Announcement

**gsgs** · September 1, 2010, 05:19 AM

Re: Sequences at Genbank!

new update after only 3 weeks:

http://magictour.free.fr/seq/mxhac.m1

the file contains the HA-nucleotide-sequences with their mutations

http://magictour.free.fr/seq/mxhac.mp

for amino-acid mutations

4948 *** HAs meanwhile, including partials
7.44M nucleotides in total (coding region only),
1504 in average (full=1701)

add 14 to the commonly used numbering here for the amino acids.
So D225G would be D239G in mxhac.mp
sorted by collection date, first those where only the collection year is known

239 mxhac.p 468 -:172 A:1 D:4307 E:369 F:1 G:74 N:18 P:4 V:1
so 1.6% have 225G , and 0.4% have 225N

nucleotides:
715 mxhac 33 -:130 A:18 G:4784 R:14 T:1
0.4% for 225N and 0.3% mixed

716 mxhac 113 -:130 A:4704 C:1 G:74 M:1 N:3 R:32 T:2
1.5% for 225G and 0.7% mixed

**mixin** · September 1, 2010, 09:10 AM

Re: Sequences at Genbank!

From the latest WHO update: 2 WHO Euro region report a case of pandemic A(H1N1) 2009 virus that developed in an immunocompromised child with reduced susceptibility to zanamivir and oseltamivir due to an aminoacid mutation at position 223 in the neuraminidase. The clinical implications of this A(H1N1) 2009 variant are being assessed and a publication is expected.

Do we have this sequence at Genbank and has the publication been released yet?

**gsgs** · September 4, 2010, 07:37 AM

Re: Sequences at Genbank!

none are at genbank with that mutation

**gsgs** · September 4, 2010, 07:38 AM

Re: Sequences at Genbank!

2191 ****** genomes, acquisition of mutations over time

maybe I'll update this and add some text and description later

**gsgs** · September 17, 2010, 05:02 AM

Re: Sequences at Genbank!

recent H3N2-HAs

Code:

                                      00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000111111111111111111111111111111111 
                                      00000000000011111111111111122222222222233333333334444444444555555555666666666666667777777777888888888999999999000000111111111222333444555555566 
                                      01122345668900122334455688900113366788912222789990133345889112335567012455667788891111233679333477788034568888012355233345789009048057013456756 
                                      70115565073689709675939029056391214312180138872372905763035892035957952216071626900125956813037901627305731234573238201495057566117314734820832 
-codon-position-----------------------112 1211 12  1   1212  12 112   1   2   2 21  2 1 21 22    2  22 111  1  2 121122 2 11  1  122   1  2      12      2 2       2  2 1221111 1     
---Index------------------------------AATGTGGCTGCGACAGAACCTATAGAAGATGAGGAGGCTCGCATACCCAGGAATAATCTTAAACAAATGTAAACCAGCATTCCCAGCAAACGGGGATGATATCGGTAAACGAGTCGTTAACCCGGGGCTGCAAGGGTCACACC 
  57 >Index/USA-2007                  ............................................................................................................................................... 
  53 >A/Brisbane/10/2007/02/06        ......A.C............................................................................................C......................................... 
  54 >Index/Brisbane-like/2007        ......................................................................G........................................................................ 
  55 >Index/Perth-like/2009           ................................A.......................A....C....C..A................T..............................G......A..T.........T.AG.. 
  56 >Index/2009/Egypt/Iowa           .......................................A.................T...C....C..G....A...G.......T.......................A...A..G......A..T...........AG.. 

  16 >A/Habana/11052/2010/04          ---...............................................................C...................T.....................................A..............AG.. 

   1 >A/Egypt/N11830/2009/11          ................................A.....................G.A....C....C..A...T......C..T..T................A.............G......A..T.........T.AG.. 
   2 >A/Thailand/CU-B1697/2009/11/1   ................................AA.T........GT..........A....C....C..A.........C......T........................G.....G....A..A.T.........T.AG.. 
   3 >A/Japan/AF2158/2009/11/1        .....................G..........A.......................A....C.AGGC..A..............C.T.....A........................G......A------------------ 
  15 >A/Acre/15093/2010/03/0          ..............G........T.....C..A................T...C..A....C....C..A...............AT............C....A.......AC...G......A..T..TG.A...T.AG.. 
  17 >A/Acre/26954/2010/04/0          ..............GA.............C..A................T...C..A....C....C..A................T............C....A.......AC...G......A..T..TG.A...T.AG.. 
  46 >A/Sao Paulo/16363/2010/07       ...............................GA.......................A....CT...C..A.........C......T..............................G...T..A..T......A.CT.AG.. 

   4 >A/Kenya/0072/2009/11/2          .......................................A.......G.........T...C....C..G....A...G.C.....T.......................A...A..G......A------------------ 
   5 >A/Kenya/0073/2009/11/2          .......................................A.................T...C....C..G....A...G.C.....T.......................A...A..G......A------------------ 
   6 >A/Egypt/N12479/2009/12          .......................................A.................T...C....C.TG....A...G......RT........G..............A...A..G......A..T...........AG.. 
   7 >A/Egypt/N13417/2009/12          ...A..A................................A........G........T...C....C..G....A...G.......T.....A.............G.G.A...A..G......A..T...........AG.T 
   8 >A/Egypt/N13578/2009/12          ..........................G.G..........A..G..............T...C....C..G....A...G...Y...T.....................G.A...A..G.....AA..T..........GAG.. 
   9 >A/Egypt/N13654/2009/12          .......................................A.................T...C....C..G....A...G...T...T.....................G.A...A..G......A..T....C..A...AG.. 
  10 >A/Egypt/N13658/2009/12          .......................................A.................T...C....C..G....A...G.......T.....................G.A...A..G......A..T....C..A...AG.. 
  11 >A/Egypt/N13908/2009/12          ----..................C................A.................T.C.C....C..G....A...G...M...TG.....................AA...A..G......A..T...........AGT. 
  12 >A/Toronto/H42220/2009/12/3      ----------------G......................A.................T...C....C..G....A...G.......T.....................G.A...A..G.C....A..TC...C..A...AG-- 
  13 >A/Nanjing/01/2010/01/1          ............CT.........................A.................T...C....C..G....A...G.......T..G....................A...AA.G......A..T...........AG.. 
  14 >A/Nagasaki/I544/2010/02/1       ---------.....................A........A...........T.....T...C....C.--------------------------------------------------------------------------- 
  18 >A/Kenya/001/2010/05/0           .................G......A...........A..A.................T...C....C..G..G.A...G.......T.......................A...A..G......A------------------ 
  19 >A/Kenya/002/2010/05/0           ........................A..............A.................T...C....C..G....A...G.......T.......................A...A..G......A------------------ 
  20 >A/Kenya/003/2010/05/1           ...................A....A..............A.................T...C....C..G....A...G.......T.......................A...A..G......A------------------ 
  21 >A/Kenya/004/2010/05/1           ........................A..............A.................T...C....C..G..G.A...G.......T..........A............A...A.CG......A------------------ 
  22 >A/Kenya/005/2010/05/1           ........................A..............A.................T...C....C..G....A...G.......T.......................A...A..G..T...A------------------ 
  23 >A/Kenya/006/2010/05/1           ........................A..............A.................T...C....C..G....A...G.......T.......................A...A..G......A------------------ 
  24 >A/Kenya/007/2010/05/1           ........................A..............A.................T...C....C..G....A...G.......T.........A.............A...A..G......A------------------ 
  25 >A/Italy/AF2157/2010/05/1        ........................A.........G....A.................T...C....C..G....A...G.......T.......................A...A..G......A------------------ 
  26 >A/Kenya/008/2010/05/1           .......................................A.................T.C.C....C..G....A...G.......TG.....A................A...A..G......A------------------ 
  27 >A/Kenya/009/2010/05/1           .......................................A.................T.C.C....C..G....A...G.......TG.....A................A...A..G......A------------------ 
  28 >A/Kenya/010/2010/05/1           .........T..............A..............A.................T...C....C..G....A...G.......T.......................A...A..G......A------------------ 
  29 >A/Kenya/011/2010/05/2           ..C...............T.....A..............A.................T...C....C..G....A...G.......T.......................A...A..G......A------------------ 
  30 >A/Kenya/012/2010/05/2           .....A....T.............A..............A.................T...C....C..G....A...G.......T.......................A...A..G......A------------------ 
  31 >A/Kenya/013/2010/05/2           ........................A..............A.................T...C....C..G....A...G.......T.......................A...A..G......A------------------ 
  32 >A/Kenya/014/2010/05/2           .G......................A..............A.................TC..C....C..G....A...G.......T.......................A...A..G......A------------------ 
  33 >A/Kenya/015/2010/05/2           .................G......AC..........A..AA...........G....T...C....C..G..G.A...G.......T.......................A...A..G......A------------------ 
  34 >A/Kenya/016/2010/05/2           ........................A..............A.................T...C....C..G....A...G.......T.......................A...A..G......A------------------ 
  35 >A/Kenya/017/2010/05/2           .......................................A.................T.C.C....C..G....A...G.......TG....T.................A...A..G......A------------------ 
  36 >A/Kenya/018/2010/05/2           ........................A..............A.................T...C....C..G....A...G.......T.......................A...A..G......A------------------ 
  37 >A/Kenya/019/2010/05/3           .......A................A..............A.................T...C....C..G....A...G.......T.......................A...A..G......A------------------ 
  38 >A/Managua/1181.03/2010/06/0     .......................................A.................T...C....C..G....A...G.......T.......A.............G.A...A..G......A..T....C..A...AG.. 
  39 >A/Managua/1422.03/2010/06/0     .......................................A.................T...C....C..G....A...G.......T.......A.............G.A...A..G......A..T....C..A...AG.. 
  40 >A/Managua/4131.04/2010/06/0     .......................................A.................T...C....C..G....A...G.......T.......A.............G.A...A..G......A..T....C..A...AG.. 
  41 >A/Managua/1807.03/2010/06/0     .....................................A.A.................T...C....C..G....A...G.......T.......A.............G.A...A..G......A..T....C..A...AG.. 
  42 >A/Managua/5806.01/2010/06/0     .......................................A.................T...C....C..G....A...G.......T.......A.............G.A...A..G......A..T....C..A...AG.. 
  43 >A/Managua/2867.01/2010/06/1     G......................................A.................T...C....C..G....A...G.......T.......A..........C..G.A...A..G......A..T....C..A...AG.. 
  44 >A/New York/20342/2010/06/1      .......................................A.................T...T....CC.G....A...G.......T......A....G...........A...A..G......A.AT.T.........AG.. 
  45 >A/New York/20343/2010/06/1      ..C.C.....................G............A.AG..............T...C....C..G....A...G.......T.....................G.A...A..G.....AA..T...........AG.. 
  47 >A/Alabama/AF2156/2010/07/1      ...........AG..............A..........CA...C.............T..GC....C..G....A.A.G..T....T.G.T.........C.........A...A..GG.....A------------------ 
  48 >A/Habana/14684/2010/08          ----------------.......................A......T..........T...C....C..G....A...G.......T.......................A..------------------------------ 
  49 >A/Habana/14685/2010/08          ----------------..................G....A.................T...C....C.TG.G..A...G.......T....................C..C..------------------------------ 
  50 >A/Habana/14686/2010/08          ----------------..................G....A..........A......T...C....C.TG.G..A...G.......T.......................C..------------------------------ 
  51 >A/Habana/14696/2010/08          ----------------....C..................A.................T...C....C.TG....A...G.......T....C..........T.......A..------------------------------ 
  52 >A/Habana/14720/2010/08          ----------------.......................A...............C.T...C....C..G....AC.AG.......T.......A.............G.A..------------------------------ 
                                                                                                                                                                                      
---Index------------------------------AATGTGGCTGCGACAGAACCTATAGAAGATGAGGAGGCTCGCATACCCAGGAATAATCTTAAACAAATGTAAACCAGCATTCCCAGCAAACGGGGATGATATCGGTAAACGAGTCGTTAACCCGGGGCTGCAAGGGTCACACC 
-codon-position-----------------------112 1211 12  1   1212  12 112   1   2   2 21  2 1 21 22    2  22 111  1  2 121122 2 11  1  122   1  2      12      2 2       2  2 1221111 1     
                                      00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000111111111111111111111111111111111 
                                      00000000000011111111111111122222222222233333333334444444444555555555666666666666667777777777888888888999999999000000111111111222333444555555566 
                                      01122345668900122334455688900113366788912222789990133345889112335567012455667788891111233679333477788034568888012355233345789009048057013456756 
                                      70115565073689709675939029056391214312180138872372905763035892035957952216071626900125956813037901627305731234573238201495057566117314734820832

**gsgs** · September 20, 2010, 04:25 AM

Re: Sequences at Genbank!

