Today at GenBank

gsgs · Feb 12, 2014

Re: Today at GenBank

A/panda/Sichuan/01-GG/2009/11/,H1N1 8 segments

http://www.ncbi.nlm.nih.gov/nuccore/KF277204.1

it has 14 mutations:

>A/panda/Sichuan/01-GG/2009,2009/11/,H1N1
G546A(1),C1412T(1)
A300G(2),A1058G(2),A1696G(2)
T198C(3),A495G(3),G849A(3),G1027A(3)
C145A(4),G798C(4)
---
G238A(6),C813T(6),C1332T(6)
---
---

this is surprisingly few . In Nov.2009 I'd expect about 25 mutations.
Let's me speculate whether the virus survived in the environment
some months without replicating.

mutations G546A(1),A300G(2),A1058G(2),C145A(4) are from
the "airplane strain" or "South Carolina strain (2009/04/26)" or "Cancun-2" strain.
I think it was from students returning from Cancun of a school in South Carolina.
It's not the Cancun-strain, that became dominant since 2010.
I have one other early sequence from that strain from Sichuan :
A/Sichuan/1/2009/05/10 from May,10 which has
G546A(1),A300G(2),A1058G(2),G37A(4),

-------------------------------------------------------------------------
here is the paper:
http://wwwnc.cdc.gov/eid/article/20/3/13-1531_article.htm
-----------------------------------------------------------------------
http://www.setbb.com/fluwiki2/viewt...74560a4f2dea4b614e9dafe32ace5&mforum=fluwiki2

The results indicated that A/Sichuan/1/2009 strain had significantly higher replication
ability and virulence than the other strains, and five unique non-synonymous mutations
were identified in important gene-encoding sequences. These mutations led to amino
acid substitutions in HA (L32I), PA (A343T), PB1 (K353R and T566A), and PB2 (T471M),
and may be critical molecular determinants for replication, virulence, and pathogenicity.

Amino acid mutations and the codon posotions:
T471M PB2(1)= C1412T
K353R, T566A PB1(2)= A1058G, A1696G
A343T PA(3)= G1027A
L32I HA(4)= C145A

Sichuan/1/2009 from Genbank; also one at Gisaid
G546A(1),C1412T(1),
A300G(2),A1058G(2),A1696G(2),
T198C(3),A495G(3),G849A(3),G1027A(3),
C145A(4),G798A(4),
Nothing for NP
G238A(6),C813T(6),C1332T(6),
Nothing for MP
Nothing for NS

Survival rates for lab mice:
20% A/Sichuan/1/2009
60% A/California/04/2009
70% A/California/07/2009
50-70% A/Fujian/1/2009, A/Shanghai/1/2009, and A/Guangdong/SWL28/2009
100% A/Shandong/1/2009, A/Beijing/3/2009, A/Jiangsu/1/2009, A/Sichuan-Wenjiang/SWL456/2009

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

checking again ... the Panda sequence is 100% identical to A/Sichuan/1, so there is a problem.

The A/Sichuan/1/2009 strain was isolated from the first reported
case of 2009 pandemic A (H1N1) influenza virus infection in China;
the patient was a Chinese student who had returned from the
United States in May 2009. The patient reported that no illness
symptoms were experienced during the flight from St. Louis to
Beijing, but fever developed on the following day during the flight
from Beijing to Sichuan. The source of infection remains unknown
[18].

--------------------------
the paper mentions
We named the virus that we isolated A/giant panda/01/Ya’an/2009 (H1N1).

but genbank has another virus
however they mention 100% identity in the 8 segments to

A/Wisconsin/629-D01313/2009 --- G546A,C1412T, May.8
A/Sichuan/1/2009
A/Sichuan/1/2009
A/Sichuan/1/2009
A/Paris/2580/2009 --- C132T , April.30
A/Sichuan/1/2009
A/California/04/2009 --- none
A/Sichuan/1/2009

so that would be just one difference to Sichuan/1 : C132T(5) and the problem remains

mixin · Feb 12, 2014

Re: Today at GenBank

Just to clarify your post a bit, the study you linked to from your forum is:
Genomic Polymorphism of the Pandemic A (H1N1) Influenza Viruses Correlates with Viral Replication, Virulence, and Pathogenicity In Vitro and In Vivo
http://www.plosone.org/article/info...+plosone/Virology+(PLoS+ONE+Alerts:+Virology)

So, looking back, have we found those mutations to be critical molecular determinants for replication, virulence, and pathogenicity?

Are these in our currently-circulating flu strain?
Amino acid mutations and the codon posotions:
T471M PB2(1)= C1412T
K353R, T566A PB1(2)= A1058G, A1696G
A343T PA(3)= G1027A
L32I HA(4)= C145A

About the panda, we don't have any reasonable explanation as to why the sequences were an exact match, even though 6 months had passed? Note that the study states

The results indicated that A/Sichuan/1/2009 strain had significantly higher replication ability

gsgs · Feb 12, 2014

Re: Today at GenBank

all the non-Cancun-substrains that we observed in 2009 died out.

A new strain emerged -probably in India IMO - in 2010
and descendents of that one still dominate this season

gsgs · Feb 15, 2014

Re: Today at GenBank

today: bull-flu

C/bovine/Minnesota/628/2013
C/bovine/Minnesota/729/2013
C/bovine/Oklahoma/660/2013

---------------------------------------------------------------------------
http://www.ncbi.nlm.nih.gov/nuccore/KF425652
Hause,B., Collin,E., Liu,R., Huang,B., Sheng,Z., Lu,W., Wang,D.,
Nelson,E.A. and Li,F.
TITLE Characterization of a novel influenza virus in cattle and swine:
Proposal for a new genus in the Orthomyxoviridae family
JOURNAL MBio 5 (1), e00031-14 (2014)
REMARK Publication Status: Online-Only
REFERENCE 2 (residues 1 to 772)
AUTHORS Hause,B., Collin,E., Liu,R., Simonson,R. and Li,F.
TITLE Direct Submission
JOURNAL Submitted (18-JUL-2013) Diagnostic Services, Newport Labs, 1524
Prairie Drive, Worthington, MN 56187, USA
collection_date="18-Feb-2013"

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

Code:

  9 >C/bovine/Minnesota/628/2013,2013/02/18                          2364 2330 2195 2049 1775    3 1219  868   
  1:552,491,548,608,538,---,538,571   A/Brevig Mission/1/1918(H1N1) 
  2:546,488,546,614,539,---,539,574   A/duck/LA/17G/1987,1987//,H3N8 
  3:549,490,543,620,540,---,553,581   A/equine/Lexington/1/1966(H7N7) 
  4:570,502,557,607,555,---,550,579   A/little yellow-shouldered bat/Guatemala/153/2009/05/(H17N10) 
  5:559,483,548,605,552,---,575,595   A/flat-faced bat/Peru/033/2010(H18N11) 
  6:598,581,567,615,585,---,622,606   B/1940 
  7:415,323,400,405,425,---,459,459   C/Ann Arbor/1/50,1950// 
  8: 20,  8, 24, 10, 19,---, 32,  8   C/swine/Oklahoma/1334/2011,2011/03/21 
  9:  0,  0,  0,  0,  0,---,  0,  0   C/bovine/Minnesota/628/2013,2013/02/18 
 10:  0,  0,  0,  0,  1,---,  0,  0   C/bovine/Minnesota/729/2013,2013/02/26 
 11:  8, 10, 23, 37,  7,---,  9, 12   C/bovine/Oklahoma/660/2013,2013/02/20

so it's the same virus as the new C/swine/Oklahoma from 2011,
only that now they found it in cattle

gsgs · Feb 19, 2014

Re: Today at GenBank

A/giant panda/Ya'an/01/2009(H1N1) today at genbank , identical to the other claimed Panda genome
more H1 from Spain, Dec.2013

NY, mixed H1 from June 2009
1,4,6 from pH1
2,3,5,7,8 from H3N2, Perth
A/New York/3720/2009/06/01(mixed)
apparently it didn't spread

gsgs · Feb 25, 2014

Re: Today at GenBank

35 HAs human Spain Dec.,Jan
50 HAs Canada , Dec.

Sparrow-H7N9

A/environment/Gainesville,2014/01/14(H1N1) segments 4,6,7

A/Utah/8/2013/08/05 (H1N1)

Iran,2013/04 , H3N2

gsgs · Apr 9, 2014

Re: Today at GenBank

70 teals and mallards from North USA , 2013 , full genome , no 17g
(52*OH,11*IO,7*WI,54*teal,14*mallard, types below)
7 H1N1 genomes, Czech, this season
3 H3N2 genomes, Czech, this season

-------------------
H10N8,H11N9,H1N8,H2N3,H2N8,H7N1,H9N2
5*H3N2,13*H3N8,7*H4N6,19*H4N8,2*H6N1,4*H6N2,2*H6N7,8*H6N8,4*H7N3
-------------------------
distances from the bird-index:

Code:

  3,  4,  3,---,  4,---,  2,  2,
  2,  2,  4,---,  0,---,  1,  2,
  3,  2,  3,---,  2,---,  2,  2,
  3,  2,  5,---,  2,---,  1,  0,
  3,  2,  5,---,  2,---,  1,  0,
  3,  2,  5,---,  2,---,  1,  0,
  4,  2,  5,---,  2,---,  2,  0,
  4,  2,  5,---,  2,---,  2,  0,
  8,  2,  5,---,  4,---,  1,  2,#
  3,  6,  3,---,  3,---,  1,  2,#
  4,  3,  4,---,  4,---,  2,  2,#
  4,  4,  4,---,  4,---,  2,  3,#
  3,  2,  4,---,  5,---,  0,  2,#
  6,  2,  6,---,  2,---,  0,  2,
  2,  3,  4,---,  3,---,  3,  1,
  2,  4,  5,---,  3,---,  3,  0,
  2,  4,  4,---,  3,---,  3,  0,
  2,  3,  9,---,  3,---,  1,  0,
  1,  6,  9,---,  4,---,  2,  1,
  3,  5,  9,---,  2,---,  0,  0,
  1,  4,  8,---,  3,---,  0,  1,
  1,  2,  9,---,  1,---,  1,  4,
  1,  3,  9,---,  1,---,  1,  4,
  4,  5,  4,---,  2,---,  0,  4,#
  2,  4,  9,---,  4,---,  0,  1,#
  1,  3,  9,---,  1,---,  0,  2,#
  3,  2, 12,---,  2,---,  2,  1,#
  3,  3,  8,---,  3,---,  1,  5,
  3,  5,  3,---,  5,---,  3,  1,
  3,  5,  3,---,  5,---,  3,  1,
  3,  3,  3,---,  2,---,  1,  1,
  3,  3,  3,---,  2,---,  1,  1,
  3,  3,  3,---,  2,---,  1,  1,
  3,  2,  3,---,  2,---,  0,  0,
  3,  2,  3,---,  2,---,  1,  0,
  4,  3,  7,---,  3,---,  0,  0,
  3,  2,  6,---,  5,---,  1,  1,
  2,  2,  6,---,  3,---,  2,  2,
  3,  2,  5,---,  2,---,  2,  2,
  3,  2,  3,---,  2,---,  2,  2,
  2,  4,  5,---,  2,---,  0,  1,
  2,  2,  4,---,  0,---,  1,  1,#
  3,  8,  5,---,  3,---,  0,  2,#
  3,  8,  5,---,  3,---,  0,  2,#
  3,  8,  5,---,  3,---,  0,  2,#
  3,  8,  5,---,  3,---,  0,  2,#
  3,  8,  5,---,  3,---,  0,  2,#
  3,  8,  5,---,  3,---,  0,  2,#
  3,  8,  5,---,  3,---,  0,  2,#
  3,  8,  5,---,  3,---,  0, 43,#
  3,  4,  9,---,  4,---,  3,  0,
  3,  4,  9,---,  3,---,  3,  0,
  2,  4,  8,---,  2,---,  3,  0,
  2,  4,  8,---,  2,---,  0,  0,
  3,  5,  8,---,  2,---,  3,  2,#
  2,  3,  3,---,  2,---,  3,  2,#
  2,  4,  4,---,  2,---,  0,  1,#
  3,  4,  3,---,  2,---,  0,  2,
  5,  4,  5,---,  2,---,  0,  1,#
  3,  3, 12,---,  2,---,  1,  1,#
  6,  4, 10,---,  2,---,  1,  4,
  6,  4, 10,---,  2,---,  1,  4,
  5,  4,  3,---,  2,---,  1,  1,
  2,  4,  4,---,  3,---,  2,  0,
  2,  4,  4,---,  3,---,  2,  0,
  2,  2,  4,---,  3,---,  1,  4,#
  2,  2,  4,---,  3,---,  1,  4,#
  2,  3,  4,---,  3,---,  1,  4,#
  4,  6,  2,---,  3,---,  1,  5,
  4,  4,  4,---,  3,---,  1,  0,
  4,  4,  4,---,  3,---,  1,  0,

Code:

                                         0000000000000000000000000000000 000000000000000000000000000 0000000000000000000000000000000000000000000  00000000000000  0000000000000 00000000000000000000000000 
                                         0000011112233344444455555666667 000111122222233333445666777 0000000111111122222233333333334444445566667  00111123333444  2222222222333 00001111111222222222222333 
                                         2666702892238944556712578457786 155155711138946788238569035 2236699000168902566722455688890002344601241  35002305567159  2566777789345 25891111225000111122358125 
                                         2347693415789568133814546994620 249324856876428567902471368 2761279014437981219237839727810493245598637  80158610353709  4347136806521 06661689397269245636149703 
                                         ------------------------------- --------------------------- -------------------------------------------  --------------  ------------- -------------------------- 
                                         KIMITVETESVVRAFNIPIVVTRKKVNATG VKTVSGERSLKVQIINRKKRQSIKSK KDAIITGVEKELLETPELRDVEIKNKEVSKSASIVNIVKTKK  RSDVDLITVITNS  STGKSSPVLSG KTAEVCRMIIVASDPLPPAISLRI 
>A/Index/birds/2000(H3N8a)               ..............................} ..........................} ..........................................}  .............}  .}..........} ....................}....} 
>A/Index/birds/North America/2000(H3N8b) ...................I..........} ...............S..........} ....................I.........P...........}  ...M........N}  .}..........} ....................}....} 
>A/BWTeal/OH/13OS2018/2013(H3N8)         .....I.............I........I.} ..S............S..........} .....A........A.....I.....D...P...........}  ...M........N}  .}..R.......} ....................}....} 
>A/AGWTeal/OH/13OS2106/2013(H3N8)        .....I.............I........I.} ..S............S..........} .....A........A.....I.....D...P...........}  ...M........N}  .}..R.......} ....................}....} 
>A/BWTeal/OH/13OS3827/2013(H3N8)         .....I........L....I........I.} ..S............S..........} .....A........A.....I.....D...P...........}  ...M........N}  .}..R....F..} ....................}....} 
>A/wood duck/OH/13OS3300/2013(H3N8)      .....I........L....I........I.} ..S............S..........} .....A........A.....I.....D...P...........}  ...M........N}  .}..R....F..} ....................}....} 
>A/AGWTeal/OH/13OS2108/2013(H3N8)        .....I.............I........I.} ..S............S..........} .....A........A.....I.....D...P...........}  ...M........N}  .}..R.......} ....................}....} 
>A/AGWTeal/OH/13OS2084/2013(H6N8)        ................V..II.KR....I.} ..S............SK.....V...} ....V.............K.I.L.....G.P..M..V.R.R.}  ...M........N}  .}..R.......} ............C.S...E.}Y...} 
>A/AGWTeal/OH/13OS2086/2013(H6N8)        ................V..II.KR....I.} ..S............SK.....V...} ....V.............K.I.L.....G.P..M..V.R.R.}  ...M........N}  .}..R.......} ............C.S...E.}Y...} 
>A/BWTeal/IO/13OS2338/2013(H4N8)         ....A..............I.A........} ..S............S....K.....} .......I..........K.I.L.....G.P.....V...R.}  .G.M........N}  .}..R.......} ..T.........C...L...}.F.V} 
>A/BWTeal/OH/13OS1773/2013(H7N3)         ...................I..........} ..S............S..........} ...............S..K.I.L....IG.P......I..R.}  ............N}  .}........N.} .........T...N....E.}...V} 
>A/AGWTeal/OH/13OS1777/2013(H7N3)        ...................I..........} ..S....K.......S..........} ...............S..K.I.L....IG.P......I..R.}  ............N}  .}........N.} .........T...N....E.}...V} 
>A/BWTeal/WI/13OS3463/2013(H3N2)         ...................I..........} ..S..DGK.......S...K......} ..................K.I.L....IG.P......I.KR.}  ...M...A...SN}  .}......I..S} R...................}....} 
>A/BWTeal/OH/13OS2104/2013(H2N3)         ......K.......................} ..S....K.......S..R.......} ..................K.I......IG.P...I..I..R.}  ..EM........N}  .}..........} .........T..........}....} 
>A/mallard/OH/13OS3856/2013(H9N2)        .....I.............I.........S} ..S....K......VS.........R} ........K.........K.I.L....IG.P...I.....R.}  ...M........N}  .}..........} ....................}....} 
>A/mallard/OH/13OS1972/2013(H2N8)        .....I.............I..........} ..S...........VS.........R} ..........K.......K.I.L....IG.P.........R.}  ...M........N}  .}..........} ....................}....} 
>A/AGWTeal/OH/13OS1775/2013(H4N8)        .....I.........T...I..........} ..S...........VS.........R} ......R..N........K.I.L....IG.P.........R.}  K..M........N}  .}I.R......S} ....................}....} 
>A/BWTeal/OH/13OS1783/2013(H4N8)         .....I.........T...I..........} ..S...........VS.........R} ......R..N........K.I.L....IG.P.........R.}  K..ME.......N}  .}I.R......S} ....................}....} 
>A/mallard/OH/13OS1966/2013(H1N8)        .....I.............I..........} ..S...........VS.........R} ..........K.......K.I.L....IG.P.........R.}  ...M........N}  .}I.R......S} ....................}....} 
>A/AGWTeal/OH/13OS2056/2013(H3N2)        .....I.............I..........} ..S...........VS..........} ..................K.I.LN...IG.P.G.......R.}  ...M....I...N}  .}..R.......} ....................}....} 
>A/BWTeal/OH/13OS2055/2013(H6N7)         .....I.............I..........} ..SI...........S.N........} .N..................I.....D...P...........}  ...M....I...N}  .}...N..I...} ....................}....} 
>A/AGWTeal/OH/13OS2070/2013(H6N7)        .....I.............I..........} ..SI...........S.N........} .N..................I.....D...P...........}  ...M....I...N}  .}...N..I...} ....................}....} 
>A/AGWTeal/WI/13OS3465/2013(H6N8)        ...L...M.G.......S.I..........} ..SI.......I...S..........} ....................I.....D...P...........}  ...T........N}  N}..........} .................S..}....} 
>A/AGWTeal/OH/13OS2050/2013(H4N6)        ................V..II.........} ..S............S..........} ...........I.......E..........Q...........}  ...M........N}  .}.E........} ....................}....} 
>A/BWTeal/OH/13OS2016/2013(H4N6)         ................V..II.........} ..S............S..........} ...........I.......E..........Q...........}  ...M........N}  .}..........} ....................}....} 
>A/NPintail/WI/13OS2778/2013(H6N2)       .......M.....V...S.I..........} .RS..........V.SK..K......} ...................E..........Q...........}  ...M....I...N}  .}......I...} .M......V.I....F....}..K.} 
>A/AGWTeal/OH/13OS1793/2013(H6N1)        ........K........S.I.....I....} I.S....K.......S..........} ............F......E.........RQ...........}  ...M....A...N}  .}..R.......} ....................}....} 
>A/AGWTeal/OH/13OS1794/2013(H6N1)        ........K........S.I.....I....} I.S....K.......S..........} ............F......E.........RQ...........}  ...M....A...N}  .}..R.......} ....................}....} 
>A/BWTeal/OH/13OS2064/2013(H4N6)         .V..........K......I..........} ..S............S..R.......} ...................E.........RQ...........}  ...M.......S.}  .}..R.......} .......I............}....} 
>A/AGWTeal/OH/13OS2063/2013(H4N6)        .V..........K......I..........} ..S............S..R.......} ...................E.........RQ...........}  ...M.......S.}  .}..R.......} .......I............}....} 
>A/AGWTeal/OH/13OS2065/2013(H4N6)        .V..........K......I..........} ..S............S..R.......} ...................E.........RQ...........}  ...M.......S.}  .}..R.......} .......I............}....} 
>A/BWTeal/IO/13OS2367/2013(H3N8)         .....I.............I..........} ..S............S..........} ...................E.........RQ..........R}  .............}  .}........N.} ....M..............V}....} 
>A/BWTeal/IO/13OS2368/2013(H4N8)         .....I............VI..........} ..P......I.....S.......R..} ...................E.........RQ...........}  ...M.M....A.N}  .}..R...I...} ....M..............V}....} 
>A/AGWTeal/OH/13OS1864/2013(H4N8)        .....I.............I..........} ..S............S..........} R...............G..E.........RQG..........}  ...M....I...N}  .}....N.I...} ....M..............V}....} 
>A/AGWTeal/OH/13OS1844/2013(H3N8)        .....I.A.......T...II......V..} ..S............S..........} R...............G..E.........RQG..........}  ...M........N}  .}..........} ....M..............V}....} 
>A/mallard/OH/13OS1989/2013(H4N8)        ..I.........K......I..........} ..S............S..........} R...............G..E.........RQG..........}  ...M.MVA....N}  .}......I...} ......K.............}....} 
>A/BWTeal/OH/13OS2020/2013(H4N6)         ...................I....R.S...} ..S.L...G.R....S..........} ...................E.........RQ...........}  ...M.MV..V..N}  .}I.R......S} ......K.............}....} 
>A/AGWTeal/OH/13OS2021/2013(H4N6)        ...................I....R.S...} ..S.L...G.R....S..........} ...................E.........RQ...........}  ...M.MV..V..N}  .}I.R......S} ......K.............}....} 
>A/AGWTeal/OH/13OS1778/2013(H3N2)        .....I.............I..........} .RS.......R....S..........} ...................E....T....RQ....D......}  ...M....I...N}  .}I.R......S} ....................}....} 
>A/BWTeal/OH/13OS1831/2013(H3N2)         .....I.............I..........} .RS.......R....S..........} ...................E.........RQ....D......}  ...M....I...N}  .}I.R......S} ....................}....} 
>A/AGWTeal/OH/13OS1867/2013(H3N2)        .....I.............I..........} ..S............S.....N....} ...................E.........RQ...I.......}  ...M....I...N}  .}I.R......S} ...G................}....} 
>A/BWTeal/IO/13OS2359/2013(H4N8)         R..........A.......I........A.} ..S....K.......S..........} ...T.............Q.E.G.......RQ...I.......}  .T.M........N}  .}..........} ....................}....} 
>A/AGWTeal/OH/13OS1840/2013(H6N8)        R..................I........A.} ..S....K.......S...K......} ...................E.........RQ...........}  ...M........N}  .}..........} .....R...T..........}....} 
>A/BWTeal/IO/13OS2349/2013(H4N8)         .....I.............I..........} ..S.........R..S........C.} ....V........G.....E.........RQ...........}  ...M........N}  .}..........} .........T..........}....} 
>A/BWTeal/IO/13OS2337/2013(H4N8)         .....I....A........I..........} ..S............S..........} ..V................E.....M...RQ...........}  ...M........N}  .}.....LI...} ...........T.N......}....} 
>A/BWTeal/IO/13OS2340/2013(H3N8)         .....I....A........I..........} ..S............S..........} ...................E.........RQ...........}  ...M........N}  .}.....LI...} ...........T.N......}....} 
>A/BWTeal/IO/13OS2357/2013(H4N8)         .....I....A........I..........} ..S............S..........} ...................E.........RQ...........}  ...M........N}  .}.....LI...} ...........T.N......}....}

Code:

                                   00000000000000000000000000000 000000000000000000000000000000 0000000000000000000000000000000000  0000000000000000  00000000000 00000000000000000 
                                   00000111113333344444555566777 000000111233333334444566677777 0000011112222233333333444455666667  0112333333444444  00122222333 00111111222222223 
                                   22666003883456856779238945156 145679777156778893358700913455 2366902691566724488899000344024441  0030155677023559  12656778345 78000125002235895 
                                   29135797478038933580496099460 249404789538256770666847456838 9612942392279231827814034057960237  5561803335833069  57734180521 16018197691613083 
                                   ----------------------------- ------------------------------ ----------------------------------  ----------------  ----------- ----------------- 
                                   KAKIESVNTKVRKRRPILVSTIKGVNSM VNTPDFEEMRKIMNRKIRYHRKLPNVKSL KAIIGKVLEREPRDVVIEVSKDSLAEIDKKLAK  GVLIPTVVTDVATSV  VRTTKPVSG SARERIIVRNYVEVE 
>A/Index/birds/2000(H3N8b)         ............................} .............................} .................................}  ...............}  ...}......} ............}...} 
>A/mallard/OH/13OS1988/2013(H4N8)  ......I..N........I.........} I.SA..K......S.....Y..F.S....} ......II.....E......R.Q..........}  .M...........NM}  ...}......} ..K........I}...} 
>A/mallard/OH/13OS1990/2013(H4N8)  ......I..N........I.........} I.SA..K......S.....Y..F.S....} ......II.....E......R.Q..........}  .M...........NM}  ...}......} ..K........I}...} 
>A/mallard/OH/13OS1982/2013(H4N8)  ......I..N........I.........} I.SA..K......S.....Y..F.S....} ......II.....E......R.Q..........}  .M...........NM}  ...}......} ..K........I}...} 
>A/mallard/OH/13OS1994/2013(H4N8)  ......I..N........I.........} I.SA..K......S.....Y..F.S....} ......II.....E......R.Q..........}  .M...........NM}  ...}......} ..K........I}...} 
>A/mallard/OH/13OS1981/2013(H4N8)  ......I..N........I.........} I.SA..K......S.....Y..F.S....} ......II.....E......R.Q..........}  .M...........NM}  ...}......} ..K........I}...} 
>A/mallard/OH/13OS1993/2013(H4N8)  ......I..N........I.........} I.SA..K......S.....Y..F.S....} ......II.....E......R.Q..........}  .M...........NM}  ...}......} ..K........I}...} 
>A/mallard/OH/13OS1985/2013(H4N8)  ......I..N........I.........} I.SA..K......S.....Y..F.S....} ......II.....E......R.Q..........}  .M...........NM}  ...}......} ..K........I}...} 
>A/mallard/WI/13OS2767/2013(H3N8)  ........M......S..I.........} ..S..........S...............} .............EA.....R.Q..........}  ....SA.I...T.N.}  ...}......} G..........I}...} 
>A/BWTeal/IO/13OS2339/2013(H4N8)   ......I...........I.........} ..S..........S...............} .............E......R.Q.........R}  ...............}  ...}....N.} ......T.....}...} 
>A/BWTeal/IO/13OS2345/2013(H3N8)   .T...N......R.....I.........} ..S..........S....H..........} .T...........E......R.Q..........}  .MM.....A....N.}  I..}....N.} ......T..D..}...} 
>A/BWTeal/IO/13OS2346/2013(H3N8)   .T...N......R.....I.........} ..S..........S....H......M...} .T...........E......R.Q..........}  .MM.....A....N.}  I..}....N.} ..K...T..D..}...} 
>A/AGWTeal/OH/13OS2094/2013(H6N8)  ..R...............I.........} ..S..........SK............F.} .............E......R.Q..D.......}  .M...........N.}  ...}......} ......T.....}...} 
>A/AGWTeal/OH/13OS1781/2013(H6N8)  Q..V......I...K...I.........} ..S......K...S...K...........} ..........G..E......R.Q.G........}  .M...........N.}  ...}......} ......T.....}...} 
>A/AGWTeal/WI/13OS3462/2013(H3N8)  ........A.........I.....I...} .SS......K...S.........S....F} .............E......R.Q..........}  .M.......E...N.}  ..A}......} ......TI....}...} 
>A/BWTeal/OH/13OS2082/2013(H6N2)   ......I...........I.........} ..S..........S...............} .............E......R.Q........T.}  .M....I......N.}  ...}...I..} ......T....I}G.G} 
>A/AGWTeal/OH/13OS2083/2013(H6N2)  ......I...........I.........} ..S.G........S...............} .............E......R.Q........T.}  .M....I......N.}  ...}...I..} ......T....I}G.G} 
>A/AGWTeal/OH/13OS2090/2013(H6N2)  ......I...........I.........} ..S..........S...............} .............E......R.Q........T.}  .M....I......N.}  ...}...I..} ......T....I}G.G} 
>A/AGWTeal/OH/13OS2097/2013(H6N8)  ......I...........I.........} ..S..........S...K...........} .............E......R.Q..........}  .M...........N.}  ...}IR...S} ......T...H.}...} 
>A/AGWTeal/OH/13OS1869/2013(H10N8) ......I...........I.I.......} ..S....K...V.S............R..} ....R.......K.I.L.IG..P......R...}  .M...........N.}  ...}IR...S} .T....T.....}...} 
>A/AGWTeal/OH/13OS2060/2013(H6N8)  ......I.........V.I.........} ..S.........IS...............} ...V.....H..KEI.L..G..P...V.RRI..}  .M...........N.}  I..}......} ......T.....}...} 
>A/mallard/WI/13OS2800/2013(H11N9) ..................I...R..S..} ..S..........S...............} ...V.......SKEILL..G..P...V.RR...}  .M...........N.}  ...}.RH...} ...D........}...} 
>A/BWTeal/OH/13OS2037/2013(H7N1)   ..................I.........} ..S..S.......S...............} .....R..D...K.I.L..G..P...V..R...}  .............N.}  ...}......} .....V.....I}...} 
>A/AGWTeal/WI/13OS3468/2013(H7N3)  .................M.N........} ..S...G.I....S...............} ............K.I.L..G.NPI..V..R...}  .MMV.........N.}  ...}......} ...........I}...} 
>A/BWTeal/IO/13OS2316/2013(H7N3)   ..R....S......K...I.........} ..S.......R..S..T...K........} R.............I..D....P..........}  ............SN.}  ...}......} ....K.T.H...}.M.} 
>A/AGWTeal/OH/13OS1861/2013(H3N8)  ....G......K.K....I..V.S..GV} ...............R.....R.......} ..V...........I..D....P....N.....}  SIM.......I....}  .K.}......} ......T..D..}...}

recombination (--> presumably sequencing error in segment 8 of A/mallard/Ohio/13OS1984/2013,H4N8
combining the 2 NS - variants ! )

gsgs · Apr 15, 2014

Re: Today at GenBank

6709 new flu-sequences today !

could be a new record

most are human USA H3N2 and H1N1 from the previous seasons

more later ....
---------------------------
flu-A:3538.flu-B:3565,H3N2:2438,H1N1:1035,H1N2:36,
3013...1997:168,1728,802,635,244,548,912,608,465,167,64,56,56,208,8,24,0

gsgs · May 1, 2014

Re: Today at GenBank

582 sequences yesterday
mostly American birds, Alaska 2006,2007

no 17G

gsgs · May 7, 2014

Re: Today at GenBank

4454 sequences today ! (2014/05/07)
ftp://ftp.ncbi.nih.gov/genomes/INFLUENZA/updates/2014-05-07/influenza_na.dat

65 India
1951 mallard
1 chicken
57 swine
518 ggluti
315 H1N1
470 H3N2
0 penguin
0 H7N9
84 Delhi
273 Mongolia
3138 Wisconsin (avian)

no 17g

4138 Avian,251 Human,57 Swine
segments:547,492,493,567,546,604,571,634
1 Bangla Desh,112 Canada,231 India,273 Mongolia,3837 USA
1974ff:157,338,871,135,300,329,151,248,417,439,263,199,56
2005ff:16,9,41,5,132,103,92,43,100,9

so, mostly old bird sequences from Wisconsin from the 70s and 80s, full genomes

we have a new closest neighbour to 1918-flu in segment 4: H1 !
It still has 263 nucleotide differences, though.
But it is from North America, so 1918-HA was probably (~70%) also from North-America
-------------edit--------down to 50% after looking at amino-acids (again)

Code:

my list of closest avian neighbors to 1918-flu from Aug.2013:

        >A/Brevig Mission/1/1918(H1N1)
-----------------segment 1-------------------------
 929  212 2280 8696 >A/duck/Manitoba_KF/1953(H10N7)
 942  215 2280 7545 >GU052882,A/turkey/Canada/1963,1963//,Canada,H6N8,1
 951  217 2280  481 >CY004591,A/blue-winged teal/ALB/286/1977,1977/08/10,Canada,H3N6,1
 960  219 2280  512 >CY004797,A/mallard duck/Alberta/106/1979,1979/08/07,Canada,H4N2,1
 960  219 2280  513 >CY004804,A/blue-winged teal/Alberta/580/1979,1979/08/11,Canada,H4N2,1
 960  219 2280  514 >CY004811,A/pintail duck/ALB/599/1979,1979/08/11,Canada,H4N2,1
 964  220 2280 7466 >GU052000,A/Canada goose/Wisconsin/902/1975,1975//,USA,H5N2,1
 973  222 2280  425 >CY004153,A/pintail/Alberta/189/82,1982/08/10,Canada,H6N6,1
 973  222 2280  426 >CY004161,A/widgeon/ALB/256/1982,1982/08/13,Canada,H6N6,1
 974  221 2268 6143 >DQ870885,A/turkey/Oregon/1971,1971//,USA,H7N3,1
 978  222 2268 6144 >DQ870891,A/turkey/Oregon/1971,1971//,USA,H7N3,1
 978  223 2280  427 >CY004169,A/blue-winged teal/ALB/266/1982,1982/08/13,Canada,H6N6,1
 978  223 2280  428 >CY004177,A/mallard/Alberta/289/82,1982/08/14,Canada,H6N6,1
 978  223 2280  429 >CY004185,A/blue-winged teal/ALB/685/1982,1982/08/20,Canada,H6N4,1
      226
------------------segment 2----------------------------
 729  166 2274 8797 >A/duck/Manitoba_KF/1953(H10N7)
 795  181 2274 2848 >CY087814,A/turkey/Ontario/6213/1966,1966/06/11,Canada,mixed,2
 800  182 2274  746 >CY015107,A/turkey/Ontario/7732/1966,1966//,Canada,H5N9,2
 809  184 2274 7113 >GQ257446,A/duck/Memphis/546/1974,1974//,USA,H11N9,2
 817  186 2274 6918 >FJ517336,A/blue goose/WI/711/1975,1975//,USA,H5N2,2
 835  190 2274  476 >CY004590,A/blue-winged teal/ALB/286/1977,1977/08/10,Canada,H3N6,2
 848  193 2274 2847 >CY087782,A/turkey/Ontario/6118/1968,1968/06/11,Canada,H8N4,2
 857  195 2274  482 >CY004629,A/mallard/Alberta/663/1979,1979/08/13,Canada,H3N5,2
 870  198 2274 2819 >CY080513,A/turkey/Wisconsin/1/1968,1968/06/11,USA,H5N9,2
 901  205 2274  414 >CY004120,A/pintail duck/ALB/628/1979,1979/08/13,Canada,H6N8,2
 985  224 2274 6796 >EU871834,A/duck/LA/17G/1987,1987//,USA,H3N8,2
      253
--------------------segment 3-------------------------
 776  167 2151  915 >CY004479,A/pintail duck/ALB/219/1977,1977/09/03,Canada,H1N1,3
 794  171 2151 1140 >CY014668,A/turkey/Wisconsin/1/1966,1966//,USA,H9N2,3
 799  172 2151 8010 >EU743083,A/turkey/CO/118899/1972,1972//,USA,H5N2,3
 808  174 2151 1101 >CY005830,A/turkey/Ontario/6118/1968,1968//,Canada,H8N4,3
 813  175 2151  862 >CY004004,A/mallard duck/ALB/250/1978,1978/08/07,Canada,H6N2,3
 818  176 2151  863 >CY004009,A/blue-winged teal/Alberta/368/1978,1978/08/07,Canada,H6N8,3
 818  176 2151  866 >CY004030,A/mallard duck/ALB/290/1978,1978/08/09,Canada,H6N2,3
 822  176 2140  401 >AF156457,A/turkey/California/189/66,1966//,USA,H9N2,3
 827  178 2151  865 >CY004023,A/mallard duck/ALB/280/1978,1978/08/08,Canada,H6N2,3
      181
---------------------segment 4---------------------------------
1685  105  623  377 >FN773073,A/Mallard/Norway/10_1671/2007,2007//,Norway,H1N1,4
1690  105  621  463 >KC895597,A/common murre/Newfoundland/AB318/2011,2011/07/21,Canada,H1N2,4
1696  103  607  458 >KC464558,A/domestic duck/Newfoundland/MW668/2010,2010/09/17,Canada,H1N1,4
1707  104  609  460 >KC464574,A/American black duck/Newfoundland/1148/2009,2009/09/25,Canada,H1N1,4
1735  105  605  376 >FN773066,A/Teal/Norway/10_993/2007,2007//,Norway,H1N2,4
1880  218 1159  168 >CY132834,A/northern shoveler/Mississippi/11OS108/2011,2011/01/08,USA,H1N1,4
1887  321 1701   37 >CY004592,A/mallard/Alberta/127/1977,1977/08/22,Canada,H1N1,4
      324
----------------------segment 5-------------------------------------
1082  162 1497  324 >A/black duck/Ohio/95/1993,1993/10/15,USA,H1N1
1082  162 1497 4063 >A/American black duck/New Brunswick/03534/2009,2009/09/10,Canada,H4N6
1088  163 1497  268 >A/mallard/Alberta/72/1994,1994/08/09,Canada,H3N6
1088  163 1497  269 >A/mallard/Alberta/142/1994,1994/08/13,Canada,H3N6
1088  163 1497  270 >A/blue-winged teal/ALB/293/1994,1994/07/01,Canada,H4N6
1088  163 1497  323 >A/mallard/Ohio/94/1993,1993//,USA,H11N3
1088  163 1497 7981 >A/turkey/IA/21089-3/1992,1992//,USA,H1N1
      164
-----------------------segment 6---------------------------------------
 840   93 1107 3393 >GU052948,A/chicken/Germany/1934,1934//,Germany,H7N1,6
 848  114 1344  722 >CY015048,A/chicken/Rostock/45/1934,1934//,Germany,H7N1,6
1023   31  303 1538 >CY099621,A/sooty tern/Western Australia/7666/1984,1984//,Australia,mixedÞN1,6
1160   39  336 1471 >CY094865,A/Pacific black duck/Western Australia/2741/1979,1979//,Australia,H6N1,6
1163  164 1410  369 >AJ416625,A/chicken/Scotland/1959,1959//,United Kingdom,H5N1,6
1205  170 1410 1371 >CY087810,A/turkey/Ontario/6213/1966,1966/06/11,Canada,mixedÞN1,6
1205  170 1410 2634 >EF607922,A/duck/PA/486/1969,1969//,USA,H6N1,6
1220  164 1344  483 >AY207532,A/turkey/Minnesota/1265/80,1980//,USA,H6N1,6
1241  175 1410 1577 >CY116744,A/mallard/Rugen/27-6/1980,1980//,Germany,mixedÞ N1,6
1255  177 1410 2120 >DQ376691,A/chicken/Taiwan/G2/87,1987//,Taiwan,H6N1,6
1255  177 1410 2121 >DQ376692,A/chicken/Taiwan/G23/87,1987//,Taiwan,H6N1,6
1258  171 1359  719 >CY014752,A/turkey/Minnesota/799/1980,1980/02/04,USA,H6N1,6
1262  178 1410  580 >AY633118,A/mallard duck/Alberta/743/1983,1983//,Canada,H9N1,6
1262  178 1410  683 >CY004492,A/mallard/Alberta/965/1979,1979/08/16,Canada,H1N1,6
1262  178 1410  695 >CY005100,A/mallard duck/Alberta/743/1983,1983/08/21,Canada,H9N1,6
1262  178 1410 2119 >DQ376690,A/duck/Taiwan/0526/72,1972//,Taiwan,H6N1,6
      180
----------------------segment 7-------------------------------------
 417   41  982 4902 >CY132002,A/mallard/Ohio/11OS2045/2011,2011/08/17,USA,mixed,7
 417   41  982 5905 >CY141133,A/red-necked grebe/Minnesota/AI10-2531/2010,2010/08/07,USA,mixed,7
 427   42  982 1079 >CY005331,A/shorebird/DE/236/2003,2003/05/30,USA,H11N9,7
 427   42  982 2341 >CY047561,A/mallard/Quebec/16566/2005,2005/08/21,Canada,H11N2,7
 427   42  982 3641 >CY097118,A/mallard/Ohio/2033/2009,2009/08/03,USA,H4N9,7
 427   42  982 3683 >CY097495,A/northern pintail/Wisconsin/2737/2009,2009/10/17,USA,H3N2,7
 427   42  982 3703 >CY097655,A/mallard/Ohio/2031/2009,2009/08/03,USA,H4N9,7
 427   42  982 4706 >CY127848,A/shorebird/Delaware Bay/230/2009,2009/05/20,USA,H6N1,7
 427   42  982 4712 >CY127896,A/shorebird/Delaware Bay/707/2009,2009/06/04,USA,H6N2,7
 427   42  982 4946 >CY132411,A/mallard/Ohio/11OS1982/2011,2011/08/08,USA,mixed,7
 427   42  982 5018 >CY133054,A/mallard/Wisconsin/10OS4194/2010,2010/11/30,USA,H11N9,7
 427   42  982 8430 >GQ923390,A/mallard/Louisiana/476670-4/2007,2007//,USA,H5N2,7
 427   42  982 8476 >GU050076,A/green winged teal/Delaware/468157-6/2006,2006//,USA,H5N2,7
 427   42  982 8996 >GU186447,A/ruddy turnstone/DE/85/2003,2003//,USA,H5N2,7
 437   43  982  959 >CY004508,A/mallard/ALB/201/1998,1998/08/11,Canada,H1N1,7
 437   43  982 10297 >A/duck/Manitoba_KF/1953(H10N7)
 437   43  982 1167 >CY011113,A/mallard/Maryland/881/2002,2002/08/29,USA,H6N2,7
 437   43  982 1375 >CY020774,A/mallard/Ohio/655/2002,2002/08/19,USA,H4N6,7
 437   43  982 2358 >CY047697,A/American black duck/New Brunswick/25182/2007,2007/09/21,Canada,H3N6,7
 437   43  982 2664 >CY053878,A/mallard/Maryland/802/2007,2007//,USA,H5N1,7
 437   43  982 2759 >CY064066,A/mallard/Minnesota/Sg-00055/2007,2007/08/02,USA,H12N5,7
 437   43  982 3338 >CY089516,A/mallard/Maryland/792/2007,2007//,USA,H5N9,7
 437   43  982 3657 >CY097286,A/mallard/Wisconsin/1538/2009,2009/08/18,USA,H4N6,7
       43
------------------segment 8----------------------

 393   33  838    2 >A/duck/Manitoba_KF/1953(H10N7)
 393   33  838  928 >CY004596,A/mallard/Alberta/127/1977,1977/08/22,Canada,H1N1,8
 393   33  838  943 >CY004815,A/mallard duck/Alberta/581/1983,1983/08/17,Canada,H4N4,8
 393   33  838 1108 >CY014905,A/mallard duck/New York/170/1982,1982/12/01,USA,H1N2,8
 393   33  838 3142 >CY117345,A/mallard/Alberta/720/1984,1984/08/09,Canada,H2N3,8
 405   34  838  920 >CY004470,A/mallard/Alberta/46/1977,1977/08/08,Canada,H1N1,8
 405   34  838  956 >CY004964,A/mallard duck/Alberta/291/1977,1977/08/28,Canada,H4N1,8
 405   34  838 1058 >CY005885,A/blue-winged teal/MN/993/1980,1980/09/04,USA,H6N6,8
 405   34  838 1894 >CY041843,A/turkey/Minnesota/1138/1980,1980//,USA,H7N3,8
 405   34  838 3100 >CY116839,A/mallard/New York/6750/1978,1978//,USA,H2N2,8
 405   34  838 6262 >EU871824,A/turkey/Ontario/84/1983,1983/01/,Canada,H5N1,8
 405   34  838 8330 >M25376,A/mallard/New York/6750/1978,1978//,USA,H2N2,8
       35



=======================================================================


what we got today


   0    0 2280    1 >A/Brevig Mission/1/1918(H1N1)
-----------------segment 1-------------------
 956  218 2280  261 >CY179554,Avian,1,H3N2,USA,1977,2316,A/mallard/Wisconsin/162/1977(H3N2))
 964  220 2280  393 >CY180619,Avian,1,H6N2,Canada,1981,2316,A/mallard/Saskatchewan/36/1981(H6N2))
 969  221 2280  280 >CY179706,Avian,1,H11N9,USA,1975,2316,A/mallard/Wisconsin/5/1975(H11N9))
 969  221 2280  488 >CY181384,Avian,1,H6N8,Canada,1981,2316,A/mallard/Saskatchewan/83/1981(H6N8))
 973  222 2280  262 >CY179562,Avian,1,H3N2,USA,1977,2316,A/mallard/Wisconsin/414/1977(H3N2))
 973  222 2280  297 >CY179850,Avian,1,H6N2,USA,1975,2316,A/green-winged teal/Alabama/563/1975(H6N2))
 973  222 2280  299 >CY179866,Avian,1,H12N5,USA,1975,2316,A/gadwall/Wisconsin/13/1975(H12N5))
 973  222 2280  402 >CY180691,Avian,1,H11N9,USA,1976,2316,A/mallard/Wisconsin/477/1976(H11N9))
 978  223 2280  260 >CY179546,Avian,1,H3N8,USA,1977,2316,A/mallard/Wisconsin/85/1977(H3N8))
---------------segment 2---------------------------------
 813  185 2274  413 >CY180762,Avian,2,H11N9,USA,1974,2293,A/duck/Minnesota/83/1974(H11N9))
 826  188 2274  301 >CY179865,Avian,2,H12N5,USA,1975,2293,A/gadwall/Wisconsin/13/1975(H12N5))
 835  190 2274  293 >CY179801,Avian,2,H6N2,USA,1975,2316,A/mallard/Wisconsin/331/1975(H6N2))
 839  191 2274   11 >CY177526,Avian,2,mixed,USA,1976,2316,A/mallard/Wisconsin/685/1976(mixed))
 844  192 2274  473 >CY181247,Avian,2,H4N6,USA,1974,2316,A/mallard/Wisconsin/14/1974(H4N6))
 861  196 2274  343 >CY180201,Avian,2,H3N8,USA,1976,2316,A/mallard/Wisconsin/383/1976(H3N8))
 861  196 2274  385 >CY180538,Avian,2,H5N2,USA,1976,2316,A/duck/Minnesota/63/1976(H5N2))
 870  198 2274   26 >CY177628,Avian,2,H6N8,USA,1974,2316,A/green-winged teal/Wisconsin/20/1974(H6N8))
 870  198 2274  291 >CY179777,Avian,2,H3N2,USA,1975,2316,A/mallard/Wisconsin/31/1975(H3N2))
 879  200 2274  490 >CY181391,Avian,2,H12N2,USA,1977,2316,A/mallard/Wisconsin/214/1977(H12N2))
 888  202 2274  450 >CY181059,Avian,2,H3N8,Canada,1982,2316,A/mallard/Saskatchewan/1/1982(H3N8))
 892  203 2274  453 >CY181083,Avian,2,H4N8,Canada,1982,2316,A/blue-winged teal/Saskatchewan/11/1982(H4N8))
 905  206 2274  156 >CY178669,Avian,2,H3N2,USA,1981,2316,A/blue-winged teal/Wisconsin/331/1981(H3N2))
 905  206 2274  194 >CY179000,Avian,2,H1N1,USA,1976,2316,A/blue-winged teal/Wisconsin/336/1976(H1N1))
 910  207 2274  187 >CY178941,Avian,2,H10N7,USA,1979,2316,A/mallard/Wisconsin/455/1979(H10N7))
 945  215 2274  162 >CY178741,Avian,2,H2N3,USA,1981,2316,A/mallard/Wisconsin/515/1981(H2N3))
-------------------segment 3---------------------
 781  168 2151  191 >CY178983,Avian,3,H3N2,USA,1976,2208,Influenza A virus (A/mallard/Wisconsin/82/1976(H3N2))
 790  170 2151  365 >CY180377,Avian,3,H4N2,USA,1976,2208,Influenza A virus (A/mallard/Wisconsin/209/1976(H4N2))
 790  170 2151  368 >CY180401,Avian,3,H4N2,USA,1976,2208,Influenza A virus (A/mallard/Wisconsin/251/1976(H4N2))
 790  170 2151  370 >CY180417,Avian,3,H4N2,USA,1976,2208,Influenza A virus (A/blue-winged teal/Wisconsin/345/1976(H4N2))
 794  171 2151  288 >CY179760,Avian,3,H4N6,USA,1975,2208,Influenza A virus (A/blue-winged teal/Wisconsin/278/1975(H4N6))
 794  171 2151  325 >CY180064,Avian,3,H11N9,USA,1976,2208,Influenza A virus (A/mallard/Wisconsin/789/1976(H11N9))
 799  172 2151  376 >CY180465,Avian,3,H4N6,USA,1974,2208,Influenza A virus (A/duck/Minnesota/104/1974(H4N6))
 799  172 2151  377 >CY180473,Avian,3,H4N6,USA,1974,2208,Influenza A virus (A/duck/Minnesota/110/1974(H4N6))
 804  173 2151  409 >CY180729,Avian,3,H3N8,USA,1974,2208,Influenza A virus (A/duck/Minnesota/53/1974(H3N8))
 804  173 2151  410 >CY180737,Avian,3,H3N8,USA,1974,2208,Influenza A virus (A/duck/Minnesota/54/1974(H3N8))
 804  173 2151  411 >CY180745,Avian,3,H3N8,USA,1974,2208,Influenza A virus (A/duck/Minnesota/56/1974(H3N8))
 808  174 2151   22 >CY177607,Avian,3,mixed,USA,1974,2208,Influenza A virus (A/blue-winged teal/Wisconsin/2/1974(mixed))
 808  174 2151  474 >CY181246,Avian,3,H4N6,USA,1974,2208,Influenza A virus (A/mallard/Wisconsin/14/1974(H4N6))
 813  175 2151    9 >CY177507,Avian,3,H11N2,USA,1975,2208,Influenza A virus (A/widgeon/Alabama/1278/1975(H11N2))
 813  175 2151   21 >CY177597,Avian,3,mixed,USA,1978,2208,Influenza A virus (A/duck/Wisconsin/1177/1978(mixed))
 813  175 2151  293 >CY179808,Avian,3,H6N2,USA,1975,2208,Influenza A virus (A/green-winged teal/Wisconsin/367/1975(H6N2))
 813  175 2151  465 >CY181174,Avian,3,mixed,USA,1978,2208,Influenza A virus (A/widgeon/Wisconsin/208/1978(mixed))
 813  175 2151  475 >CY181254,Avian,3,H6N8,USA,1974,2208,Influenza A virus (A/mallard/Wisconsin/13/1974(H6N8))
 813  175 2151  483 >CY181318,Avian,3,H6N8,USA,1978,2208,Influenza A virus (A/widgeon/Wisconsin/27/1978(H6N8))
 818  176 2151  262 >CY179552,Avian,3,H3N2,USA,1977,2208,Influenza A virus (A/mallard/Wisconsin/162/1977(H3N2))
 818  176 2151  340 >CY180184,Avian,3,H3N8,USA,1976,2208,Influenza A virus (A/mallard/Wisconsin/316/1976(H3N8))
 818  176 2151  341 >CY180192,Avian,3,H3N8,USA,1976,2208,Influenza A virus (A/mallard/Wisconsin/317/1976(H3N8))
 818  176 2151  464 >CY181165,Avian,3,H6N8,USA,1978,2208,Influenza A virus (A/widgeon/Wisconsin/86/1978(H6N8))
 818  176 2151  472 >CY181230,Avian,3,H6N2,USA,1974,2208,Influenza A virus (A/mallard/Wisconsin/15/1974(H6N2))
 818  176 2151  486 >CY181342,Avian,3,H9N1,USA,1974,2177,Influenza A virus (A/mallard/Wisconsin/24/1974(H9N1))
 822  177 2151   19 >CY177579,Avian,3,H3N2,USA,1975,2208,Influenza A virus (A/duck/Minnesota/36/1975(H3N2))
-------------------segment 4-------------------------
1546  263 1701   64 >CY181369,Avian,4,H1N1,USA,1983,1744,Influenza A virus (A/green-winged teal/Wisconsin/585/1983(H1N1))
1893  322 1701   36 >CY179395,Avian,4,H1N1,USA,1979,1752,Influenza A virus (A/widgeon/Wisconsin/505/1979(H1N1))
1904  324 1701   62 >CY180796,Avian,4,H1N1,USA,1976,1752,Influenza A virus (A/mallard/Wisconsin/683/1976(H1N1))
1904  324 1701   63 >CY180804,Avian,4,H1N1,USA,1976,1752,Influenza A virus (A/mallard/Wisconsin/795/1976(H1N1))
---------------------segment 5---------------------
1088  163 1497  356 >CY180311,Avian,5,H3N8,USA,1983,1540,Influenza A virus (A/mallard/Wisconsin/603/1983(H3N8))
1122  168 1497   23 >CY177615,Avian,5,mixed,USA,1978,1540,Influenza A virus (A/widgeon/Wisconsin/278/1978(mixed))
1122  168 1497  374 >CY180455,Avian,5,H4N2,USA,1979,1540,Influenza A virus (A/mallard/Wisconsin/637/1979(H4N2))
1122  168 1497  487 >CY181372,Avian,5,H1N1,USA,1983,1532,Influenza A virus (A/green-winged teal/Wisconsin/585/1983(H1N1))
1128  169 1497  141 >CY178562,Avian,5,H4N2,USA,1982,1540,Influenza A virus (A/blue-winged teal/Wisconsin/259/1982(H4N2))
----------------------segment 6------------------------
1241  175 1410   21 >CY180037,Avian,6,H1N1,USA,1979,1434,Influenza A virus (A/mallard/Wisconsin/654/1979(H1N1))
1241  175 1410   28 >CY180710,Avian,6,H9N1,USA,1979,1433,Influenza A virus (A/green-winged teal/Wisconsin/562/1979(H9N1))
1248  176 1410   12 >CY179013,Avian,6,H6N1,USA,1979,1433,Influenza A virus (A/mallard/Wisconsin/541/1979(H6N1))
1248  176 1410   18 >CY179941,Avian,6,H1N1,USA,1979,1434,Influenza A virus (A/mallard/Wisconsin/73/1979(H1N1))
1255  177 1410   40 >CY181339,Avian,6,H9N1,USA,1974,1433,Influenza A virus (A/mallard/Wisconsin/24/1974(H9N1))
1257  169 1344    6 >CY178529,Avian,6,H6N1,USA,1982,1379,Influenza A virus (A/blue-winged teal/Wisconsin/377/1982(H6N1))
1262  178 1410   10 >CY178971,Avian,6,mixedÞN1,USA,1976,1433,Influenza A virus (A/mallard/Wisconsin/81/1976(mixed))
-------------------------segment 7------------------------------
 468   46  982  229 >CY179284,Avian,7,H3N8,USA,1983,1002,Influenza A virus (A/mallard/Wisconsin/1636/1983(H3N8))
 478   47  982  453 >CY181086,Avian,7,H3N8,Canada,1982,1002,Influenza A virus (A/mallard/Saskatchewan/14/1982(H3N8))
 478   47  982  454 >CY181094,Avian,7,H3N8,Canada,1982,1002,Influenza A virus (A/widgeon/Saskatchewan/33/1982(H3N8))
 478   47  982  476 >CY181274,Avian,7,H11N9,USA,1978,1002,Influenza A virus (A/blue-winged teal/Wisconsin/151/1978(H11N9))
 488   48  982   67 >CY177967,Avian,7,H4N6,USA,1984,1002,Influenza A virus (A/mallard/Wisconsin/2106/1984(H4N6))
-------------------------segment 8--------------------------------
 381   32  838  367 >CY180416,Avian,8,H4N2,USA,1976,865,Influenza A virus (A/blue-winged teal/Wisconsin/345/1976(H4N2))
 393   33  838  111 >CY178330,Avian,8,H11N9,USA,1980,865,Influenza A virus (A/mallard/Wisconsin/261/1980(H11N9))
 393   33  838  286 >CY179759,Avian,8,H4N6,USA,1975,865,Influenza A virus (A/blue-winged teal/Wisconsin/278/1975(H4N6))
 393   33  838  379 >CY180512,Avian,8,H2N3,USA,1976,865,Influenza A virus (A/mallard/Wisconsin/793/1976(H2N3))
 393   33  838  380 >CY180520,Avian,8,H6N9,USA,1975,865,Influenza A virus (A/duck/Minnesota/1/1975(H6N9))
 393   33  838  393 >CY180624,Avian,8,H6N1,USA,1975,865,Influenza A virus (A/duck/Minnesota/2/1975(H6N1))
 393   33  838  395 >CY180640,Avian,8,H6N1,USA,1975,865,Influenza A virus (A/duck/Minnesota/56/1975(H6N1))
 405   34  838   41 >CY177770,Avian,8,H3N8,USA,1981,865,Influenza A virus (A/mallard/Wisconsin/415/1981(H3N8))

