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Today at GenBank

Re: Today at GenBank

17g is still around, although it's rare
at least in segments 5 and 8

http://www.ncbi.nlm.nih.gov/nuccore/KJ413562
http://www.ncbi.nlm.nih.gov/pubmed/25056712


the paper suggests the teals bring it from Mexico or South America.
Remember, 17g was mammalian-like in the AT-content.
So this gives again speculation about flu in tapirs,piccaries or such



Code: 
  1 >KJ413562,A/blue-winged teal/LA/AI13-1334/2013,2013/03/20,USA,H4N2

  2:127,157,130,332, 54,464, 96, 41   A/duck/LA/17G/1987,1987//,H3N8 
  3: 12, 20, 14,332, 15,467,  8, 15   A/mallard/Mississippi/390/2010,2010/01/17,H3N8 
  8: 10, 14,  9,332, 13,465,  9, 22   A/American coot/Oregon/20589-007/2007,2007/12/17,H3N8 
  9:  9, 16,  7,333, 14,467,  8, 22   A/northern pintail/California/HKWF792/2007,2007/11/28,H3N8 
 11:135,162,136,335, 12,467, 90, 15   A/cinnamon teal/California/44287-325/2007,2007/01/27,H3N8 
 22:116,140,138,119, 11, 21, 91, 14   A/mallard/California/JN808/2006,2006/12/06,H4N2 
 38: 45, 35, 49,---,148,---, 28,---   A/Avian/Index/North America 
 45: 75, 61, 72,---,150,---, 46,---   1980//,A/Avian/Index/North America,HxNx,USA,Avian 
 48: 29, 31, 26,---,  3,---,  2,  2   A/American green-winged teal/Ohio/12OS4717/2012,2012/10/13,USA,?
 49: 22, 29, 26,441,  8,435,  7, 15   A/northern shoveler/Illinois/12OS5294/2012,2012/11/10,USA,H10N3

http://www.ncbi.nlm.nih.gov/nuccore/CY053821
http://www.ncbi.nlm.nih.gov/nuccore/CY076405
http://www.ncbi.nlm.nih.gov/nuccore/EU871828



http://www.ncbi.nlm.nih.gov/nuccore/CY111585
> draft sequence
I think they should sequence it again, full genome.
It's one of the rare viruses from the "17g"-strain,
which has a high AT-score, usually only seen in mammals.

Maybe this one went (back) from mammals to mallards

Code: 
                                                           00000000000000000000000 000000000000000000000000000 0000000000000000000000000000000 0 00000000000000000000000000000000000  00000000000000 0000000000000000000000000000 
                                                           01112444445555555666677 011111222333333344455556667 0000001122233333333334444455677 5 00000011111122223333334444444444444  01222222222333 0000001111111112222222222233 
                                                           90199567780123468027806 505577019116778823777881455 2256660446912223568880003755411 6 11133500023818990115552334455577999  92335666778035 4678891223557790112234578925 
                                                           68492135808149776776320 482429054474453630367174548 2851350119422380652780490624867 7 02634205946643035382375034602623689  71493679131811 8704741897570879466714318103 
                                                           ----------------------- --------------------------- ------------------------------- - -----------------------------------  -------------- ---------------------------- 
                                                           VTVAIIILVVRVTIVDKLETTK KLSGEMVRQNMLANERIRVLKEAEVS KPDIVSVECRDKIVKIKQEVSSASEATISK  YQGVGYRVINLVRLDRRFPVVQITTIRSRVTNYN  VTLANGEKSILQ SREVSTVIIIAVTITDLPIELGLSSI 
>A/Index/birds/2000(H3N8a)                                 ......................} ..........................} ..............................} } ..................................}  ....}........} ....................}......} 
>A/Index/birds/North America/2000(H3N8b)                   ........I.............} .............S............} .............I.......P........} } .......M...................N......}  ....}........} ....................}......} 
>A/Brevig Mission/1/1918(H1N1)                             .AIS...M.....V.N..K..R} R............SD...LI....MN} .LN...A.Y..RV.....D..L....S..R} } ..DI..IM..M..P...Y...K.........S..}  .AI.}.EGRN..K} ..K..........V.N...K}....N.} 
>A/duck/LA/17G/1987,1987//,H3N8                            I...VV...I......RI....} EIA.DI.KKS..SSDKVK...DTD..} ....IA........R.RP..IKS.D..VN.} } HK..NH.MTH.IKINKK.SLI.VSNV..KL.S.S}  ...T}S..R.VF.} N...PS.V..VIN.N.FAV.}METFNT} 
>A/cinnamon teal/California/44287-325/2007,2007/01/27,H3N8 I...VVVMI.QII....I.IS.} .IT.DIIK.--ISSDKVK..RDTD..} ....IA...KN...RVRP.I.KSNDS..N.} } --..SH.MTH.IKINKK.SL......K.....F.}  ...T}S..R.V..} N..APS.VTLVIN.N.FAV.}METFNT} 
>A/pekin duck/California/P30/2006,2006/03/06,H4N2          I...VV.M..QII.I..I..S.} .ITCDIIK.SIISSDKVK..RDTD..} ....IA.K.K....RVRP.I.KSND...N.} } HK..NH.MTH.IKINKK.SL......K.....F.}  I..T}S..R.V..} NW.APSIVTLVIN.N.FAV.}METFNT} 
>A/mallard/California/JN808/2006,2006/12/06,H4N2           ------------------..S.} .I--DIIK----------------..} R..VIA..--------------------N.} } ---------------------------...A.F.}  ...T}S..R.V..} N..APS.VTLVIN.N.FAV.}METFNT}
 
Re: Today at GenBank

influenza virus at genbank today
(H1N1)
A/sloth bear/District of Columbia/6365/2013/02/25(H1N1))
must be a zoo-bear in Washington DC who got it from humans

not the first bear with flu -- we had the Pandas in 2009
with strangely conserved sequences (-->maybe errors)


http://www.ncbi.nlm.nih.gov/nuccore/KM244081
/isolation_source="nasal swab; zoo"

no paper


get it from daily updates -- not so easy, takes a while
get it from normal genbank-search "niman said:the front door") (takes some days to update) easier


the India/UK strain (of course)

185 mutations in 4 years, 46 per year, unusually many.
~35 per year would be normal

closest match is ...


---------edit----------------
http://www.funbuz.com/why-do-animals-sometimes-kill-their-babies/
March 31, 2014
The point when Khali, a sloth bear at the Smithsonian’s National Zoo in Washington, D.c.,
went into work in late December a year ago,
Right away subsequently, all the sloth bears fell sick with an influenza infection

[
 
Re: Today at GenBank

H1n1 , usa, 2014 , some all 8 segments , some 467

2014/09/17,1513 sequences
146 swine
484 2013(H1N1)
747 2014(H1N1)
56 canine
6 equine
8 seal
28 chicken

---------------------------------------------
there is an insertion of 3 amino-acids ([..TSL..]TSL ) at position 308 in the 16 ****** HAs at genbank
listed below. 11 of these were recent and from New York. It was first seen in A/NL/602/2009 which
was used in several experiments.

We had one other insertion in HA of 2 amino-acids ([..KK..]KK ) at position 172 that was seen
in 4 Italian swine sequences only in Sept.2009

so the previous 3 (resp.2) previous amino-acids got repeated.


>CY148123,A/Netherlands/602/2009,2009//,Netherlands,H1N1,Human
>CY086993,A/New York/3251/2009,2009//,USA,H1N1,Human
>CY167332,A/Tennessee/F1052A/2010,2010/02/09,USA,H1N1,Human
>CY176450,A/Kowloon/INS3_638/2011,2011/02/08,Hong Kong,H1N1,Human
>CY181817,A/Nicaragua/AGA2-36/2011,2011/10/15,Nicaragua,H1N1,Human
>CY188881,A/New York/WC-LVD-13-009/2013,2013/12/09,USA,H1N1,Human
>CY189001,A/New York/WC-LVD-13-024/2013,2013/12/25,USA,H1N1,Human
>CY189265,A/New York/WC-LVD-14-028/2014,2014/01/20,USA,H1N1,Human
>CY189297,A/New York/WC-LVD-14-032/2014,2014/01/27,USA,H1N1,Human
>CY189361,A/New York/WC-LVD-14-040/2014,2014/02/11,USA,H1N1,Human
>CY189369,A/New York/WC-LVD-14-041/2014,2014/02/13,USA,H1N1,Human
>CY189377,A/New York/WC-LVD-14-042/2014,2014/02/20,USA,H1N1,Human
>CY189401,A/New York/WC-LVD-14-045/2014,2014/03/06,USA,H1N1,Human
>CY188801,A/New York/WC-LVD-14-047/2014,2014/03/07,USA,H1N1,Human
>CY189449,A/New York/WC-LVD-14-052/2014,2014/03/11,USA,H1N1,Human
>CY189489,A/New York/WC-LVD-14-057/2014,2014/03/27,USA,H1N1,Human

----------------------------------------------------------------------
We added additional HA glycosylation sites to influenza A/Netherlands/602/2009
recombinant (rpH1N1) viruses, reflecting their temporal appearance in previous
seasonal H1N1 viruses. Additional glycosylations resulted in substantially
attenuated infection in mice and ferrets, whereas deleting HA glycosylation
sites from a pre-pandemic virus resulted in increased pathogenicity in mice.
-----------------------------------------------------------------
we genetically modified two viruses, A/Netherlands/602/09 (H1N1pdm09) and
A/Netherlands/26/07 (H1N1), and inserted or deleted glycosylation sites on the
head of HA and showed that binding efficiency of DC-SIGN to HA and subsequent
infection rates are determined by the extent of glycosylation on the head of HA.
-----------------------------------------------------------
A/Netherlands/602/09-Δ276 and a mutant that contains three additional glycosylation
sites that are present in A/Netherlands/26/07 (A/Netherlands/602/09-VN54 N125 N160).
-----------------------------------------
http://www.flutrackers.com/forum/showthread.php?t=113913
ferrets infected with swine flu lost more weight than those exposed to seasonal flu,
and the swine flu virus was more widespread in the animals’ bodies.
Fouchier et.al. : ferrets passed [Nl/602] to each other through the air as easily as seasonal flu.
Tumpey et.al. : ferrets transmit [CA/09] less efficiently than seasonal flu
---------------------------------------------------------
 
Re: Today at GenBank

today 34 H5N8 genomes from South Korea, early 2014
all very similar to each other

15,09,17,--,03,--,17,14
amino-acids away from the bird index in the 8 segments


closest neighbors in the 8 segments :

Code: 
>KJ508897,Avian,1,H5N8,South Korea,2014/01/18,2308,A/broiler duck/Korea/H29/2014



----------segment 1------------- 
 119   27 2266 11637 >JQ973691,A/duck/Jiangsu/k1203/2010,2010/12/05,China,H5N8,Avian,1
 122   28 2280 11814 >JX534562,A/wild duck/Shandong/628/2011,2011/04/14,China,H5N1,Avian,1
 149   34 2280 11808 >JX507352,A/duck/Jiangsu/m234/2012,2012/01/18,China,H5N2,Avian,1
 214   49 2280 3699 >CY091624,A/duck/Guangdong/wy11/2008,2008/06/06,China,H5N5,Avian,1
----------segment 2------------- 
 140   32 2274 11886 >KC282877,A/duck/Jiangsu/1-15/2011,2011/01/12,China,H4N2,Avian,2
 153   35 2274 11507 >JQ041393,A/duck/Eastern China/1111/2011,2011/01/,China,H5N2,Avian,2
 206   47 2274 11508 >JQ041394,A/goose/Eastern China/1112/2011,2011/01/,China,H5N2,Avian,2
----------segment 3------------- 
 158   34 2151 11912 >KC282878,A/duck/Jiangsu/1-15/2011,2011/01/12,China,H4N2,Avian,3
 172   37 2151 11556 >JQ041397,A/duck/Eastern China/1111/2011,2011/01/,China,H5N2,Avian,3
 232   50 2151 10847 >GU727668,A/duck/Eastern China/108/2008,2008/12/15,China,H5N1,Avian,3
----------segment 4------------- 
 275   47 1704 4942 >JX534565,A/wild duck/Shandong/628/2011,2011/04/14,China,H5N1,Avian,4
 281   48 1704 4883 >JQ973694,A/duck/Jiangsu/k1203/2010,2010/12/05,China,H5N8,Avian,4
 316   54 1704 4936 >JX507355,A/duck/Jiangsu/m234/2012,2012/01/18,China,H5N2,Avian,4
----------segment 5------------- 
 106   16 1497 11437 >JX534550,A/wild duck/Shandong/1/2011,2011/04/12,China,H5N1,Avian,5
 113   17 1497 11433 >JX507356,A/duck/Jiangsu/m234/2012,2012/01/18,China,H5N2,Avian,5
 120   18 1497 11439 >JX534566,A/wild duck/Shandong/628/2011,2011/04/14,China,H5N1,Avian,5
 128   19 1479 11290 >JQ973695,A/duck/Jiangsu/k1203/2010,2010/12/05,China,H5N8,Avian,5
 220   33 1497 12417 >KJ413835,A/breeder duck/Korea/Gochang1/2014,2014/01/16,South Korea,H5N8,Avian,5
----------segment 6------------- 
 186   26 1394 1571 >JQ973696,A/duck/Jiangsu/k1203/2010,2010/12/05,China,H5N8,Avian,6
 191   27 1413 1639 >KJ476674,A/duck/Zhejiang/6D18/2013,2013/12/14,China,H5N8,Avian,6
 198   28 1413 1638 >KJ476673,A/duck/Zhejiang/W24/2013,2013/11/14,China,H5N8,Avian,6
 205   29 1413 1635 >KJ413836,A/breeder duck/Korea/Gochang1/2014,2014/01/16,South Korea,H5N8,Avian,6
 559   79 1413 1622 >KF667707,A/common shelduck/Mongolia/2185/2011,2011/10/09,Mongolia,H3N8,Avian,6
----------segment 7------------- 
  91    9  982 12087 >JQ041413,A/duck/Eastern China/1111/2011,2011/01/,China,H5N2,Avian,7
  91    9  982 12505 >KC282882,A/duck/Jiangsu/1-15/2011,2011/01/12,China,H4N2,Avian,7
 173   17  982 12371 >JX534568,A/wild duck/Shandong/628/2011,2011/04/14,China,H5N1,Avian,7
----------segment 8------------- 
 119   10  838 7146 >JQ041417,A/duck/Eastern China/1111/2011,2011/01/,China,H5N2,Avian,8
 131   11  838 7375 >KC282883,A/duck/Jiangsu/1-15/2011,2011/01/12,China,H4N2,Avian,8
 143   12  838 7147 >JQ041418,A/goose/Eastern China/1112/2011,2011/01/,China,H5N2,Avian,8
 214   18  838 7296 >JX534569,A/wild duck/Shandong/628/2011,2011/04/14,China,H5N1,Avian,8


difference in 1/100 percent
difference in number of nucleotides
nucleotides available
number in database
name


kumamoto:16,11,16,03,17,15
1111:16,08,18,04,18,14
1-15:14,07,17,05,17,14
628:16,07,22,04,16,15
 