I made a picture :

http://magictour.free.fr/panflu/h3_tt6c.GIF

some(~300) "old" viruses most from early 2007,
Wisconsin/05 -like were removed.
The index is almost Brisbane/10/2007

it ignores mutations that occur only once in the list, as usual

it just considers changes to the index, 3 or more different
nucleotides at one position are treated as 2 different
(--> some "bias", sigh) to make it easier
------edit----hmm, I should use another color for these

it would be useful to include GISAID sequences here (agreed ?)
but this is forbidden by their terms of use
if you have registered (agreed ?)
and presumably not supported, since you would have to
download all their H3-sequences and build my database.
So, I think it doesn't exist and we can only get this from genbank.

here is the mutation table:

http://magictour.free.fr/panflu/H3_TT.L6Z

compressed with gzip

I only had a brief look at it and noted indication for
recombination or lab-error in

A/Cheongju/H471/2008/02/28 + A/Cheongju/H473/2008/04/15
with parents
A/Cheongju/H380/2007/09/19 + A/Cheongju/H383/2007/10/10
and
A/Boston/44/2008/02/19 + many similars

here is an example how "polymorphism jumping"
should look in the pictures:

http://magictour.free.fr/panflu/jump2.GIF

two black vertical lines A,B such that
some horizontal lines are intersected by A
some by B
and some by both

**gsgs** · October 13, 2010, 01:26 AM

Re: Sequences at Genbank!

below is a Boston update with now 64 genomes from Boston

we must have had a first Boston table in this thread
with 42 genomes - I can't find it now

Code:

                                     00000000000011111111111222 000000000111111122222 0000000111112 000000000000000000011111 000000000111 0000011111 00000 0000000 
                                     12344455667801235577899111 133456689455666800222 0012468445581 001133455666677788911456 123467889123 0136712233 01446 0334445 
                                     21966848373835460756923689 466570347307489717001 4974304025934 014649544045525959378063 597018290447 2515492439 75090 9260183 
                                     60904060992882070982932376 136033645902882206671 0019239181406 495500309707806328015860 082209870384 6069241828 54820 7371142 
-codon-position----------------------   12  1 1    12 1 1              1 2  12    12  1         1 1 111 1    11 1  1 1 1 1 1  1  1        2 121       1    1212 11 
---Index-----------------------------CGCCGGGCTGCCGGGAATGATAGGGG CAATAGGCCAATTGATGCAAA GCGCCTGGCGCAA AGCCGGAATGGGTAGCTAGGACGG TGCTCAGCGGGC CTGGAGTTCC GTAGG CGATCCG 
   1 >A/******/index/2009/02/01      .......................... ..................... ............. ........................ ............ .......... ..... ....... 
   2 >A/Boston/132/2009/06/19        ......A................... ..................... ............. ..A..................... ............ ........T. ..... ....... 
   3 >A/Boston/118/2009/06/20        ......A................... .....A...........T... ............. ..A..................... ............ .......... ..... ....... 
   4 >A/Boston/108/2009/06/16        ...........T.............. .....AA..........T... ...T......... G.................T..T.. .A.......A.. ..A.G..... ..... ....... 
   5 >A/Boston/126/2009/06/20        ...........T.............. .....AA..........T... .T.T......... G.................T..T.. .A.......A.. ..A.G..... ..... ....... 
   6 >A/Boston/121/2009/06/19        ...........T.............. .....AA..........T... ...T...A..... G..........A......T..TA. .A..A....A.. ..A.G..... ..... .....T. 
   7 >A/Boston/120/2009/06/19        ...........T.............. .....AA..........T... ...T...A..... G..........A......T..TA. .A..A....A.. ..A.G..... ..... .....T. 
   8 >A/Boston/151/2009/07/06        ...........T.............. ....GA............... ...T......... G.................T..T.. .A.......A.. ..A.G..... ..... ....... 
   9 >A/Boston/147/2009/07/09        .A.........T.............. ....GA...........T... ............. G.................T..T.. .A.......A.. ..A.G..... ..... ....... 
  10 >A/Boston/124/2009/06/26        .A.........T.............. .....A...........T... ............. GT................T..T.. .A.......A.. ..A.G..... ..... ....... 
  11 >A/Boston/140/2009/06/22        ...........T.............. .....A...........T... ............. G.................T..T.. CA.......A.. ..A.G..... ..... ....... 
  12 >A/Boston/129/2009/06/22        ...........T............T. .....A...........T... ............. G............G....T..T.. CA.......A.. ..A.G..... ..... ....... 
  13 >A/Boston/138/2009/06/18        ...........T............T. .....A...........T... ............. G..T.........G.T..T.GT.. CA.......A.. ..A.G..... ..... ....... 
  14 >A/Boston/110/2009/06/11        ...........T............T. .....A...........T... ............. G..T.........G....T.GT.. CA.......A.. ..A.G..... ..... ....... 
  15 >A/Boston/146/2009/07/01        ...........T.............. .....A...........T... ............. G.................T..T.. CA.......A.. ..A.G..... ..... ....... 
  16 >A/Boston/117/2009/06/26        ...........T.............A .....A...........T... ............. G.................T..T.. CA.......A.. ..A.G..... A.... .A..... 
  17 >A/Boston/125/2009/06/17        ...........T.............A .....A...........T... ............. G.................T..T.. .A.......A.. ..A.G..... A.... .A..... 
  18 >A/Boston/137/2009/06/20        ...........T.............A .....A..........AT... ............. G.................T..T.. .A.......A.. ..A.G..... A.... .A..... 
  19 >A/Boston/106/2009/06/15        ...........T.............A .....A..........AT... ............. G.................T..T.. .A.......A.. ..A.G..... A.... .A..... 
  20 >A/Boston/135/2009/06/18        ...........T.............A .....A...........T... ............. G.................T..T.. .A.......A.. ..A.G..... A.... .A..... 
  21 >A/Boston/142/2009/06/30        ...........T.............A .....A...........T... ............. G.................T..T.. .A.......A.. ..A.G..... ..... ....... 
  22 >A/Boston/130/2009/06/21        ...........T.............A TG...A...........T... ............. G.................T..T.. .A.......A.. ..A.G..... .C... ....... 
  23 >A/Boston/115/2009/06/13        ...........T.............A TG...A...........T... ............. G.................T..T.. .A.......A.. ..A.G..... .C... ....... 
  24 >A/Boston/109/2009/06/15        ...........T.............A .....A...........T... ............. G.................T..T.. .A.......A.. ..A.G..... ..... ....... 
  25 >A/Boston/113/2009/06/15        ...........T.............A .....A...........T... ............. G.................T..T.. .A.......A.. ..A.G..... ..... ....... 
  26 >A/Boston/133/2009/06/18        ...........T.............A .....R...........T... ............. G.................T..T.. .A.......A.. ..A.G..... ..... ....... 
  27 >A/Boston/131/2009/06/24        ...........T.............. .....A...........T... ............. G.................T..T.. .A.......A.. ..A.G..... ..... ....... 
  28 >A/Boston/103/2009/06/15        ...........T.............. .....A...........T... ............. G.................T..T.. .A.......A.. ..A.G..... ..... ....... 
  29 >A/Boston/144/2009/07/09        .......................A.. ..................... ............. ............A........T.. .A.......AA. ..A.G..... ...AA ..G.... 
  30 >A/Boston/123/2009/06/18        .......A...............A.. ..................... ............. ............A........T.. .A.......AA. ..A.G..... ...AA ..G.... 
  31 >A/Boston/149/2009/07/01        ..T....A...............A.. ...C...........C..... .....C....... ............A........T.. .A.......AA. ..A.G..... ...AA ..G.... 
  32 >A/Boston/152/2009/06/29        ..T....A...............A.. ...C...........C..... .....C....... ............A........T.. .A.......AA. ..A.G..... ...AA ..G.... 
  33 >A/Boston/96/2009/06/13         .......................A.. ..................... ............. .T..........A........T.. .A.......AA. ..A.G..... ...AA ..G.... 
  34 >A/Boston/127/2009/06/17        ...A....C..............A.. ..................... ............. ............A........T.. .A.......AA. ..A.G..... ...AA ..G.... 
  35 >A/Boston/703/2009/12/02        ...A....C..............A.. ..............G...... ............. ............A........T.. .A.......AA. ..A.G..... ...AA ..G.... 
  36 >A/Boston/584/2009/10/07        ...A....C..............A.. ..............G...... .T........... .......C....A........T.. .A.......AA. ..A.G..... ...AA ..G.... 
  37 >A/Boston/663/2009/11/16        .......................A.. ..................... ............. ............A........T.. .A.......AA. ..A.G..... ...AA ..G.... 
  38 >A/Boston/145/2009/07/09        ................G......A.. ..................... ............. ............A........T.. .A.......AA. ..A.G..... ...AA ..G.... 
  39 >A/Boston/148/2009/07/07        ......................AA.. ..................... ............. ............A........T.. .A.......AA. ..A.G..... ...AA ..G.... 
  40 >A/Boston/682/2009/11/17        ...............G..A...AA.. ........TGG..A....... ..A.......T.. ....A.......A.A.C..A.T.. .A.......AA. ..A.G..... ...AA A.G.... 
  41 >A/Boston/648/2009/11/12        ...............G..A...AA.. ........TGG..A....... ..A.......T.. ....A.......A.A.C..A.T.. .A.......AA. ..A.G..... ...AA A.G.... 
  42 >A/Boston/634/2009/11/09        ..............A....G...A.. ..........G..A....... ..A.......T.. ....A.......A...C..A.T.. .A.......AA. ..A.G..... ...AA ..G.... 
  43 >A/Boston/655/2009/11/13        .......................A.. ..........G..A....... ..A......AT.. ....A.T.....A...C..A.T.. .A.......AA. ..A.G..... ...AA ..G...T 
  44 >A/Boston/653/2009/11/13        ....................C..A.. ..........G..A....... ..A......AT.. ....A.T.....A...C..A.T.. .A.......AA. ..A.G..... ...AA ..G...T 
  45 >A/Boston/112/2009/06/13        ....................C..A.. ..................... ............. ............A........T.A .A.......AA. ..A.G..... ...AA ..G.... 
  46 >A/Boston/122/2009/06/22        .......................A.. ..................... ............. ............A........T.. .A.......AA. ..A.G..... ...AA ..G.... 
  47 >A/Boston/658/2009/11/13        .......................A.. ................A.... ............. ............A........T.. .A.......AA. ..A.G..... ...AA ..G.... 
  48 >A/Boston/591/2009/10/18        .......................A.. ..................... ............. ............A........T.. .A.......AA. ..A.G..... ...AA ..G.... 
  49 >A/Boston/595/2009/10/24        .........A..AA...C.....A.. ...........CC.....GGG A.....A.A..TC .......G.A..A......A.T.. .ATC.....AAT ..AAGA.... ...AA ..G.T.. 
  50 >A/Boston/602/2009/10/29        .........A..AA...C.....A.. ...........CC.....GGG A.....A.A..TC .......G.A..A......A.T.. .ATC.....AAT ..AAGA.... ...AA ..G.T.. 
  51 >A/Boston/701/2009/11/27        .........A..AA...C.....A.. ............C.....GGG A.....A.A..TC .......G.A..A......A.T.. .ATC.....AAT ..AAGA.... ...AA ..G.T.. 
  52 >A/Boston/698/2009/11/23        ............AAA.G......A.. ............C.....GGG A...........C ............A......A.T.A .AT..C...AAT ..A.GA..T. ...AA ..G.... 
  53 >A/Boston/672/2009/11/15        ............A..........A.. ............C.....GGG A...........C ............A......A.T.. .AT..C...AAT ..A.GA.... ...AA ..G.... 
  54 >A/Boston/154/2009/08/18        ....A..................A.. ..................... ....T........ ............A......A.T.. .A.....T.AA. ..A.G..C.T ...AA ..G.... 
  55 >A/Boston/116/2009/06/29        ....A..................A.. ..................... ....T........ ............A........T.. .A.....T.AA. ..A.G..C.T ...AA ..G.... 
  56 >A/Boston/143/2009/07/08        .......................A.. ..................... ............. ............A..T.....T.. .A.......AA. ..A.G..... ...AA ..G.... 
  57 >A/Boston/606/2009/11/02        .......................A.. ..................... ............. ............A........T.. .A.......AA. ..A.G.C... ...AA ..G.... 
  58 >A/Boston/134/2009/06/26        .......................A.. ..................... ............. ............A........T.. .A.......AA. ..A.G.C... ...AA ..G.... 
  59 >A/Boston/141/2009/06/25        .......................A.. ..................... ............. ............A........T.. .A.......AA. .CA.G..... ...AA ..G.... 
  60 >A/Boston/681/2009/11/17        .....A....T..........G.A.. ..G....T............. ............. .....A..C.T.A....G...T.. .A....A.AAA. TCA.G..... ..GAA ..G.... 
  61 >A/Boston/666/2009/11/16        .....A....T..........G.A.. ..G....T............. ............. .....A..C.T.A....G...T.. .A....A.AAA. T.A.G..... ..GAA ..G.... 
  62 >A/Boston/612/2009/11/02        .....A....T..........G.A.. ..G....T............. ............. .....A..C.T.A....G...T.. .A....A.AAA. T.A.G..... ..GAA ..G.... 
  63 >A/Boston/704/2009/12/03        .....A....T..........G.A.. ..G....T............. ............. .....A..C.T.A....G...T.. .A....A.AAA. T.A.G..... ..GAA ..G.... 
  64 >A/Boston/153/2009/07/15        T..................G...A.. ..................... ............. ............A........T.. .A.......AA. ..A.G..... ...AA ..GC... 
  65 >A/Boston/136/2009/06/26        T..................G...A.. .................T... ............. ............A........T.. .A.......AA. ..A.G..... ...AA ..GC... 
  66 >A/Cancun-NY/Index/2009/04/15   .......................A.. ..................... ............. ............A........T.. .A.......AA. ..A.G..... ...AA ..G.... 
                                                                                                                                                                   
---Index-----------------------------CGCCGGGCTGCCGGGAATGATAGGGG CAATAGGCCAATTGATGCAAA GCGCCTGGCGCAA AGCCGGAATGGGTAGCTAGGACGG TGCTCAGCGGGC CTGGAGTTCC GTAGG CGATCCG 
-codon-position----------------------   12  1 1    12 1 1              1 2  12    12  1         1 1 111 1    11 1  1 1 1 1 1  1  1        2 121       1    1212 11 
                                     00000000000011111111111222 000000000111111122222 0000000111112 000000000000000000011111 000000000111 0000011111 00000 0000000 
                                     12344455667801235577899111 133456689455666800222 0012468445581 001133455666677788911456 123467889123 0136712233 01446 0334445 
                                     21966848373835460756923689 466570347307489717001 4974304025934 014649544045525959378063 597018290447 2515492439 75090 9260183 
                                     60904060992882070982932376 136033645902882206671 0019239181406 495500309707806328015860 082209870384 6069241828 54820 7371142

132 and 118 are the "airplane"-strain, but 118 got segment 2 by reassortment from
the Boston strain

then 25 genomes from the "Boston strain"
and 37 from the Cancun-strain

The "Boston-strain" is a substrain from the pre-Cancun/Mexico-City strain,
I had called it the Manitoba-strain before, so let's stick to
"Manitoba-strain".

markers for the Manitoba-strain are:
C888T(1) , G603A(2) , C2076T(2) , A4G(4) , G930T(4) ,

888 mxpb26 57 -:1 C:1124 T:57
603 mxpb1b 120 -:1 A:117 G:2092 N:2 R:1
2076 mxpb1b 146 -:3 A:44 C:2064 T:102
4 mxhac 172 -:782 A:3993 G:171 R:1
930 mxhac 204 -:290 A:9 C:1 G:4453 K:6 T:188

057,1124
117,2092
102,2064
171,3993
188,4453

the list of substrains is here:

h5n1experts.org - h5n1experts Resources and Information.

http://h5n1experts.org/forum/showpost.php?p=1133

h5n1experts.org is your first and best source for all of the information you’re looking for. From general topics to more of what you would expect to find here, h5n1experts.org has it all. We hope you find what you are searching for!