my list of closest avian neighbors to 1918-flu from Aug.2013:

        >A/Brevig Mission/1/1918(H1N1)
 929  212 2280 8696 >A/duck/Manitoba_KF/1953(H10N7)
 729  166 2274 8797 >A/duck/Manitoba_KF/1953(H10N7)
 776  167 2151  915 >CY004479,A/pintail duck/ALB/219/1977,1977/09/03,Canada,H1N1,3
1887  321 1701   37 >CY004592,A/mallard/Alberta/127/1977,1977/08/22,Canada,H1N1,4
1082  162 1497  324 >A/black duck/Ohio/95/1993,1993/10/15,USA,H1N1
1163  164 1410  369 >AJ416625,A/chicken/Scotland/1959,1959//,United Kingdom,H5N1,6
 417   41  982 4902 >CY132002,A/mallard/Ohio/11OS2045/2011,2011/08/17,USA,mixed,7
 393   33  838    2 >A/duck/Manitoba_KF/1953(H10N7)

 956  218 2280  261 >CY179554,H3N2,USA,1977,2316,A/mallard/Wisconsin/162/1977(H3N2)
 813  185 2274  413 >CY180762,H11N9,USA,1974,2293,A/Minnesota/83/1974(H11N9)
 781  168 2151  191 >CY178983,H3N2,USA,1976,2208,A/mallard/Wisconsin/82/1976(H3N2)
1546  263 1701   64 >CY181369,H1N1,USA,1983,1744,A/green-winged teal/Wisconsin/585/1983(H1N1)
1088  163 1497  356 >CY180311,H3N8,USA,1983,1540,A/mallard/Wisconsin/603/1983(H3N8)
1241  175 1410   21 >CY180037,H1N1,USA,1979,1434,A/mallard/Wisconsin/654/1979(H1N1)
 468   46  982  229 >CY179284,H3N8,USA,1983,1002,A/mallard/Wisconsin/1636/1983(H3N8)
 381   32  838  367 >CY180416,H4N2,USA,1976,865,A/blue-winged teal/Wisconsin/345/1976(H4N2)

I used to have a file named "7birds" containing avian genomes closely related to 1918-flu,
especially in segment 2, where just 7 avian, (not caught from humans or swine), sequences
were available from that 1918-like avian segment 2 substrain, which died in the 1980s
the 7 birds were:
>A/blue goose/WI/711/1975
>A/blue-winged teal/ALB/286/197/08/10/
>A/duck/Memphis/546/1974
>A/mallard duck/ALB/663/1979/08/13/
>A/pintail duck/ALB/628/1979/08/13
>A/turkey/Ontario/6118/1968///
>A/turkey/Ontario/7732/1966///

with the new update of old sequences from Wisconsin, that extinct substrain has now extended
to 55 birds (latest from 1983), forming 2 subsubstrains, 24 sequences of which are in the
more 1918flu-like subsubstrain (latest from 1982).
Apparently in the ~1960s the Eurasian segment 2 went into North America and slowly replaced
the American, 1918flu-like one. Since then there was almost no further mixing and the
North-American and Eurasian segment-2 strains evolved separated again.
see attached picture 55bird.gif

in the 70s it was discovered that flu-A comes from wild waterfowl. Then in 1976 the swine-flu ...
so presumably at that time they collected lots of bird-samples in USA,Canada - but sequencing
was expensive so they waited until now, presumably storing the samples in liquid nitrogene

gsgs · May 16, 2014

Re: Today at GenBank

May,13 : India,Bhutan,Mongolia
May,15: 15 Thailand Swine H1N1, 2009 -- no "smoking pigs" , afaics

May,16:
6471 sequences today !

3 penguin genomes :
distance to the index: 13,10,13,--,11,--,02,15

Code:

   0    0 2280    1 >KJ729356,A/Adelie penguin/Antarctica/184/2013(H11N2)
----------segment 1------------- 
 442  101 2280 2795 >A/mallard/WI/169/1975,1975//,H5N3
 657  150 2280 1164 >A/mallard duck/New York/90/1982,1982/12/01,H6N8
 657  150 2280 1181 >A/chicken/Pennsylvania/1370/1983,1983//,H5N2
----------segment 2------------- 
 996   75  753 8856 >A/semi-palmated sandpiper/New Jersey/237/1990,1990/05/26,H3N6
1474  182 1234 8812 >A/mallard/New Zealand/449-68/2004,2004//,H1N2
1509  218 1444 8871 >A/American black duck/New Brunswick/03532/2009,2009/09/10,H4N6
1525  347 2274    2 >A/Brevig Mission/1/1918(H1N1)
1539  350 2274 3443 >A/blue goose/WI/711/1975,1975//,H5N2
1556  354 2274  595 >A/blue-winged teal/ALB/286/1977,1977/08/10,H3N6
----------segment 3------------- 
 953  205 2151 1097 >A/chicken/Chile/184240-4322/2002,2002//,H7N3
 953  205 2151 7892 >A/chicken/Chile/184240-1/2002,2002//,H7N3
 962  207 2151  213 >A/chicken/Chile/4957/02,2002//,H7N3
 962  207 2151 1012 >A/cinnamon teal/Bolivia/4537/2001,2001//,H7N3
 962  207 2151 4289 >A/semipalmated sandpiper/Delaware/2144/2000,2000//,H11N6
 971  208 2142  214 >A/chicken/Chile/4322/02,2002//,H7N3
 971  209 2151  212 >A/chicken/Chile/176822/02,2002//,H7N3
1055  227 2151 6276 >A/rosy-billed pochard/Argentina/CIP051-269/2007,2007/05/13,H6N8
1073  231 2151 7155 >A/rosy-billed pochard/Argentina/CIP051-559/2007,2007//,H9N2
1075   63  586 2539 >A/kelp gull/Argentina/LDC4/2006,2006//,H13N9
1078  232 2151 5222 >A/rosy-billed pochard/Argentina/CIP051-557/2007,2007/05/,H6N2
1083  233 2151 5224 >A/rosy-billed pochard/Argentina/CIP051-925/2008,2008/02/,H6N2
1087  234 2151 5223 >A/rosy-billed pochard/Argentina/CIP051-575/2007,2007/05/,H6N8
1109  211 1901 3698 >A/red-winged tinamou/Argentina/MP1/2008,2008/04/,H1N1
1115  240 2151 6275 >A/rosy-billed pochard/Argentina/CIP051-1977/2010,2010/06/29,H6N2
1263  198 1567 8771 >A/mallard/New Zealand/1613-39/2004,2004//,H2N7
1306  281 2151 1058 >A/turkey/Massachusetts/3740/1965,1965//,H6N2
1306  281 2151 3873 >A/whiskered tern/Egypt/04/2004,2004/12/05,H6N2
1306  281 2151 8293 >A/turkey/Massachusetts/3740/1965,1965//,H6N2
1311  282 2151 5881 >A/turkey/Massachusetts/3740/1965,1965/06/11,H6N2
1311  282 2151 6206 >A/duck/Egypt/053/2005,2005/02/05,H6N2
1315  283 2151 4405 >A/chicken/Alabama/1975,1975//,H4N8
----------segment 4------------- 
2188  371 1695 4426 >A/ruddy turnstone/Delaware/2762/1987,1987/05/20,H11N2,USA
2525  427 1691 4790 >A/tern/Australia/752/1975,1975//,H11N9,Australia
2613  443 1695 4425 >A/ruddy turnstone/Delaware/2589/1987,1987/05/20,H11N1,USA
2625  445 1695 2193 >A/herring gull/Delaware Bay/2610/1987,1987/05/20,H11N1,USA
----------segment 5------------- 
 414   62 1497 2936 >A/turkey/CO/118899/1972,1972//,H5N2
 447   67 1497   13 >A/gull/Maryland/5/1977,1977//,H11N9
 460   69 1497  863 >A/gull/Maryland/19/1977,1977/04/04,H2N9
 460   69 1497 2844 >A/gull/Maryland/19/1977,1977//,H2N9
 460   69 1497 7356 >A/gull/Maryland/18/1977,1977/08/01,H2N9
 627   94 1497  706 >A/sanderling/New Jersey/766/1986,1986/05/12,H2N7
----------segment 6------------- 
 943  133 1410 10194 >A/turkey/Wisconsin/1/1966,1966//,H9N2
 950  134 1410 1196 >A/duck/Hong Kong/293/1978,1978//,H7N2
 950  134 1410 2400 >A/duck/Hong Kong/301/1978,1978//,H7N2
 950  134 1410 7488 >A/duck/Hokkaido/5/1977,1977//,H3N2
1000  141 1410  947 >A/mallard/ALB/250/1978,1978/08/07,H6N2
1000  141 1410  952 >A/pintail/ALB/367/1978,1978/08/10,H6N2
1000  141 1410 1136 >A/mallard/Alberta/354/1978,1978/08/10,H4N2
1000  141 1410 1531 >A/mallard/Alberta/205/1978,1978/08/10,H6N2
1000  141 1410 1541 >A/duck/Hong Kong/784/1979,1979/10/10,H9N2
1007  140 1389  795 >A/turkey/Wisconsin/1/1966,1966//,H9N2
----------segment 7------------- 
 121    1   82 5943 >A/northern waterthrush/Maine/CTR-AIV21/2006,2006/08/05,
 185    2  108 5931 >A/western wood-pewee/Washington/CTR-AIV09/2006,2006/07/26,
 305   30  981  502 >A/blue-winged teal/Alberta/96/76 ,1976//,H4N8
 305   30  981 1197 >A/mallard/ALB/210/1977,1977/08/30,H4N8
 316   31  981 1195 >A/redhead duck/ALB/74/1977,1977/08/08,H4N6
 326   32  981   48 >A/turkey/Oregon/71,1971//,H7N3
 326   32  981 1044 >A/mallard/ALB/25/1976,1976/08/11,H3N1
 326   32  981 1166 >A/mallard/ALB/676/1979,1979/08/13,H3N6
 326   32  981 1198 >A/mallard/ALB/161/1977,1977/09/03,H4N6
 326   32  981 8510 >A/turkey/Oregon/1971,1971/03/,H7N3
 336   33  981 1548 >A/turkey/Oregon/1971,1971//,H7N3
 336   33  981 3331 >A/duck/PA/486/1969,1969//,H6N1
 336   33  981 6712 >A/turkey/Oregon/1/1971,1971/06/11,mixed
 346   34  981 1074 >A/gadwall duck/Alberta/291/1977,1977/09/01,H7N3
 346   34  981 1219 >A/blue-winged teal/ALB/295/1977,1977/09/01,H7N3
 346   34  981 1220 >A/widgeon/Alberta/284/1977,1977/09/01,H7N3

3297 Human, 3013 Avian , 120 Swine

avian from 2012 , two "17g" - segments 5,6 Ohio,Illinois

lab-H7N9
lab-H1
Houston,H3N2,Jan,2013
Nicaragua,Georgia,Uganda,
5 Canada 70s-80s

Sweden mallards 2002-2009

ftp://ftp.ncbi.nih.gov/genomes/INFLUENZA/updates/2014-05-16/influenza_na.dat

genbank, 2014/05/17 , 112159 avian flu-A sequences meanwhile (lab-strains excluded)
12994,12942,12879,18731,12583,15184,13633,13213 from the 8 segments
time to update my files .... bitsb1,...,bitsb82 last update was Aug.2013,
bitx1...bitx82 with 10924,10825,10842,--,10577,--,11568,8820+2385..., sequences

gsgs · May 20, 2014

Re: Today at GenBank

wild chickens in Shanghai ?