Re: Today at GenBank

Brazil,H3N2,June 2014
A/Italy/3/2013(H7N7))
A/breeder duck/France/090045b/2009(H5N3))
A/chicken/Egypt/14VIR784-11-133AL/2013(H5N1))
H9N2 China 2010/12/01
A/duck/Quang Ninh/13c1-2-1/2013(H5N2))
A/duck/Mongolia/256/2014 (H5N2))
A/muscovy duck/Long An/86/2014(H5N1))
A/swan/Germany/R65/2008(H5N1))


etc.

1369 in total today , after none the last 4 days

no H5N8 from Europe yet
China 2013/11/13 2280 Influenza A virus (A/mallard/Shanghai/SH-9/2013(H5N8))
[this is from the Gochang1 type, not the Buan2=Donglim3 type which is in Europe]

ftp://ftp.ncbi.nih.gov/genomes/INFLUENZA/updates/2014-12-03/influenza_na.dat

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

Code: 
>A/Index/birds/2000(H3N8a)                 0, 0, 0,--, 0,--, 0, 0
>Index Qinghai                             9, 8,10,--, 7,--,14,18
>A/Ck/Egypt/14VIR784-11-133AL/2013(H5N1)  14,11,18,--,11,--,12,22
>A/Ck/Egypt/14VIR784-5-1318S/2013(H5N1)   17,13,22,--, 8,--,15,25
>A/Dk/Egypt/14VIR784-4-133AD/2013(H5N1)   20,10,22,--,12,--,13,24
>A/Dk/Egypt/14VIR784-6-1328S/2013(H5N1)   18,13,22,--,12,--,13,24
 
Re: Today at GenBank

H1N2 in Beijing last season:

KJ484586,H1N2,2013/12/27,A/Beijing/13-31/2013(H1N2)
KJ484585,H1N2,2013/12/20,A/Beijing/13-8/2013(H1N2)
KJ484587,H1N2,2014/01/07,A/Beijing/14-3/2014(H1N2)
KJ484588,H1N2,2014/01/10,A/Beijing/14-30/2014(H1N2)
ftp://ftp.ncbi.nih.gov/genomes/INFLUENZA/updates/2014-12-04/

http://www.ncbi.nlm.nih.gov/nuccore/KJ484586

NA from the Czech/2012 H3N2 strain


I can't find this mentioned anywhere, only swinish or avian H1N2

http://www.ncbi.nlm.nih.gov/pubmed/25209152
A human-like H1N2 influenza virus detected during an outbreak of acute respiratory
disease in swine in Brazil.
2010-2011

http://www.ncbi.nlm.nih.gov/pubmed/25467861
Novel triple reassortant H1N2 influenza viruses bearing six internal genes of the
pandemic 2009/H1N1 influenza virus were detected in pigs in China.
winter of 2012,
HA from Euroswine , NA from US-swine H1N2, rest from ******=pH1N1/2009

Characterization of an artificial swine-origin influenza virus with the same gene
combination as H1N1/2009 virus: a genesis clue of pandemic strain.
 
update Dec.30 after many days of silence

ftp://ftp.ncbi.nih.gov/genomes/INFLU...fluenza_na.dat

seals Germany , H10N7

>KP137827,A/harbour seal/Germany/1/2014,2014//,H10N7,1

02,09,06,--,03,--,01,03
segment 2 is a bit unusual

192 44 2280 >CY165733,A/mallard/Sweden/101010/2009,2009/11/03,Sweden,H4N6,Avian,1
259 59 2274 >CY055173,A/aquatic bird/India/NIV-17095/2007,2007/12/23,India,H11N1,Avian,2
106 23 2151 >KM213387,A/ruddy turnstone/Iceland/2899/2013,2013/05/23,Iceland,H5N1,Avian,3
164 27 1646 >CY183991,A/mallard/Sweden/133546/2011,2011/11/23,Sweden,H10N4,Avian,4
155 23 1475 >JX566128,A/mallard/Sweden/107892/2009,2009/12/12,Sweden,H2N3,Avian,5
233 33 1416 >CY185451,A/domestic duck/Republic of Georgia/1/2010,2010/04/28,Georgia,H10N7,Avian,6
81 8 982 >CY165719,A/mallard/Sweden/100881/2009,2009/11/01,Sweden,H4N6,Avian,7
143 12 838 >HQ244411,A/Anas crecca/Spain/1460/2008,2008/01/26,Spain,H7N9,Avian,8


 
no, not even at GISAID.
And European,Russian,Japanese,Korean(since Nov.) only at gisaid

there are some unclear descriptions in the OIE-reports or such mentioning other Korean sequences,
presumably the closest matches from genbank in HA
and some % of differences comparing some H5N8 or H5N2

but I haven't seen anything hinting at what segments were involved in the reassortment,
how close to the avian consensus, what strain (17g ?? unlikely)

what way was taken, (Alaska ?) what species
 
full genome,China,2014/06/29,A/duck/Jiangxi/NCDZT1123/2014(H5N6)
full genome,China,2014/06/29,A/duck/Jiangxi/NCDZT1126/2014(H5N6)


ftp://ftp.ncbi.nih.gov/genomes/INFLU...fluenza_na.dat http://www.ncbi.nlm.nih.gov/nuccore/kp090436



best neighbors in the 8 segments:

Code: 
[FONT=Arial][SIZE=10px]0    0 2280    1 >KP090436,A/duck/Jiangxi/NCDZT1123/2014,2014/06/29,China,H5N6,Avian,1

----------segment 1-------------
  74   17 2280    2 >KP090444,A/duck/Jiangxi/NCDZT1126/2014,2014/06/29,China,H5N6,Avian,1
114   26 2280 13373 >KJ754142,A/duck/Guangdong/GD01/2014,2014/03/,China,H5N6,Avian,1
131   30 2280 13291 >KM234812,A/duck/Jiangxi/JXA132023/2013,2013/12/17,China,H5N2,Avian,1
131   30 2280 13377 >KM496962,A/chicken/Laos/LPQ001/2014,2014/03/12,Laos,H5N6,Avian,1
135   31 2280 13378 >KM496974,A/duck/Laos/XBY004/2014,2014/03/12,Laos,H5N6,Avian,1
140   32 2280 13290 >KM234807,A/duck/Jiangxi/JXA131996/2013,2013/12/17,China,H5N2,Avian,1
153   35 2280 13384 >AB979452,A/muscovy duck/Vietnam/LBM631/2014,2014/04/15,Viet Nam,H5N1,Avian,1
153   35 2280 13385 >AB979460,A/duck/Vietnam/LBM632/2014,2014/04/15,Viet Nam,H5N1,Avian,1
153   35 2280 13386 >AB979468,A/duck/Vietnam/LBM633/2014,2014/04/15,Viet Nam,H5N1,Avian,1
153   35 2280 13387 >AB979476,A/muscovy duck/Vietnam/LBM634/2014,2014/04/15,Viet Nam,H5N1,Avian,1
153   35 2280 13388 >AB979484,A/muscovy duck/Vietnam/LBM635/2014,2014/04/15,Viet Nam,H5N1,Avian,1
153   35 2280 13389 >AB979492,A/muscovy duck/Vietnam/LBM636/2014,2014/04/15,Viet Nam,H5N1,Avian,1
153   35 2280 13390 >AB979500,A/duck/Vietnam/LBM638/2014,2014/04/15,Viet Nam,H5N1,Avian,1
153   35 2280 13391 >AB979508,A/duck/Vietnam/LBM639/2014,2014/04/15,Viet Nam,H5N1,Avian,1
171   39 2280 13300 >KM234819,A/duck/Jiangxi/JXA131986/2013,2013/12/17,China,mixed,Avian,1
232   53 2280 12341 >CY146697,A/duck/Hunan/S4220/2011,2011/11/13,China,H5N1,Avian,1
276   63 2280 13056 >AB824276,A/duck/Quang Ninh/21/2013,2013/04/10,Viet Nam,H5N1,Avian,1
...
289   66 2280 10830 >KF735641,A/barn swallow/Hong Kong/1161/2010,2010/03/29,Hong Kong,H5N1,Avian,1
...
399   91 2280 8225 >CY036242,A/grey heron/Hong Kong/1046/2008,2008//,Hong Kong,H5N1,Avian,1
...
434   99 2280 6783 >CY036210,A/grey heron/Hong Kong/3088/2007,2007//,Hong Kong,H5N1,Avian,1

----------segment 2-------------
105   24 2274 13326 >KM496963,A/chicken/Laos/LPQ001/2014,2014/03/12,Laos,H5N6,Avian,2
105   24 2274 13327 >KM496975,A/duck/Laos/XBY004/2014,2014/03/12,Laos,H5N6,Avian,2
110   25 2271 13249 >KM234820,A/duck/Jiangxi/JXA131986/2013,2013/12/17,China,mixed,Avian,2
114   26 2274 13322 >KJ754143,A/duck/Guangdong/GD01/2014,2014/03/,China,H5N6,Avian,2
118   27 2271 13241 >KM234813,A/duck/Jiangxi/JXA132023/2013,2013/12/17,China,H5N2,Avian,2
118   27 2271 13251 >KM234872,A/chicken/Jiangxi/JXA132321/2013,2013/12/22,China,H5,Avian,2
127   29 2274    2 >KP090444,A/duck/Jiangxi/NCDZT1126/2014,2014/06/29,China,H5N6,Avian,1
171   39 2274 13333 >AB979453,A/muscovy duck/Vietnam/LBM631/2014,2014/04/15,Viet Nam,H5N1,Avian,2
171   39 2274 13334 >AB979461,A/duck/Vietnam/LBM632/2014,2014/04/15,Viet Nam,H5N1,Avian,2
171   39 2274 13335 >AB979469,A/duck/Vietnam/LBM633/2014,2014/04/15,Viet Nam,H5N1,Avian,2
171   39 2274 13336 >AB979477,A/muscovy duck/Vietnam/LBM634/2014,2014/04/15,Viet Nam,H5N1,Avian,2
171   39 2274 13337 >AB979485,A/muscovy duck/Vietnam/LBM635/2014,2014/04/15,Viet Nam,H5N1,Avian,2
171   39 2274 13338 >AB979493,A/muscovy duck/Vietnam/LBM636/2014,2014/04/15,Viet Nam,H5N1,Avian,2
171   39 2274 13339 >AB979501,A/duck/Vietnam/LBM638/2014,2014/04/15,Viet Nam,H5N1,Avian,2
171   39 2274 13340 >AB979509,A/duck/Vietnam/LBM639/2014,2014/04/15,Viet Nam,H5N1,Avian,2
233   53 2271 13242 >KM234772,A/chicken/Jiangxi/JXA131985/2013,2013/12/17,China,H6N2,Avian,2
250   57 2274 11735 >JN646700,A/duck/Zhejiang/224/2011,2011/02/,China,H5N1,Avian,2
...
259   59 2274 10830 >KF735642,A/barn swallow/Hong Kong/1161/2010,2010/03/30,Hong Kong,H5N1,Avian,2
...
325   74 2274 8252 >CY036243,A/grey heron/Hong Kong/1046/2008,2008//,Hong Kong,H5N1,Avian,2
...
338   77 2274 6793 >CY036211,A/grey heron/Hong Kong/3088/2007,2007//,Hong Kong,H5N1,Avian,2
...
365   82 2241 5689 >GU052492,A/chicken/Hong Kong/D-06-0947/2006,2006//,Hong Kong,H5N1,Avian,2
...
388   87 2238 4644 >EF123920,A/duck/Guangxi/4830/2005,2005//,China,H5N1,Avian,2