Manitoba,10,C1408T,4,G0298A,5,G1143A,5,G0316A,6,A0 742G,6,C0888T,1,G0603A,2,C2076T,2,A0004G,4,G0930T, 4

the last genomes from that Manitoba-strain in Boston were from early July 2009,
later genomes are all Cancun.
So, why did Cancun take over ? Was it more fit ?
I think it's just that the Manitoba-wave had ended and the virus had died.
Then Cancun was re-introduced in fall from New-York or elsewhere.

Manitoba/Boston mutations were also seen in:

Code:

AUS,1
Addis Ababa,2
Alabama,2
Alaska,1
Amman,2
Ancona,2
Ankara,4
Athens,2
Australia,8
Bahia,6
Bamako,1
Beijing,1
Belgorod,1
Bishkek,1
Blore,1
Boston,102
California,8
Canada-MB,30
Canada-SK,5
Catalonia,1
Dhule,2
Finland,2
Frankfurt,2
GER-MV,2
Gifu-C,1
Guam,5
Guangdong,1
Guayaquil,1
Hamburg,1
IL,1
Indiana,3
Italy,7
Kavala,2
Korea,2
Kuwait,1
Lisboa,2
Maine,2
Managua,1
Massachusetts,4
Mexico City,15
Mississippi,4
Moscow,2
Mum,2
NY,41
Netherlands,1
New Hampshire,1
New Mexico,1
New York,60
Newark,1
Norway,2
Nsk,4
Odense,1
Ontario,30
Parana,2
Paris,5
Pavia,2
Pennsylvania,2
Port Au Prince,1
Pune,11
Rhode Island,12
Rio Grande do Sul,5
Rio de Janeiro,15
Roma,2
San Diego,1
San Salvador,2
Santa Catarina,3
Santo Domingo,4
Sao Paulo,9
Shandong,5
Shanghai,4
Shizuoka,5
Silver Spring,18
Singapore,14
South Carolina,3
Swine,2
THA,50
Taipei,3
Taiwan,7
Texas,82
Thailand,10
Thessaloniki,6
Tokushima,5
Toronto,10
Vermont,2
Wakayama,1
Wisconsin,5
Yakutsk,1
Yaroslavl,1
turkey,6

both, A4G(4) and G930T(4) were in :

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

1,Alabama/2009/07/26
25,A/Boston/2009/06/13 - 07/09
1,Indiana/2009
1,Maine/2009/05/09
2,Massachusetts/2009/05/07
2,Mississippi/2009/10/06 - 12/01
19,NY/2009/04/28 - 06/23
6,Ontario/2009/06/15 - 09/07
3,turkey/Ontario/2009/10/23 - 11/03
1,Pennsylvania/2009
3,Rhode Island/2009/04/28 - 04/30
6,Silver Spring/2009/06/18
17,Texas/2009/06/15 - 10/19
2,Toronto/2009/06/09 - 06/17
1,Vermont/2009/05/04
1,Wisconsin/2009/11/27

1,Ankara/2009/11/11
1,Finland/2009/05/28
1,Frankfurt/2009/11/23
1,Italy/2009/06/17
1,Kavala/2010/01/12
1,Lisboa/2009/06/19
1,Norway/2009/08/11
1,Paris/2009/06/02
1,Thessaloniki/2010/01/13

1,Parana/2009/07/12
2,Rio Grande do Sul/2009/07/23 - 07/29
7,Rio de Janeiro/2009/07/02 - 2010/02/18
1,San Salvador/2009/11/06
1,Santo Domingo/2009/06/10
4,Sao Paulo/2009/05/27 - 08/09

1,Guam/2009/08/06
1,Korea/2009/09/22
3,Pune/2009/07/ - 09/10
1,Shandong/2009/05/10
1,Shizuoka/2009/06/15
1,Singapore/2009/06/14
23,Thailand/2009/06/13 - 09/25
1,Taiwan/2009/05/28
1,Tokushima/2009/06/02

3,Bahia/2010/03/19
1,Dhule/2009/08/
1,Mum/2009/07/
1,Nsk/2009/09/07
1,Santa Catarina/2009/06/01

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

91 in North America: 2009/04/28 - 2009/11/27
16 in Latin America: 2009/05/27 - 2010/02/18
9 in Europe: 2009/05/28 - 2010/01/13
33 in Asia: 2009/05/10 - 2009/09/22

**gsgs** · October 15, 2010, 07:46 AM

Re: Sequences at Genbank!

new sequences from Thailand

Code:

                                           000000011111111111111111111111112222222 0000000000000000000000000000000000112 00001 0000000000000000011111111111 00000000001111111 00000000001 000000000000000000000000000000000000000 0000000000 
                                           004778902234466666666666666666990011111 0000000000000000000344444444456999390 00096 0111234566778999900012234445 23445667780112224 02346777880 000011144566777777777777777778888899999 1112233457 
                                           034158266851422333333333444558791901677 1111111122222222223268899999990179067 04430 0045482105012002328978850691 95577463963344579 27115144685 233444809906000111111111244671122844445 1253966152 
                                           961428109113089012346789012469900495303 1234578901234567890127912347843230316 90500 4644914658719061096211228442 81946832858738720 06651126359 834502922303679023456789427354657367890 2183167754 
-codon-position----------------------------    2  1  1  2 12 1212 12 11  21     11 2 12 2 12 12 12 12   1 2 122    1 12   1  1 11 1  1 212 1       1 121    1        1      2 2 11  122   1 1 21   2  121212 12 1211 111  2112 12 1122  1  1 
---Index-----------------------------------AGAGGCCAGAAGCAGTCAGTCTAGTCATGAACGCACGGC ATCCGCTCTACTTTTCCTACCCATAGATCGGGACAGC CGGCC AGCGGAAAGTAGAGTCGTAAGAGCCCTA GGGAGGAAGCCGGGTCA TCGTGTAGTCC TTCCAAGGGAGTAATTCAGGCCTAAAGTATCTTGTGACG CAAGAGACTG 
   1 >A/******/index/2009/02/01            ....................................... ..................................... ..... ............................ ................. ........... ....................................... .......... 
   2 >A/Nonthaburi/102/2009/05/06          .......G..G............................ ................................G.... ...T. -----G...............------- A...........A.... ..AC..GA... ......T................................ .......... 
   3 >A/Thailand/104/2009/05/06            .......G..G............................ ................................G.... ...T. .....G..................T... A...........A.... ..AC..G.... ......T................................ .......... 
   4 >A/Thailand/CU-H340/2009/08/          ....................................R.. ......................G.......A.....T ..... -...A...........T.G.....T... A...........A.... -.A...G.... ...A................................... .......... 
   5 >A/Thailand/CU-B5/2009/06/13          .....T................................. ......................G.......A.....T ..... G...............T.G.....T... A.......A...A..T. ..A...G.... .........G............................. .......... 
   6 >A/Thailand/CU-H572/2009/09/03        G...A.T.A...A.......................A.. ......................G........A...A. ..T.. G...............T.G.....T... A...........A..T. ..A...G.... .......AA.AC........................... ......G... 
   7 >A/Thailand/CU-H300/2009/07/26        ---------------------CTAGTC.........--- ----------..C.A.T.C......A.A.-------- ----- ................T.......T... ----------------- ..A...G.--- ..................................GACGA --------.. 
   8 >A/Thailand/CU-H302/2009/07/27        ---------------------CTAGTC.......----- -------------------..---------------- ----- ................T.......T... ----------------- ..A...G.--- ..................................GACGA .....----- 
   9 >A/Thailand/CU-H243/2009/07/17        --------------------.CTAGT..........--- .A...ACT.C.................---------- ----- .........A......T.......T... ----------------- ..A...G.--- ..........A........................---- ......G... 
  10 >A/Thailand/THB0423/2009/07/21        --------------------------------------- ------------------------------------- ----- G............T..T.......T..C ----------------- ----------- --------------------------------------- ---------- 
  11 >A/Thailand/CU-H139/2009/07/07        -------------GTGAGAGGCTTG..GA....------ --------AT.C.C..T.T........A--------- ----- ................T.......T... ----------------- ..A...G.--- GGG..G.......GAG.....ACT.....C.C..GACGA .......... 
  12 >A/Thailand/PMKSV0305/2009/08/02      --------------------------------------- ------------------------------------- ----- ................T.G.....T... ----------------- ----------- --------------------------------------- ---------- 
  13 >A/Thailand/CU-H203/2009/07/13        --------------------..............G.... -----A...CT.CC.AAA.....AGTT---------- ----- ................T.......T... ----------------- ..A...G.--- ...............................CC...... .......... 
  14 >A/Thailand/THB0402/2009/07/15        --------------------------------------- ------------------------------------- ----- G...............T.G.....T... ----------------- ----------- --------------------------------------- ---------- 
  15 >A/Thailand/CU-H134/2009/07/07        -------------CCGAGCGGCTAGT.G.....T----- -----ACTCTAC...T...........A--------- ----- ................T.......T... ----------------- ..A...G.--- .....G......GGAG.....ACTC..A.C.C..----- .......... 
  16 >A/Thailand/THB0434/2009/07/27        --------------------------------------- ------------------------------------- ----- G...............T.G.....T... ----------------- ----------- --------------------------------------- ---------- 
  17 >A/Thailand/THB0442/2009/07/29        --------------------------------------- ------------------------------------- ----- G...............T.G.....T... ----------------- ----------- --------------------------------------- ---------- 
  18 >A/Thailand/0440-00-N0/2009/07/29     --------------------------------------- ------------------------------------- ----- G...............T.G.....T... ----------------- ----------- --------------------------------------- ---------- 
  19 >A/Thailand/THB0435/2009/07/28        --------------------------------------- ------------------------------------- ----- G......G........T.G.....T... ----------------- ----------- --------------------------------------- ---------- 
  20 >A/Thailand/0445-00-N0/2009/07/30     --------------------------------------- ------------------------------------- ----- G......G........T.G.....T... ----------------- ----------- --------------------------------------- ---------- 
  21 >A/Thailand/THB0444/2009/07/29        --------------------------------------- ------------------------------------- ----- G...............T.G.....T... ----------------- ----------- --------------------------------------- ---------- 
  22 >A/Thailand/THB0437/2009/07/28        --------------------------------------- ------------------------------------- ----- G...............T.G...A.T... ----------------- ----------- --------------------------------------- ---------- 
  23 >A/Thailand/CU-H85/2009/07/01         -------------------------T.GA.--------- --AA...........T...........A--------- ----- G...............T.---------- ----------------- .TA...G.A-- .............................C.C..GACG- .......... 
  24 >A/Thailand/THB0474/2009/08/10        --------------------------------------- ------------------------------------- ----- G...............T.G.....T... ----------------- ----------- --------------------------------------- ---------- 
  25 >A/Thailand/CU-H109/2009/07/03        --------------------GCTAGTC...--------- -----....CT...C.T.C......T.AT-------- ----- -........A......T.---------- ----------------- ..A...G.--- ...............................C..GA--- .......... 
  26 >A/Thailand/THB0438/2009/07/28        --------------------------------------- ------------------------------------- ----- G...............T.G.....T... ----------------- ----------- --------------------------------------- ---------- 
  27 >A/Thailand/CU-H216/2009/07/15        --------------------..............G.... ...GT.GTC..................---------- ----- -...............T.......T.-- ----------------- ..A...G.--- ........A.A.......................----- .GG....... 
  28 >A/Thailand/PMKD0030/2009/09/25       --------------------------------------- ------------------------------------- ----- G...............T.G.....T... ----------------- ----------- --------------------------------------- ---------- 
  29 >A/Thailand/0316-00-N0/2009/06/23     --------------------------------------- ------------------------------------- ----- G...............T.G.....T... ----------------- ----------- --------------------------------------- ---------- 
  30 >A/Thailand/CU-H133/2009/07/06        -----------------------..T....--------- ----A......................A--------- ----- ................T.......T... ----------------- ..A...G.--- ............GGA.TCATT....C.A.C.C..----- .......... 
  31 >A/Thailand/THB0419/2009/07/20        --------------------------------------- ------------------------------------- ----- G............A..T.G.....T... ----------------- ----------- --------------------------------------- ---------- 
  32 >A/Thailand/THB0428/2009/07/22        --------------------------------------- ------------------------------------- ----- G............A..T.G.....T... ----------------- ----------- --------------------------------------- ---------- 
  33 >A/Thailand/THB0454/2009/08/03        --------------------------------------- ------------------------------------- ----- G............A..T.G.....T... ----------------- ----------- --------------------------------------- ---------- 
  34 >A/Thailand/THB0433/2009/07/27        --------------------------------------- ------------------------------------- ----- G............A..T.G....AT... ----------------- ----------- --------------------------------------- ---------- 
  35 >A/Thailand/THB0427/2009/07/22        --------------------------------------- ------------------------------------- ----- G............A..T.G.....T... ----------------- ----------- --------------------------------------- ---------- 
  36 >A/Thailand/CU-H128/2009/07/06        --------------------.....TC...--------- TCGTA................T...T.AT-------- ----- ................T.......T... ----------------- ..A...G.--- .............................C.C..GACG- .......--- 
  37 >A/Thailand/THB0420/2009/07/20        --------------------------------------- ------------------------------------- ----- G...............T.G.....T... ----------------- ----------- --------------------------------------- ---------- 
  38 >A/Thailand/CU-H393/2009/08/14        --------------------................... --A........................A--------- ----- ................T.......T... ----------------- ..A...G..-- ....CG............................----- .......... 
  39 >A/Thailand/THB0472/2009/08/07        --------------------------------------- ------------------------------------- ----- G...............T.G.....T... ----------------- ----------- --------------------------------------- ---------- 
  40 >A/Thailand/THA0364/2009/07/22        --------------------------------------- ------------------------------------- ----- G..A............T.G.....T... ----------------- ----------- --------------------------------------- ---------- 
  41 >A/Thailand/THB0415/2009/07/16        --------------------------------------- ------------------------------------- ----- G...............T.G.....T... ----------------- ----------- --------------------------------------- ---------- 
  42 >A/Thailand/CU-H427/2009/08/19        --------------------.........G....G.... TC.GA......................A--------- ----- ................T.......T... ----------------- ..A...G..-- ........A.A.......................----- A......... 
  43 >A/Thailand/CU-H429/2009/08/20        -------------GTGA.A..CT..T........G..TT -C.GA......................A--------- ----- ........................T... ----------------- ..A...G.--- ........A.A.......................----- A....----- 
  44 >A/Nonthaburi/104/2009/05/10          --------------------------------------- ------------------------------------- ----- -----G...............------- ----------------- ..AC..GA... --------------------------------------- ---------- 
  45 >A/Thailand/CU-H122/2009/07/04        ---------------------------...--------- ----A.CTC..................A--------- ----- ..................---------- ----------------- ..A...G.--- ............................CC.CC.GA--- .....----- 
  46 >A/Thailand/CU-H132/2009/07/06        ---------------------...........------- -------------------..---------------- ----- ................T.......T... ----------------- ..A...G.--- .............................C.CC.GAC.- .....----- 
  47 >A/Thailand/CU-H491/2009/08/01        --------------------.......G........A.. --.GA......................A--------- ----- .........A..............T... ----------------- -.A-------- ....CG..A.A....................C....... ...A.----- 
  48 >A/Thailand/0419-00-N0/2009/06/23     --------------------------------------- ------------------------------------- ----- .........A....GA........T... ----------------- ----------- --------------------------------------- ---------- 
  49 >A/Thailand/CU-H106/2009/07/          -...................................A.. ....................T.........A.....T ..... .........A....GA........T... A...........A.... ..A...G.... .........G............................. .......... 
  50 >A/Thailand/PMKD0028/2009/09/24       --------------------------------------- ------------------------------------- ----- .........A....GA........TT.. ----------------- ----------- --------------------------------------- ---------- 
  51 >A/Thailand/0404-00-N0/2009/07/17     --------------------------------------- ------------------------------------- ----- .........A....GA........TT.. ----------------- ----------- --------------------------------------- ---------- 
  52 >A/Thailand/CU-H130/2009/07/06        --------------------..........--------- ------...CT..CCTAA...T.AGTT.T-------- ----- .........A..............T... ----------------- ..A...G.--- ........A.A..................C.C..GACGA ....------ 
  53 >A/Thailand/THB0390/2009/07/13        --------------------------------------- ------------------------------------- ----- .A.......A.A...........AT... ----------------- ----------- --------------------------------------- ---------- 
  54 >A/Thailand/34-9913/2010/07/14        --------------------------------------- ------------------------------------- ----- --------.A.A---------------- ----------------- ----------- --------------------------------------- ---------- 
  55 >A/Bangkok/INS426/2010/02/25          ....A.........................G.A...A.. ..................................G.. ..... .A.A.....A...........G..T... A.T.A.......AA... ..A...G.... ........A.A......................A..... ......G... 
  56 >A/Bangkok/INS425/2010/02/25          ................................A...A.. ..................................G.. ..... .A.......A...........G..T... A.T.A.......AA... ..A...G.... ........A.A......................A..... ......G... 
  57 >A/Thailand/CU-H567/2009/09/02        G...A.T.A...A.......................A.. ...............................A..... ..T.. .........A..............T... A...........AA... ..A...G.... ........A.A............................ ......G... 
  58 >A/Thailand/CU-H847/2009/10/26        G...A.T.A...A.......................A.. ...............................A..G.. ..... ..T......A...........G..T... A.......A...AA... ..A...G..T. .......AA.A............................ ......G... 
  59 >A/Thailand/CU-H910/2009/11/09        ....A.T.A...A.......................A.. ...............................A.T... ..... ..T......A...........G..T... A..G.A....T.AAC.. ..A...G.... ........A.AC........................... ......G... 
  60 >A/Thailand/CU-H1222/2010/01/13       G.G.A....G.A......................G.A.. ......................G........A...A. ..... ..T......A...........G..T... A..G.A....T.AAC.. ..A...G..T. .......AA.AC........................... ......G... 
  61 >A/Thailand/CU-C161/2009/08/26        G.G.A....G.A......................G.A.. ...............................A..G.. ..... ..T......A...........G..T... A...........AA... ..A...G.... .......AA.AC........................... ......G... 
  62 >A/Thailand/CU-H9/2009/06/17          ..G......G.A........................A.. ..................................... .A... ....A....A..G.........A.T... A......G...TAA... ..A...G.... ........A.A............................ ....G.G... 
  63 >A/Thailand/CU-H276/2009/07/          ..R......R..........................A.. ....................T.........A...... .A... -...A....A..G...........T... A......G....A...- ..A...G.... ........A.A............................ .......... 
  64 >A/Thailand/CU-B938/2009/08/          ..G.................................A.. ....................T.........A.....T .A... G........A..G.........A.T... A..........TAA..- ..A...G.... ...A................................... .......... 
  65 >A/Bangkok/INS427/2010/03/04          ....................................A.. ...................T................. ..... .........A..........A...T..C A...........AA... ..A...G.... ........A.A............................ ......G... 
  66 >A/Bangkok/INS424/2010/02/23          .A........T.........................A.. ..................................... ..... .........A..............T... A...........AA... ..A...G.... ........A.A............................ ......G... 
  67 >A/Bangkok/INS428/2010/03/04          .........................T....G.....A.. .................................T... ..... ......G..A..........A...T... A...........AA... ..A...G.... ........A.A............................ ......G... 
  68 >A/Thailand/34-9936/2010/07/14        --------------------------------------- ------------------------------------- ----- ------G..A..---------------- ----------------- ----------- --------------------------------------- ---------- 
  69 >A/Thailand/CU-H94/2009/07/02         --------------------------........----- ----------.GACC.TC.........A--------- ----- .........A....C.TC---------- ----------------- .TA...G.--- .............................C.CC.....C .......... 
  70 >A/Thailand/34-9943/2010/07/14        --------------------------------------- ------------------------------------- ----- -----....A..---------------- ----------------- ----------- --------------------------------------- ---------- 
  71 >A/Thailand/CU-H354/2009/08/08        --------------------.......G.G......A.. -----A..CT...C.TTC...T--------------- ----- .........A..............T... ----------------- -.A.------- .....G..A.A.......................G---- ......G... 
  72 >A/Thailand/34-9937/2010/07/14        --------------------------------------- ------------------------------------- ----- ------..CA..---------------- ----------------- ----------- --------------------------------------- ---------- 
  73 >A/Thailand/CU-H137/2009/07/07        -------------CCGTGCGGCTAGT.......T..ATT -----.....................T---------- ----- .........A..G....C......T... ----------------- G.A...G.--- GGG..G..A.A..GAG.....ACT.....C.C..G---- ....G.G... 
  74 >A/Thailand/34-9912/2010/07/14        --------------------------------------- ------------------------------------- ----- ------..CA..---------------- ----------------- ----------- --------------------------------------- ---------- 
  75 >A/swine/Thailand/CU-RA75/2010/01/    -..A.T.........................A..GT..T -------------------T..G......AA.....T T...T -.......CA..G......G..A.T.C. AA....GG.T.TAA... ..A.ACG...T ....................................... .....A.TGA 
  76 >A/swine/Thailand/CU-RA114/2010/01/   .A.A.T.........................A..GT..T ...................T..G......AA.....T T...T -........A..G......G..A.T.C. AA....GG.T.T.A..- ..A.ACG.... ..............................T........ .....A.TGA 
  77 >A/swine/Thailand/CU-RA15/2010/01/    ...A.T.........................A..GT..T -------------------T..G......AA.....T T...T -........A..G......G..A.T.C. AA....GG.T.TAA..- ..A.ACG.... ....................................... .....A.TGA 
  78 >A/swine/Thailand/CU-RA29/2009/12/    -..A.T.........................A..GT... -------------------T..G.......A.....T ....T .........A..G...A.....A.T.C. A......G.T.TAA... ..A.A.G.... ..............................T........ .......TG. 
  79 >A/swine/Thailand/CU-RA4/2009/11/     -..A.T.........................A..GT... --.................T..G.......A.....T -...T .........A..G......G..A.T.C. A......G.T.TAA..C ..A.A.G.... ....................................... .......TG. 
  80 >A/swine/Thailand/CU-RA9/2009/11/     -..A.T.........................A..GT... --.................T..G.......A.....T -...T .........A..G.........A.T... A......G.T.TAA..C ..A.A.G...T ....................................... .......TG. 
  81 >A/Thailand/THB0421/2009/07/20        --------------------------------------- ------------------------------------- ----- .........A..G.........A.T... ----------------- ----------- --------------------------------------- ---------- 
  82 >A/Thailand/CU-H75/2009/06/30         ----------------------TAGTC....-------- -------ACCTAC..T...........A--------- ----- .........A..G.....---------- ----------------- G.A...G.A-- ........A....................C.C..GACG- ....G.G... 
  83 >A/Thailand/THB0441/2009/07/28        --------------------------------------- ------------------------------------- ----- .........A..G.........A.T... ----------------- ----------- --------------------------------------- ---------- 
  84 >A/Thailand/CU-H126/2009/07/06        --------------------.............------ -----.C....................AT-------- ----- .........A..G.....---------- ----------------- ..A...G.--- ........A.A..................C.CC.G---- ...A------ 
  85 >A/Thailand/THB0389/2009/07/13        --------------------------------------- ------------------------------------- ----- .........A..G.........A.T... ----------------- ----------- --------------------------------------- ---------- 
  86 >A/Thailand/CU-H143/2009/07/07        --------------------GCTAGTC.........A.. -----.....................T---------- ----- .........A..G...........T... ----------------- ..A...G.--- ........A.A..G.G..........C.......----- ....G.G--- 
  87 >A/Thailand/PMKE0009/2009/08/28       --------------------------------------- ------------------------------------- ----- .........A..............T... ----------------- ----------- --------------------------------------- ---------- 
  88 >A/Thailand/CU-H140/2009/07/07        --------------------.CTAGTC.........--- -----......................A--------- ----- .........A..G...........T... ----------------- ..A...G.--- ........A.A.GGA.TCATT...CCCACC.C..----- ....G----- 
  89 >A/Thailand/THB0411/2009/07/16        --------------------------------------- ------------------------------------- ----- .........A..G.........A.T... ----------------- ----------- --------------------------------------- ---------- 
  90 >A/Thailand/CU-H104/2009/07/02        --------------------.............G----- -A.GA....CT...C.T..........A--------- ----- .........A..G...........T... ----------------- ..A...G.--- ........A...................CC.CC.----- ....G.G... 
  91 >A/Thailand/THB0408/2009/07/15        --------------------------------------- ------------------------------------- ----- ....A....AG.G.........A.T... ----------------- ----------- --------------------------------------- ---------- 
  92 >A/Thailand/THB0405/2009/07/15        --------------------------------------- ------------------------------------- ----- ....A....AG.G.........A.T... ----------------- ----------- --------------------------------------- ---------- 
  93 >A/Thailand/CU-H199/2009/07/13        --------------------................A.. -----A...CT.CC.............A--------- ----- .........A..G...........T... ----------------- ..A...G.--- --------------------------------------- .GG.G.G... 
  94 >A/Thailand/CU-H313/2009/07/29        -------------------------T..........A.. -----AC.ACT..CCTT....---------------- ----- .........A..G...........T... ----------------- ..A...G..-- .....G..A.A.......................GACGA ....G.G... 
  95 >A/Thailand/CU-H119/2009/07/04        --------------------------------------- -A................T......A.A--------- ----- .........A......T.---------- ----------------- ..A...G.--- .............................C.C..GA--- .......... 
  96 >A/Thailand/CU-H88/2009/07/01         --------------------GC............----- ---........................A--------- ----- .........A..G.....---------- ----------------- ..A...G.--- ........A....................C.C..GACG- ....G.G... 
  97 >A/Cancun-NY/Index/2009/04/15         ....................................A.. ..................................... ..... .........A..............T... A...........AA... ..A...G.... ........A.A............................ ......G... 
                                                                                                                                                                                                                                             
---Index-----------------------------------AGAGGCCAGAAGCAGTCAGTCTAGTCATGAACGCACGGC ATCCGCTCTACTTTTCCTACCCATAGATCGGGACAGC CGGCC AGCGGAAAGTAGAGTCGTAAGAGCCCTA GGGAGGAAGCCGGGTCA TCGTGTAGTCC TTCCAAGGGAGTAATTCAGGCCTAAAGTATCTTGTGACG CAAGAGACTG 
-codon-position----------------------------    2  1  1  2 12 1212 12 11  21     11 2 12 2 12 12 12 12   1 2 122    1 12   1  1 11 1  1 212 1       1 121    1        1      2 2 11  122   1 1 21   2  121212 12 1211 111  2112 12 1122  1  1 
                                           000000011111111111111111111111112222222 0000000000000000000000000000000000112 00001 0000000000000000011111111111 00000000001111111 00000000001 000000000000000000000000000000000000000 0000000000 
                                           004778902234466666666666666666990011111 0000000000000000000344444444456999390 00096 0111234566778999900012234445 23445667780112224 02346777880 000011144566777777777777777778888899999 1112233457 
                                           034158266851422333333333444558791901677 1111111122222222223268899999990179067 04430 0045482105012002328978850691 95577463963344579 27115144685 233444809906000111111111244671122844445 1253966152 
                                           961428109113089012346789012469900495303 1234578901234567890127912347843230316 90500 4644914658719061096211228442 81946832858738720 06651126359 834502922303679023456789427354657367890 2183167754 
          
.
.