Avian 3 H9N2 China 2014/03 2151
Influenza A virus (A/wild chicken/Shanghai/C1/2014(H9N2))
c
KJ726694 Avian 4 H9N2 China 2014/03 1683
Influenza A virus (A/wild chicken/Shanghai

KJ726724

ftp://ftp.ncbi.nih.gov/genomes/INFLUENZA/updates/2014-05-20/

no paper

http://www.ncbi.nlm.nih.gov/nuccore/KJ726724

Ge,F., Liu,J., Ju,H. and Yang,D.
TITLE Genotypic evolution and antigenic drift of H9N2 influenza viruses
in Shanghai of China
JOURNAL Unpublished

Submitted (20-APR-2014) Veterinary Disease Diagnostic Center,
Shanghai Animal Disease Control Center, No. 30 Lane 855 Hongjing
Road Changning Dc, Shanghai, Shanghai 201103, China

===================================
The Shanghai Shanghai Wild Wild chicken chicken farming Shanghai Wild chicken farming
techniques CCTV7 agricultural world of Genuine Wild chicken farming techniques VCD discs
and books(Chinese Edition)
NONG YE JIAO YU SHENG XIANG CHU BAN SHE
Verlag:
ISBN 10: 7887485614 / ISBN 13: 9787887485618
=============================================

gsgs · Jun 12, 2014

Re: Today at GenBank

human HAs from 2014 , USA,Japan,Korea

list: ftp://ftp.ncbi.nih.gov/genomes/INFLUENZA/updates/2014-06-12/influenza_na.dat
fasta: ftp://ftp.ncbi.nih.gov/genomes/INFLUENZA/updates/2014-06-12/influenza.fna

also on May,10:
ftp://ftp.ncbi.nih.gov/genomes/INFLUENZA/updates/2014-06-10/influenza_na.dat
Cuba July,2013
India

maybe I can analize it and add mutation tables here later

H1:

Code:

                                                                                  0000000000000000000000000000000000000000000111111111111111111111111111111111 
                                                                                  0000001112233333444445555556666677788899999000000111111112223333444455556666 
                                                                                  0135792686714589013563333790055723501902569114568024567793472238004624670125 
                                                                                  6607830857380770815952578945718868947801466271680155871310970736380076392063 
-codon-position------------------------------------------------------------------- 1      2   1        11 1  21 1     11     1       2  1   12 11 21 2 1 1 2   
---Index--------------------------------------------------------------------------GGTAGCTGGACGGAAGGAGTTCACAATGGTTGGTGGGAGCAACGGTTGGTGTGTGGTACACTCAGCCAAGGATTAT 
   1 >CY187663|A/Japan/3745/2014(H1N1)) hemagglutinin (HA) gene,                  ...T...T..T.A.......C..TCG.C..A.....AG...GAA.CC.....A.A.CG.....GAT...A..C..C       32     27 ,     32     27       1:>CY187663|A/Japan/3745/2014(H1N1)) hemagglutinin (HA) gene,                  
   2 >CY187727|A/Washington/3809/2014(H1N1)) hemagglutinin (HA) gene,             ...T...T..T.A.......C..TCG.T..A.....AG...GAA.CC.....A.A.CG.....GAT...A.....C       28     26 ,     28     26       2:>CY187727|A/Washington/3809/2014(H1N1)) hemagglutinin (HA) gene,             
   3 >CY187641|A/California/3723/2014(H1N1)) hemagglutinin (HA) gene,             ...T...T..T.A.......C..TCG.C..A.....AG...GAA.CC.....A.A.CG.....GAT...A.....C       28     26 ,     28     26       3:>CY187641|A/California/3723/2014(H1N1)) hemagglutinin (HA) gene,             
   4 >CY187640|A/Arizona/3722/2014(H1N1)) hemagglutinin (HA) gene,                ..........T.A.......C...CG.C..A.....AG...G...CC.....A.A..G.....GAT...A.....C       22     20 ,     22     20       4:>CY187640|A/Arizona/3722/2014(H1N1)) hemagglutinin (HA) gene,                
   5 >CY187710|A/Montana/3792/2014(H1N1)) hemagglutinin (HA) gene,                ..........T.A.......C...CG.C..A.....AG...G...CC....AA.A..G.....GAT...A.....C       21     21 ,     21     21       5:>CY187710|A/Montana/3792/2014(H1N1)) hemagglutinin (HA) gene,                
   6 >CY187658|A/Hawaii/3740/2014(H1N1)) hemagglutinin (HA) gene,                 ..........T.A.......C...CG.C..A.....AG...G...CC....AA.A..G.....GAT...A.....C       22     21 ,     22     21       6:>CY187658|A/Hawaii/3740/2014(H1N1)) hemagglutinin (HA) gene,                 
   7 >CY187636|A/Alabama/3718/2014(H1N1)) hemagglutinin (HA) gene,                ..........T.A.......C...CG.C..A.....AG...G...CC.....A.A..G.....GAT...A.....C       26     20 ,     26     20       7:>CY187636|A/Alabama/3718/2014(H1N1)) hemagglutinin (HA) gene,                
   8 >CY187672|A/Japan/3754/2014(H1N1)) hemagglutinin (HA) gene,                  ..C.......T.A.......C...CG.C..A.....AG...G..ACC.....A.AA.G...C.GAT...A.....C       26     24 ,     26     24       8:>CY187672|A/Japan/3754/2014(H1N1)) hemagglutinin (HA) gene,                  
   9 >CY187653|A/Guam/3735/2014(H1N1)) hemagglutinin (HA) gene,                   ..C.......T.A..A....C...CG.C..A.....AG...G..ACC.....A.AA.G...C.GAT...A.....C       25     25 ,     25     25       9:>CY187653|A/Guam/3735/2014(H1N1)) hemagglutinin (HA) gene,                   
  10 >CY187725|A/Utah/3807/2014(H1N1)) hemagglutinin (HA) gene,                   ..C.......T.A..A....C...CG.C..A.....AG...G..ACC.....A.AA.G...C.GAT...A.....C       28     25 ,     28     25      10:>CY187725|A/Utah/3807/2014(H1N1)) hemagglutinin (HA) gene,                   
  11 >CY187651|A/Guam/3733/2014(H1N1)) hemagglutinin (HA) gene,                   ..C.......T.A..A....C...CG.C..A.....AG...G..ACC.....A.AA.G...C.GAT...A.....C       25     25 ,     25     25      11:>CY187651|A/Guam/3733/2014(H1N1)) hemagglutinin (HA) gene,                   
  12 >CY187654|A/Guam/3736/2014(H1N1)) hemagglutinin (HA) gene,                   ..C.......T.A..A....C...CG.C..A.....AG...G..ACC.....A.AA.G...C.GAT...A.....C       27     25 ,     27     25      12:>CY187654|A/Guam/3736/2014(H1N1)) hemagglutinin (HA) gene,                   
  13 >CY187652|A/Guam/3734/2014(H1N1)) hemagglutinin (HA) gene,                   ..C.......T.A..A....C...CG.C..A.....AG...G..ACC.....A.AA.G...C.GAT...A.....C       25     25 ,     25     25      13:>CY187652|A/Guam/3734/2014(H1N1)) hemagglutinin (HA) gene,                   
  14 >CY187715|A/New York/3797/2014(H1N1)) hemagglutinin (HA) gene,               ..C.......T.A..A....C...CG.C.CA.....AG...G..ACC.....A.AA.GT..C.GAT...A.....C       27     27 ,     27     27      14:>CY187715|A/New York/3797/2014(H1N1)) hemagglutinin (HA) gene,               
  15 >CY187650|A/Georgia/3732/2014(H1N1)) hemagglutinin (HA) gene,                ..C.......T.A..A....C...CG.C.CA.....AG...G..ACC.....A.AA.GT..C.GAT...A.....C       28     27 ,     28     27      15:>CY187650|A/Georgia/3732/2014(H1N1)) hemagglutinin (HA) gene,                
  16 >CY187634|A/Alabama/3716/2014(H1N1)) hemagglutinin (HA) gene,                ..C.......T.A..A....C...CG.C.CA.....AG...G..ACC.....A.AA.GT..C.GAT...A.....C       28     27 ,     28     27      16:>CY187634|A/Alabama/3716/2014(H1N1)) hemagglutinin (HA) gene,                
  17 >CY187713|A/New York/3795/2014(H1N1)) hemagglutinin (HA) gene,               ..C.......T.A..A....C...CG.C.CA.....AG...G..ACC.....A.AA.GT..C.GAT...A.....C       27     27 ,     27     27      17:>CY187713|A/New York/3795/2014(H1N1)) hemagglutinin (HA) gene,               
  18 >CY187635|A/Alabama/3717/2014(H1N1)) hemagglutinin (HA) gene,                ..C.......T.A..A....C...CG.C.CA.....AG...G..ACC.....A.AA.GT..C.GAT...A.....C       28     27 ,     28     27      18:>CY187635|A/Alabama/3717/2014(H1N1)) hemagglutinin (HA) gene,                
  19 >CY187644|A/California/3726/2014(H1N1)) hemagglutinin (HA) gene,             ..C.......T.A..A....C...CG.C.CA.....AG.T.G..ACC.....A.AA.GT..C.GAT...A.....C       29     28 ,     29     28      19:>CY187644|A/California/3726/2014(H1N1)) hemagglutinin (HA) gene,             
  20 >CY187711|A/New Jersey/3793/2014(H1N1)) hemagglutinin (HA) gene,             ..C.......T.A..A....C...CG.C.CA.....AG...G..ACC.....A.AA.GT..C.GAT...A.....C       29     27 ,     29     27      20:>CY187711|A/New Jersey/3793/2014(H1N1)) hemagglutinin (HA) gene,             
  21 >CY187720|A/Ohio/3802/2014(H1N1)) hemagglutinin (HA) gene,                   ..C.......T.A..A....C...CG.C.CA.....AG...G..ACC.....A.AA.GT..C.GAT...A.....C       30     27 ,     30     27      21:>CY187720|A/Ohio/3802/2014(H1N1)) hemagglutinin (HA) gene,                   
  22 >CY187683|A/Japan/3765/2014(H1N1)) hemagglutinin (HA) gene,                  ..C.......T.AGGA....C...CG.C..A.....AG..GG..ACC.....A.AA.GT..C.GAT...A.....C       31     29 ,     31     29      22:>CY187683|A/Japan/3765/2014(H1N1)) hemagglutinin (HA) gene,                  
  23 >CY187666|A/Japan/3748/2014(H1N1)) hemagglutinin (HA) gene,                  ..C.......T.AGGA....C...CG.C..A.....AG..GG..ACC.....A.AA.GT..C.GAT...A.....C       29     29 ,     29     29      23:>CY187666|A/Japan/3748/2014(H1N1)) hemagglutinin (HA) gene,                  
  24 >CY187665|A/Japan/3747/2014(H1N1)) hemagglutinin (HA) gene,                  ..C.......T.AG.A....C...CG.C..A.....AG..GG..ACC.....A.AA.GT..C.GAT...A.....C       29     28 ,     29     28      24:>CY187665|A/Japan/3747/2014(H1N1)) hemagglutinin (HA) gene,                  
  25 >CY187684|A/Japan/3766/2014(H1N1)) hemagglutinin (HA) gene,                  ..C.......T.AG.A....C...CG.C..A....AAG..GG..ACC.....ACAA.GT..C.GAT...A.....C       30     30 ,     30     30      25:>CY187684|A/Japan/3766/2014(H1N1)) hemagglutinin (HA) gene,                  
  26 >CY187671|A/Japan/3753/2014(H1N1)) hemagglutinin (HA) gene,                  ..C.......T.AG.A....C...CG.C..A....AAG..GG..ACC.....ACAA.GT..C.GAT...A.....C       30     30 ,     30     30      26:>CY187671|A/Japan/3753/2014(H1N1)) hemagglutinin (HA) gene,                  
  27 >CY187664|A/Japan/3746/2014(H1N1)) hemagglutinin (HA) gene,                  ..C.......T.AG.A....C...CG.C..A.....AG..GG..ACC.....ACAA.GT..C.GAT...A.....C       29     29 ,     29     29      27:>CY187664|A/Japan/3746/2014(H1N1)) hemagglutinin (HA) gene,                  
  28 >CY187660|A/Hawaii/3742/2014(H1N1)) hemagglutinin (HA) gene,                 ..C.......T.AG.A....C...CG.C..A.....AG...G..ACC.....A.AA.GT..C.GAT...A.....C       29     27 ,     29     27      28:>CY187660|A/Hawaii/3742/2014(H1N1)) hemagglutinin (HA) gene,                 
  29 >CY187649|A/District of Columbia/3731/2014(H1N1)) hemagglutinin (HA) gene,   A.C.......T.A..A..A.C...CG.C..A...A.AG...G..ACC.....A.AA.GT..C.GAT.G.A.....C       30     30 ,     30     30      29:>CY187649|A/District of Columbia/3731/2014(H1N1)) hemagglutinin (HA) gene,   
  30 >CY187706|A/Maryland/3788/2014(H1N1)) hemagglutinin (HA) gene,               A.C.......T.A..A..A.C...CG.C..A...A.AG...G..ACC.....A.AA.GT..C.GAT.G.A.....C       30     30 ,     30     30      30:>CY187706|A/Maryland/3788/2014(H1N1)) hemagglutinin (HA) gene,               
  31 >CY187716|A/New York/3798/2014(H1N1)) hemagglutinin (HA) gene,               ..C.......T.A..A....C...CG.C..A.....AG...G..ACC.....A.AA.GT..C.GAT...AA....C       31     27 ,     31     27      31:>CY187716|A/New York/3798/2014(H1N1)) hemagglutinin (HA) gene,               
  32 >CY187659|A/Hawaii/3741/2014(H1N1)) hemagglutinin (HA) gene,                 ..........T.A.......CA..CGCC..A..C..AG...G...CC.....A.A...T....GAT..GAA....C       25     25 ,     25     25      32:>CY187659|A/Hawaii/3741/2014(H1N1)) hemagglutinin (HA) gene,                 
  33 >CY187722|A/Oklahoma/3804/2014(H1N1)) hemagglutinin (HA) gene,               ...G......T.A.......CA..CGCC..A..C..AG...G...CC.....A.A..G.....GAT..GAA....C       26     26 ,     26     26      33:>CY187722|A/Oklahoma/3804/2014(H1N1)) hemagglutinin (HA) gene,               
  34 >CY187661|A/Hawaii/3743/2014(H1N1)) hemagglutinin (HA) gene,                 ..........T.A.......C...CGCC..A..C..AG...G...CC.....A.A..G.....GAT..GAA....C       24     24 ,     24     24      34:>CY187661|A/Hawaii/3743/2014(H1N1)) hemagglutinin (HA) gene,                 
  35 >CY187673|A/Japan/3755/2014(H1N1)) hemagglutinin (HA) gene,                  ..........T.A.......C...CGCC..A..C..AG.T.G...CC.....A.A..G.....GAT..GAAG...C       26     26 ,     26     26      35:>CY187673|A/Japan/3755/2014(H1N1)) hemagglutinin (HA) gene,                  
  36 >CY187689|A/Korea/3771/2014(H1N1)) hemagglutinin (HA) gene,                  ..........T.A.......C...CGCC..A..C..AG.T.G...CC.....A.A..G.....GAT..GAAG...C       27     26 ,     27     26      36:>CY187689|A/Korea/3771/2014(H1N1)) hemagglutinin (HA) gene,                  
  37 >CY187668|A/Japan/3750/2014(H1N1)) hemagglutinin (HA) gene,                  ..........T.A.......C...CGCC..A..C..AG.T.G...CC.....A.A..G.....GAT..GAAG...C       26     26 ,     26     26      37:>CY187668|A/Japan/3750/2014(H1N1)) hemagglutinin (HA) gene,                  
  38 >CY187648|A/Delaware/3730/2014(H1N1)) hemagglutinin (HA) gene,               ..........T.A.......C...CGCC..A..C..AG...G...CC.....A.A..G.....GAT..GAAG...C       25     25 ,     25     25      38:>CY187648|A/Delaware/3730/2014(H1N1)) hemagglutinin (HA) gene,               
  39 >CY187714|A/New York/3796/2014(H1N1)) hemagglutinin (HA) gene,               ..........T.A.......C...CGCC..A..C..AG...G...CC.....A.A..G......AT..GAAG...C       26     24 ,     26     24      39:>CY187714|A/New York/3796/2014(H1N1)) hemagglutinin (HA) gene,               
  40 >CY187643|A/California/3725/2014(H1N1)) hemagglutinin (HA) gene,             .........GT.A.......C...CGCC..A..C..AG...G...CC.....A.A..G.....GAT...AA....C       28     24 ,     28     24      40:>CY187643|A/California/3725/2014(H1N1)) hemagglutinin (HA) gene,             
  41 >CY187662|A/Idaho/3744/2014(H1N1)) hemagglutinin (HA) gene,                  ..........T.A.......C...CGCC..A..C..AG...G...CC.....A.A..G.....GAT...AA....C       24     23 ,     24     23      41:>CY187662|A/Idaho/3744/2014(H1N1)) hemagglutinin (HA) gene,                  
  42 >CY187721|A/Ohio/3803/2014(H1N1)) hemagglutinin (HA) gene,                   ..........T.A.......C...CGCC..A.....AG...G...CC.....A.A..G....TGAT...A.....C       25     22 ,     25     22      42:>CY187721|A/Ohio/3803/2014(H1N1)) hemagglutinin (HA) gene,                   
  43 >CY187638|A/Alaska/3720/2014(H1N1)) hemagglutinin (HA) gene,                 ......C...T.A.......C.C.CGCCA.A.A...AG...G...CCA....A.A..G.G...GAT...A....GC       28     28 ,     28     28      43:>CY187638|A/Alaska/3720/2014(H1N1)) hemagglutinin (HA) gene,                 
  44 >CY187639|A/Alaska/3721/2014(H1N1)) hemagglutinin (HA) gene,                 ......C...T.A.......C.C.CGCCA.A.A...AG...G...CCA....A.A..G.G...GAT...A....GC       28     28 ,     28     28      44:>CY187639|A/Alaska/3721/2014(H1N1)) hemagglutinin (HA) gene,                 
  45 >CY187705|A/Louisiana/3787/2014(H1N1)) hemagglutinin (HA) gene,              ..........T.A.......C.C.CGCCA.A.....AG...G...CCA....A.A..G.....GAT...A.....C       26     24 ,     26     24      45:>CY187705|A/Louisiana/3787/2014(H1N1)) hemagglutinin (HA) gene,              
  46 >CY187686|A/Kansas/3768/2014(H1N1)) hemagglutinin (HA) gene,                 ..........T.A......CC.C.CGCCA.A.....AG...G...CCA....A.A..G.....GAT...A.....C       26     25 ,     26     25      46:>CY187686|A/Kansas/3768/2014(H1N1)) hemagglutinin (HA) gene,                 
  47 >CY187642|A/California/3724/2014(H1N1)) hemagglutinin (HA) gene,             ..........T.A.......C...CGCCA.A.....AG...G...CCA....A.A..G.....GAT...A.....C       25     23 ,     25     23      47:>CY187642|A/California/3724/2014(H1N1)) hemagglutinin (HA) gene,             
  48 >CY187646|A/Connecticut/3728/2014(H1N1)) hemagglutinin (HA) gene,            ..........T.A.......C...CGCC..A.....AG...G...CCA....A.A..G.....GAT...A.....C       23     22 ,     23     22      48:>CY187646|A/Connecticut/3728/2014(H1N1)) hemagglutinin (HA) gene,            
  49 >CY187726|A/Utah/3808/2014(H1N1)) hemagglutinin (HA) gene,                   ..........T.A.......C...CGCC..A.....AG...G...CCA....A.A..G.....GAT...A.....C       25     22 ,     25     22      49:>CY187726|A/Utah/3808/2014(H1N1)) hemagglutinin (HA) gene,                   
  50 >CY187670|A/Japan/3752/2014(H1N1)) hemagglutinin (HA) gene,                  ........A.T.A.......C...CGCC..AA....AG...G...CCAA...A.A..G.....GAT...A.....C       25     25 ,     25     25      50:>CY187670|A/Japan/3752/2014(H1N1)) hemagglutinin (HA) gene,                  
  51 >CY187718|A/North Carolina/3800/2014(H1N1)) hemagglutinin (HA) gene,         ........A.T.A.......C...CGCC..AA....AG...G...CCAA...A.A..G.....GAT...A.....C       25     25 ,     25     25      51:>CY187718|A/North Carolina/3800/2014(H1N1)) hemagglutinin (HA) gene,         
  52 >CY187677|A/Japan/3759/2014(H1N1)) hemagglutinin (HA) gene,                  ..........T.A.......C...CGCC..A.....AG...G...CCA....A.A..G.....GAT...A.....C       25     22 ,     25     22      52:>CY187677|A/Japan/3759/2014(H1N1)) hemagglutinin (HA) gene,                  
  53 >CY187717|A/New York/3799/2014(H1N1)) hemagglutinin (HA) gene,               ..........T.A.......C...CGCC..A.....AG...G...CCA....A.A..G.....GAT...A...C.C       25     23 ,     25     23      53:>CY187717|A/New York/3799/2014(H1N1)) hemagglutinin (HA) gene,               
  54 >CY187707|A/Massachusetts/3789/2014(H1N1)) hemagglutinin (HA) gene,          ....A.....T.A...A...C...CG.C..A.....AG...G...CC.....A.A.CG.....GAT...A...C.C       26     24 ,     26     24      54:>CY187707|A/Massachusetts/3789/2014(H1N1)) hemagglutinin (HA) gene,          
  55 >CY187708|A/Massachusetts/3790/2014(H1N1)) hemagglutinin (HA) gene,          ....A.....T.A...A...C...CG.C..A.....AG...G...CC.....A.A.CG.....GATA..A...C.C       26     25 ,     26     25      55:>CY187708|A/Massachusetts/3790/2014(H1N1)) hemagglutinin (HA) gene,          
  56 >CY187656|A/Guam/3738/2014(H1N1)) hemagglutinin (HA) gene,                   .A...T...GTAA....G..C...CG.C..A.....AGA..G...CC.A.A.A.A..G.....GATA..A.....C       29     29 ,     29     29      56:>CY187656|A/Guam/3738/2014(H1N1)) hemagglutinin (HA) gene,                   
  57 >CY187655|A/Guam/3737/2014(H1N1)) hemagglutinin (HA) gene,                   .A...T...GTAA....G..C...CG.C..A.....AGA..G...CC.A.A.A.A..G.....GATA..A.....C       30     29 ,     30     29      57:>CY187655|A/Guam/3737/2014(H1N1)) hemagglutinin (HA) gene,                   
  58 >CY187657|A/Guam/3739/2014(H1N1)) hemagglutinin (HA) gene,                   .A...T...GTAA....G..C...CG.C..A.....AGA..G...CC.A.A.A.A..G.....GATA..A.....C       29     29 ,     29     29      58:>CY187657|A/Guam/3739/2014(H1N1)) hemagglutinin (HA) gene,                   
  59 >CY187692|A/Korea/3774/2014(H1N1)) hemagglutinin (HA) gene,                  .....T....TAA....G.CC...CG.C..A.....AGA..G...CC.....A.A..G.....GATA..A..C..C       27     27 ,     27     27      59:>CY187692|A/Korea/3774/2014(H1N1)) hemagglutinin (HA) gene,                  
  60 >CY187687|A/Korea/3769/2014(H1N1)) hemagglutinin (HA) gene,                  .....T....TAA....G.CC...CG.C..A.....AGA..G...CC.....A.A..G.....GATA..A..C..C       28     27 ,     28     27      60:>CY187687|A/Korea/3769/2014(H1N1)) hemagglutinin (HA) gene,                  
  61 >CY187681|A/Japan/3763/2014(H1N1)) hemagglutinin (HA) gene,                  .....T....TAA....G..C...CG.C..A.....AGA..G...CC..C..A.A..G....TGAT...A.....C       26     26 ,     26     26      61:>CY187681|A/Japan/3763/2014(H1N1)) hemagglutinin (HA) gene,                  
  62 >CY187688|A/Korea/3770/2014(H1N1)) hemagglutinin (HA) gene,                  .....T....TAA....G..C...CG.C..A.....AGA..G...CC..C..A.A..G....TGAT...A.....C       26     26 ,     26     26      62:>CY187688|A/Korea/3770/2014(H1N1)) hemagglutinin (HA) gene,                  
  63 >CY187703|A/Korea/3785/2014(H1N1)) hemagglutinin (HA) gene,                  .....T....TAA....G..C...CG.C..A.....AGA..G...CC.....A.A..G.....GAT...A.....C       25     24 ,     25     24      63:>CY187703|A/Korea/3785/2014(H1N1)) hemagglutinin (HA) gene,                  
  64 >CY187669|A/Japan/3751/2014(H1N1)) hemagglutinin (HA) gene,                  .....T.....AA....G..C...CG.C..A.....AGA..G...C......A.A..G..T..GAT...A.....C       23     23 ,     23     23      64:>CY187669|A/Japan/3751/2014(H1N1)) hemagglutinin (HA) gene,                  
  65 >CY187667|A/Japan/3749/2014(H1N1)) hemagglutinin (HA) gene,                  .....T.....AA....G..C...CG.C..A.....AGA..G...C......A.A..G..T..GAT...A.....C       23     23 ,     23     23      65:>CY187667|A/Japan/3749/2014(H1N1)) hemagglutinin (HA) gene,                  
  66 >A/******/index/2009/02/01                                                   ............................................................................        0      0 ,      0      0      66:>A/******/index/2009/02/01                                                   
                                                                                                                                                               
