..G......GAG....G..A......C........ ..T...AGA...
C..T.A..T......A.....A..T...GG.....A .......C..........C ----------------------------------------- AA.....C.GA..G......GAG....G..A......C........ ..T...AGA...
C..T.A..T......A.....A..T...GG.....A .......C..........C ----------------------------------------- AA.....C.GA..G......GAG....G..A......C........ ..T...AGA...
C..T.A..T......A.....A..T...GG.....A .......C..........C ----------------------------------------- AA.....C.GA..G......GAG....G..A......C........ ..T...AGA...
C....A..T......A.....A..T....G.....A .......C..........C ----------------------------------------- AA.......GA..G......GAG....G..AG.....C........ A.....AGA...
C....A..T.A....AT.G..A..T....G.....A .......C......G...C ----------------------------------------- AA.......GA..G......GAG....G..AG.....C........ A..AG.AGA.T.
C....A..T.A....AT.G..A..T....G.....A .......C......G...C ----------------------------------------- AA.......GA..G......GAG....G..AG.....C........ A..AG.AGA.T.
C....A..T......A.....A..T....G...... ------------------- ----------------------------------------- AA.......GA..G......GAG....G..AG.....C........ ------------
C....A..T.....CA...A.A.GT....G.....A TT..GG..A.T.CG.TA.. ----------------------------------------- AA.......GAG.G......GAG....G..AG.....C........ .....A...G..
C....A..T.....CA...A.A.GT....G.....A TT..GG..A.T.CG.TA.. ----------------------------------------- AA.......GAG.G......GAG....G..AG.....C........ .....A...G..
------------------------------------ ------------------- ----------------------------------------- A............G......G..A...G....A............. ------------
------------------------------------ ------------------- ----------------------------------------- ..A..........G...C.C.....A......A.........GA.. ------------
------------------------------------ ------------------- ----------------------------------------- ..A..........G...C.C.....A......A.........GA.. ------------
------------------------------------ ------------------- ----------------------------------------- .A..G...T...CG..........A...............C..... ------------
------------------------------------ ------------------- ----------------------------------------- .A......T...CG..........A...............C..... ------------
------------------------------------ ------------------- ----------------------------------------- .A...........G.............................A.G ------------
------------------------------------ ------------------- GCC..ATT..TC.GG..C.T....AATG....C........ .A...........G.........T.........TACT......A.. ------------
------------------------------------ ------------------- .CC..ATT..TC.GG..C.T....AATG....C........ .A...........G.........T.........TACT......A.. ------------
------------------------------------ ------------------- ----------------------------------------- .A...........G...........A...............C.... ------------
------------------------------------ ------------------- ----------------------------------------- .A....A.T...CG................A............... ------------
------------------------------------ ------------------- ----------------------------------------- .A..G........G................................ ------------
.........T...................G...... ------------------- ....G...T................................ ---------------------------------------------- ------------
------------------------------------ ------------------- ......................................G.. ---------------------------------------------- ------------
------------------------------------ ------------------- ----------------------------------------- AA...........G......G.G......C...........C.... ------------
.....AA.....GA........C..C.T..A..CA. ------------------- ........T......C................CT......C AA...G....A..G.C....G.G....G..A......CA....... ------------
.....AA.....GA........C..C.T..A..CA. ------------------- ........T......C................CT......C AA...G....A..G.C....G.G....G..A......CA....... ------------
....C.AT....G.................A..... ------------------- ...............................A......... AA........A..G......G.G....G..A......C........ ------------
------------------------------------ ------------------- .........T..........T..........A......... AA........A..G.C....G.G....G..A......C........ ------------
------------------------------------ ------------------- ...G..T...........G..T................... .A..G........G............C........G.......A.. ------------
------------------------------------ ------------------- ...G..............G...................G.. .A...........G.........A..C........G.......A.. ------------
------------------------------------ ------------------- ----------------------------------------- .A.C.........G..............GC.........G...A.. ------------
------------------------------------ ------------------- ----------------------------------------- .A...........GT........T..........A....G...A.. ------------
------------------------------------ ------------------- ----------------------------------------- .A...........G.........T..........A........A.. ------------
------------------------------------ ------------------- ----------------------------------------- .A...........G.........T..........ACT......A.. ------------
------------------------------------ ------------------- ----------------------------------------- .A....A......GT........T...................A.. ------------
------------------------------------ ------------------- ----------------------------------------- .A...........G.............................A.. ------------
------------------------------------ ------------------- ----------------------------------------- .A...........G..............G..............A.. ------------
------------------------------------ ------------------- ----------------------------------------- .A...........G..G....................C.....A.. ------------
------------------------------------ ------------------- ----------------------------------------- .A.C.........G...............C.........G...A.. ------------
.....A..T..A........A.....T..G.AG... ------------------- GA..G.......A...A.....A..T..TT.........A. AA........A..G....A.G......G..A......C.....A.. ------------
.....A..T..A........A.....T..G.AG... ..C...C..TTA....... G......T........A.....A.....TT.....T...A. AA........A..G....A.G......G..A......C.....A.. ............
.....A..T..A........A.....T..G.AG... ..C...C..TTA....... .......T........A.....A.....TT.....T...A. AA........A..G....A.G......G..A......C.....A.. ............
------------------------------------ ..C...C..TTA....... G......T........A.....A.....TT.........A. AA........A..G....A.G......G..A......C.....A.G ............
.....A..T....................G...... ------------------- ............A.......TT.........A....T.... AA........A..G.CG...G.G....G..A......C........ ------------
.............................G...... ..........T........ ........T................................ ---------------------------------------------- A...........
......A.....G.................A..... ..........T........ ........T................................ ---------------------------------------------- ............
.....A..T....................G...... ....G.....T........ .......................C......C...G..A... AA...........G......G.G....................... ........A...
....C.AT....G.................A..... ....G.....T........ .........Y..........T..........A......... .............................................G .........G..
.....A..T....................G...... ....G.....T........ .......................C......C...G..A... AA...........G......G.G....................... ........A...
.....A..T...........A........G...... ..CT......TA....... -........T...................A......T.... AA........A..G......G.G....G..A......C........ .T..........
C....A..T......A........T....G...... ..CT......TA....... ----------------------------------------- AA.......GA..G......G.G....G..A......C........ ........A...
.....A..T....................G...... ................... ............................T............ AA...........G......G.G....................... .T..........
.....A..T....................G...... A.................. .......................C......C...G..A... AA........A..G......G.G....G..A......C........ ........A...
TGCCTGGCCCTGAGAGCCAGGCTACTCAAAGGATCG GCTCAATTGCCGTAAGTGT ATTAAGCCCCCTCAATCTAAGCGTGCCACCTCTCACCTACT CGGTAAGTGAGATACTATGTATAGGGTAATGTCAGACTTATTAGAA GCCTTGGAGACA
12 1 12 1 21 2 2 1 1 12 1 2 2 1 1 1 1 22 1 2 1 12 1 12112111 2 1 2
000000000000000000000000001111111111 0000000000011111111 00000000000000000000000000000111111111111 0000000000000000000000000000000000000000000000 000000000000
002233333344455556667788990012234555 1123333578901222344 00011112222333445555667888999000111111222 0111111222222333444445555556666677777778888899 011233333446
331855779923401346890238134551681067 1460069102949349644 16900230111116683488293457008129134569047 4001788225789236037890256880367800136671233817 157515579168
156517593966614730732641307012020642 1173669685971393659 59325156023899837902732360697208912114086 5254439122051463854321851580969104156825389396 861511790687
Attached Files