.
.

polymorphisms that occur only once in this Thailand table are omitted,
as usual.

this looks to me as if there are quite some sequencing-errors, lab-errors.
Sequences from USA look "better".

See i.e. the examples with many mutations at the start of
a sequence e.g. segment 2 in H128 or sement 1 in H137
the swine sequences look as if they are from the "pre-Cancun"-strain,
but with T658A(4),
so maybe they got a new segment 4 by reassortment.
(this is also in H119,H94,B938,(H106))
H9 has a new segment 8, H427:7+8,H216:7

**gsgs** · October 22, 2010, 05:37 AM

Re: Sequences at Genbank!

one post for the searchengines

new genbank release
ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt

genbank Release 180.0 is out for download at ftp://ftp.ncbi.nih.gov/genbank

125764384 loci, 118551641086 bases, from 125764384 reported sequences

1475 compressed files with about 250MB each when uncompressed

genbank growth:

http://magictour.free.fr/seq/gbst6.GIF

Entries Bases Species
------------------------------------------------
16403297 14891556303 Homo sapiens
7871531 8892650030 Mus musculus
2179595 6458987847 Rattus norvegicus
2190848 5362571338 Bos taurus
3892658 5037718386 Zea mays
3219186 4784078545 Sus scrofa
1698243 3125621603 Danio rerio
228238 1352920226 Strongylocentrotus purpuratus
1243345 1197439938 Oryza sativa Japonica Group
1756913 1187717551 Nicotiana tabacum
1424202 1147136093 Xenopus (Silurana) tropicalis
1212433 1049762304 Drosophila melanogaster
213953 1002175163 Pan troglodytes
2294285 1002146700 Arabidopsis thaliana
1452602 943091356 Canis lupus familiaris
660621 913979288 Vitis vinifera
810333 891564107 Gallus gallus
1880599 887191622 Glycine max
82244 823113612 Macaca mulatta
1216415 748356051 Ciona intestinalis

viruses are in
1439. 250MB,gbvrl1.seq - Viral sequence entries, part 1.
1440. 205MB,gbvrl10.seq - Viral sequence entries, part 10.
1441. 250MB,gbvrl11.seq - Viral sequence entries, part 11.
1442. 250MB,gbvrl12.seq - Viral sequence entries, part 12.
1443. 250MB,gbvrl13.seq - Viral sequence entries, part 13.
1444. 250MB,gbvrl14.seq - Viral sequence entries, part 14.
1445. 226MB,gbvrl15.seq - Viral sequence entries, part 15.
1446. 250MB,gbvrl2.seq - Viral sequence entries, part 2.
1447. 250MB,gbvrl3.seq - Viral sequence entries, part 3.
1448. 250MB,gbvrl4.seq - Viral sequence entries, part 4.
1449. 146MB,gbvrl5.seq - Viral sequence entries, part 5.
1450. 250MB,gbvrl6.seq - Viral sequence entries, part 6.
1451. 250MB,gbvrl7.seq - Viral sequence entries, part 7.
1452. 250MB,gbvrl8.seq - Viral sequence entries, part 8.
1453. 250MB,gbvrl9.seq - Viral sequence entries, part 9.
---------------------------------
3580MB

Division Entries Bases
-----------------------------------------------
VRL1 70349 67339165
VRL10 44782 60282471
VRL11 62262 72140806
VRL12 58034 72255432
VRL13 61433 68435260
VRL14 59745 72773685
VRL15 59155 65373216
VRL2 73130 64084261
VRL3 70820 62797248
VRL4 69207 70548710
VRL5 36491 39712342
VRL6 48364 77592072
VRL7 63408 70096717
VRL8 61865 72467087
VRL9 65661 69894570
---------------------------------------------
VRL.. 839045 935898472

I haven't downloaded and examined these yet.
The last release ~1/4 year ago had 135526 flu-sequences
most common viruses at genbank were:

334250 ,Human immunodeficiency virus 1
135526 ,Influenza
066844 ,Hepatitis C virus
033422 ,Hepatitis B virus
015728 ,Simian immunodeficiency virus
013235 ,Hepatitis C virus subtype 1b
011545 ,Porcine reproductive and respiratory syndrome virus
010096 ,Rabies virus
006706 ,Hepatitis C virus subtype 1a
004781 ,Newcastle disease virus
004747 ,Hepatitis A virus
004740 ,Torque teno virus
004507 ,Human herpesvirus 5
004093 ,Measles virus
003883 ,Human immunodeficiency virus 2
003813 ,GB virus C
003703 ,Human rotavirus A
003509 ,Human metapneumovirus
003122 ,Human respiratory syncytial virus
003056 ,Hepatitis E virus
002993 ,Human enterovirus 71
002837 ,Dengue virus 2
002732 ,Human echovirus 30
002723 ,Human T-lymphotropic virus 1
002553 ,Dengue virus 3
002543 ,Dengue virus 1
002373 ,Influenza A virus (A/equine/Newmarket/1/1993(H3N8))
002355 ,Infectious bronchitis virus
002301 ,Feline immunodeficiency virus
002273 ,JC polyomavirus
002187 ,Human herpesvirus 8
001955 ,Human poliovirus 1
001945 ,Rotavirus A
001877 ,Citrus tristeza virus
001877 ,Bovine viral diarrhea virus 1
001840 ,West Nile virus
001830 ,Infectious bursal disease virus
001778 ,BK polyomavirus
001740 ,Human papillomavirus
001669 ,Human rhinovirus sp.
001612 ,Equine infectious anemia virus
001554 ,Hepatitis C virus subtype 3a
001433 ,Porcine circovirus 2
001422 ,Human herpesvirus 1
001391 ,Japanese encephalitis virus
001248 ,Human papillomavirus type 16
001221 ,Human herpesvirus 4
001206 ,Foot-and-mouth disease virus - type O
001181 ,Classical swine fever virus
001112 ,African swine fever virus
001085 ,Human parvovirus B19
001032 ,Cucumber mosaic virus
000990 ,Hepatitis delta virus
000989 ,Turnip mosaic virus
000951 ,Human herpesvirus 2
000940 ,Human bocavirus
000934 ,Feline coronavirus
000872 ,Small ruminant lentivirus
000865 ,Human endogenous retrovirus K
000863 ,Buggy Creek virus
000821 ,Mumps virus
000818 ,Canine distemper virus
000803 ,Human enterovirus B
000802 ,Rubella virus
000796 ,Human immunodeficiency virus
000788 ,Foot-and-mouth disease virus - type A
000786 ,Tomato spotted wilt virus
000772 ,Tick-borne encephalitis virus
000766 ,Infectious salmon anemia virus
000753 ,Dengue virus 4
000743 ,Swine hepatitis E virus
000733 ,Beet necrotic yellow vein virus
000725 ,Potato virus Y
000724 ,Eastern equine encephalitis virus
000711 ,Equine arteritis virus
000709 ,Chikungunya virus
000707 ,Simian foamy virus
000703 ,Human echovirus 11
000703 ,Human coxsackievirus A16
000665 ,Human rhinovirus C
000652 ,Bovine rotavirus
000646 ,Bluetongue virus
000643 ,Influenza A virus (A/northern
000638 ,Human parechovirus
000624 ,Puumala virus

------------edit--------------

Sequences at Genbank! - FluTrackers News and Information

http://www.flutrackers.com/forum/showthread.php?p=367766&highlight=135526#post367766

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

LOCUS: 70349 73130 70819 69207 36491
48364 63407 61865 65661 44781
62262 58034 61433 59745 59155
DEFINITION: 70347 73130 70820 69207 36490
48364 63406 61864 65661 44781 62262 58034 61433 59745 59153
//:

70349 6006 6006
73130 3168 3168
70820 3070 3070
69207 3445 3445
36491 10429 10429
48364 48364 48364
63408 18325 18324
61865 5457 5457
65661 6890 6890
44782 5402 5402
62262 5275 5275
58034 6407 6407
61433 6740 6740
59745 10522 10522
59155 4596 4612
-----------------------
904706 144096 144111

maybe someone else out there is doing this work also and will
find this by typing those numers into a searchengine
flutrackers-search only accepts blank as a word-separator

144117 flu-sequences , up from 135526 in 2010/08/19
211M nucleotides , file with 19MB compressed

why are there still zero google-hits for
144117,influenza,genbank,135526 ?
I don't understand this. Everyone seriously working with flu
should be searching for a file with all genbank influenza seuences
in computer readable format

**gsgs** · November 22, 2010, 01:48 AM

Re: Sequences at Genbank!

reassortment in India , August 2009

http://www.springerlink.com/content/x3w8247347m8161v/fulltext.html

I get :

Code:

-m-m-r-m   A/Eastern India/107/2009/08
-m-r-r--   A/KOL/2086/2009
-m-r-r-r   A/KOL/2449/2009
-m-r-r-r   A/KOL/2465/2009

-:unknown
m:******=pandemic,new,swine,flu (2009)
r=Russian flu = semi-pandemic China/Russia(1977) = seasonal H1N1

at least two different reassortment patterns

not one complete genome, so we don't know what segments are
from what strain

1.2 years of delay until we hear about this reassortment.
Apparantly it didn't spread to other countries - else they would have
told us ... or not ?

**gsgs** · December 2, 2010, 05:06 AM

Re: Sequences at Genbank!

116 HAs from Sendai,Japan,2009
all are Cancun

Code:

                                     000000000000000000000000000000000111111111111111111111111      
                                     000011112233334444455566677888999000000112222233344444556      
                                     013912465923590134406624534079246011356471558926800058248      
                                     730060477049609164643710838418141279268912791315003858268      
-codon-position----------------------11  2  222  2 1 1 2 2  1111 11 21  2    1  2  1  221  112      
---Index-----------------------------GCTAATCGCTCCGGAAATTAAATGTACGGACTCAGCATGGGTAGATGCGGGCCCGGG      
   1 >A/******/index/2009/02/01      .........................................................      
   2 >A/Sendai/TU460/2009(H1N1)      ...T................G..AA..........................T.....      
   3 >A/Sendai/TU433/2009(H1N1)      ...T................G..AA..........................T.....      
   4 >A/Sendai/TU489/2009(H1N1)      ...T................G..AA..........................T.....      
   5 >A/Sendai/TU588/2009(H1N1)      ...T................G..AA..........................T.....      
   6 >A/Sendai/TU490/2009(H1N1)      ...T................G..AA..............A...........T.....      
   7 >A/Sendai/TU496/2009(H1N1)      ...T........A.......G..AA..........................T.....      
   8 >A/Sendai/TU526/2009(H1N1)      ...T........A.......G..AA..........................T.....      
   9 >A/Sendai/TU530/2009(H1N1)      ...T........A.......G..AA..........................T.....      
  10 >A/Sendai/TU529/2009(H1N1)      ...T........A.......G..AA..........................T.....      
  11 >A/Sendai/TU589/2009(H1N1)      ...T........A.......G..AA..........................T.....      
  12 >A/Sendai/TU398/2009(H1N1)      .......................AA..........................T.....      
  13 >A/Sendai/TU378/2009(H1N1)      ...................G...AA..........................T.....      
  14 >A/Sendai/TU426/2009(H1N1)      ...................G...AA..........................T.....      
  15 >A/Sendai/TU555/2009(H1N1)      ...................G...AA..........................T.....      
  16 >A/Sendai/TU1001/2009(H1N1)     ...................G...AA..........................T.....      
  17 >A/Sendai/TU384/2009(H1N1)      ...................G...AA.......................A..T.....      
  18 >A/Sendai/TU444/2009(H1N1)      ....G..................AA..........................T.....      
  19 >A/Sendai/TU451/2009(H1N1)      ....G..................AA..........................T.....      
  20 >A/Sendai/TU466/2009(H1N1)      ....G..................AA..........................T.....      
  21 >A/Sendai/TU468/2009(H1N1)      ....G..................AA..........................T.....      
  22 >A/Sendai/TU474/2009(H1N1)      ....G..................AA..........................T.....      
  23 >A/Sendai/TU477/2009(H1N1)      ....G..................AA..........................T.....      
  24 >A/Sendai/TU499/2009(H1N1)      ....G..................AA..........................T.....      
  25 >A/Sendai/TU528/2009(H1N1)      ....G..................AA..........................T.....      
  26 >A/Sendai/TU1003/2009(H1N1)     ....G..................AA..........................T.....      
  27 >A/Sendai/TU524/2009(H1N1)      ....G..................AA..........................T.....      
  28 >A/Sendai/TU531/2009(H1N1)      ....G..................AA..........................T...A.      
  29 >A/Sendai/TU498/2009(H1N1)      .......................AA..........................T...A.      
  30 >A/Sendai/TU586/2009(H1N1)      .......................AA..........................T.....      
  31 >A/Sendai/TU1015/2009(H1N1)     .......................AA..........................T.....      
  32 >A/Sendai/TU373/2009(H1N1)      .......................AA.....................A....T.....      
  33 >A/Sendai/TU399/2009(H1N1)      .................C......A..........................T.....      
  34 >A/Sendai/TU408/2009(H1N1)      .................C......A..............A...........T.....      
  35 >A/Sendai/TU412/2009(H1N1)      ........................A....G.........A...........T.....      
  36 >A/Sendai/TU407/2009(H1N1)      .......................AA..............A....G......T.....      
  37 >A/Sendai/TU377/2009(H1N1)      .................C.....AA..............A....G......T.....      
  38 >A/Sendai/TU387/2009(H1N1)      ...............T.C.....AA..............A....G......T.....      
  39 >A/Sendai/TU380/2009(H1N1)      .................C.....AA..............A....G.A.A..T.....      
  40 >A/Sendai/TU413/2009(H1N1)      .................C.....AA...................G....A.T.....      
  41 >A/Sendai/TU455/2009(H1N1)      .................C......A........................A.T.....      
  42 >A/Sendai/TU445/2009(H1N1)      ...............T.C......A..........................T.....      
  43 >A/Sendai/TU376/2009(H1N1)      .........C.....T.C......A..........................T.....      
  44 >A/Sendai/TU386/2009(H1N1)      .........C.....T.C......A...................G......T.....      
  45 >A/Sendai/TU417/2009(H1N1)      ...............T.C......A...................G......T.A...      
  46 >A/Sendai/TU461/2009(H1N1)      .................C......A...................G......T.A...      
  47 >A/Sendai/TU439/2009(H1N1)      .................C......A...................G......T.A...      
  48 >A/Sendai/TU395/2009(H1N1)      .................C......A....G..............G......T.A...      
  49 >A/Sendai/TU406/2009(H1N1)      .......A.........C......A...................G......T.A...      
  50 >A/Sendai/TU438/2009(H1N1)      .................C......A...................G......T.A...      
  51 >A/Sendai/TU394/2009(H1N1)      .................C......A...........G..A....G......T.A...      
  52 >A/Sendai/TU409/2009(H1N1)      .................C...G..A...........G..A....G......T.A...      
  53 >A/Sendai/TU400/2009(H1N1)      .................C...G..A...........G..A....G......T.....      
  54 >A/Sendai/TU414/2009(H1N1)      .................C......A...........G.......G......T.....      
  55 >A/Sendai/TU415/2009(H1N1)      .................C......A...A........C......G......T.....      
  56 >A/Sendai/TU443/2009(H1N1)      .................C......A..............A....GG.....T.....      
  57 >A/Sendai/TU397/2009(H1N1)      ...............T.C......A........G..........GG.....T.....      
  58 >A/Sendai/TU432/2009(H1N1)      ...............T.C......A........G..........GG.....T.....      
  59 >A/Sendai/TU450/2009(H1N1)      ...............T.C......A........G..........GG.....T.....      
  60 >A/Sendai/TU527/2009(H1N1)      ...............T.C......A........G..........GG.....T.....      
  61 >A/Sendai/TU462/2009(H1N1)      ...............T.C......A........G..........GG.....T.....      
  62 >A/Sendai/TU556/2009(H1N1)      ...............T.C......A........G..........GG.....T.....      
  63 >A/Sendai/TU453/2009(H1N1)      ...............T.C......A........G..........G....A.T.A...      
  64 >A/Sendai/TU454/2009(H1N1)      .................C......A........G.................T.....      
  65 >A/Sendai/TU483/2009(H1N1)      ........................A...............A..........T.....      
  66 >A/Sendai/TU502/2009(H1N1)      ........................A...............A..........T.....      
  67 >A/Sendai/TU1004/2009(H1N1)     ........................A...............A..........T.....      
  68 >A/Sendai/TU497/2009(H1N1)      ........................A.............A.A..........T.....      
  69 >A/Sendai/TU459/2009(H1N1)      ..............G.........A.............A.A..........T.....      
  70 >A/Sendai/TU1007/2009(H1N1)     ..............G.........A.............A.A..........T.....      
  71 >A/Sendai/TU1005/2009(H1N1)     ..............G.........A...............A..........T.....      
  72 >A/Sendai/TU491/2009(H1N1)      ..................A.....A..A............A..........T.....      
  73 >A/Sendai/TU458/2009(H1N1)      ..................A.....A..A............A........A.T...A.      
  74 >A/Sendai/TU512/2009(H1N1)      ..................A.....A..A...........AA.......AA.T.....      
  75 >A/Sendai/TU514/2009(H1N1)      ........................A..............AA..........T.....      
  76 >A/Sendai/TU615/2009(H1N1)      ............A...........A.....T.........A..........T.....      
  77 >A/Sendai/TU619/2009(H1N1)      ........................A.....T.........A..........T.....      
  78 >A/Sendai/TU616/2009(H1N1)      ........................A...............A..........T.....      
  79 >A/Sendai/TU582/2009(H1N1)      ............A...........A...............A..........T.....      
  80 >A/Sendai/TU446/2009(H1N1)      .............A.........AA......C...................T.....      
  81 >A/Sendai/TU441/2009(H1N1)      .............A.........AA......C...................T.A...      
  82 >A/Sendai/TU447/2009(H1N1)      .............A.........AA......C.................A.T...A.      
  83 >A/Sendai/TU476/2009(H1N1)      ...........T...........AA..........................T.....      
  84 >A/Sendai/TU563/2009(H1N1)      .......................AA.A........................T.....      
  85 >A/Sendai/TU612/2009(H1N1)      ..C.G..................AA..........................T.....      
  86 >A/Sendai/TU628/2009(H1N1)      ..C.G..................AA..........................T.A...      
  87 >A/Sendai/TU452/2009(H1N1)      A.....T............G...AA..........................T.....      
  88 >A/Sendai/TU436/2009(H1N1)      A.....T............G...AA..........................T..A..      
  89 >A/Sendai/TU440/2009(H1N1)      A.....T............G...AA...................G......T.....      
  90 >A/Sendai/TU579/2009(H1N1)      ......T............G...AA..........................T.....      
  91 >A/Sendai/TU620/2009(H1N1)      ......T............G...AA..........................T.....      
  92 >A/Sendai/TU565/2009(H1N1)      ...T................G..AA.......................A..T.....      
  93 >A/Sendai/TU617/2009(H1N1)      ...T................G..AA..........................T.....      
  94 >A/Sendai/TU1006/2009(H1N1)     ...........T...........AA..................A.......T....A      
  95 >A/Sendai/TU385/2009(H1N1)      .................C.....AA..............A....G......T....A      
  96 >A/Sendai/TU392/2009(H1N1)      .................C......A...........G..A....G....A.T.AAA.      
  97 >A/Sendai/TU393/2009(H1N1)      .................C......A..........TG.......G....A.T.AA..      
  98 >A/Sendai/TU396/2009(H1N1)      .........C.....T.C......A..........T.............A.T.AA..      
  99 >A/Sendai/TU430/2009(H1N1)      .T.......C.....T.C......A...................G......T.....      
 100 >A/Sendai/TU467/2009(H1N1)      .................C......A...........G.......G......T.A...      
 101 >A/Sendai/TU481/2009(H1N1)      .................C......A...........G..A....G......T.A...      
 102 >A/Sendai/TU416/2009(H1N1)      .......A.........C......A............C..A...G......T.A...      
 103 >A/Sendai/TU431/2009(H1N1)      .T......T...............A...A........C..A...G..T...T.....      
 104 >A/Sendai/TU463/2009(H1N1)      ........T.......G.......AG..A........C..A...G..T...T.....      
 105 >A/Sendai/TU464/2009(H1N1)      ................G.......AG..A........C..A.T.G..T...T.....      
 106 >A/Sendai/TU420/2009(H1N1)      ........T.......G.......AG..A........C.AA.T.G..TA..T.....      
 107 >A/Sendai/TU622/2009(H1N1)      ........T...............A...A........C..A...G..T...T.....      
 108 >A/Sendai/TU402/2009(H1N1)      ........T.......G.......A............C.....A.......T.....      
 109 >A/Sendai/TU429/2009(H1N1)      ........................A..........................T.....      
 110 >A/Sendai/TU437/2009(H1N1)      ..........T...........C.A.......T..................TT....      
 111 >A/Sendai/TU428/2009(H1N1)      ..........T...........C.A.......T................A.TT.AA.      
 112 >A/Sendai/TU418/2009(H1N1)      ........................A...................G....A.T...A.      
 113 >A/Sendai/TU538/2009(H1N1)      ...............T.C......A.A......G.....A....GG...A.T.....      
 114 >A/Sendai/TU533/2009(H1N1)      .....C.......A.........AA.........A...............AT.....      
 115 >A/Sendai/TU613/2009(H1N1)      .....C.......A.........AA.........A......C........AT.....      
 116 >A/Sendai/TU618/2009(H1N1)      .....C.......A.........AA.........A......C........AT.....      
 117 >A/Sendai/TU587/2009(H1N1)      ............A...........A...............A..A..A.A..T.....      
 118 >A/Cancun-NY/Index/2009/04/15   ........................A..........................T.....      
                                                                                                    
---Index-----------------------------GCTAATCGCTCCGGAAATTAAATGTACGGACTCAGCATGGGTAGATGCGGGCCCGGG      
-codon-position----------------------11  2  222  2 1 1 2 2  1111 11 21  2    1  2  1  221  112      
                                     000000000000000000000000000000000111111111111111111111111      
                                     000011112233334444455566677888999000000112222233344444556      
                                     013912465923590134406624534079246011356471558926800058248      
                                     730060477049609164643710838418141279268912791315003858268

**gsgs** · December 15, 2010, 09:16 AM

Re: Sequences at Genbank!

sequences from La Gloria, March and early April at genbank !

early Mexico:

Code:

                                       00011 000000111 001111112 000001111111111 000000111111 0000000011 00000 00
                                       02225 001233129 891347780 267780012233467 233368011111 1133477703 14589 14
                                       91447 017526709 267284974 661121871937040 904868913456 0018545852 13313 54
                                       99557 561210895 399261486 096974038601840 816435284357 2361326609 18973 37
-codon-position------------------------  2 2 21    2   1  211    2 222     1 1 2 111    2      11  1       21    
---Index-------------------------------GAAGA AAAACTGGC CCTTCACGT TCAAGCGGGCGACGA GGATAGGCCGCG TAGGCAAGAA AATTG CT
--------------"original"--------------
   1 >A/******/index/2009/02/01        ..... ......... ......... ............... ............ .......... ..... ..
   2 >A/Mexico/InDRE4487/2009/04/14    ..G.. ......... A........ ...G........... ............ .......... ..... ..
   3 >A/Mexico/4115/2009/04/07         ..G.. ......... A.....T.. ............... ............ .......... ..... ..

---------"Northern"-----------
  19 >A/Mexico/4646/2009/04/20         ..... ........T --------- ............... ..C.G.AT.... .......... .G... --
  20 >A/Mexico/LaGloria-8/2009/03/25   RG... ........T .T.C.C... ...G..........- .......T.... CG........ ..... .C
  21 >A/Mexico/LaGloria-3/2009/04/03   RG... ........T .T.C.C... ...G........... .R.....T..YR AG........ ..... .C
  22 >A/Mexico/LaGloria-4/2009/03/24   RG... GR......T .T.C.C... ...G..........C .R.....T..YR N......... ..... .C
   4 >A/Mexico/3955/2009/04/03         ----- --------- --------- Y.G....A..A..A. ------------ .......... ....A --
   5 >A/Mexico/4108/2009/04/03         ..... ......... .....C... .......A..A..A. .......T.... .......... ....A ..
   6 >A/Mexico/4627/2009/04/20         ----- --------- --------- .......AA...... .......T.... ........T. ----- --
   7 >A/Mexico/4176/2009/04/13         ----- .....C... .....C... ............... .......T.... .......A.. ----- ..
   8 >A/Mexico/4269/2009/04/15         ....G ..C...A.. ....AC... .T.........G... .......T.... .......... ..K.. ..
   9 >A/Mexico/4486/2009/04/14         ....G ....T.... .....C... .....TA.....T.. .......TT... .......... ..... ..

----------"pre-Cancun"--------------
  10 >A/Mexico/4603/2009/04/19         ..... ......... .......A. ............T.. A........A.. ..R..G...C ..... ..
  11 >A/Mexico/4635/2009/04/20         ..... ...G..... ......... ....A.......T.. A....A...A.. ..A..R...C ..... --
  12 >A/Mexico/4595/2009/04/20         ...A. --------- --------- ............T.. A........A.. ..A..G...C ----- T.
  13 >A/Mexico/4283/2009/04/15         ----- --------- ......... ............T.. A........A.. ---------- ----- T.
  14 >A/Mexico/4482/2009/04/14         ----- ......... ........C ............T.. A........A.. ..A.TG.... ...C. ..
  15 >A/Mexico/4502/2009/04/17         ----- .......A. --------- .........T..T.. ------------ ---------- ----- --
  16 >A/Mexico/4604/2009/04/19         ..... ......... ..C...... ............T.. A..C.....A.. ..AA.G.... T.... ..
  17 >A/Mexico/4575/2009/04/20         ----- --------- --------- ............T.. ------------ ..A..G.... ----- --
  18 >A/Mexico/4593/2009/04/20         ----- --------- --------- ............... ------------ ..A..GG... ----- --
                                                                                                                 
---Index-------------------------------GAAGA AAAACTGGC CCTTCACGT TCAAGCGGGCGACGA GGATAGGCCGCG TAGGCAAGAA AATTG CT
-codon-position------------------------  2 2 21    2   1  211    2 222     1 1 2 111    2      11  1       21    
                                       00011 000000111 001111112 000001111111111 000000111111 0000000011 00000 00
                                       02225 001233129 891347780 267780012233467 233368011111 1133477703 14589 14
                                       91447 017526709 267284974 661121871937040 904868913456 0018545852 13313 54
                                       99557 561210895 399261486 096974038601840 816435284357 2361326609 18973 37

4108 is presumably Edgar Hernandez from La Gloria

the other "LaGloria" sequences have some further mutations,
strongly related, maybe a family.

Also "R","Y" - nucleotides, unclear signals, which I interpret as difficult sequencing,
old samples,possible contamination, unusual method.
Compare with the A/Swine/4/Mexico/ sequences (link) which had also many
such signals an the A/Swine/Alberta sequences from May 2009 (link) with
many mutations.

All the La Gloria sequences - and maybe just only those - have the two "Northern"
markers which were subsequently found in Canada and Northern USA.

This makes me a bit less confident that ** started in Jan. or Feb. 2009
in one single host (which I still consider likely, >50% though)
The LaGloria outbreak, characterized by the 2 "Northern" markers, looks a bit different.
It would have been interesting to further track back these 2 markers.