---Index--------------------------------------------------------------------------GGTAGCTGGACGGAAGGAGTTCACAATGGTTGGTGGGAGCAACGGTTGGTGTGTGGTACACTCAGCCAAGGATTAT 
-codon-position------------------------------------------------------------------- 1      2   1        11 1  21 1     11     1       2  1   12 11 21 2 1 1 2   
                                                                                  0000000000000000000000000000000000000000000111111111111111111111111111111111 
                                                                                  0000001112233333444445555556666677788899999000000111111112223333444455556666 
                                                                                  0135792686714589013563333790055723501902569114568024567793472238004624670125 
                                                                                  6607830857380770815952578945718868947801466271680155871310970736380076392063

gsgs · Jun 14, 2014

Re: Today at GenBank

11 full genomes from Zhejiang:

KF042117 Avian 1 H9N9 China 2013/03 2280 A/chicken/Zhejiang/C11/2013(H9N9)
KF042111 Avian 1 H7N9 China 2013/04 2280 A/chicken/Zhejiang/C481/2013(H7N9)
KF042112 Avian 1 H7N9 China 2013/04 2280 A/chicken/Zhejiang/C483/2013(H7N9)
KF042113 Avian 1 H9N2 China 2013/04 2280 A/chicken/Zhejiang/C484/2013(H9N2)
KF042114 Avian 1 H9N2 China 2013/04 2280 A/chicken/Zhejiang/C487/2013(H9N2)
KF042115 Avian 1 H9N2 China 2013/04 2280 A/chicken/Zhejiang/C494/2013(H9N2)
KF042116 Avian 1 H9N2 China 2013/04 2280 A/chicken/Zhejiang/C497/2013(H9N2)
KF042073 Avian 1 H7N3 China 2013/03 2280 A/duck/Zhejiang/DK10/2013(H7N3)
KF042074 Avian 1 H7N3 China 2013/03 2280 A/duck/Zhejiang/DK16/2013(H7N3)
KF042109 Avian 1 H7N9 China 2013/04 2280 A/pigeon/Zhejiang/P1/2013(H7N9)
KF042110 Avian 1 H7N9 China 2013/04 2280 A/pigeon/Zhejiang/P2/2013(H7N9)

Code:

  1 >A/Index/H7N9-China/2013/03/,H7N9                              2280 2274 2151 1683 1497 1398  982  838   
  1:  0,  0,  0,  0,  0,  0,  0,  0   A/Index/H7N9-China/2013/03/,H7N9 
  2:  0,  0,  0,  0,  0,  0, 20,  0   A/Index_newMP/H7N9-China/2013/03/,H7N9 
  3:  1,---,  0,  0,  0,  1,  1,  1   A/environment/Guangdong/25/2013,2013/04/26,H7N9 
  4:---,---,---,  1,  3,  1,  1,  1   A/environment/Guangdong/30/2013,2013/04/26,H7N9 
  5: 37, 28,  3,  2, 33,  0,  0, 33   A/Huizhou/01/2013,2013/08/08,H7N9 
  6: 38, 27, 35,  1, 36,  3,  1, 35   A/Guangdong/02/2013,2013/11/04,H7N9 
  7:  0,  0,  0,  0,  0,  0,  0,  0   A/Index/H7N9-China/2013/03/,H7N9 
  8:  0,  0,  0,  0,  0,  0, 20,  0   A/Index_newMP/H7N9-China/2013/03/,H7N9 
  9:  0,  0,  0,  0,  0,  0,  0,  0   A/Index/H7N9-China/2013/01/31,H7N9,China,throat-swab,65m,E1 
 10: 14,  8, 17,  0, 12,  0, 13, 17   A/poultry/index/East-China/2010,2009//,H9N2 (+H7+N9) 
 11: 32, 29, 19,  1, 15,  3, 20,  0   A/chicken/Shanghai/S1358/2013,2013/04/03,China,H7N9 
 12: 32, 29, 19,  0,  2,  4, 20,  0   A/chicken/Jiangsu/SC099/2013,2013/04/16,China,H7N9 
 13:---,---,---,---,---,  0,---,---   A/Shanghai/4987T/2013,2013/04/17,China,H7N9 
 14: 12, 21, 13,  1, 23,  2, 16, 10   A/chicken/Shanghai/S1080/2013,2013/04/03,China,H7N9 
 15:---,---,---,---,---,  0,---,---   A/Shanghai/4778T/2013,2013/04/10,China,H7N9 
 16:  6,---,---,  1,---,  0,---,---   A/Hangzhou/2/2013,2013/04/01,China,H7N9 
 17:---,---,---,---,---,  0,---,---   A/chicken/Zhejiang/C11/2013,2013/03/,China,H9N9,6 
 18: 29,  0,  0,  1,  0,  1, 18,  0   A/chicken/Jiangsu/SC537/2013,2013/04/16,China,H7N9 
 19:---,---,---,  0,---,  1,---,---   A/Shanghai/4842T/2013,2013/04/13,China,H7N9 
 20: 21,---,---,  9,---,---,---,---   A/Shanghai/4659T/2013,2013/02/27,China,H7N9 
 21:---,---,---,---,---,  6,---,---   A/Shanghai/4798T/2013,2013/04/12,China,H7N9 
 22:---,---,---, 40,---,---,---,---   A/duck/Zhejiang/12/2011|2011/06/|China|H7N3|4 
 23:---,---,---,---,---, 12,---,---   A/chicken/Jiangsu/RD5/2013(H10N9) 
 24:---,---,---, 14,---,---,---,---   A/Shanghai/4655T/2013,2013/02/26,China,H7N9 
 25: 17,---,---, 14,---,---,---,---   A/Shanghai/4665T/2013,2013/03/05,China,H7N9 
 26:---,---,---,---,---,  4,---,---   A/Shanghai/4821T/2013,2013/04/12,China,H7N9 
 27:  0,  1,  8,  2,  0,  5,  2,  2   A/Shanghai/4664T/2013,2013/03/05,China,H7N9 
 28:  0,  0,  0,  0,  0,  2, 10,  0   A/chicken/Zhejiang/SD019/2013,2013/04/11,China,H7N9 
 29:  0,  0,  2,  0,  0,  4,  5,  0   A/environment/Shanghai/S1088/2013,2013/04/03,China,H7N9 
 30:  0,  0,  0,  0,  0,  4,  1,  0   A/chicken/Shanghai/S1055/2013,2013/04/03,China,H7N9 
 31:  0,  0,  0,  1,  0,  5,  1,  0   A/chicken/Shanghai/S1053/2013,2013/04/03,China,H7N9 
 32:  0,  0,  0,  0,  1,  2,  1,  0   A/pigeon/Shanghai/S1421/2013,2013/04/03,China,H7N9 
 33:  0,  0,  1,  0,  0,  2,  1,  0   A/chicken/Shanghai/S1413/2013,2013/04/03,China,H7N9 
 34:  0,  0,  0,  0,  0,  0,  0,  0   A/Anhui/1/2013,H7N9 
 35:  1,  0,  0,  0,  0,  1,  0,  0   A/Shanghai/02/2013,2013/03/05,China,H7N9 
 36:  1,  0,  0,  0,  0,  0,  0,  0   A/Shanghai/2/2013,H7N9 
 37:  2,  1,  0,  1,  0,  0,  0,  1   A/Hangzhou/1/2013,2013/03/24,China,H7N9 
 38:  2,  1,  0,  1,  0,  0,  0,  1   A/Hangzhao/1/2013,2013/03/24,H7N9,China,throat-swab,, 
 39:  0,  0,  0,  1,  0,  0,  0,  0   A/chicken/Shanghai/S1410/2013,2013/04/03,China,H7N9 
 40:  0,  0,  0,  2,  0,  0,  0,  1   A/wild pigeon/Jiangsu/SD001/2013,2013/04/17,China,H7N9 
 41:  0,  0,  0,  6,  0,  2,  1,  1   A/chicken/Zhejiang/DTID-ZJU01/2013,2013/04/,China,H7N9 
 42:  1,  0,  0,  1,  0,  0,  1,  0   A/chicken/Guangdong/SD641/2013,2013/05/03,China,H7N9 
 43:  1,  0,  0,  1,  1,  2,  0,  0   A/environment/Fujian/SC337/2013,2013/04/30,China,H7N9 
 44:  0,  0,  0,  2,  0,  0,  0,  3   A/chicken/Jiangsu/SC035/2013,2013/04/16,China,H7N9 
 45:  0,  0,  0,  0,  0,  0,  0,  1   A/duck/Anhui/SC702/2013,2013/04/16,China,H7N9 
 46:  5,  3,  0,  0,  2,  0,  0,  1   A/Fujian/1/2013,2013/04/24,China,H7N9 
 47:---,---,---,  1,---,  0,  2,---   A/Jiangsu/1/2013/03/30,H7N9,China,,45f,E1 
 48:  0,  0, 16,  0,  0,  0,  0,  0   A/chicken/Zhejiang/SD033/2013,2013/04/11,China,H7N9 
 49:  0,  0, 16,  0,  0,  2,  1,  1   A/Zhejiang/DTID-ZJU01/2013,2013//,H7N9 
 50:---,---,---,---,---,  0,---,---   A/Shanghai/5058T/2013,2013/04/19,China,H7N9 
 51: 18, 31,  0,  1, 11,  0,  1,  1   A/chicken/Jiangxi/SD001/2013,2013/05/03,China,H7N9 
 52:---,---,---,---,---,  0,---,---   A/Shanghai/4862T/2013,2013/04/14,China,H7N9 
 53:  0, 14, 17,  0, 12,  5, 23, 15   A/chicken/Zhejiang/SD007/2013,2013/04/22,China,H7N9 
 54:---,---,---,  0,---,  0,---,---   A/Shanghai/4701T/2013,2013/04/06,China,H7N9 
 55:---,---,---,---,---,  0,---,---   A/Shanghai/4774T/2013,2013/04/10,China,H7N9 
 56:  0,  4,  1,  1,  2,  0, 20,  2   A/environment/Nanjing/2913/2013,2013/03/29,China,H7N9 
 57:  0,  4,  1,  1,  2,  0, 20,  2   A/environment-poultry_cage/Nanjing/2913/2013/03/29,H7N9 
 58:  2,---,---,  2,---,  5,---,---   A/Hangzhou/3/2013,2013/04/08,China,H7N9 
 59:  2,---,---,  2,  2,  5,---,  4   A/Hangzhou/3/2013/04/02,H7N9,m79 
 60:  2,  0, 16,  2,  2,  4, 21,  4   A/Zhejiang/HZ1/2013/4/,H7N9 
 61:---,---,---,---,---,  0,---,---   A/Shanghai/4819T/2013,2013/04/12,China,H7N9 
 62:  2,  7,  0,  1, 10,  4, 20,  1   A/Nanjing/1/throat_swab/2013/03/28,H7N9 
 63:---,---,---,---,---,  0,---,---   A/Shanghai/4700/2013,2013/04/05,China,H7N9 
 64:  9,  0, 14,  1, 23,  0, 20, 20   A/environment/Shanghai/S1438/2013,2013/04/03,China,H7N9 
 65:  2,  0, 14,  1, 22,  0, 19,  9   A/environment/Shanghai/S1436/2013,2013/04/03,China,H7N9 
 66:---,---,---,  1,---,  1,---,---   A/Shanghai/5083T/2013,2013/04/20,China,H7N9 
 67: 10, 28, 13,  1,  1,  0, 19, 23   A/environment/Shanghai/S1437/2013,2013/04/03,China,H7N9 
 68:---,---,---,  1,---,  1,---,---   A/Shanghai/5240T/2013,2013/04/25,China,H7N9 
 69: 13,  1,  7,  1, 22,  0, 17,  1   A/environment/Shanghai/S1439/2013,2013/04/03,China,H7N9 
 70:---,---,---,  1,---,  1,---,---   A/Shanghai/5180T/2013,2013/04/23,China,H7N9 
 71:  1,  1,  1,  1,  2,  1, 22,  0   A/Taiwan/T02081/2013,2013/04/22,Taiwan,H7N9 
 72:  2,  1,  3,  1,  0,  1, 22,  0   A/Taiwan/S02076/2013,2013/04/22,Taiwan,H7N9 
 73:  0,  0,  1,  2,  0,  0, 21,  0   A/homing pigeon/Jiangsu/SD184/2013,2013/04/20,China,H7N9 
 74:  0,  0,  0,  1,  0,  0, 21,  0   A/pigeon/Shanghai/S1423/2013,2013/04/03,China,H7N9 
 75:  0,  0,  0,  1,  0,  4, 20,  0   A/chicken/Jiangsu/S002/2013,2013/04/16,China,H7N9 
 76:  0,---,---,  0,---,  0,---,---   A/environment/Hangzhou/34/2013,2013/04/04,China,H7N9 
 77:  0, 21, 16,  0,  0,  2,  1,  0   A/duck/Zhejiang/SC410/2013,2013/04/16,China,H7N9 
 78:  1, 32,  0,  0, 11,  0,  2,  1   A/environment/Shandong/SD049/2013,2013/05/03,China,H7N9 
 79:  1, 31,  0,  0, 11,  0,  2,  1   A/environment/Shandong/SD039/2013,2013/05/03,China,H7N9 
 80:  0, 31,  0,  1, 11,  0,  1,  0   A/pigeon/Shanghai/S1069/2013,2013/04/02,China,H7N9 
 81:  0, 31,  0,  1, 11,  0,  1,  0   A/chicken/Shanghai/S1076/2013,2013/04/03,China,H7N9 
 82:  0, 31,  0,  1, 11,  0,  2,  0   A/chicken/Shanghai/S1079/2013,2013/04/03,China,H7N9 
 83:  0, 31,  0,  1, 11,  0,  1,  0   A/chicken/Shanghai/S1078/2013,2013/04/03,China,H7N9 
 84:  1, 31,  0,  1, 12,  0,  1,  0   A/chicken/Shanghai/S1077/2013,2013/04/03,China,H7N9 
 85:  0, 30,  0,  2, 13,  0,  2,  0   A/environment/Henan/SD429/2013,2013/04/24,China,H7N9 
 86:  0, 31,  0,  1, 11,  1,  2,  0   A/environment/Henan/SC232/2013,2013/04/24,China,H7N9 
 87:  0,---,  0,  0, 11,---,  1,  0   A/Nanchang/1/2013,2013/04/24,China,H7N9 
 88:  1, 32,  0,  1, 11,  2,  1,  0   A/environment/Shandong/SD038/2013,2013/05/03,China,H7N9 
 89:  3,  5,  1,  7, 23,  5,  1,  2   A/Shanghai/1/2013,H7N9 
 90:  1,  0,  0,  1,  0,  0,  1,  2   A/Wuxi/2/2013,2013/03/31,H7N9 
 91:  0,  0,  0,  0,  0,  2,  0,  1   A/Wuxi/1/2013,2013/04/02,H7N9 
 92:  2,  5,  1,  2,  2,  5, 20,  3   A/environment/Wuxi/1/2013,2013/04/02,H7N9 
 93: 29, 23, 39, 30, 26,---, 27, 32   A/Chicken/Wenzhou/89/2013,2013//,H7N7 
 94: 40, 20, 33,  2, 26,  2,  0, 36   A/Hong Kong/470129/2013,2013/11/11,H7N9 
 95:  0,  0,  0,  0,  0,  0,  0,  0   A/Index/H7N9-China/2013/03/,H7N9 
 96:  0,  0,  0,  0,  0,  0, 20,  0   A/Index_newMP/H7N9-China/2013/03/,H7N9 
 97: 14,  8, 17,  0, 12,  0, 13, 17   A/poultry/index/East-China/2010,2009//,H9N2 (+H7+N9) 
 98:  8,  4,  3,  2,  1,  5,  1,  4   A/Zhejiang/DTID-ZJU10/2013,2013/10/14,China,H7N9 
 99:  8,---,---,---,---,---,---,---   A/Zhejiang/DTID-ZJU10-b/2013,2013/10/14,China,H7N9 
100:---,---,---,  3,---,---,---,---   A/environment/Shenzhen/1/2013,2013/10/,China,H7N9 
101:  1,  0,  0,  1,  1,  2, 21,  0   KF997838,A/Shanghai/5190T/2013,2013/05/,H7N9 
102:---,---,  0,  2,  1,  2, 24,  0   KF997840,A/Shanghai/5190T-clone2/2013,2013/05/,H7N9 
103: 37, 27,  3,  2, 34,  0,  0, 32   KF662944,A/Guangdong/1/2013,2013/08/10,China,H7N9 
104: 37, 28,  3,  2, 33,  0,  0, 33   A/Huizhou/01/2013,2013/08/08,China,H7N9 
105: 38, 27, 35,  1, 36,  3,  1, 35   A/Guangdong/02/2013,2013/11/,China,H7N9 
106:---,---,---,  4, 39,  0,  5, 39   KJ023067,A/Guangdong/03/2013,2013/12/15,H7N9 
107:---, 27, 37,  2, 36,  4,  0, 36   KJ023072,A/Guangdong/04/2013,2013/12/16,H7N9 
108: 41, 29, 37,  2, 37,  3,  1, 36   KJ023079,A/Guangdong/05/2013,2013/12/17,H7N9 
109: 32, 31, 21,---, 12,---, 25, 47   KJ128369,A/pigeon/Shanghai/JC1/2013,2013/04/,H9N2 
110: 40, 20, 33,  2, 26,  2,  0, 36   A/Hong Kong/470129/2013,2013/11/11,H7N9 
111: 14, 12, 19,452, 13,---, 23,  3   A/chicken/Zhejiang/C11/2013,2013/03/,China,H9N9Avian 
112:  0,  0,  0,  1,  0,  0,  1,  1   A/chicken/Zhejiang/C481/2013,2013/04/,China,H7N9Avian 
113:  0,  2,  0,  1,  3,  0, 21,  1   A/chicken/Zhejiang/C483/2013,2013/04/,China,H7N9Avian 
114:  7, 18, 16,454, 38,466, 22, 14   A/chicken/Zhejiang/C484/2013,2013/04/,China,H9N2Avian 
115:  7, 18, 18,452,  0,466, 23, 45   A/chicken/Zhejiang/C487/2013,2013/04/,China,H9N2Avian 
116: 14, 12, 18,454, 13,466, 23, 46   A/chicken/Zhejiang/C494/2013,2013/04/,China,H9N2Avian 
117:  0, 31, 18,452,  0,466, 23, 45   A/chicken/Zhejiang/C497/2013,2013/04/,China,H9N2Avian 
118: 78,104,115,459, 96,497,109,112   A/duck/Zhejiang/6D18/2013,2013/12/14,China,H5N8Avian 
119:143,106, 70,---,122,455, 92,101   A/duck/Zhejiang/DK10/2013,2013/03/,China,H7N3Avian 
120:132,106, 70,---,122,457, 92,102   A/duck/Zhejiang/DK16/2013,2013/03/,China,H7N3Avian 
121: 77,103,113,460, 98,496,108,110   A/duck/Zhejiang/W24/2013,2013/11/14,China,H5N8Avian 
122: 13, 12, 18,  0, 24,  1, 23, 45   A/pigeon/Zhejiang/P1/2013,2013/04/,China,H7N9Avian 
123: 34, 28, 17,  2, 24,  1, 23, 42   A/pigeon/Zhejiang/P2/2013,2013/04/,China,H7N9Avian 

