Sequences at Genbank!

[gsgs]

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%3Adoi%2F10.1371%2Fjournal.pone.0020698#pone-0020698-t001

these were in Russia (also Ukraine ?) in 2009 with reassortments,
presumably severe cases

Sichuan/1/2009(H1N1)
included in my russ8 table :

                                       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

[mixin]

Re: Sequences at Genbank!

gs:

presumably severe cases

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.

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.

[gsgs]

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

[mixin]

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

[mixin]

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

[mixin]

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.

[gsgs]

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

--------------------------------------

[gsgs]

Re: Sequences at Genbank!

new genomes from Chile, summer 2010
went to Sydney ? seen there one month later



pH1,HA since May,2010

[gsgs]

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

[gsgs]

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.

[gsgs]

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

[gsgs]

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

                                            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/2011/09/13/1111179108.DCSupplemental/pnas.201111179SI.pdf

[gsgs]

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

                                  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)

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)
NY2M+11)
Mex2M+14)
ZhejM+13)
WI2WI+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/2011/12/02/86.1.11.DC1/TableS1.pdf

they also have 13 "culsters" (~13 introductions into UK)

[gsgs]

Re: Sequences at Genbank!

33 HAs from Freiburg-city, SW-Germany early 2011
6 different introductions

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

[gsgs]

Re: Sequences at Genbank!

looking again at the genbank sequences ...
I think the Chi-strain , chi1 and chi2 that
circulated in Mexico,Ecuador,USA in 2010/2011
did emerge from Mexican viruses from late 2009,
it survived summer 2010 in Mexico or South America
or even South Africa, where it was seen.
And then it reassorted and emerged again in late 2010.
It was never seen in Asia, from where usually the
new strains are coming. So the European H1N1v
in 2010/11, which was first seen in India, May 2010.

I'm not aware of other examples, where a virus
from USA or Europe had descendents around
in the next season.
Except one H3N2 in 2001 or such, which I called "dynasty virus",
A/NY/301(2001/01/21(H3N2)
but this was a rare substrain, most viruses were different.

-----------------------------------
A/Mexico/UASLP-026/2009/11/13
A/Mexico/InDRECTRLA/2010/01 (is it really from 2010, not 2011)
Mex/INER 10,13,14
Habana
South Africa