And then we have 4487(April 14) and 4115(April 7) with the strangely few mutations(unusual,rare),
making me speculate that these viruses survived for months in frozen pork or in the
environment without replicating.
Maybe these were the mother and daughter from the Mexico-City hospital,
Mexico presumably won't tell us. My emails to Mexico (INDRE,scientists,journalists)
in 2009 invain.

**sharon sanders** · December 15, 2010, 09:49 AM

Re: Sequences at Genbank!

Thanks Gs.

**gsgs** · December 17, 2010, 01:15 AM

Re: Sequences at Genbank!

Close-of-data for the upcoming GenBank Release 181.0 occurred on
Tuesday December 14 2010, at approximately 1:30am EST.

ftp://ftp.ncbi.nih.gov/genbank/
ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt
to be updated soon
--------updated now (2010/12/21)--------------

Uncompressed,the Release 181.0 flatfiles require roughly 468 GB (sequence files only)

Release Date Base Pairs Entries
180 Oct 2010 118551641086 125764384
181 Dec 2010 122082812719 129902276

BCT (bacterial and archeal) : 63 files (+3)
CON (constructed) : 143 files (+1)
ENV (Environmental Samples) : 33 files (+3)
EST (Expressed Sequence Tag) : 427 files (+5)
GSS (Genome Survey Sequence) : 224 files (+7)
INV (invertebrate) : 26 files (+1)
PAT (patent) : 138 files (+10)
PLN (plant) : 44 files (+1)
TSA (Transcriptome Shotgun Assembly) : 15 files (+3)
VRL (viral) : 16 files (+1)

files are copressed and contain ~300MB uncompressed

1. PRI - primate
2. ROD - rodent
3. MAM - other mammals
4. VRT - other vertebrate
5. INV - invertebrate
6. PLN - plant, fungal, and algal
7. BCT - bacterial
8. VRL - viral
9. PHG - bacteriophage
10. SYN - synthetic
11. UNA - unannotated
12. EST - expressed sequence tags)
13. PAT - patent sequences
14. STS - sequence tagged sites)
15. GSS - genome survey sequences)
16. HTG - high throughput genomic sequences)
17. HTC - high throughput cDNA sequences)
18. ENV - Environmental
19. CON - Constructed

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

3.5B new base pairs, biggest increase since April 2007

158 Feb 2007 71292211453 67218344
159 Apr 2007 75742041056 71802595
160 Jun 2007 77248690945 73078143
161 Aug 2007 79525559650 76146236
162 Oct 2007 81563399765 77632813
163 Dec 2007 83874179730 80388382
164 Feb 2008 85759586764 82853685
165 Apr 2008 89172350468 85500730
166 Jun 2008 92008611867 88554578
167 Aug 2008 95033791652 92748599
168 Oct 2008 97381682336 96400790
169 Dec 2008 99116431942 98868465
170 Feb 2009 101467270308 101815678
171 Apr 2009 102980268709 103335421
172 Jun 2009 105277306080 106073709
173 Aug 2009 106533156756 108431692
174 Oct 2009 108560236506 110946879
175 Dec 2009 110118557163 112910950
176 Feb 2010 112326229652 116461672
177 Apr 2010 114348888771 119112251
178 Jun 2010 115624497715 120604423
179 Aug 2010 117476523128 122941883
180 Oct 2010 118551641086 125764384
181 Dec 2010 122082812719 129902276

I think I'm not updating my flu-database with this release 181
but rather wait until 182 or later

**gsgs** · January 7, 2011, 11:27 AM

Re: Sequences at Genbank!

remember Argentina, mid 2009 and our concern about possible
bad mutations ?
Now lots of sequences were upoaded to genbank.
(after 1.5 years into the pandemic)

to me they look quite normal.

192 Cancun (3 of these in Brazil are the "Russia"-strain)
29 pre-Cancun (24 of these in Brazil are the "Manitoba"-strain)
15 original Mexico ( 4 of these are the "Sto Domingo"-strain)

9 with A716G (aka D225G) , most from Brazil

South American HAs :

Code:

                                                00000000000000000000000000000000000000001111111111111111111111111111111111111111111111 
                                                00011111333334444555666666677777888899990000011111122333334444455666666666666666666666 
                                                07944578014690357169055789901127167733681556800447868245880223345677777777788888888999 
                                                48515524250309218616378270385667770104336016937031861919348894767902345678901234567245 
-codon-position---------------------------------1 2 12112 1  1 11  2  1     12  1  1 1 22 11 2   1       11 1  1 1212 12 12 12 12 1 2  
---Index----------------------------------------AGCTCACAGAGAGACGAAGCTGTCGAAAGAGCGCCGGAAACTGGTACCCGAGAGACCTCAAACGGAAGGGTCTCTACAGTGTAAGT 
   1 >A/******/index/2009/02/01                 ...................................................................................... 
 104 >A/Bogota/224,2009/04/25                   ---------------------.................------------------------------------------------ 
 106 >A/Bogota/176,2009/04/27                   ---------------------.................------------------------------------------------ 
 107 >A/Guayaquil/3,2009/07/                    .........................................--------------------------------------------- 
 108 >A/Colombia/213,2009/04/30                 ---------------------.................------------------------------------------------ 
 109 >A/Colombia/08,2009/04/25                  -...A.............NNN.................------------------------------------------------ 
 110 >A/Colombia/450,2009/05/06                 ---------------------.................------------------------------------------------ 
 138 >A/Guayaquil/4,2009/07/                    -.......................................---------------------------------------------- 
 140 >A/Guayaquil/2,2009/07/                    -........................................--------------------------------------------- 
  38 >A/Minas Gerais/65,2009/04/24              -------------------------------....................................................... 
 141 >A/Ecuador/FLE1269,2009/07/01              ----------.......................................................--------------------- 
 142 >A/Peru/FLA8689,2009/06/27                 ----------..................................................G....--------------------- 
 143 >A/Peru/FLA9494,2009/07/07                 ----------...........A............T.........................G....--------------------- 
 144 >A/Peru/FLA9813,2009/07/10                 ----------...........A............T......G..................G....--------------------- 
 145 >A/Chile/9113,2009/05/19                   ....A................A............T......--------------------------------------------- 
 147 >A/Ecuador/FLE2399,2009/07/15              ----------............A.................GCA.................G....--------------------- 
 146 >A/Ecuador/FLE2354,2009/06/14              ----------...........A............T.....GCA...............T......--------------------- 
 101 >A/Parana/2529,2009/06/30                  ...................A......................................T........................... 
 102 >A/Sao Paulo/1454,2009/04/29               ..........................................................T........................... 
 103 >A/Sao Paulo/2303,2009/06/01               ..........................................................T........................... 
 139 >A/La Paz/WR0096T,2009/06/22               ..........................................................T......GGCATAGCTGTAGAATATTAA 
  77 >A/Rio de Janeiro/4707,2009/07/23          ---------T...................G......T.....................T........................... 
  78 >A/Peru/FLA9726,2009/07/04                 ----------..........................T.....................T......--------------------- 
  81 >A/Sao Paulo/43812,2009/07/03              ....................................T...............G.....T........................... 
  96 >A/Rio Grande do Sul/9116,2009/08/02       -...................................T.....................T........................... 
  97 >A/Guayaquil/1,2009/05/                    -....G..............................T....--------------------------------------------- 
  80 >A/Santa Catarina/6235,2009/07/26          -...................................T.....................T........................... 
  79 >A/Rio Grande do Sul/5395,2009/07/23       G...................................T.....................T........................... 
  82 >A/Rio de Janeiro/9685,2009/08/10          G...................................T.....................T..............------------- 
  83 >A/Rio de Janeiro/5090,2009/07/23          G...................................T.....................T........................... 
  84 >A/Rio Grande do Sul/7019,2009/07/29       G...................................T.....................T........................... 
  85 >A/Sao Paulo/53838,2009/08/01              G...........................A.......T.....................T........................... 
  86 >A/Rio de Janeiro/491,2010/02/18           G...................................T.....................T........................... 
  87 >A/Sao Paulo/53823,2009/08/01              G...................................T.....................T........................... 
  88 >A/Santa Catarina/423,2009/06/01           G...................................T.....................T........................... 
  89 >A/Parana/4597,2009/07/12                  G...................................T.....................T........................... 
  90 >A/Sao Paulo/2233,2009/05/27               G...................................T.....................T........................... 
  91 >A/Rio de Janeiro/7131,2009/08/01          G............................G......T.....................T........................... 
  92 >A/Rio de Janeiro/7455,2009/08/04          G............................G......T.....................T........................... 
  93 >A/Rio de Janeiro/14601,2009/08/24         G............................G......T.....................T........................... 
  94 >A/Sao Paulo/57831,2009/08/09              G...................................T.....................T........................... 
  95 >A/Rio de Janeiro/2459,2009/07/02          G...................................T.....................T........................... 
  98 >A/Bahia/162,2010/03/19                    G...................................T.T.....C......A.A....T....A...................... 
  99 >A/Bahia/161,2010/03/19                    G........T....................T.....T.T.....C......A.A....T....A...................... 
 100 >A/Bahia/160,2010/03/19                    G........T.........A..........T.....T.T.....C......A.A....T....A...................... 