  2 >A/Index_newMP/H7N9-China/2013/03/,H7N9                        2280 2274 2151 1683 1497 1398  982  838   
111: 14, 12, 19,452, 13,---,  4,  3   A/chicken/Zhejiang/C11/2013,2013/03/,China,H9N9Avian 
112:  0,  0,  0,  1,  0,  0, 21,  1   A/chicken/Zhejiang/C481/2013,2013/04/,China,H7N9Avian 
113:  0,  2,  0,  1,  3,  0,  3,  1   A/chicken/Zhejiang/C483/2013,2013/04/,China,H7N9Avian 
114:  7, 18, 16,454, 38,466,  4, 14   A/chicken/Zhejiang/C484/2013,2013/04/,China,H9N2Avian 
115:  7, 18, 18,452,  0,466, 17, 45   A/chicken/Zhejiang/C487/2013,2013/04/,China,H9N2Avian 
116: 14, 12, 18,454, 13,466,  4, 46   A/chicken/Zhejiang/C494/2013,2013/04/,China,H9N2Avian 
117:  0, 31, 18,452,  0,466,  4, 45   A/chicken/Zhejiang/C497/2013,2013/04/,China,H9N2Avian 
118: 78,104,115,459, 96,497,109,112   A/duck/Zhejiang/6D18/2013,2013/12/14,China,H5N8Avian 
119:143,106, 70,---,122,455, 93,101   A/duck/Zhejiang/DK10/2013,2013/03/,China,H7N3Avian 
120:132,106, 70,---,122,457, 93,102   A/duck/Zhejiang/DK16/2013,2013/03/,China,H7N3Avian 
121: 77,103,113,460, 98,496,108,110   A/duck/Zhejiang/W24/2013,2013/11/14,China,H5N8Avian 
122: 13, 12, 18,  0, 24,  1,  4, 45   A/pigeon/Zhejiang/P1/2013,2013/04/,China,H7N9Avian 
123: 34, 28, 17,  2, 24,  1,  4, 42   A/pigeon/Zhejiang/P2/2013,2013/04/,China,H7N9Avian

Code:

  1 >A/Index/H7N9-China/2013/03/,H7N9                              2280 2274 2151 1683 1497 1398  982  838   
  1:  0,  0,  0,  0,  0,  0,  0,  0   A/Index/H7N9-China/2013/03/,H7N9 
 10: 14,  8, 17,  0, 12,  0, 13, 17   A/poultry/index/East-China/2010,2009//,H9N2 (+H7+N9) 
 89:  3,  5,  1,  7, 23,  5,  1,  2   A/Shanghai/1/2013,H7N9 
 98:  8,  4,  3,  2,  1,  5,  1,  4   A/Zhejiang/DTID-ZJU10/2013,2013/10/14,China,H7N9 
108: 41, 29, 37,  2, 37,  3,  1, 36   KJ023079,A/Guangdong/05/2013,2013/12/17,H7N9 
110: 40, 20, 33,  2, 26,  2,  0, 36   A/Hong Kong/470129/2013,2013/11/11,H7N9 
111: 14, 12, 19,452, 13,---, 23,  3   A/chicken/Zhejiang/C11/2013,2013/03/,China,H9N9Avian 
112:  0,  0,  0,  1,  0,  0,  1,  1   A/chicken/Zhejiang/C481/2013,2013/04/,China,H7N9Avian 
113:  0,  2,  0,  1,  3,  0, 21,  1   A/chicken/Zhejiang/C483/2013,2013/04/,China,H7N9Avian 
114:  7, 18, 16,454, 38,466, 22, 14   A/chicken/Zhejiang/C484/2013,2013/04/,China,H9N2Avian 
115:  7, 18, 18,452,  0,466, 23, 45   A/chicken/Zhejiang/C487/2013,2013/04/,China,H9N2Avian 
116: 14, 12, 18,454, 13,466, 23, 46   A/chicken/Zhejiang/C494/2013,2013/04/,China,H9N2Avian 
117:  0, 31, 18,452,  0,466, 23, 45   A/chicken/Zhejiang/C497/2013,2013/04/,China,H9N2Avian 
118: 78,104,115,459, 96,497,109,112   A/duck/Zhejiang/6D18/2013,2013/12/14,China,H5N8Avian 
119:143,106, 70,---,122,455, 92,101   A/duck/Zhejiang/DK10/2013,2013/03/,China,H7N3Avian 
120:132,106, 70,---,122,457, 92,102   A/duck/Zhejiang/DK16/2013,2013/03/,China,H7N3Avian 
121: 77,103,113,460, 98,496,108,110   A/duck/Zhejiang/W24/2013,2013/11/14,China,H5N8Avian 
122: 13, 12, 18,  0, 24,  1, 23, 45   A/pigeon/Zhejiang/P1/2013,2013/04/,China,H7N9Avian 
123: 34, 28, 17,  2, 24,  1, 23, 42   A/pigeon/Zhejiang/P2/2013,2013/04/,China,H7N9Avian 

  2 >A/Index_newMP/H7N9-China/2013/03/,H7N9                        2280 2274 2151 1683 1497 1398  982  838   
  1:  0,  0,  0,  0,  0,  0, 20,  0   A/Index/H7N9-China/2013/03/,H7N9 
  2:  0,  0,  0,  0,  0,  0,  0,  0   A/Index_newMP/H7N9-China/2013/03/,H7N9 
 10: 14,  8, 17,  0, 12,  0,  8, 17   A/poultry/index/East-China/2010,2009//,H9N2 (+H7+N9) 
 89:  3,  5,  1,  7, 23,  5, 20,  2   A/Shanghai/1/2013,H7N9 
 98:  8,  4,  3,  2,  1,  5, 21,  4   A/Zhejiang/DTID-ZJU10/2013,2013/10/14,China,H7N9 
108: 41, 29, 37,  2, 37,  3, 21, 36   KJ023079,A/Guangdong/05/2013,2013/12/17,H7N9 
110: 40, 20, 33,  2, 26,  2, 20, 36   A/Hong Kong/470129/2013,2013/11/11,H7N9 
111: 14, 12, 19,452, 13,---,  4,  3   A/chicken/Zhejiang/C11/2013,2013/03/,China,H9N9Avian 
112:  0,  0,  0,  1,  0,  0, 21,  1   A/chicken/Zhejiang/C481/2013,2013/04/,China,H7N9Avian 
113:  0,  2,  0,  1,  3,  0,  3,  1   A/chicken/Zhejiang/C483/2013,2013/04/,China,H7N9Avian 
114:  7, 18, 16,454, 38,466,  4, 14   A/chicken/Zhejiang/C484/2013,2013/04/,China,H9N2Avian 
115:  7, 18, 18,452,  0,466, 17, 45   A/chicken/Zhejiang/C487/2013,2013/04/,China,H9N2Avian 
116: 14, 12, 18,454, 13,466,  4, 46   A/chicken/Zhejiang/C494/2013,2013/04/,China,H9N2Avian 
117:  0, 31, 18,452,  0,466,  4, 45   A/chicken/Zhejiang/C497/2013,2013/04/,China,H9N2Avian 
118: 78,104,115,459, 96,497,109,112   A/duck/Zhejiang/6D18/2013,2013/12/14,China,H5N8Avian 
119:143,106, 70,---,122,455, 93,101   A/duck/Zhejiang/DK10/2013,2013/03/,China,H7N3Avian 
120:132,106, 70,---,122,457, 93,102   A/duck/Zhejiang/DK16/2013,2013/03/,China,H7N3Avian 
121: 77,103,113,460, 98,496,108,110   A/duck/Zhejiang/W24/2013,2013/11/14,China,H5N8Avian 
122: 13, 12, 18,  0, 24,  1,  4, 45   A/pigeon/Zhejiang/P1/2013,2013/04/,China,H7N9Avian 
123: 34, 28, 17,  2, 24,  1,  4, 42   A/pigeon/Zhejiang/P2/2013,2013/04/,China,H7N9Avian 

 10 >A/poultry/index/East-China/2010,2009//,H9N2 (+H7+N9)          2280 2274 2151 1683 1497 1398  982  838   
 89: 15, 11, 16,  7, 14,  5, 12, 17   A/Shanghai/1/2013,H7N9 
 98: 15, 11, 20,  2, 13,  5, 14, 22   A/Zhejiang/DTID-ZJU10/2013,2013/10/14,China,H7N9 
108: 28, 22, 22,  2, 29,  3, 14, 32   KJ023079,A/Guangdong/05/2013,2013/12/17,H7N9 
109: 21, 24, 18,---,  9,---, 12, 38   KJ128369,A/pigeon/Shanghai/JC1/2013,2013/04/,H9N2 
110: 28, 13, 18,  2, 21,  2, 13, 31   A/Hong Kong/470129/2013,2013/11/11,H7N9 
111: 17, 10, 15,452, 12,---, 10, 21   A/chicken/Zhejiang/C11/2013,2013/03/,China,H9N9Avian 
112: 15,  8, 17,  1, 12,  0, 14, 19   A/chicken/Zhejiang/C481/2013,2013/04/,China,H7N9Avian 
113: 15,  7, 17,  1, 14,  0,  9, 19   A/chicken/Zhejiang/C483/2013,2013/04/,China,H7N9Avian 
114: 14, 14, 16,454, 36,466, 10, 17   A/chicken/Zhejiang/C484/2013,2013/04/,China,H9N2Avian 
115: 14, 14, 13,452, 12,466, 10, 35   A/chicken/Zhejiang/C487/2013,2013/04/,China,H9N2Avian 
116: 17, 10, 13,454, 12,466, 10, 39   A/chicken/Zhejiang/C494/2013,2013/04/,China,H9N2Avian 
117: 15, 23, 13,452, 12,466, 10, 35   A/chicken/Zhejiang/C497/2013,2013/04/,China,H9N2Avian 
118: 71,100,106,459, 92,497,105,103   A/duck/Zhejiang/6D18/2013,2013/12/14,China,H5N8Avian 
119:138,100, 59,---,124,455, 87, 95   A/duck/Zhejiang/DK10/2013,2013/03/,China,H7N3Avian 
120:128,100, 59,---,124,457, 87, 96   A/duck/Zhejiang/DK16/2013,2013/03/,China,H7N3Avian 
121: 71, 99,105,460, 94,496,104,102   A/duck/Zhejiang/W24/2013,2013/11/14,China,H5N8Avian 
122: 17, 10, 13,  0, 16,  1, 10, 38   A/pigeon/Zhejiang/P1/2013,2013/04/,China,H7N9Avian 
123: 22, 21, 16,  2, 16,  1, 10, 33   A/pigeon/Zhejiang/P2/2013,2013/04/,China,H7N9Avian 