----------segment 3-------------
  18    4 2151    2 >KP090444,A/duck/Jiangxi/NCDZT1126/2014,2014/06/29,China,H5N6,Avian,1
  55   12 2151 13251 >KM234808,A/duck/Jiangxi/JXA131996/2013,2013/12/17,China,H5N2,Avian,3
  55   12 2151 13252 >KM234814,A/duck/Jiangxi/JXA132023/2013,2013/12/17,China,H5N2,Avian,3
  55   12 2151 13259 >KM234821,A/duck/Jiangxi/JXA131986/2013,2013/12/17,China,mixed,Avian,3
  55   12 2151 13278 >KM234930,A/duck/Jiangxi/JXA132718/2014,2014/01/01,China,mixed,Avian,3
  65   14 2151 13261 >KM234873,A/chicken/Jiangxi/JXA132321/2013,2013/12/22,China,H5,Avian,3
  79   17 2151 13332 >KJ754144,A/duck/Guangdong/GD01/2014,2014/03/,China,H5N6,Avian,3
  83   18 2151 13343 >AB979454,A/muscovy duck/Vietnam/LBM631/2014,2014/04/15,Viet Nam,H5N1,Avian,3
  83   18 2151 13344 >AB979462,A/duck/Vietnam/LBM632/2014,2014/04/15,Viet Nam,H5N1,Avian,3
  83   18 2151 13345 >AB979470,A/duck/Vietnam/LBM633/2014,2014/04/15,Viet Nam,H5N1,Avian,3
  83   18 2151 13346 >AB979478,A/muscovy duck/Vietnam/LBM634/2014,2014/04/15,Viet Nam,H5N1,Avian,3
  83   18 2151 13347 >AB979486,A/muscovy duck/Vietnam/LBM635/2014,2014/04/15,Viet Nam,H5N1,Avian,3
  83   18 2151 13348 >AB979494,A/muscovy duck/Vietnam/LBM636/2014,2014/04/15,Viet Nam,H5N1,Avian,3
  83   18 2151 13349 >AB979502,A/duck/Vietnam/LBM638/2014,2014/04/15,Viet Nam,H5N1,Avian,3
  83   18 2151 13350 >AB979510,A/duck/Vietnam/LBM639/2014,2014/04/15,Viet Nam,H5N1,Avian,3
  92   20 2151 13337 >KM496976,A/duck/Laos/XBY004/2014,2014/03/12,Laos,H5N6,Avian,3
  93   20 2150 13336 >KM496964,A/chicken/Laos/LPQ001/2014,2014/03/12,Laos,H5N6,Avian,3
125   27 2151 12301 >CY146699,A/duck/Hunan/S4220/2011,2011/11/13,China,H5N1,Avian,3
153   33 2151 10797 >KF735643,A/barn swallow/Hong Kong/1161/2010,2010/03/31,Hong Kong,H5N1,Avian,3
167   36 2151 11734 >JN646707,A/duck/Zhejiang/224/2011,2011/02/,China,H5N1,Avian,3
167   36 2151 11735 >JN646708,A/duck/Zhejiang/2242/2011,2011/02/,China,H5N1,Avian,3
167   36 2151 11736 >JN646709,A/duck/Zhejiang/2243/2011,2011/02/,China,H5N1,Avian,3
167   36 2151 11737 >JN646710,A/duck/Zhejiang/2244/2011,2011/02/,China,H5N1,Avian,3
167   36 2151 11739 >JN646712,A/duck/Zhejiang/2248/2011,2011/02/,China,H5N1,Avian,3
181   39 2151 11733 >JN646706,A/duck/Zhejiang/213/2011,2011/02/,China,H5N1,Avian,3
190   41 2151 8214 >CY036244,A/grey heron/Hong Kong/1046/2008,2008//,Hong Kong,H5N1,Avian,3
195   42 2151 11832 >JX534588,A/wild duck/Fujian/1/2011,2011/03/10,China,H5N1,Avian,3
199   43 2151 11833 >JX534596,A/wild duck/Fujian/2/2011,2011/03/11,China,H5N1,Avian,3
209   45 2151 6764 >CY036212,A/grey heron/Hong Kong/3088/2007,2007//,Hong Kong,H5N1,Avian,3
...
274   59 2151 5660 >EF124657,A/little egret/Hong Kong/718/2006,2006//,Hong Kong,H5N1,Avian,3
...
278   60 2151 5191 >GU186737,A/chicken/Ninh Binh/209/2005,2005//,Viet Nam,H5N1,Avian,3

----------segment 4-------------
  17    3 1704    2 >KP090444,A/duck/Jiangxi/NCDZT1126/2014,2014/06/29,China,H5N6,Avian,1
  52    9 1704 5705 >KJ754145,A/duck/Guangdong/GD01/2014,2014/03/,China,H5N6,Avian,4
  99   17 1704 5709 >KM496970,A/duck/Laos/LPQ002/2014,2014/03/12,Laos,H5N6,Avian,4
  99   17 1704 5710 >KM496972,A/chicken/Laos/XBY003/2014,2014/03/12,Laos,H5N6,Avian,4
  99   17 1704 5711 >KM496977,A/duck/Laos/XBY004/2014,2014/03/12,Laos,H5N6,Avian,4
  99   17 1704 5712 >KM496982,A/duck/Laos/XBY004/2014,2014/03/12,Laos,H5N6,Avian,4
105   18 1704 5708 >KM496965,A/chicken/Laos/LPQ001/2014,2014/03/12,Laos,H5N6,Avian,4
211   36 1704 5718 >AB979455,A/muscovy duck/Vietnam/LBM631/2014,2014/04/15,Viet Nam,H5N1,Avian,4
211   36 1704 5719 >AB979463,A/duck/Vietnam/LBM632/2014,2014/04/15,Viet Nam,H5N1,Avian,4
211   36 1704 5720 >AB979471,A/duck/Vietnam/LBM633/2014,2014/04/15,Viet Nam,H5N1,Avian,4
211   36 1704 5721 >AB979479,A/muscovy duck/Vietnam/LBM634/2014,2014/04/15,Viet Nam,H5N1,Avian,4
211   36 1704 5722 >AB979487,A/muscovy duck/Vietnam/LBM635/2014,2014/04/15,Viet Nam,H5N1,Avian,4
211   36 1704 5723 >AB979495,A/muscovy duck/Vietnam/LBM636/2014,2014/04/15,Viet Nam,H5N1,Avian,4
211   36 1704 5724 >AB979503,A/duck/Vietnam/LBM638/2014,2014/04/15,Viet Nam,H5N1,Avian,4
211   36 1704 5725 >AB979511,A/duck/Vietnam/LBM639/2014,2014/04/15,Viet Nam,H5N1,Avian,4
264   45 1704 5078 >JX534565,A/wild duck/Shandong/628/2011,2011/04/14,China,H5N1,Avian,4
269   46 1704 4793 >JQ973694,A/duck/Jiangsu/k1203/2010,2010/12/05,China,H5N8,Avian,4
293   50 1704 4844 >JQ041402,A/goose/Eastern China/1112/2011,2011/01/,China,H5N2,Avian,4
305   52 1704 5255 >JX507355,A/duck/Jiangsu/m234/2012,2012/01/18,China,H5N2,Avian,4
311   53 1704 4843 >JQ041401,A/duck/Eastern China/1111/2011,2011/01/,China,H5N2,Avian,4
322   55 1704 5567 >KM504101,A/duck/Shandong/Q1/2013,2013/04/25,China,H5N8,Avian,4
328   56 1704 5642 >KJ413834,A/breeder duck/Korea/Gochang1/2014,2014/01/16,South Korea,H5N8,Avian,4
340   58 1704 5653 >KJ508961,A/Baikal teal/Korea/H52/2014,2014/01/20,South Korea,H5N8,Avian,4
357   61 1704 4099 >CY091635,A/duck/Guangdong/wy19/2008,2008/06/06,China,H5N5,Avian,4
...
559   92 1644 1917 >DQ992790,A/duck/Hunan/324/2006,2006//,China,H5N1,Avian,4
...
576   98 1701 1377 >EU329186,A/wild duck/Hunan/211/2005,2005//,China,H5N1,Avian,4

----------segment 5-------------
   6    1 1497    2 >KP090444,A/duck/Jiangxi/NCDZT1126/2014,2014/06/29,China,H5N6,Avian,1
  60    9 1497 12895 >KM234815,A/duck/Jiangxi/JXA132023/2013,2013/12/17,China,H5N2,Avian,5
  60    9 1497 12906 >KM234877,A/duck/Jiangxi/JXA132323/2013,2013/12/22,China,,Avian,5
  60    9 1497 12907 >KM234874,A/chicken/Jiangxi/JXA132321/2013,2013/12/22,China,H5,Avian,5
  66   10 1497 12894 >KM234809,A/duck/Jiangxi/JXA131996/2013,2013/12/17,China,H5N2,Avian,5
  66   10 1497 12903 >KM234823,A/duck/Jiangxi/JXA131986/2013,2013/12/17,China,mixed,Avian,5
  93   14 1497 12985 >KM496966,A/chicken/Laos/LPQ001/2014,2014/03/12,Laos,H5N6,Avian,5
  93   14 1497 12986 >KM496978,A/duck/Laos/XBY004/2014,2014/03/12,Laos,H5N6,Avian,5
  93   14 1497 12992 >AB979456,A/muscovy duck/Vietnam/LBM631/2014,2014/04/15,Viet Nam,H5N1,Avian,5
  93   14 1497 12993 >AB979464,A/duck/Vietnam/LBM632/2014,2014/04/15,Viet Nam,H5N1,Avian,5
  93   14 1497 12994 >AB979472,A/duck/Vietnam/LBM633/2014,2014/04/15,Viet Nam,H5N1,Avian,5
  93   14 1497 12995 >AB979480,A/muscovy duck/Vietnam/LBM634/2014,2014/04/15,Viet Nam,H5N1,Avian,5
  93   14 1497 12996 >AB979488,A/muscovy duck/Vietnam/LBM635/2014,2014/04/15,Viet Nam,H5N1,Avian,5
  93   14 1497 12997 >AB979496,A/muscovy duck/Vietnam/LBM636/2014,2014/04/15,Viet Nam,H5N1,Avian,5
  93   14 1497 12998 >AB979504,A/duck/Vietnam/LBM638/2014,2014/04/15,Viet Nam,H5N1,Avian,5
  93   14 1497 12999 >AB979512,A/duck/Vietnam/LBM639/2014,2014/04/15,Viet Nam,H5N1,Avian,5
106   16 1497 12981 >KJ754146,A/duck/Guangdong/GD01/2014,2014/03/,China,H5N6,Avian,5
167   25 1497 11935 >CY146701,A/duck/Hunan/S4220/2011,2011/11/13,China,H5N1,Avian,5
180   27 1497 11366 >JN646721,A/duck/Zhejiang/224/2011,2011/02/,China,H5N1,Avian,5
...
247   37 1497 8098 >CY036254,A/magpie robin/Hong Kong/1097/2008,2008//,Hong Kong,H5N1,Avian,5
...
293   44 1497 6780 >CY036214,A/grey heron/Hong Kong/3088/2007,2007//,Hong Kong,H5N1,Avian,5
...
347   52 1497 4470 >KC261670,A/duck/Jiangsu/26/2004,2004/05/,China,H3N2,Avian,5

----------segment 6-------------
  28    4 1391    2 >KP090444,A/duck/Jiangxi/NCDZT1126/2014,2014/06/29,China,H5N6,Avian,1
  72   10 1380 2011 >KJ754147,A/duck/Guangdong/GD01/2014,2014/03/,China,H5N6,Avian,6
  77    9 1159 2016 >KM496983,A/duck/Laos/XBY004/2014,2014/03/12,Laos,H5N6,Avian,6
  91   11 1208 2014 >KM496973,A/chicken/Laos/XBY003/2014,2014/03/12,Laos,H5N6,Avian,6
  94   13 1380 2012 >KM496967,A/chicken/Laos/LPQ001/2014,2014/03/12,Laos,H5N6,Avian,6
  94   13 1380 2015 >KM496979,A/duck/Laos/XBY004/2014,2014/03/12,Laos,H5N6,Avian,6
  97   12 1227 2013 >KM496971,A/duck/Laos/LPQ002/2014,2014/03/12,Laos,H5N6,Avian,6
246   34 1380 1829 >KJ200743,A/duck/Guangdong/S1419/2011,2011/03/09,China,H6N6,Avian,6
347   48 1380 1818 >KJ200823,A/duck/Guangdong/S4251/2010,2010/12/10,China,H6N6,Avian,6
384   53 1380  767 >CY109764,A/duck/Shantou/1984/2007,2007/08/,China,H6N6,Avian,6