   2 >A/Argentina/19464,2009/06/11              ......................A...................................T........................... 
   3 >A/Chile/1624,2009/06/15                   ......................A...................................T........................... 
   4 >A/Argentina/HNRG107,2009/07/02            ......................A...................................T........................... 
   5 >A/Chile/36,2009/05/25                     ......................A...................................T........................... 
   6 >A/Argentina/08AR,2009/07/21               ......................A...................................T........................... 
   7 >A/Argentina/HNRG104,2009/06/19            ......................A...................................T........................... 
   8 >A/Minas Gerais/14602,2009/08/22           ......................A...................................T........................... 
   9 >A/Argentina/HNRG37,2009/06/22             ......................A...................................T........................... 
  10 >A/Chile/3905,2009/07/07                   ......................A...................................T........................... 
  11 >A/Argentina/19911,2009/06/24              ......................A...................................T........................... 
  12 >A/Argentina/19531,2009/06/15              ......................A...................................T........................... 
  13 >A/Chile/42,2009/05/25                     ......................A...................................T........................... 
  14 >A/Argentina/HNRG23,2009/07/27             ..............T.......A...................................T........................... 
  15 >A/Argentina/HNRG82,2009/07/22             ..............T.......A...................................T........................... 
  16 >A/Argentina/HNRG15,2009/07/20             ..............T.......A.......T...........................T........................... 
  17 >A/Alagoas/97,2010/03/05                   -..................A..A.......T..................A........T........................... 
  18 >A/Alagoas/166,2010/03/22                  ........T......A...A..A..........................A........T........................... 
  19 >A/Alagoas/201,2010/03/26                  ........T......AG..A..A...C......................A........T........................... 
  20 >A/Alagoas/143,2010/03/13                  ........T......AG..A..A...C...T..................A........T........................... 
  21 >A/Alagoas/119,2010/03/10                  ........T......A...A..A..........................A........T........................... 
  22 >A/Alagoas/171,2010/03/24                  ........T......A......A..........................A........T........................... 
  23 >A/Alagoas/266,2010/03/31                  ........T......A......A..........................A.......YT........................... 
  24 >A/Alagoas/140,2010/03/15                  ......................A..........................A........T........................... 
  25 >A/Argentina/HNRG102,2010/01/15            .A....................A......G...................AG.......T........................... 
  26 >A/Argentina/HNRG16,2009/06/29             ......................A......G............................T........................... 
  27 >A/Rio de Janeiro/5826,2009/07/28          ......................A......G......................G.....T........................... 
  28 >A/Sao Paulo/53206,2009/07/19              ......................A......G............................T........................... 
  29 >A/Sao Paulo/53225,2009/08/01              ......................A....G.G............................T........................... 
  30 >A/Uruguay/6,2009/08/03                    ------................A....G...............A..............T....----------------------- 
  31 >A/Uruguay/3,2009/05/31                    ------................A....................A..............T....----------------------- 
  32 >A/Uruguay/19,2009/07/10                   ------................A....................A..............T....----------------------- 
  33 >A/Uruguay/8,2009/05/30                    ------T...............A....................A..............T....----------------------- 
  34 >A/Chile/4406,2009/07/17                   ......T...............A...................................T........................... 
  35 >A/Paraguay/FLE1726,2009/07/10             ----------............A...................................T......--------------------- 
  36 >A/Argentina/HNRG106,2009/06/27            ......................A...................................T........................... 
  37 >A/Peru/FLE1410,2009/07/22                 ----------...C........A...................................T......--------------------- 
  39 >A/Uruguay/23,2009/06/04                   ------..............A.A...................................T....----------------------- 
  40 >A/Colombia/450,2009/05/06                 -.................-------------------------------------------------------------------- 
  41 >A/Santiago/3221,2009/06/30                -.....................A..................--------------------------------------------- 
  42 >A/Santiago/2009,2009/06/18                -.....................A....................A------------------------------------------ 
  43 >A/Santiago/21579,2009/07/05               ......................A....................------------------------------------------- 
  44 >A/Peru/FLA9065,2009/07/06                 ----------............A................................A..T......--------------------- 
  45 >A/Chile/8886,2009/05/18                   ......................A..................--------------------------------------------- 
  46 >A/Uruguay/9,2009/08/05                    ------................A................................A..T....----------------------- 
  47 >A/Chile/8947,2009/05/17                   ......................A..................--------------------------------------------- 
  48 >A/Chile/2911,2009/06/25                   ......................A........................T..G.......T........................... 
  49 >A/Chile/2851,2009/06/20                   ......................A........................T..G.......T........................... 
  50 >A/Puerto Montt/Bio87,2009/06/19           ......................A........................T..........T........................... 
  51 >A/Argentina/19656,2009/06/18              ......................A...................................T........................... 
  52 >A/Argentina/HNRG66,2009/07/10             ......................A...................................T........................... 
  53 >A/Chile/2909,2009/06/25                   ......................A...................................T........................... 
  54 >A/Chile/3467,2009/07/02                   ......................A...................................T........................... 
  55 >A/Sao Paulo/55115,2009/08/05              ......................A...................................T........................... 
  56 >A/Argentina/HNRG13,2009/06/05             ......................A...................................T........................... 
  57 >A/Argentina/07AR,2009/07/15               ..........A...........A...................................T........................... 
  58 >A/Argentina/19618,2009/06/12              ..........A...........A...................................T........................... 
  59 >A/Argentina/FLE0116,2009/06/11            ----------A...........A...................................T......--------------------- 
  60 >A/Sao Paulo/55312,2009/08/05              ...C......A...........A.A.................................T........................... 
  61 >A/Bahia/15525,2009/09/05                  ...C......A...........A.A...RR............................T.................---------- 
  62 >A/Bahia/231,2010/04/01                    ......................A......R............................T........................... 
  63 >A/Peru/FLE0603,2009/07/13                 ----------............A.................................T.T......--------------------- 
  64 >A/Chile/3369,2009/07/01                   ......................A...................................T........................... 
  65 >A/Venezuela/FLE2525,2009/07/20            ----------............A...................................T......--------------------- 
  66 >A/Argentina/07-09GP,2009/05/30            ......................A...................................T........................... 
  67 >A/Uruguay/4,2009/06/25                    ------................A...................................T....----------------------- 
  68 >A/Chile/4181,2009/07/09                   ..T...................A...................................T........................... 
  69 >A/Chile/4182,2009/07/10                   ..T...................A...................................T........................... 
  70 >A/Paraguay/FLE1703,2009/07/06             ----------........A...A...................................T......--------------------- 
  71 >A/Uruguay/40,2009/07/04                   ------................A...................................T....----------------------- 
  72 >A/Peru/FLE1066,2009/07/11                 ----------............A..................................CT......--------------------- 
  73 >A/Peru/FLA9857,2009/07/09                 ----------............A..................................CT......--------------------- 
  74 >A/Peru/FLE1051,2009/07/09                 ----------............A..................................CT......--------------------- 
  75 >A/Bahia/12606,2009/08/18                  ......................A.............................G.....T........................... 
  76 >A/Santa Catarina/478,2009/06/11           ----------............A...................................T........................... 
 105 >A/Peru/FLE2275,2009/07/15                 ----------.G......A...A...................A..T....G.......T......--------------------- 
 111 >A/Peru/FLE2031,2009/07/18                 ----------.G.C........A...................................T......--------------------- 
 112 >A/Rio de Janeiro/290,2009/05/24           ----------------......A...................................T........................... 
 113 >A/Parana/937,2010/05/11                   .....G.G..............A..G..........A............A........T..G...--------------------- 
 114 >A/Parana/881,2010/05/17                   -....G.G..............A..G..........A............A........T..G........................ 
 115 >A/Parana/927,2010/04/19                   ......................A..G..........A............A........T..G........................ 
 116 >A/Parana/914,2010/03/26                   .......G..............A..G..........A............A........T..G........................ 
 117 >A/Argentina/HNRG5,2009/06/22              ......................A...................................T..G........................ 
 118 >A/Chile/32,2009/05/25                     ......................A...................................T........................... 
 119 >A/Chile/3056,2009/06/26                   ......................A..............G....................T........................... 
 120 >A/Chile/3123,2009/06/26                   ......................A..............G....................T........................... 
 121 >A/Chile/3295,2009/06/30                   ......................A...................................T........................... 
 122 >A/Argentina/HNRG21,2009/07/01             ......................A...................................T........................... 
 123 >A/Argentina/HNRG31,2009/06/17             ......................A...................................T........................... 
 124 >A/Chile/56,2009/05/26                     ......................A...................................T........................... 
 125 >A/Chile/2994,2009/06/26                   ......................A...................................T........................... 
 126 >A/Chile/3242,2009/06/30                   ......................A...................................T........................... 
 127 >A/Argentina/HNRG41,2009/06/26             ......................A...................................T........................... 
 128 >A/Rio Grande do Sul/7108,2009/07/29       ......................A...................................T........................... 
 129 >A/Bogota/0466N,2009/06/25                 ............A.........AT...........A............T.........T........................... 
 130 >A/Argentina/HNRG72,2009/06/19             ......................A...................................T........................... 
 131 >A/Argentina/HNRG48,2009/06/25             ......................A...................................T........................... 
 132 >A/Sao Paulo/2193,2009/05/29               ......................A...................................T........................... 
 133 >A/Chile/1599,2009/06/15                   ......................A...................................T........................... 
 134 >A/Chile/1600,2009/06/15                   ......................A...................................T........................... 
 135 >A/Chile/4064,2009/07/09                   ......................A...................................T........................... 
 136 >A/Uruguay/38,2009/06/29                   ------................A...................................T....----------------------- 
 137 >A/Chile/3553,2009/07/02                   ......................A...................................T........................... 
 148 >A/Guayaquil/5,2009/07/                    -................G....A.................---------------------------------------------- 
 149 >A/Peru/FLA9506,2009/07/08                 ----------.......G....A......................T............T......--------------------- 
 150 >A/Paraguay/FLE1714,2009/07/10             ----------.......G....A...................................T......--------------------- 
 151 >A/Paraguay/FLE1767,2009/07/03             ----------.......G....A...................................T......--------------------- 
 152 >A/Chile/4257,2009/07/13                   ...C..................A...................................T........................... 
 153 >A/Uruguay/11,2009/08/07                   ------................A...................................T....----------------------- 
 154 >A/Sao Paulo/54392,2009/08/01              ......................A...................................T.....A..................... 
 155 >A/Rio Grande do Sul/4509,2009/07/18       ...................A..A...................................T.....A..................... 
 156 >A/Alagoas/115,2010/03/05                  ...................A..A...................................T........................... 
 157 >A/Alagoas/96,2010/03/02                   ...................A..A..........................A........T........................... 
 158 >A/Rio de Janeiro/88,2010/03/04            ...................A..A..........................A........T........................... 
 159 >A/Peru/FLA9527,2009/07/09                 ----------............A..........................A........T......--------------------- 
 160 >A/Quito/WR1589N,2009/10/21                ......................A..........................A........T......GGCATAGCTGTAGAATATTAA 
 161 >A/Uruguay/35,2009/07/14                   ------................A...................................T....----------------------- 
 162 >A/Argentina/HNRG36,2009/06/21             ......................A...................................TG.......................... 
 163 >A/Argentina/HNRG42,2009/06/27             ......................A.......................T...........TG.......................... 
 164 >A/Argentina/HNRG44,2009/06/30             ......................A.......................T...........T........................... 
 165 >A/Argentina/HNRG39,2009/06/23             ......................A.........A.............T...........T........................... 
 166 >A/Chile/3220,2009/06/30                   ......................A.........A.........................T........................... 
 167 >A/Argentina/HNRG91,2009/07/05             ......................A...................................T........................... 
 168 >A/Sao Paulo/53845,2009/08/02              ......................A.....A.............................T........................... 
 169 >A/Argentina/HNRG8,2009/06/11              ......................A.....A........................--------------------------------- 
 170 >A/turkey/Chile/28317-6504-3,2009/08/17    ......................A...................................T....----------------------- 
 171 >A/Argentina/HNRG30,2009/06/17             ......................A...................................T....----------------------- 
 172 >A/Castro/JXP,2009/06/11                   ......................A...................................T........................... 
 173 >A/Argentina/HNRG20,2009/06/19             ......................A...................................T....----------------------- 
 174 >A/Bogota/WR0090N,2009/06/16               ............A.........AT...........A............T.........T......GGCATCTA.AGTGTA.A.TT. 
 175 >A/Chile/8949,2009/05/18                   ......................A..................--------------------------------------------- 
 176 >A/Peru/FLE0785,2009/07/07                 ----------............A............................A......T......--------------------- 
 177 >A/Argentina/HNRG32,2009/06/22             ......................A...................................T........................... 
 178 >A/Paraguay/FLA9595,2009/06/17             ----------............A........T..........................T......--------------------- 
 179 >A/SW/Argentina/SAGiles-31215,2009/06/24   ......................A........T..........................T........................... 
 180 >A/Chile/31,2009/05/25                     ......................A...................................T........................... 
 181 >A/Chile/1598,2009/06/15                   ......................A...................................T........................... 
 182 >A/Uruguay/39,2009/07/04                   ------................A...................................T....----------------------- 
 183 >A/Sao Paulo/2056,2009/05/20               .A....................A...................................T........................... 
 184 >A/Uruguay/10,2009/07/10                   ------................A...................................T....----------------------- 
 185 >A/Mato Grosso/2329,2009/05/28             ......................A...................................T.....................T..... 
 186 >A/Peru/FLE1338,2009/07/17                 ----------............A...................................T......--------------------- 
 187 >A/Chile/4438,2009/07/20                   ......................A...................................T........................... 
 188 >A/Paraguay/FLE1685,2009/07/01             ----------............A..................C................T......--------------------- 
 189 >A/Rio Grande do Sul/4772,2009/07/20       .........T............A...................................T........................... 
 190 >A/Argentina/FLE2161,2009/07/01            ----------............A...................................T......--------------------- 
 191 >A/Chile/3586,2009/07/03                   ....................A.A...................................T........................... 
 192 >A/Rio Grande do Sul/4782,2009/07/20       ....................A.A...................................T........................... 
 193 >A/Chile/2009,2009/06/18                   ......................A...................................T........................... 
 194 >A/Chile/180,2009/05/29                    ......................A...............................G...T........................... 
 195 >A/Chile/2239,2009/06/19                   ......................A...............................G...T........................... 
 196 >A/Chile/1586,2009/06/13                   ......................A...................................T........................... 
 197 >A/Peru/FLA9735,2009/07/08                 ----------.G..........A...................................T......--------------------- 
 198 >A/Peru/FLE0768,2009/07/08                 ----------.G..........A...................................T......--------------------- 
 199 >A/Peru/FLE1118,2009/07/11                 ----------.G..........A...................................T......--------------------- 
 200 >A/Chile/3935,2009/07/07                   ......................A...................................T........................... 
 201 >A/Peru/FLA9395,2009/07/02                 ----------............A.................................A.T......--------------------- 
 202 >A/Peru/FLA8651,2009/06/26                 ----------............A.................................A.T......--------------------- 
 203 >A/Santiago/3827,2009/07/07                -------G..............A........................--------------------------------------- 
 204 >A/Argentina/FLE0140,2009/06/17            ----------............A...................................T......--------------------- 
 205 >A/Argentina/HNRG14,2009/05/27             ......................A...................................T........................... 
 206 >A/Chile/3349,2009/07/01                   ......................A...................................T........................... 
 207 >A/Argentina/HNRG83,2009/06/17             ......................A...................................T........................... 
 208 >A/Santa Catarina/460,2009/06/10           ......................A...................................T........................... 
 209 >A/Argentina/HNRG17,2009/06/01             ......................A...................................T........................... 
 210 >A/Chile/2362,2009/06/22                   ......................A...................................T........................... 
 211 >A/Argentina/HNRG45,2009/06/16             ......................A...................................T........................... 
 212 >A/Chile/88,2009/05/27                     ......................A...................................T........................... 
 213 >A/Argentina/HNRG3,2009/06/18              ......................A...................................T........................... 
 214 >A/Argentina/HNRG105,2009/06/24            ......................A...................................T........................... 
 215 >A/Chile/3244,2009/06/30                   ......................A...................................T........................... 
 216 >A/Sao Paulo/2275,2009/05/29               ......................A...................................T........................... 
 217 >A/Chile/28,2009/05/23                     ......................A...................................T........................... 
 218 >A/Chile/158,2009/05/28                    ......................A...................................T........................... 
 219 >A/Argentina/HNRG84,2009/07/05             ......................A...................................T........................... 
 220 >A/Chile/40,2009/05/25                     ......................A...................................T........................... 
 221 >A/Chile/3819,2009/07/06                   ......................A...................................T........................... 
 222 >A/Chile/1603,2009/06/15                   ......................A...................................T........................... 
 223 >A/Chile/3019,2009/06/26                   ......................A...................................T........................... 
 224 >A/Chile/95,2009/05/27                     ......................A...................................T........................... 
 225 >A/Sao Paulo/2261,2009/05/29               ......................A...................................T........................... 
 226 >A/Argentina/HNRG49,2009/06/16             ......................A...................................T........................... 
 227 >A/Distrito Federal/2611,2009/06/05        ......................A...................................T........................... 
 228 >A/Chile/3361,2009/07/01                   ......................A...................................T........................... 
 229 >A/Chile/3760,2009/07/06                   ......................A...................................T........................... 
 230 >A/Argentina/HNRG40,2009/06/24             ......................A..........T........................T........................... 
 231 >A/Argentina/19527,2009/06/15              ......................A..........T........................T........................... 
 232 >A/Argentina/HNRG33,2009/06/24             ......................A...................................T........................... 
 233 >A/Chile/3375,2009/07/01                   ......................A................G..................T...T....................... 
 234 >A/Chile/3766,2009/07/06                   ......................A................G..................T...T....................... 
 235 >A/Argentina/19659,2009/05/18              ......................A...................................T........................... 
 236 >A/Santa Catarina/459,2009/06/11           ......................A...........M.......................T........................... 
 237 >A/Argentina/HNRG18,2009/07/01             ......................A...................................T........................... 
 238 >A/Cancun-NY/Index/2009/04/15              ......................A...................................T........................... 
                                                                                                                                       
---Index----------------------------------------AGCTCACAGAGAGACGAAGCTGTCGAAAGAGCGCCGGAAACTGGTACCCGAGAGACCTCAAACGGAAGGGTCTCTACAGTGTAAGT 
-codon-position---------------------------------1 2 12112 1  1 11  2  1     12  1  1 1 22 11 2   1       11 1  1 1212 12 12 12 12 1 2  
                                                00000000000000000000000000000000000000001111111111111111111111111111111111111111111111 
                                                00011111333334444555666666677777888899990000011111122333334444455666666666666666666666 
                                                07944578014690357169055789901127167733681556800447868245880223345677777777788888888999 
                                                48515524250309218616378270385667770104336016937031861919348894767902345678901234567245

Announcement

Sequences at Genbank!

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