 89 >A/Shanghai/1/2013,H7N9                                        2280 2274 2151 1683 1497 1398  982  838   
  1:  3,  5,  1,  7, 23,  5,  1,  2   A/Index/H7N9-China/2013/03/,H7N9 
 10: 15, 11, 16,  7, 14,  5, 12, 17   A/poultry/index/East-China/2010,2009//,H9N2 (+H7+N9) 
 98:  9,  9,  5,  9, 24, 11,  2,  7   A/Zhejiang/DTID-ZJU10/2013,2013/10/14,China,H7N9 
108: 41, 31, 36,  9, 38,  9,  2, 39   KJ023079,A/Guangdong/05/2013,2013/12/17,H7N9 
109: 32, 34, 21,---, 22,---, 24, 50   KJ128369,A/pigeon/Shanghai/JC1/2013,2013/04/,H9N2 
110: 40, 23, 32, 10, 31,  8,  1, 38   A/Hong Kong/470129/2013,2013/11/11,H7N9 
111: 14, 15, 19,455, 22,---, 22,  5   A/chicken/Zhejiang/C11/2013,2013/03/,China,H9N9Avian 
112:  4,  6,  1,  7, 23,  5,  2,  3   A/chicken/Zhejiang/C481/2013,2013/04/,China,H7N9Avian 
113:  3,  7,  1,  7, 25,  6, 20,  3   A/chicken/Zhejiang/C483/2013,2013/04/,China,H7N9Avian 
114:  7, 21, 16,456, 42,469, 21, 14   A/chicken/Zhejiang/C484/2013,2013/04/,China,H9N2Avian 
115:  7, 21, 18,457, 23,468, 22, 47   A/chicken/Zhejiang/C487/2013,2013/04/,China,H9N2Avian 
116: 14, 15, 18,456, 22,469, 22, 48   A/chicken/Zhejiang/C494/2013,2013/04/,China,H9N2Avian 
117:  4, 33, 17,457, 23,468, 22, 47   A/chicken/Zhejiang/C497/2013,2013/04/,China,H9N2Avian 
118: 78,103,115,463, 97,496,108,114   A/duck/Zhejiang/6D18/2013,2013/12/14,China,H5N8Avian 
119:143,106, 69,---,122,457, 91,103   A/duck/Zhejiang/DK10/2013,2013/03/,China,H7N3Avian 
120:132,106, 69,---,122,459, 91,104   A/duck/Zhejiang/DK16/2013,2013/03/,China,H7N3Avian 
121: 77,102,113,463,100,494,107,113   A/duck/Zhejiang/W24/2013,2013/11/14,China,H5N8Avian 
122: 14, 15, 18,  7, 28,  7, 22, 47   A/pigeon/Zhejiang/P1/2013,2013/04/,China,H7N9Avian 
123: 35, 31, 16,  8, 27,  7, 22, 45   A/pigeon/Zhejiang/P2/2013,2013/04/,China,H7N9Avian 

 98 >A/Zhejiang/DTID-ZJU10/2013,2013/10/14,China,H7N9              2268 2177 2130 1649 1497 1398  982  838   
  1:  8,  4,  3,  2,  1,  5,  1,  4   A/Index/H7N9-China/2013/03/,H7N9 
 10: 15, 11, 20,  2, 13,  5, 14, 22   A/poultry/index/East-China/2010,2009//,H9N2 (+H7+N9) 
 89:  9,  9,  5,  9, 24, 11,  2,  7   A/Shanghai/1/2013,H7N9 
 98:  0,  0,  0,  0,  0,  0,  0,  0   A/Zhejiang/DTID-ZJU10/2013,2013/10/14,China,H7N9 
108: 42, 32, 40,  4, 38,  9,  2, 41   KJ023079,A/Guangdong/05/2013,2013/12/17,H7N9 
109: 32, 33, 25,---, 13,---, 26, 52   KJ128369,A/pigeon/Shanghai/JC1/2013,2013/04/,H9N2 
110: 41, 24, 37,  5, 28,  8,  1, 41   A/Hong Kong/470129/2013,2013/11/11,H7N9 
111: 15, 15, 22,458, 14,---, 24,  8   A/chicken/Zhejiang/C11/2013,2013/03/,China,H9N9Avian 
112:  9,  4,  3,  3,  2,  5,  2,  5   A/chicken/Zhejiang/C481/2013,2013/04/,China,H7N9Avian 
113:  8,  5,  3,  3,  4,  6, 22,  5   A/chicken/Zhejiang/C483/2013,2013/04/,China,H7N9Avian 
114:  6, 20, 19,460, 40,467, 23, 19   A/chicken/Zhejiang/C484/2013,2013/04/,China,H9N2Avian 
115:  6, 20, 22,459,  1,468, 24, 50   A/chicken/Zhejiang/C487/2013,2013/04/,China,H9N2Avian 
116: 15, 15, 22,460, 14,467, 24, 51   A/chicken/Zhejiang/C494/2013,2013/04/,China,H9N2Avian 
117:  9, 33, 21,459,  1,468, 24, 50   A/chicken/Zhejiang/C497/2013,2013/04/,China,H9N2Avian 
118: 76,106,118,461, 97,496,110,116   A/duck/Zhejiang/6D18/2013,2013/12/14,China,H5N8Avian 
119:142,106, 73,---,124,454, 93,106   A/duck/Zhejiang/DK10/2013,2013/03/,China,H7N3Avian 
120:131,106, 73,---,124,457, 93,107   A/duck/Zhejiang/DK16/2013,2013/03/,China,H7N3Avian 
121: 76,105,116,462, 99,494,109,115   A/duck/Zhejiang/W24/2013,2013/11/14,China,H5N8Avian 
122: 14, 15, 22,  2, 26,  7, 24, 50   A/pigeon/Zhejiang/P1/2013,2013/04/,China,H7N9Avian 
123: 34, 30, 19,  4, 25,  7, 24, 47   A/pigeon/Zhejiang/P2/2013,2013/04/,China,H7N9Avian 

108 >KJ023079,A/Guangdong/05/2013,2013/12/17,H7N9                  2280 2270 2151 1683 1497 1398  982  838   
  1: 41, 29, 37,  2, 37,  3,  1, 36   A/Index/H7N9-China/2013/03/,H7N9 
 10: 28, 22, 22,  2, 29,  3, 14, 32   A/poultry/index/East-China/2010,2009//,H9N2 (+H7+N9) 
 89: 41, 31, 36,  9, 38,  9,  2, 39   A/Shanghai/1/2013,H7N9 
 98: 42, 32, 40,  4, 38,  9,  2, 41   A/Zhejiang/DTID-ZJU10/2013,2013/10/14,China,H7N9 
108:  0,  0,  0,  0,  0,  0,  0,  0   KJ023079,A/Guangdong/05/2013,2013/12/17,H7N9 
109: 46, 39, 38,---, 33,---, 26, 27   KJ128369,A/pigeon/Shanghai/JC1/2013,2013/04/,H9N2 
110: 10, 25, 27,  2, 41,  6,  1,  8   A/Hong Kong/470129/2013,2013/11/11,H7N9 
111: 43, 31, 35,451, 38,---, 24, 40   A/chicken/Zhejiang/C11/2013,2013/03/,China,H9N9Avian 
112: 42, 29, 37,  2, 38,  3,  2, 38   A/chicken/Zhejiang/C481/2013,2013/04/,China,H7N9Avian 
113: 41, 29, 37,  2, 39,  4, 22, 38   A/chicken/Zhejiang/C483/2013,2013/04/,China,H7N9Avian 
114: 41, 36, 34,452, 54,465, 23, 46   A/chicken/Zhejiang/C484/2013,2013/04/,China,H9N2Avian 
115: 41, 36, 33,451, 37,469, 24, 22   A/chicken/Zhejiang/C487/2013,2013/04/,China,H9N2Avian 
116: 43, 32, 33,452, 38,465, 24, 26   A/chicken/Zhejiang/C494/2013,2013/04/,China,H9N2Avian 
117: 42, 38, 33,451, 37,469, 24, 22   A/chicken/Zhejiang/C497/2013,2013/04/,China,H9N2Avian 
118: 85,105,113,458,106,499,108,100   A/duck/Zhejiang/6D18/2013,2013/12/14,China,H5N8Avian 
119:142,108, 77,---,127,457, 91, 98   A/duck/Zhejiang/DK10/2013,2013/03/,China,H7N3Avian 
120:132,108, 77,---,127,459, 91,100   A/duck/Zhejiang/DK16/2013,2013/03/,China,H7N3Avian 
121: 86,103,111,459,108,497,107,101   A/duck/Zhejiang/W24/2013,2013/11/14,China,H5N8Avian 
122: 42, 32, 33,  2, 42,  5, 24, 25   A/pigeon/Zhejiang/P1/2013,2013/04/,China,H7N9Avian 
123: 47, 36, 35,  4, 41,  5, 24, 22   A/pigeon/Zhejiang/P2/2013,2013/04/,China,H7N9Avian

gsgs · Jun 21, 2014

Re: Today at GenBank

19 Mexico human H3 and H1 genomes 2003-2014: 4,0,7,1,1,0,2,0,3,1,0,0
--------------------------------------
Indonesia H5N1, segment 4 ,
24 * 2008, 29*2010, 15*2011
ftp://ftp.ncbi.nih.gov/genomes/INFLUENZA/updates/2014-06-20/

not yet included in the main list, which has these counts of H5N1-HAs from Indonesia 2008-2014:
17,1,11,0,8,0,0
----------------------------------

gsgs · Jul 4, 2014

Re: Today at GenBank

1230 sequences today, mainly USA human 2013/4, segments 4,6,7
1170 human,29 avian, 31 swine ;
the counts for the segments are: 8,8,8,375,8,417,286,120
USA:990,Vietnam:105,India:94,Finland:29,Canada:8,China:4
7,7,98,91,33,0,275,719 from 2007,...,2014

676 H3N2
360 B
151 H1N1
94 Mumbai
15 India

ftp://ftp.ncbi.nih.gov/genomes/INFLUENZA/updates/2014-07-04/influenza_na.dat

gsgs · Jul 9, 2014

Re: Today at GenBank

KF357795,2013/04/06,A/duck/Zhejiang/4613/2013(H3N2)
KF357794,2013/04/06,A/duck/Zhejiang/4625/2013(H3N2)
KF357796,2013/04/06,A/duck/Zhejiang/4637/2013(H3N2)
KF357797,2013/04/08,A/duck/Zhejiang/4812/2013(H3N8)
KJ439816,2013/12/14,A/duck/Zhejiang/6D4/2013(H3N2)
KJ439817,2013/12/14,A/duck/Zhejiang/6D7/2013(H3N2)
KJ439821,2013/11/14,A/duck/Zhejiang/D1-1/2013(H3N6)
KJ439822,2013/11/14,A/duck/Zhejiang/D1-2/2013(H3N6)
KJ439823,2013/11/14,A/duck/Zhejiang/D1-3/2013(H3N6)
KJ439824,2013/11/14,A/duck/Zhejiang/D1-6/2013(H3N8)
KJ439814,2013/10/16,A/duck/Zhejiang/D11/2013(H3N2)
KJ439815,2013/10/16,A/duck/Zhejiang/D13/2013(H3N2)
KJ439818,2013/10/16,A/duck/Zhejiang/D16/2013(H3N3)
KJ439819,2013/10/16,A/duck/Zhejiang/D17/2013(H3N3)
KJ439820,2013/10/16,A/duck/Zhejiang/D18/2013(H3N3)

http://www.ncbi.nlm.nih.gov/nuccore/KF357795
Molecular characterization and phylogenetic analysis of H3 subtype
avian influenza viruses isolated from domestic ducks in Zhejiang
Province in China
JOURNAL Virus Genes (2014) In press
PUBMED 24748106
http://www.ncbi.nlm.nih.gov/pubmed/24748106
In 2013, 15 avian influenza viruses (AIVs), H3N2 (n = 7), H3N3 (n = 3), H3N6 (n = 3),
and H3N8 (n = 2), were isolated from domestic ducks in Zhejiang Province in China.
These strains were characterized by whole genome sequencing with subsequent
phylogenetic analysis and genetic comparison. Phylogenetic analysis of all eight
viral genes showed that these strains clustered in the AIV Eurasian lineage.
Analysis of the neuraminidase (NA) gene indicates that a re-assortment event
between H3 and H9N2 AIV occurred in these ducks. The molecular markers
analyzed over the genome of all viruses indicated that these strains were
low-pathogenic AIVs. Although there was no evidence of re-assortment in
subtype H3 AIVs among the avian species' and mammalian hosts in this study,
continued surveillance is needed considering the important role of domestic
ducks in AIV re-assortment.

========================================

all 15 are distant from human H7N9

this flu in domestic Chinese ducks is maybe slowly mutating away from the bird-index = avian consensus,
since they have (slightly) more amino-acid differences from the bird-index than average
mallards/wild waterfowl in the inner segments:

Code:

              segment                                      1  2  3  5  7  8
---------------------------------------------------------------------------
  1 >A/Index/birds/2000(H3N8a)                             0, 0, 0, 0, 0, 0
  7 >KF357795,A/duck/Zhejiang/4613/2013,2013/04/06,H3N2    3, 4, 1, 4, 1, 2
  8 >KF357794,A/duck/Zhejiang/4625/2013,2013/04/06,H3N2    2, 6, 2, 4, 1, 2
  9 >KF357796,A/duck/Zhejiang/4637/2013,2013/04/06,H3N2    3, 6, 1, 4, 1, 2
 10 >KF357797,A/duck/Zhejiang/4812/2013,2013/04/08,H3N8    4, 7, 5, 9, 1, 1
 11 >KJ439816,A/duck/Zhejiang/6D4/2013,2013/12/14,H3N2    11, 9, 4, 3, 2, 5
 12 >KJ439817,A/duck/Zhejiang/6D7/2013,2013/12/14,H3N2     5, 5, 6, 3, 1, 5
 13 >KJ439821,A/duck/Zhejiang/D1-1/2013,2013/11/14,H3N6    8, 7, 5, 4, 2, 3
 14 >KJ439822,A/duck/Zhejiang/D1-2/2013,2013/11/14,H3N6    8, 7, 5, 4, 2, 3
 15 >KJ439823,A/duck/Zhejiang/D1-3/2013,2013/11/14,H3N6    7, 7, 5, 4, 2, 3
 16 >KJ439824,A/duck/Zhejiang/D1-6/2013,2013/11/14,H3N8    7, 7, 5, 4, 2, 3
 17 >KJ439814,A/duck/Zhejiang/D11/2013,2013/10/16,H3N2     2, 7, 5, 1, 1, 1
 18 >KJ439815,A/duck/Zhejiang/D13/2013,2013/10/16,H3N2     2, 4, 5, 1, 3, 1
 19 >KJ439818,A/duck/Zhejiang/D16/2013,2013/10/16,H3N3     2, 4, 5, 1, 1, 1
 20 >KJ439819,A/duck/Zhejiang/D17/2013,2013/10/16,H3N3     2, 4, 5, 1, 0, 1
 21 >KJ439820,A/duck/Zhejiang/D18/2013,2013/10/16,H3N3     2, 4, 5, 1, 0, 1

gsgs · Jul 15, 2014

Re: Today at GenBank

2014/07/15 , big update

3830 sequences, all flu-A

segment-counts: 449+443+445+576+454+496+513+454=3830
97 avian,8 environment,941 human, 160 reassortant,2624 swine
1453 H1N1,1452 H3N2,721 H1N2,88 H5N1
1406 China, 1224 Hong Kong,755 Chile, 160 USA, 160 Lab,80 Vietnam,17 Russia,
17 Australia, 11 Iran
2007,...,2014:1+6+13+312+1529+1343+250+216 [+160 non]

58 human,2014,from China, segment 4

nucleotide-fasta-file: ftp://ftp.ncbi.nih.gov/genomes/INFLUENZA/updates/2014-07-15/influenza.fna

gsgs · Jul 22, 2014

Re: Today at GenBank

16 H3N2,Mumbai,2009,2010 , segments 6 and 7
50 avian genomes USA from 2007, no 17g

gsgs · Aug 1, 2014

Re: Today at GenBank

56 Mongolia ducks, segments 1,2,5,7,8

0,1,2,... differences from the index:

1,18,13,6,6,5,1,11:4,14:1
0,10,18,6,13,5,2,8:2,10:1
-
-
4,15,17,8,2,1,3,8:2,10:3,11:1,12:1
-
28,19,5,1,12:1,14:3
4,8,4,1, ... 15*,8*,10*,1*,2*,1*

Today at GenBank

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