----------segment 7-------------
  30    3  982    2 >KP090444,A/duck/Jiangxi/NCDZT1126/2014,2014/06/29,China,H5N6,Avian,1
  50    5  982 13991 >KM234810,A/duck/Jiangxi/JXA131996/2013,2013/12/17,China,H5N2,Avian,7
  50    5  982 13992 >KM234816,A/duck/Jiangxi/JXA132023/2013,2013/12/17,China,H5N2,Avian,7
  50    5  982 14023 >KM234934,A/duck/Jiangxi/JXA132718/2014,2014/01/01,China,mixed,Avian,7
  50    5  982 14100 >KJ754148,A/duck/Guangdong/GD01/2014,2014/03/,China,H5N6,Avian,7
  50    5  982 14104 >KM496968,A/chicken/Laos/LPQ001/2014,2014/03/12,Laos,H5N6,Avian,7
  50    5  982 14105 >KM496980,A/duck/Laos/XBY004/2014,2014/03/12,Laos,H5N6,Avian,7
  71    7  982 14004 >KM234875,A/chicken/Jiangxi/JXA132321/2013,2013/12/22,China,H5,Avian,7
112   11  982 14000 >KM234824,A/duck/Jiangxi/JXA131986/2013,2013/12/17,China,mixed,Avian,7
132   13  982 13004 >CY146703,A/duck/Hunan/S4220/2011,2011/11/13,China,H5N1,Avian,7
138   12  866 13360 >AB780497,A/duck/Vietnam/OIE-2212/2012,2012/08/11,Viet Nam,H5N1,Avian,7
142   14  982 12257 >KC436114,A/oriental magpie robin/Hong Kong/470.1/2011,2011//,Hong Kong,H5N1,Avian,7
142   14  982 12383 >JN646735,A/duck/Zhejiang/224/2011,2011/02/,China,H5N1,Avian,7
142   14  982 12384 >JN646736,A/duck/Zhejiang/2242/2011,2011/02/,China,H5N1,Avian,7
...
173   17  982 10100 >JN055394,A/Muscovy duck/Vietnam/18151/2009,2009/04/08,Viet Nam,H5N1,Avian,7
...
173   17  982 8806 >CY036248,A/grey heron/Hong Kong/1046/2008,2008//,Hong Kong,H5N1,Avian,7
...
183   18  982 7405 >CY036216,A/grey heron/Hong Kong/3088/2007,2007//,Hong Kong,H5N1,Avian,7
----------segment 8-------------
  24    2  823    2 >KP090444,A/duck/Jiangxi/NCDZT1126/2014,2014/06/29,China,H5N6,Avian,1
  48    4  823 10482 >KM234811,A/duck/Jiangxi/JXA131996/2013,2013/12/17,China,H5N2,Avian,8
  48    4  823 10483 >KM234817,A/duck/Jiangxi/JXA132023/2013,2013/12/17,China,H5N2,Avian,8
  48    4  823 10494 >KM234878,A/duck/Jiangxi/JXA132348/2013,2013/12/22,China,,Avian,8
  60    5  823 10495 >KM234876,A/chicken/Jiangxi/JXA132321/2013,2013/12/22,China,H5,Avian,8
  60    5  823 10568 >KJ754149,A/duck/Guangdong/GD01/2014,2014/03/,China,H5N6,Avian,8
  60    5  823 10573 >KM496981,A/duck/Laos/XBY004/2014,2014/03/12,Laos,H5N6,Avian,8
  72    6  823 10572 >KM496969,A/chicken/Laos/LPQ001/2014,2014/03/12,Laos,H5N6,Avian,8
  85    7  823 10579 >AB979459,A/muscovy duck/Vietnam/LBM631/2014,2014/04/15,Viet Nam,H5N1,Avian,8
  85    7  823 10580 >AB979467,A/duck/Vietnam/LBM632/2014,2014/04/15,Viet Nam,H5N1,Avian,8
  85    7  823 10581 >AB979475,A/duck/Vietnam/LBM633/2014,2014/04/15,Viet Nam,H5N1,Avian,8
  85    7  823 10582 >AB979483,A/muscovy duck/Vietnam/LBM634/2014,2014/04/15,Viet Nam,H5N1,Avian,8
  85    7  823 10583 >AB979491,A/muscovy duck/Vietnam/LBM635/2014,2014/04/15,Viet Nam,H5N1,Avian,8
  85    7  823 10584 >AB979499,A/muscovy duck/Vietnam/LBM636/2014,2014/04/15,Viet Nam,H5N1,Avian,8
  85    7  823 10585 >AB979507,A/duck/Vietnam/LBM638/2014,2014/04/15,Viet Nam,H5N1,Avian,8
  85    7  823 10586 >AB979515,A/duck/Vietnam/LBM639/2014,2014/04/15,Viet Nam,H5N1,Avian,8
121   10  823 9682 >CY146704,A/duck/Hunan/S4220/2011,2011/11/13,China,H5N1,Avian,8
170   14  823 8539 >KF735646,A/barn swallow/Hong Kong/1161/2010,2010/04/03,Hong Kong,H5N1,Avian,8
194   16  823 9319 >JX534593,A/wild duck/Fujian/1/2011,2011/03/10,China,H5N1,Avian,8
194   16  823 9320 >JX534601,A/wild duck/Fujian/2/2011,2011/03/11,China,H5N1,Avian,8
206   17  823 9214 >JN646742,A/duck/Zhejiang/224/2011,2011/02/,China,H5N1,Avian,8
...
230   19  823 6713 >CY036249,A/grey heron/Hong Kong/1046/2008,2008//,Hong Kong,H5N1,Avian,8
...
243   20  823 5711 >CY036217,A/grey heron/Hong Kong/3088/2007,2007//,Hong Kong,H5N1,Avian,8
...
279   23  823 4662 >CY030909,A/goose/Yunnan/3798/2006,2006//,China,H5N1,Avian,8
...
291   24  823 3889 >EF124521,A/goose/Guangxi/4289/2005,2005//,China,H5N1,Avian,8[/SIZE][/FONT]

best match outside Jiangxi :
26,24,17,9,14,10,5,5 mutations or 1.14,1.05,0.79,0.52,0.93,0.72,0.50,0.60 promille away

best match from 2012 or earlier :
42,57,27,45,25,34,10,10 mutations or 1.84,2.50,1.25,2.64,1.67, 2.46,1.01,1.21 prozent away

A/duck/Hunan/S4220/2011,2011/11/13,China,H5N1 : 42,--,27,--,25,--,10,10

25,15,16,--,08,--,20,26 and 20,23,16,--,08,--,16,26 amino-acids away from the bird index,
so a poultry (including domestic duck) virus and not a wild bird/mallard virus
segments 2,3,4,(5),7,8 are of Fujian(2005)-type


these 2 H5N6 have Y52H(NP)
see : http://www.ncbi.nlm.nih.gov/pubmed/25505067


showing the great diversity of avian influenza in China ...

-----------edit 2015/01/17------------------
10 more genomes today , H5N1,H5N6

Code: 
13 >Index Fujian  
  1: 62, 42, 30, 56, 41,429, 27, 31   P090436,A/duck/Jiangxi/NCDZT1123/2014,2014/06/29,China,H5N6
  2: 59, 47, 30, 56, 42,428, 24, 31   KP090444,A/duck/Jiangxi/NCDZT1126/2014,2014/06/29,China,H5N6
  3: 57, 37, 33, 55, 40,424, 22, 29   KM251532,A/Anas_crecca/Hubei/Chenhu1623-5/2014,H5N6
  4: 56, 37, 32, 57, 40,425, 22, 29   KM251533,A/chicken/Sichuan/NCJPL1/2014,H5N6
  5: 56, 37, 35, 55, 40,425, 21, 29   KM251534,A/duck/Sichuan/NCJPL7/2014,H5N6
  6: 56, 37, 32, 58, 40,425, 23, 27   KM251535,A/duck/Sichuan/NCXJ15/2014,H5N6
  7: 56, 36, 32, 57, 40,423, 23, 29   KM251536,A/duck/Sichuan/NCXJ16/2014,H5N6
  8: 56, 36, 32, 57, 40,423, 23, 29   KM251537,A/duck/Sichuan/NCXJ24/2014,H5N6
  9: 55, 32, 22, 58, 42, 46, 23, 32   KM251539,A/duck/Sichuan/NCXN10/2014,H5N1
 10: 53, 31, 29, 56, 41, 48, 24, 31   KM251540,A/duck/Sichuan/NCXN11/2014,H5N1
 11: 56, 36, 33, 54, 40,425, 22, 27   KM251538,A/environment/Sichuan/NCLL1/2014,H5N6
 12: 53, 32, 29, 56, 41, 48, 23, 31   KM251541,A/pigeon/Sichuan/NCXN29/2014,H5N1
 13:  0,  0,  0,  0,  0,  0,  0,  0   Index Fujian


Code: 
[FONT=Arial][SIZE=2]                                                      0001 2 001111 0 00011 0 00
                                                      5685 0 002466 7 24701 4 34
                                                      1016 4 349588 5 34001 1 60
                                                      0736 9 363836 9 64489 8 65
-codon-position--------------------------------------- 1      1       2 2   1  
---Index----------------------------------------------GAAC T TGCTGG T ACGAA A CG
2 >KM251533,A/chicken/Sichuan/NCJPL1/2014,H5N6        AC.T . ...C.. . C.... . T.
3 >KM251534,A/duck/Sichuan/NCJPL7/2014,H5N6           AC.T . CA.CAA . C.... . T.
1 >KM251532,A/Anas_crecca/Hubei/Chenhu1623-5/2014,H5N6..C. . CA..AA . ...C. . ..
7 >KM251538,A/environment/Sichuan/NCLL1/2014,H5N6     ..C. . CA..AA . ..... . ..
4 >KM251535,A/duck/Sichuan/NCXJ15/2014,H5N6           ..C. . ...... . ...C. . ..
5 >KM251536,A/duck/Sichuan/NCXJ16/2014,H5N6           .... C ..T... C .TA.G G .A
6 >KM251537,A/duck/Sichuan/NCXJ24/2014,H5N6           .... C ..T... C .TA.G G .A
[/SIZE][/FONT]
 
Last edited by a moderator:
GenBank Accession Numbers KP307954-KP307961 represent sequences
from the 8 segments of Influenza A virus
(A/turkey/BC/FAV10/2014(H5N2)).

http://www.ncbi.nlm.nih.gov/nuccore/KP307954


the Canada virus has too many mutations to be a direct descendent
in segments 1,3,4,7,8 of the Korea-Jan-2014 strain

but the common ancester could have been in summer or fall 2013



compared with the Korea-H5N8 index we have these changes:
(some of these probably preceed Korea,Jan,2014)


nucleotide mutations:
>A/turkey/BC/FAV10/2014,2014/12/02
1,11,C126T,C498T,C705T,G745A,A753G,C891T,T975C,C1041T,C1998A,T2064C,G2070A
2,0
3,14,T174C,C645A,T654C,C720A,A777G,G837A,G859T,G894A,A927G,T1422C,C1498T,T1578C,T1581C,C1678T
4,14,C22T,G31A,A111G,G267A,A404G,A714G,C715A,G853A,C1107T,C1110T,C1155A,A1485G,G1535T,A1590G
5,0
6,0
7,0
8,2,T99C,A270G

amino-acid mutations:
>A/turkey/BC/FAV10/2014,2014/12/02
1,1,E249K
2,0
3,2,A287S,P560S
4,6,L8F,V11I,K135R,R239S,V285M,R512I
5,0
6,0
7,0
 
> the Canada virus has too many mutations to be a direct descendent
> in segments 1,3,4,7,8 of the Korea-Jan-2014 strain

I have to retract that.
Looking at the mutations in detail, I see that almost all
of the Canadian mutations in 1,3,4,7,8 are new ones,
additional ones, adding to the pre-H5N8 circulating viruses
in addition to the Korea-Jan.2014 strain.

So, it could well be a direct descendent of the Korea-virus.
But then there are unusually many mutations Jan-Dec,
41 in 1,2,4,7,8 in 11 months or ~70 per year,
while I'd expected 40-50 per year.

maybe the Korea virus oversummered in the environment for ~1/2 year
(as did the Suffolk/Hungary virus in 2007)
--------------------------

it's the same lab, that "created" all these extra mutations in the
Alberta swine with mexflu in May 2009, remember ? See below.
Probably they know this ... maybe that's the reason for the delay.
We'll see soon, when other labs release H5Nx sequences...

Submitted (22-DEC-2014) Canadian Food Inspection Agency, National
Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg,
Manitoba R3E 3M4, Canada
DNASTAR Lasergene v. 12
Sequencing Technology :: Sanger dideoxy sequencing


http://www.ncbi.nlm.nih.gov/nuccore/GQ150325.1

Submitted (11-MAY-2009) NCFAD, Canadian Food Inspection Agency,
1015 Arlington Street, Winnipeg, Manitoba R3E 3M4, Canada
/note="embryonated chicken eggs passage 1CE-3dpi"
 
3153=376+408+366+429+377+431+368+398 China Avian segments from 2013,2014 today
serotypes H5,6,7,9,10, N2,3,5,6,7,8 most are H10 , many are mixed (==> reassortment)
ftp://ftp.ncbi.nih.gov/genomes/INFLU...fluenza_na.dat

I make it 478 viruses, distinguishing "clone a","clone b" etc of the 1337(!) mixed segments
mixed viruses are a bit hard to handle at genbank (IMO) [they disagree...]

2003:16,2005:72,2006:48,2008:81,2009:130,2012:8,
2013(Jan-Nov):1012,2013Dec:682,2014(-Apr.20):1004

chicken:1913,duck:1181,environment:35,goose:24

Jiangxi:2943,Shenzhen:94,Dongguan:82,Shantou:24,Ni ngbo:10

1337 mixed,480 H9N2,344 H10N8,288 H10N6,280 H10N3,208 H5N6,104H10N7,72 H10N5

only the one from Ningbo of these is a little related to Korea-Europe-America H5N8
A/duck/Ningbo/3262/2013/10/20,mixed H5N6,H5N8
segment 6 (NA) with 24 differences is a new closest to Korean N8
segments 3,4,5,7 are also somehow close, but others from 2011 are closer


http://magictour.free.fr/BITSCG0b.GIF
 
gyrfalcon Asian H5N8 from Washington, 2014/12/08 at genbank
segment 1segment 2segment 3segment 4segment 5segment 6segment 7segment 8

and H5N2 pintail from 2014/12/08:
(A/Northern pintail/Washington/40964/2014(H5N2)).
segment 1segment 2segment 3segment 4segment 5segment 6segment 7segment 8


mutation table :
Code: 
                                                                                    00000000000000111111111111111111111122 000000000000000000111111111111111111111222 0000000000000000000000000000111111111111111111111111111111122 00000000000000000000000000000000000000000001111111111111111111 0000000000000111111 000000000000000000000001111111 000000000000 00000000000
                                                                                    13445567777789000223444555678888999900 001122344566788999000111223444456778899002 0111112244555666777888888899000001123334444555556666788999911 00000111122222223333344444445666677778888990000111134444555667 1123445568889023344 000111123445556678899990011112 122245556678 02223344567
                                                                                    24497850458897034565028038411338125967 235701378059033589017279567044495587758365 5027785956268145228123578936005791163891249045783779649188913 23388118901234680124801666792333711790555162249015934788139780 1256452831298761547 229135700082563692200584504898 836822790295 01336812597
                                                                                    62486875530615581400959771109794103840 433719079459514143871494734736993850236477 8894535762312254040987902496263460902944248627812185726136223 80148140526540759895948689482126845187038292312705700358650111 1089402576271201665 256489476665586915867554046807 974402980743 61497070218
-codon-position---------------------------------------------------------------------        1           2 111   11                   1          2             1     1 1   1     1      1    1      1  1     21 11       1           1 1 1    1        2 2211 1   12   1   11   2       1    12  1          1    1    2 11       1   1  2   111     2     2   1  21  1 212   11
---Index----------------------------------------------------------------------------CCCCACACGACGCTTACATGGAACCACGTATTCATCTG CAACCAAGGAGAGAATTGGTCCGAGAATACTCTGCCTGCTTA ATGTAAGAGGTGTGCTCCCTCGGGCGGTTTAACCTGCTTTTTCGTTTTAACACTTTGGGAT GGGAAAATCCCGTTGCCTCGCAAGATACGGATGACTAAGGGCGGAACCCCATTCACAGATTC ATGATAAAACTCGCTCACG GAAGTCACCTCGTGCAGGAAATAGGAACCT GCGAAAATACCT CGAAACTGGCT
   1 >Index/h5n8b/Korea-2014,2014/01/01,Korea,H5N8,Avian,1                          ...................................... .......................................... ............................................................. .............................................................. ................... .............................. ............ ...........        0      0 ,      0      0       1:>Index/h5n8b/Korea-2014,2014/01/01,Korea,H5N8,Avian,1                          
   2 >Index/h5n8b2_2-21/Korea-2014,2014/01/01,Korea,H5N8,Avian,1                    T..................................... .......................................... ............................................................. .............................................................. ................... .............................. ............ ...........        1      1 ,      1      1       2:>Index/h5n8b2_2-21/Korea-2014,2014/01/01,Korea,H5N8,Avian,1                    
   3 >Index/h5n8b1_22-38/Korea-2014,2014/01/01,H5N8,Avian,1                         ......................C............... .......................................... ............................................................. ....................................GC......................C. .....G.....T....... .............................. ............ ...........        6      6 ,      6      6       3:>Index/h5n8b1_22-38/Korea-2014,2014/01/01,H5N8,Avian,1                        
   4 >A/baikal teal/Korea/Donglim3/2014,2014/01/17                                  ......................C............... .......................................... ............................................................. ....................................GC........T.............C. .....G.....T....... .............................. ............ ...........        8      7 ,      8      7       4:>A/baikal teal/Korea/Donglim3/2014,2014/01/17                                  
   5 >A/mallard/Korea/W452/2014,2014/02/05                                          ......................C............... .......................................... ...................................A......................... ....................................GC..A............A......C. ..A..G.....T....... .............................. ............ ...........       16     10 ,     16     10       5:>A/mallard/Korea/W452/2014,2014/02/05                                          
   6 >A/broiler Dk/Korea/Buan2/2014,2014/01/17                                      ...................................... .....G.................................... .......G.................A................................... .....................................C......................C. .....G.....T....... .............................. ............ ...........       11      7 ,     11      7       6:>A/broiler Dk/Korea/Buan2/2014,2014/01/17                                      
   7 >A/Ck/kumamoto/1-7/2014,2014/04/13                                             ...................................... .....................................A.... ....G............A.......A..........T........................ .............................................................. ................... .............................. ............ ...........       23      5 ,     23      5       7:>A/Ck/kumamoto/1-7/2014,2014/04/13                                            
   8 >A/turkey/BC/FAV10/2014,2014/12/02,Canada,H5N2,Avian,1                         T..T...TAG..TC..T..................ACA ------------------------------------------ ...C..........ACA....AT..A..............C.T...CC..T.......... ..A..G........A......G...........GA....A.......TTA....G..TG... ------------------- ------------------------------ ............ ...........      311    127 ,     41     36       8:>A/turkey/BC/FAV10/2014,2014/12/02,Canada,H5N2,Avian,1                        
   9 >KP307973,A/Northern pintail/Washington/40964/2014,2014/12/08,USA,H5N2,Avian   T..T...TAG..TC..T..................ACA ------------------------------------------ ...C..........ACA....AT..A..............C.T...CC..T.......... ..A..G........A.....AG...........GA....A.......TTA....G..TG... ------------------- ------------------------------ ............ ...........      308    128 ,     38     37       9:>KP307973,A/Northern pintail/Washington/40964/2014,2014/12/08,USA,H5N2,Avian  
  10 >KP307981,A/gyrfalcon/Washington/41088-6/2014,2014/12/08,USA,H5N8,Avian        T..T...TAG..T...T..................ACA .......A..A...............G............... ...C..........ACA....AT...................T...CC..T.......... ..A..G........A......G...........GA....A.......TT.....G..TG... ..AG........A...... .............................. ............ ...........       69     38 ,     69     38      10:>KP307981,A/gyrfalcon/Washington/41088-6/2014,2014/12/08,USA,H5N8,Avian        
  11 >h5n8pre1:k1203;1-15;1-15;628;628;k1203;1-15;1-15                              .TT.GTG...TT..GG.GCA...ATGT..GCGTGC... T.GT..G.AGAGAGG.CA.CTAACAC.CGTCT.A.TGATCC. GCA.GG.CAACAC.....T.T........CG.TT....CG.C..C...GG.GTC.CAA.GC C..GG.GATTTACC.ATCAAT.G.GCCTAACC...C..A.ATAAGGT...GCCT.TC..C.T GC..C.GGCTC..TCAGTA AG.A.TGTT.T.AATGAA.GGCGTAG.TTC .TAGG.G..TTC TAG.GACAATC      197    184 ,    197    184      11:>h5n8pre1:k1203;1-15;1-15;628;628;k1203;1-15;1-15                              
  12 >h5n8pre2:628;1111;1111;k1203;sd1;6d18;1111;1111                               .TT.GTG...TT..GG.GCAAG.ATGTACGCGTGC... TGGT..G.AGAGAGG.CA.CTAACAC.CGTCT.A.TGATCC. GCA.GG.CAACAC.....T.T........CG.TT....CG.C..C...GG.GTC.CAA.GC AAAGG.GATTTACC.AT.GAT.GAGCCTAACCA..C....AT.AG.T...GC.T.TC..C.T GC..C.GGCTC..TCAGTA AGGAGTGT.GTACATGA...G.GT.GGTTC .TAGG.G..TTC .AG.GACAATC      203    187 ,    203    187      12:>h5n8pre2:628;1111;1111;k1203;sd1;6d18;1111;1111                              
  13 >H5N8pre3:m234;1112;1112;m234;m234;goch1;628;1112                              .TT.GTG...TT..GG.GCAAG.ATGTACGCGTG.... TGGTT.G..GA.AGGGCAAC.AACACGCGTC.C.ATGATCCC GAA.GGA.A.CACAT..ATGT..AT.ACCCGGTTCATGCG...ACC..GG.GTCCCAAAGC C..GG.GATTTACC.ATCAAT.G.GCCTAACC...C..A.ATAAGGT...GCCT.TC..C.T GC..C.GGCTC..TCA.TA A.GAGTGT.GTACATGA.G.G.GT.GGTTC ATAGGGGGGTT. ...C.AC.ATC      274    204 ,    274    204      13:>H5N8pre3:m234;1112;1112;m234;m234;goch1;628;1112                              
  14 >H5N8pre4:wy11;008;108;wy19;wy11;90;008;1904                                   .TT.GTG...TT..GG.GCA.G.ATGT.CGCGTGC... T.GTTGGA.GA.AGGGCAAC.AATAC.CGTCTC.A.GATCCC GCA.GGA.AACACA...ATG...AT.ACCCGGTTC..GCG.C.ACC..GG.GTCCCAAAGC AA.GG.GATTTACC.AT.AAT.GAGCCTAACCA..C....ATAAG.T...GC.T.TC..C.T GC.G..GGCTC.ATCA.TA A..AC..TT...GATGAAGGGCGTAGGTTC ATAGGGGGGTT. T..C.A.AATC      400    201 ,    400    201      14:>H5N8pre4:wy11;008;108;wy19;wy11;90;008;1904                                  
                                                                                                                                                                                                                                                                                                                                                                              
---Index----------------------------------------------------------------------------CCCCACACGACGCTTACATGGAACCACGTATTCATCTG CAACCAAGGAGAGAATTGGTCCGAGAATACTCTGCCTGCTTA ATGTAAGAGGTGTGCTCCCTCGGGCGGTTTAACCTGCTTTTTCGTTTTAACACTTTGGGAT GGGAAAATCCCGTTGCCTCGCAAGATACGGATGACTAAGGGCGGAACCCCATTCACAGATTC ATGATAAAACTCGCTCACG GAAGTCACCTCGTGCAGGAAATAGGAACCT GCGAAAATACCT CGAAACTGGCT
-codon-position---------------------------------------------------------------------        1           2 111   11                   1          2             1     1 1   1     1      1    1      1  1     21 11       1           1 1 1    1        2 2211 1   12   1   11   2       1    12  1          1    1    2 11       1   1  2   111     2     2   1  21  1 212   11
                                                                                    00000000000000111111111111111111111122 000000000000000000111111111111111111111222 0000000000000000000000000000111111111111111111111111111111122 00000000000000000000000000000000000000000001111111111111111111 0000000000000111111 000000000000000000000001111111 000000000000 00000000000
                                                                                    13445567777789000223444555678888999900 001122344566788999000111223444456778899002 0111112244555666777888888899000001123334444555556666788999911 00000111122222223333344444445666677778888990000111134444555667 1123445568889023344 000111123445556678899990011112 122245556678 02223344567
                                                                                    24497850458897034565028038411338125967 235701378059033589017279567044495587758365 5027785956268145228123578936005791163891249045783779649188913 23388118901234680124801666792333711790555162249015934788139780 1256452831298761547 229135700082563692200584504898 836822790295 01336812597
                                                                                    62486875530615581400959771109794103840 433719079459514143871494734736993850236477 8894535762312254040987902496263460902944248627812185726136223 80148140526540759895948689482126845187038292312705700358650111 1089402576271201665 256489476665586915867554046807 974402980743 61497070218


the gyrfalcon has 10+13+14+15+7+9+1+0=69 differences to the Korea sequences from January.
And it has only one such difference that goes towards candidate ancestor viruses,
you would expect more such differences, if the Korea sequences had time to evolve
since the common ancester.
So, this looks like it did descend from the Korean virus almost directly, despite the 69 differences.
Maybe the Korea virus lay in the water or came from
frozen meat without mutating for ~6 months .
This would be a rare observation, like the B.Mathews Turkey in 2007.

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

on 2015/02/11 we had at genbank:
KM251533,Avian,1-8,H5N6,China,2014/04/27,A/chicken/Sichuan/NCJPL1/2014
KM251534,Avian,1-8,H5N6,China,2014/04/27,A/duck/Sichuan/NCJPL7/2014
KM251535,Avian,1-8,H5N6,China,2014/04/27,A/duck/Sichuan/NCXJ15/2014
KM251536,Avian,1-8,H5N6,China,2014/04/27,A/duck/Sichuan/NCXJ16/2014
KM251537,Avian,1-8,H5N6,China,2014/04/27,A/duck/Sichuan/NCXJ24/2014
KM251539,Avian,1-8,H5N1,China,2014/04/27,A/duck/Sichuan/NCXN10/2014
KM251540,Avian,1-8,H5N1,China,2014/04/27,A/duck/Sichuan/NCXN11/2014
KM251538,Environment,1-8,H5N6,China,2014/04/27,A/environment/Sichuan/NCLL1/2014
KM251541,Avian,1-8,H5N1,China,2014/04/27,A/pigeon/Sichuan/NCXN29/2014
 
gsgs said:
gyrfalcon Asian H5N8 from Washington, 2014/12/08 at genbank
segment 1segment 2segment 3segment 4segment 5segment 6segment 7segment 8

and H5N2 pintail from 2014/12/08:
(A/Northern pintail/Washington/40964/2014(H5N2)).
segment 1segment 2segment 3segment 4segment 5segment 6segment 7segment 8


mutation table :
Code: 
00000000000000111111111111111111111122 000000000000000000111111111111111111111222 0000000000000000000000000000111111111111111111111111111111122 00000000000000000000000000000000000000000001111111111111111111 0000000000000111111 000000000000000000000001111111 000000000000 00000000000
13445567777789000223444555678888999900 001122344566788999000111223444456778899002 0111112244555666777888888899000001123334444555556666788999911 00000111122222223333344444445666677778888990000111134444555667 1123445568889023344 000111123445556678899990011112 122245556678 02223344567
24497850458897034565028038411338125967 235701378059033589017279567044495587758365 5027785956268145228123578936005791163891249045783779649188913 23388118901234680124801666792333711790555162249015934788139780 1256452831298761547 229135700082563692200584504898 836822790295 01336812597
62486875530615581400959771109794103840 433719079459514143871494734736993850236477 8894535762312254040987902496263460902944248627812185726136223 80148140526540759895948689482126845187038292312705700358650111 1089402576271201665 256489476665586915867554046807 974402980743 61497070218
-codon-position--------------------------------------------------------------------- 1 2 111 11 1 2 1 1 1 1 1 1 1 1 1 21 11 1 1 1 1 1 2 2211 1 12 1 11 2 1 12 1 1 1 2 11 1 1 2 111 2 2 1 21 1 212 11
---Index----------------------------------------------------------------------------CCCCACACGACGCTTACATGGAACCACGTATTCATCTG CAACCAAGGAGAGAATTGGTCCGAGAATACTCTGCCTGCTTA ATGTAAGAGGTGTGCTCCCTCGGGCGGTTTAACCTGCTTTTTCGTTTTAACACTTTGGGAT GGGAAAATCCCGTTGCCTCGCAAGATACGGATGACTAAGGGCGGAACCCCATTCACAGATTC ATGATAAAACTCGCTCACG GAAGTCACCTCGTGCAGGAAATAGGAACCT GCGAAAATACCT CGAAACTGGCT
1 >Index/h5n8b/Korea-2014,2014/01/01,Korea,H5N8,Avian,1 ...................................... .......................................... ............................................................. .............................................................. ................... .............................. ............ ........... 0 0 , 0 0 1:>Index/h5n8b/Korea-2014,2014/01/01,Korea,H5N8,Avian,1
2 >Index/h5n8b2_2-21/Korea-2014,2014/01/01,Korea,H5N8,Avian,1 T..................................... .......................................... ............................................................. .............................................................. ................... .............................. ............ ........... 1 1 , 1 1 2:>Index/h5n8b2_2-21/Korea-2014,2014/01/01,Korea,H5N8,Avian,1
3 >Index/h5n8b1_22-38/Korea-2014,2014/01/01,H5N8,Avian,1 ......................C............... .......................................... ............................................................. ....................................GC......................C. .....G.....T....... .............................. ............ ........... 6 6 , 6 6 3:>Index/h5n8b1_22-38/Korea-2014,2014/01/01,H5N8,Avian,1
4 >A/baikal teal/Korea/Donglim3/2014,2014/01/17 ......................C............... .......................................... ............................................................. ....................................GC........T.............C. .....G.....T....... .............................. ............ ........... 8 7 , 8 7 4:>A/baikal teal/Korea/Donglim3/2014,2014/01/17
5 >A/mallard/Korea/W452/2014,2014/02/05 ......................C............... .......................................... ...................................A......................... ....................................GC..A............A......C. ..A..G.....T....... .............................. ............ ........... 16 10 , 16 10 5:>A/mallard/Korea/W452/2014,2014/02/05
6 >A/broiler Dk/Korea/Buan2/2014,2014/01/17 ...................................... .....G.................................... .......G.................A................................... .....................................C......................C. .....G.....T....... .............................. ............ ........... 11 7 , 11 7 6:>A/broiler Dk/Korea/Buan2/2014,2014/01/17
7 >A/Ck/kumamoto/1-7/2014,2014/04/13 ...................................... .....................................A.... ....G............A.......A..........T........................ .............................................................. ................... .............................. ............ ........... 23 5 , 23 5 7:>A/Ck/kumamoto/1-7/2014,2014/04/13
8 >A/turkey/BC/FAV10/2014,2014/12/02,Canada,H5N2,Avian,1 T..T...TAG..TC..T..................ACA ------------------------------------------ ...C..........ACA....AT..A..............C.T...CC..T.......... ..A..G........A......G...........GA....A.......TTA....G..TG... ------------------- ------------------------------ ............ ........... 311 127 , 41 36 8:>A/turkey/BC/FAV10/2014,2014/12/02,Canada,H5N2,Avian,1
9 >KP307973,A/Northern pintail/Washington/40964/2014,2014/12/08,USA,H5N2,Avian T..T...TAG..TC..T..................ACA ------------------------------------------ ...C..........ACA....AT..A..............C.T...CC..T.......... ..A..G........A.....AG...........GA....A.......TTA....G..TG... ------------------- ------------------------------ ............ ........... 308 128 , 38 37 9:>KP307973,A/Northern pintail/Washington/40964/2014,2014/12/08,USA,H5N2,Avian
10 >KP307981,A/gyrfalcon/Washington/41088-6/2014,2014/12/08,USA,H5N8,Avian T..T...TAG..T...T..................ACA .......A..A...............G............... ...C..........ACA....AT...................T...CC..T.......... ..A..G........A......G...........GA....A.......TT.....G..TG... ..AG........A...... .............................. ............ ........... 69 38 , 69 38 10:>KP307981,A/gyrfalcon/Washington/41088-6/2014,2014/12/08,USA,H5N8,Avian
11 >h5n8pre1:k1203;1-15;1-15;628;628;k1203;1-15;1-15 .TT.GTG...TT..GG.GCA...ATGT..GCGTGC... T.GT..G.AGAGAGG.CA.CTAACAC.CGTCT.A.TGATCC. GCA.GG.CAACAC.....T.T........CG.TT....CG.C..C...GG.GTC.CAA.GC C..GG.GATTTACC.ATCAAT.G.GCCTAACC...C..A.ATAAGGT...GCCT.TC..C.T GC..C.GGCTC..TCAGTA AG.A.TGTT.T.AATGAA.GGCGTAG.TTC .TAGG.G..TTC TAG.GACAATC 197 184 , 197 184 11:>h5n8pre1:k1203;1-15;1-15;628;628;k1203;1-15;1-15
12 >h5n8pre2:628;1111;1111;k1203;sd1;6d18;1111;1111 .TT.GTG...TT..GG.GCAAG.ATGTACGCGTGC... TGGT..G.AGAGAGG.CA.CTAACAC.CGTCT.A.TGATCC. GCA.GG.CAACAC.....T.T........CG.TT....CG.C..C...GG.GTC.CAA.GC AAAGG.GATTTACC.AT.GAT.GAGCCTAACCA..C....AT.AG.T...GC.T.TC..C.T GC..C.GGCTC..TCAGTA AGGAGTGT.GTACATGA...G.GT.GGTTC .TAGG.G..TTC .AG.GACAATC 203 187 , 203 187 12:>h5n8pre2:628;1111;1111;k1203;sd1;6d18;1111;1111
13 >H5N8pre3:m234;1112;1112;m234;m234;goch1;628;1112 .TT.GTG...TT..GG.GCAAG.ATGTACGCGTG.... TGGTT.G..GA.AGGGCAAC.AACACGCGTC.C.ATGATCCC GAA.GGA.A.CACAT..ATGT..AT.ACCCGGTTCATGCG...ACC..GG.GTCCCAAAGC C..GG.GATTTACC.ATCAAT.G.GCCTAACC...C..A.ATAAGGT...GCCT.TC..C.T GC..C.GGCTC..TCA.TA A.GAGTGT.GTACATGA.G.G.GT.GGTTC ATAGGGGGGTT. ...C.AC.ATC 274 204 , 274 204 13:>H5N8pre3:m234;1112;1112;m234;m234;goch1;628;1112
14 >H5N8pre4:wy11;008;108;wy19;wy11;90;008;1904 .TT.GTG...TT..GG.GCA.G.ATGT.CGCGTGC... T.GTTGGA.GA.AGGGCAAC.AATAC.CGTCTC.A.GATCCC GCA.GGA.AACACA...ATG...AT.ACCCGGTTC..GCG.C.ACC..GG.GTCCCAAAGC AA.GG.GATTTACC.AT.AAT.GAGCCTAACCA..C....ATAAG.T...GC.T.TC..C.T GC.G..GGCTC.ATCA.TA A..AC..TT...GATGAAGGGCGTAGGTTC ATAGGGGGGTT. T..C.A.AATC 400 201 , 400 201 14:>H5N8pre4:wy11;008;108;wy19;wy11;90;008;1904

---Index----------------------------------------------------------------------------CCCCACACGACGCTTACATGGAACCACGTATTCATCTG CAACCAAGGAGAGAATTGGTCCGAGAATACTCTGCCTGCTTA ATGTAAGAGGTGTGCTCCCTCGGGCGGTTTAACCTGCTTTTTCGTTTTAACACTTTGGGAT GGGAAAATCCCGTTGCCTCGCAAGATACGGATGACTAAGGGCGGAACCCCATTCACAGATTC ATGATAAAACTCGCTCACG GAAGTCACCTCGTGCAGGAAATAGGAACCT GCGAAAATACCT CGAAACTGGCT
-codon-position--------------------------------------------------------------------- 1 2 111 11 1 2 1 1 1 1 1 1 1 1 1 21 11 1 1 1 1 1 2 2211 1 12 1 11 2 1 12 1 1 1 2 11 1 1 2 111 2 2 1 21 1 212 11
00000000000000111111111111111111111122 000000000000000000111111111111111111111222 0000000000000000000000000000111111111111111111111111111111122 00000000000000000000000000000000000000000001111111111111111111 0000000000000111111 000000000000000000000001111111 000000000000 00000000000
13445567777789000223444555678888999900 001122344566788999000111223444456778899002 0111112244555666777888888899000001123334444555556666788999911 00000111122222223333344444445666677778888990000111134444555667 1123445568889023344 000111123445556678899990011112 122245556678 02223344567
24497850458897034565028038411338125967 235701378059033589017279567044495587758365 5027785956268145228123578936005791163891249045783779649188913 23388118901234680124801666792333711790555162249015934788139780 1256452831298761547 229135700082563692200584504898 836822790295 01336812597
62486875530615581400959771109794103840 433719079459514143871494734736993850236477 8894535762312254040987902496263460902944248627812185726136223 80148140526540759895948689482126845187038292312705700358650111 1089402576271201665 256489476665586915867554046807 974402980743 61497070218


the gyrfalcon has 10+13+14+15+7+9+1+0=69 differences to the Korea sequences from January.
And it has only one such difference that goes towards candidate ancestor viruses,
you would expect more such differences, if the Korea sequences had time to evolve
since the common ancester.
So, this looks like it did descend from the Korean virus almost directly, despite the 69 differences.
Maybe the Korea virus lay in the water or came from
frozen meat without mutating for ~6 months .
This would be a rare observation, like the B.Mathews Turkey in 2007.

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

on 2015/02/11 we had at genbank:
KM251533,Avian,1-8,H5N6,China,2014/04/27,A/chicken/Sichuan/NCJPL1/2014
KM251534,Avian,1-8,H5N6,China,2014/04/27,A/duck/Sichuan/NCJPL7/2014
KM251535,Avian,1-8,H5N6,China,2014/04/27,A/duck/Sichuan/NCXJ15/2014
KM251536,Avian,1-8,H5N6,China,2014/04/27,A/duck/Sichuan/NCXJ16/2014
KM251537,Avian,1-8,H5N6,China,2014/04/27,A/duck/Sichuan/NCXJ24/2014
KM251539,Avian,1-8,H5N1,China,2014/04/27,A/duck/Sichuan/NCXN10/2014
KM251540,Avian,1-8,H5N1,China,2014/04/27,A/duck/Sichuan/NCXN11/2014
KM251538,Environment,1-8,H5N6,China,2014/04/27,A/environment/Sichuan/NCLL1/2014
KM251541,Avian,1-8,H5N1,China,2014/04/27,A/pigeon/Sichuan/NCXN29/2014
Click to expand...

Thank you, gsgs! I hadn't heard about the B. Matthews case:

https://en.wikipedia.org/wiki/Bernard_Matthews_Farms

If something like that happened at a big farm again it should be traceable, though if this traces back to a big farm with no importation history, I'd wonder about cockfighting in the area. Those types of operations likely would not report sick birds or keep records of importations.

http://www.thestar.com/news/canada/2008/03/01/1200_birds_euthanized_after_cockfighting_bust.html
http://www.avtimes.net/news/british...change-plea-in-us-cockfighting-case-1.1127173
 
> Thank you, gsgs! I hadn't heard about the B. Matthews case:
> https://en.wikipedia.org/wiki/Bernard_Matthews_Farms

the direct wiki-link to the outbreak is:
https://en.wikipedia.org/wiki/2007_B..._H5N1_outbreak
The sequences were quickly released, after only some days and there were only
4 differences from the Hungarian virus. However, it took months until BM finally
admitted that trucks from Hungary were the most likely source.
The Hungarian/BM sequences had considerably fewer mutations than other
related viruses, suggesting a 1/2-1 year freeze, afair.
This is the best direct example for such a freeze, afaik. We had some examples of slow
evolution over longer time, e.g. some segments HK70s --> China ~2000, see the slow
evolution thread. But this BM was a whole virus with lots of related viruses available.
I wrote email to DEFRA about it - no reaction. I've never seen this mentioned in papers
or newspapers.

Now, these Korea sequences could be a similar case, it should become clearer, when
the European and Taiwanese sequences from this season are published.
Strangely these events are often associated with severe outbreaks, much improved
viruses. H1N1 in 1977, H5N1 in China 2002, H3N8 in Alaska, ... and now maybe H5N8

> If something like that happened at a big farm again it should be traceable, though if this
> traces back to a big farm with no importation history,

the sequences should show it

> I'd wonder about cockfighting in the area. Those types of operations likely would not
> report sick birds or keep records of importations.
> http://www.thestar.com/news/canada/2...ting_bust.html
> http://www.avtimes.net/news/british-...case-1.1127173

I don't think cockfighting is an issue here.
We have lots of clear evidence about wild birds meanwhile, wigeons, teals, crane, swans.
The cocks may only add to that, but the main spread is likely by waterfowl.
And if cocks were related to the possible freeze, then it would be Korean or Chinese cocks
in summer 2014, - America got the additional mutations.

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

I added the 3 Taiwan sequences, they have still more mutations.
Complete mutation table below, mutations that only occur once
in the list are included (and not skipped, as I usually do)

Code: 
[FONT=Arial][SIZE=2]                                                                                    00000000000000000000000000000000000001111111111111111111111111111111111111111222222222 000000000000000000000000000011111111111111111111111111111111111111111111111112222222222 0000000000000000000000000000000000000000000000000011111111111111111111111111111111111111111111111111111111112222222 000000000000000000000000000000000000000000000000000000000000000000000000000000000000011111111111111111111111111111111 00000000000000000000000000000000000000000000000000001111111111111111111111 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000111111111111111111111111111 0000000000000000000000000000000 000000000000000000000000000000000000000000000000000
                                                                                    01112222333333444444556667777777888890000111222223333444455555666678888899999000001112 000111222333445666678888899900000001111111111222233334444455556667777788899990000011122 0001111122233334444555556666777777788888888999999900000000111112233333333444444455555566666666788888889999990000111 000000000000011111111122222222222333333333333344444444444455555666666677777788888899900000111123344444444455555566667 00011111122222333344444444455555666788888888899999990000111111122222334444 000000000000011111111111111122222222233333333334444444455555556666666777777777778888999999999000000001111122222222333333 0011222233334445555566666777888 001112222222222223333333333444445555566666677777778
                                                                                    82390226011347245669785790455889079970134125005682588028901338234711233801259067790266 239357015345780235901334558901133470122245579056825790444718995770158977745890035602705 1590277859900231568225681445022678812345789023566900455799113462612336899001234904577801347789634577991258890277113 001222334478811245588900123456689001123344688901223456667902559133347811257900555815622459015923602347788811366947780 56812357934569056702455668927789358712245679901135781127033445702367154447 122233444589901123334455677902444556900111236770000145822445672335689012467899992249000135688023445560448922344588012356 2808346822782781278901227129156 091680111123355670134456889112352344503459911336781
                                                                                    86089274025923043898687595513064151655481926034049036959175071051409779451038140915436 430837192084794795956146914385725917624591794673131487369381693174285102943691745791837 8818945357902598625354122564904270198709024979767926738468094637047255934484274862758184271895792478671133621823283 781028010124814074501527654053756595890159749248794596894882241512688145851847038827923192705710548703957856503011711 19410534216877649520406580520953744162507704764887511762701365931005165695 524507258391644900580479514676069282469026109272568126657695804672976379751812485837367235315296470424368079758179170242 5059734447870433298802172534437 697599014954926100532537089670677249247611459890897
-codon-position---------------------------------------------------------------------1 1 2 2      1    1       11   2 2 2       1         2 1 1  1      1 1            2  1                  1      1    1   2    2  22       1               2   1 1   1        11  11   1   2 21 1  21 2    1 1 1   1    1        1  1  2 1     2   1    12 11  11           1      2  1 1      2     122211 112  1    12 1 1      2  22   2 1 11 22211 21 1 1  1  2  12     122    11     2         1        2  12      1                                 21       2     2 2      1 2            2  2  1 1 1   221 2 2 1  2 1    1 1     1   1 1    2  1  1   2   1   11   1     22 2       1  1  1  1   1     2 21    22   1  12     2           1     1 211       2 11   2 1       2121 2  11211  111 1112 111 1
---Index----------------------------------------------------------------------------ACGGGCCATGAGCTACCCACACACCCGAACGATCCGTTTACTAGACATGAGTAGAACCACCATGCGGTAATTCCATCCTGGGGAAA CACGACCAAAAAGGAACGAGTAAGATTGGATCAGCAGACCACGGAGGACCGACTACTACTTCTTTAGGCCCTCCGCGCGTTTCGAAA AAGTGTAAGATCATGTGGCTGGGTGCGTACCCACATCGGGGCGGAGGTGCTTAAAACACTAGGCGTACCTTATCTTTCTCGTTCTTGAACACTACATGAGTATCAGGGCGAGAGT AATTCGGGGTTAAAACGACTACCGCGTTGGGCCCCCTCCCGCAGCTAAAATGCGATACAGTGCTGATTGAACAATATAGGGTCCGGAAGCCCCAATCAGTTCTAGCTAGAGAATGTC ATTATTTGAGTGAAAGATCCTAGGCTTAAGAAACGTCTTTCTCGCCGGTTAGGGGCAGCGACATCCTCCAGCCG GGAATAAAGTTTACGAAACTGTTCATATCCCTATCCTCGAAGCAATAGATTAAACGCTTTGGGCGGATTAATGATGGACTGAAGGAATGTTAAAAGGCGCAAGACCATTGATTGGTTAAT AGAGCGGAACCTAGCAAACTAGTCCGGCCTA CTCGAGGGGTAAAAAAAACATCAACCCATGTGTAAAGATTACGGATCATTC
   1 >Index/h5n8b/Korea-2014,2014/01/01,Korea,H5N8,Avian,1                          ...................................................................................... ....................................................................................... ................................................................................................................... ..................................................................................................................... .......................................................................... ........................................................................................................................ ............................... ...................................................        0      0 ,      0      0       1:>Index/h5n8b/Korea-2014,2014/01/01,Korea,H5N8,Avian,1                         
   2 >Index/h5n8b2_2-21/Korea-2014,2014/01/01,Korea,H5N8,Avian,1                    .T.................................................................................... ....................................................................................... ................................................................................................................... ..................................................................................................................... .......................................................................... ........................................................................................................................ ............................... ...................................................        1      1 ,      1      1       2:>Index/h5n8b2_2-21/Korea-2014,2014/01/01,Korea,H5N8,Avian,1                   
   3 >Index/h5n8b1_22-38/Korea-2014,2014/01/01,H5N8,Avian,1                         .......................................................C.............................. ....................................................................................... ................................................................................................................... ...........................................................................G.C.....................................C. .....................G......................T............................. ........................................................................................................................ ............................... ...................................................        6      6 ,      6      6       3:>Index/h5n8b1_22-38/Korea-2014,2014/01/01,H5N8,Avian,1                        
   4 >A/baikal teal/Korea/Donglim3/2014,2014/01/17                                  .......................................................C.............................. ..........G............................................................................ ................................................................................................................... ...........................................................................G.C...........T.........................C. .....................G......................T............................. ........................................................................................................................ ............................... ...................................................        8      8 ,      8      8       4:>A/baikal teal/Korea/Donglim3/2014,2014/01/17                                 
   5 >A/mallard/Korea/W452/2014,2014/02/05                                          .......................................................C.............................. ....................................................................................... ..................................G........T....................A.................................................. .........................................T...........................C.....G.C..A....................A.............C. ...........A.........G......................T............................. ......................................A........A........................................................................ ............................... ...................................................       16     16 ,     16     16       5:>A/mallard/Korea/W452/2014,2014/02/05                                         
   6 >A/broiler Dk/Korea/Buan2/2014,2014/01/17                                      ....................................................................C................. .......G.........................................T...................T................. .........G................................A........................................................................ .............................................................................C.....................................C. ...............A.....G......................T............................. ........................................................................................................................ ............................... ...................................................       11     11 ,     11     11       6:>A/broiler Dk/Korea/Buan2/2014,2014/01/17                                     
   7 >A/Ck/kumamoto/1-7/2014,2014/04/13                                             ...A.........C........................................................................ ...........G......................................A........G..............A............ ......G....T..................A...........A....................T...T......C.......................G................ ....................................................T....................G..............................A............ ...........................................................A.............. ..........................................A....................................................A....G................... ............................... ..................T.....................C..........       23     23 ,     23     23       7:>A/Ck/kumamoto/1-7/2014,2014/04/13                                            
   8 >A/turkey/BC/FAV10/2014,2014/12/02,Canada,H5N2,Avian,1                         .T.................T.....TA.G.....T.C...T...................................A.CA...... --------------------------------------------------------------------------------------- .....C...................A.C.A..G....A.T..A.G...............................C..T....CC.....T....................... ....T..A.....G................A...............G.......................GA.......A..........TTA..........G....T..G..... -------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------------------ ............................... .C..............G..................................      322    322 ,     41     41       8:>A/turkey/BC/FAV10/2014,2014/12/02,Canada,H5N2,Avian,1                        
   9 >KP307973,A/Northern pintail/Washington/40964/2014,2014/12/08,USA,H5N2,Avian   .T.................T.....TA.G.....T.C...T..T................................A.CA...... --------------------------------------------------------------------------------------- .....C...................A.C.A.......A.T..A.................................C..T....CC.....T....................... .......A.....G................A.............A.G.......................GA.......A..........TTA..........G....T..G..... -------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------------------ ............................... ...................................................      319    319 ,     38     38       9:>KP307973,A/Northern pintail/Washington/40964/2014,2014/12/08,USA,H5N2,Avian  
  10 >KP307981,A/gyrfalcon/Washington/41088-6/2014,2014/12/08,USA,H5N8,Avian        .T.................T.....TA.G.....T.....T...................................A.CA...... ............A...TA..............C..T...T...........G......T.............TT....A....AG.. .....C............T......A.C.A.......AAT.......................................T....CCA....T................T...... .......A.....G................A....A..........G.......................GA.......A..........TT....T..C...G....T..G..... ........G..A....G.......................TC.....A...A...................... .....CG.......................A..............AG...............................AC...A...................................C .........T..................... ...................................................       69     69 ,     69     69      10:>KP307981,A/gyrfalcon/Washington/41088-6/2014,2014/12/08,USA,H5N8,Avian       
  11 >A/GS/TW/0103/2015.2015/01/09,H5N8,Taiwan,Avian                                .T.......A....G.T.G......TA.G...C.T.................G............A..........A.CA...... --------------------------------------------------------------------------------------- G....C.........C..........AC...........T............G.C..............A.........T....CC.....T...........T........... .......A..C..G..A.........................CA..G...........G........G...A.......A...T...T..TT.....GA....G....T.....A.. -------------------------------------------------------------------------- ......................C.......A..C.....GG..G.AG..............A............C...A....A....A..G..G............CA..........C ........................T...... ..........................T..................C.....      231    231 ,     70     70      11:>A/GS/TW/0103/2015.2015/01/09,H5N8,Taiwan,Avian                               
  12 >A/GS/TW/0104/2015(H5N2),2015/01/09,Taiwan,H5N2,Avian                          -------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------------- .......A.....G...................T............G....................G...AG......A..........TT.....GAC..CG....T........ -------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------------------ ......................A.T...... ---------------------------------------------------      551    551 ,     18     18      12:>A/GS/TW/0104/2015(H5N2),2015/01/09,Taiwan,H5N2,Avian                         
  13 >A/GS/TW/01042/2015(H5N3),2015/01/12,Taiwan,H5N3,Avian                         -------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------- G....C.....................C...........T......A.....G.C.......T......A.........T....CC.....T...........T........... .......A.....G........T.......................G....................G...A.......A..........TT.....GA....G....T........ -------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------------------ ........G...............T...... ........A.................T..................C.....      399    399 ,     32     32      13:>A/GS/TW/01042/2015(H5N3),2015/01/12,Taiwan,H5N3,Avian                        
  14 >h5n8pre1:k1203;1-15;1-15;628;628;k1203;1-15;1-15                              ....A.......T..T....GTG......TT......G.G.C....GC..A......A..TG.AT....GCG.TGC.........G T...GT...G...AG..AGA.GG...CA..C...T...A....AC.AC.....CGTC....T.....A..TG..AT...C.C..... .G.CA.GG.C...G..AA.C..AC.........T..T............T.C.G..T.T.............C..G..C..C......G.G..GT.C.....C..AA.....G.C ...C.C.....GG.G....A.TT.TACC...A..T.CA..A...T..G......GCCT.A....ACC.......C...A.A.T.AAGG.T...G.C....CT...T.C.....C..T ...GC...............C......G..G.C...TC........A.C......T..........C.AG.T.A .A.GC.........A........T..G.T........T................T....AA..TA.G.........A...A....GG..C..G...T.A..G..TT......C....... ....T.AG....G....G.....T...T.CG T......A...G...........GA...CA.A....A....T......C..      197    197 ,    197    197      14:>h5n8pre1:k1203;1-15;1-15;628;628;k1203;1-15;1-15                             
  15 >h5n8pre2:628;1111;1111;k1203;sd1;6d18;1111;1111                               ............T..T....GTG......TTC.....G.G......GC..A..AG..A..TG..T.AC.GCG.TGC.......... TG..GT...G...AG..AGA.GG...CA..CT..T...A..T.AC.AC.....CGTC....T.....A..TG..AT...C.C..... .G.CA.GG.C......AA.C..AC.........T..T..............C.G..T.T.............C..G..C..C......G.G..GT.C..A..C..AA..AGAGCC .....AAAAC.GG.G....A.TT.TACC...A..T..G..A...T..G.....AGCCT.A....ACC.A.....C.....A.T..AG..T...G.C.....T...T.C....GC..T ...GC...............C......G..G.C...TC.................T..........C.AG.T.A .A.G........G.A....G...T.CG.T....................G..G.TA...CA..T..G.........A.........G.....G...T..A.G.GTT......C....... G...T.AG....G....G.....T...T.C. .......A...G...........GA...CA......A....T......CG.      203    203 ,    203    203      15:>h5n8pre2:628;1111;1111;k1203;sd1;6d18;1111;1111                              
  16 >H5N8pre3:m234;1112;1112;m234;m234;goch1;628;1112                              G.....A....AT..T....GTGT.....TT......G.G......GC..A..AG..AGTTG..T.AC.GCG.TG.....A...G. TG..GTT.GG....G..A.AAGG..GCAAGC..A...CA.G..AC.ACT..GTCGTC...C.C.C.A.A.TG..AT...CCC....C .GAAA.GGA...G.A.A..CTAACAT....AT.T.GT...AT...A.CA.CC.G.GTGTCGT..ACCTT.GGCT.G.T..ACCT...GG.G.AGTGCT..CCC.GAAA....G.C GGA..C.....GG.G..GTA.TT.TACC...AA.T.CA..A...T..G......GCCT.A....ACC.......C...A.AGT.AAGG.T...G.C....CT...T.C.G...C..T ...GC...............C......G..G.C...TC....T............T..........C.A.TT.A AAG......CCCG.A....G...T..G.T....................G....TA...CA..T..G.........A....G....G.....G...T....G.GTT......C....... ...ATAAG...CGA.GGGTGG..T.A.T... ....G.T.....C..G........A...C....GGGA....T......C..      274    274 ,    274    274      16:>H5N8pre3:m234;1112;1112;m234;m234;goch1;628;1112                             
  17 >H5N8pre4:wy11;008;108;wy19;wy11;90;008;1904                                   ..A..G.GC.G.T..T.T..GTG.T..G.TT..T.A.GCG..G.GTGCAGAC..G.TA..TGC.T..C.GCGTTGC.T...AAG.. T.TAGTTG.G..A.GG.A.A.GGACGCAA.C.....A.A...AATAAC.....CGTCG...TCC.T..A..G..ATAT.C.CT..GC .G.CA.GGA.C.....AA.C..ACA...G.A..T.G....AT...A.C..CC.G.GT.TC..........G.C..G..C.ACC.....GAG.GGT.C...C.C..AAA....G.C .....AA....GG.GT...AGTTATACCAA.A..T..ATTA...TA.GGCCT.AGCCT.ACATGACC.A.....C.C...A.T.AAG.TT...GGC.....T...TGC..A..C..T GGCGCACA.AC.GGG.GCTT..AATCCGGAGGCAACTCCA...A.T...CGAAAATGAT.GTGATTCTA..TTA .A.....GA..G.TAGGGTCAG..G..ATT.CG.ATCT...AT.GC..G.CG.G..TCCGA.AT.AGCCGGCAG.AAG..AGT.AGGC.CC.GTG.TTA..GAGTTG..ACCCAACCGG. .AGAT.AG..T.G.T.GG.GGA.T..ATT.. T.TA.A...CG.CGG..G.GCTG.AT.G.AC.A...AGCC.TAAG.TGC.T      400    400 ,    400    400      17:>H5N8pre4:wy11;008;108;wy19;wy11;90;008;1904                                  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
---Index----------------------------------------------------------------------------ACGGGCCATGAGCTACCCACACACCCGAACGATCCGTTTACTAGACATGAGTAGAACCACCATGCGGTAATTCCATCCTGGGGAAA CACGACCAAAAAGGAACGAGTAAGATTGGATCAGCAGACCACGGAGGACCGACTACTACTTCTTTAGGCCCTCCGCGCGTTTCGAAA AAGTGTAAGATCATGTGGCTGGGTGCGTACCCACATCGGGGCGGAGGTGCTTAAAACACTAGGCGTACCTTATCTTTCTCGTTCTTGAACACTACATGAGTATCAGGGCGAGAGT AATTCGGGGTTAAAACGACTACCGCGTTGGGCCCCCTCCCGCAGCTAAAATGCGATACAGTGCTGATTGAACAATATAGGGTCCGGAAGCCCCAATCAGTTCTAGCTAGAGAATGTC ATTATTTGAGTGAAAGATCCTAGGCTTAAGAAACGTCTTTCTCGCCGGTTAGGGGCAGCGACATCCTCCAGCCG GGAATAAAGTTTACGAAACTGTTCATATCCCTATCCTCGAAGCAATAGATTAAACGCTTTGGGCGGATTAATGATGGACTGAAGGAATGTTAAAAGGCGCAAGACCATTGATTGGTTAAT AGAGCGGAACCTAGCAAACTAGTCCGGCCTA CTCGAGGGGTAAAAAAAACATCAACCCATGTGTAAAGATTACGGATCATTC
-codon-position---------------------------------------------------------------------1 1 2 2      1    1       11   2 2 2       1         2 1 1  1      1 1            2  1                  1      1    1   2    2  22       1               2   1 1   1        11  11   1   2 21 1  21 2    1 1 1   1    1        1  1  2 1     2   1    12 11  11           1      2  1 1      2     122211 112  1    12 1 1      2  22   2 1 11 22211 21 1 1  1  2  12     122    11     2         1        2  12      1                                 21       2     2 2      1 2            2  2  1 1 1   221 2 2 1  2 1    1 1     1   1 1    2  1  1   2   1   11   1     22 2       1  1  1  1   1     2 21    22   1  12     2           1     1 211       2 11   2 1       2121 2  11211  111 1112 111 1
                                                                                    00000000000000000000000000000000000001111111111111111111111111111111111111111222222222 000000000000000000000000000011111111111111111111111111111111111111111111111112222222222 0000000000000000000000000000000000000000000000000011111111111111111111111111111111111111111111111111111111112222222 000000000000000000000000000000000000000000000000000000000000000000000000000000000000011111111111111111111111111111111 00000000000000000000000000000000000000000000000000001111111111111111111111 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000111111111111111111111111111 0000000000000000000000000000000 000000000000000000000000000000000000000000000000000
                                                                                    01112222333333444444556667777777888890000111222223333444455555666678888899999000001112 000111222333445666678888899900000001111111111222233334444455556667777788899990000011122 0001111122233334444555556666777777788888888999999900000000111112233333333444444455555566666666788888889999990000111 000000000000011111111122222222222333333333333344444444444455555666666677777788888899900000111123344444444455555566667 00011111122222333344444444455555666788888888899999990000111111122222334444 000000000000011111111111111122222222233333333334444444455555556666666777777777778888999999999000000001111122222222333333 0011222233334445555566666777888 001112222222222223333333333444445555566666677777778
                                                                                    82390226011347245669785790455889079970134125005682588028901338234711233801259067790266 239357015345780235901334558901133470122245579056825790444718995770158977745890035602705 1590277859900231568225681445022678812345789023566900455799113462612336899001234904577801347789634577991258890277113 001222334478811245588900123456689001123344688901223456667902559133347811257900555815622459015923602347788811366947780 56812357934569056702455668927789358712245679901135781127033445702367154447 122233444589901123334455677902444556900111236770000145822445672335689012467899992249000135688023445560448922344588012356 2808346822782781278901227129156 091680111123355670134456889112352344503459911336781
                                                                                    86089274025923043898687595513064151655481926034049036959175071051409779451038140915436 430837192084794795956146914385725917624591794673131487369381693174285102943691745791837 8818945357902598625354122564904270198709024979767926738468094637047255934484274862758184271895792478671133621823283 781028010124814074501527654053756595890159749248794596894882241512688145851847038827923192705710548703957856503011711 19410534216877649520406580520953744162507704764887511762701365931005165695 524507258391644900580479514676069282469026109272568126657695804672976379751812485837367235315296470424368079758179170242 5059734447870433298802172534437 697599014954926100532537089670677249247611459890897
[/SIZE][/FONT]
 
another American H5 at genbank, the teal with H5N1 from Washington, the 4th full genome from America.
It has new segments 2,3,6,8 from American wild birds. 3,8 are new ; 2,5 also common in the other 3.
--------------------------------------------------------------------------- the new American wild-bird segments that went into Asian H5 have these amino-acid mutations:

segment 2 : T59S,N328D,N375S,K353R,R215K
segment 5 : V105M,A286V,S450N,R452K,N492S,S377N

segment 3 : P271H,V323I,E382D,V387I,S400P
segment 8 : L27M,R59H,S291N(=S38N in NS2)

9 of these were previously found in avian viruses that went into mammals
and caused widespread outbreaks and created new strains :
[from my list "avhu" of ~250 such mutations]

N375S(2) : 1918 [7865,4214],{2816,3755}
R215K(2) : EQ63 [9597,3165],{5626,1128}
V105M(5) : 1918,NL2003,EQ63,SwEU [5253,6898],{1272,4918}
S450N(5) : EQ63 [5605,6454],{443,5823}
V323I(3) : triple [8196,4592],{3223,3580}
E382D(3) : triple,1918 [12041,967],{5913,883}
V387I(3) : SwEU [11163,1825],{5640,1141}
S400P(3) : triple, L in 1918,A in EQ63, N in SwEU [4468,5447,132,86,0],{674,3359,30,74,0}
S291N(8) : SwEU [7142,1041],3980,379}

EQ63= Equine H3N8 (since 1963)
NL2003= vet in NL poultry H7N7 outbreak 2003
SwEU = European Swine H1N1 (1978)
triple = USA-triple reassortant into swine (H3N2 and H1N1) in 1997


at first sight this looks astonishing, you'll have to check, how common these mutations are.
So I added the counts in avian genbank sequences. All in [] and American in {}
[maybe I should consider wild birds only and sort out poultry sequences --> maybe later]
Nothing really unusual, most unusual are E382D(3),V387I(3),S291N(9) with a 7%,13%,14% chance

so, these 9 muatations out of my list of critical mammalean mutations,
that we now already see in the acquired new American segments in the 4 available viruses,
these 9 are ~8 times more likely to occur in America than in Eurasia.

The question is, can this evil H5 gather new segments by reassortment and new mutations
so to become pandemic.We can use the data from previous pandemics and panzootics to
find clues. H5 could try to reassort with mammalean viruses, but this is not so likely,
a mammalean and an avian virus together in the same cell, how would they get there ?
But H5 reassorting with avian wild viruses is common. Can it produce a pandemic
(avian) virus that way ? And how likely will it ?

------------------------------------------------------------------------------------------- ------------edit----------------
segment 3 of the H5N1 - teal is the most unusual wrt. this, it has 5 amino-acid mutations
and 4 of these appear in the list. That's the case for only 260 from 11500 other full
segment 3 or 4%. 200 of these from USA or Canada.
 
we have 9 American H5-type-Asia genomes at genbank now

>KP739418,A/American green-winged teal/Washington/195750/2014,2014/12/29,USA,H5N1
>KP307973,A/Northern pintail/Washington/40964/2014,2014/12/08,USA,H5N2
>KP739402,A/chicken/Oregon/41613-2/2014,2014/12/16,USA,H5N8
>KP739378,A/chicken/Washington/61-9/2014,2014/12/30,USA,H5N2
>KP739386,A/domestic duck/Washington/61-16/2014,2014/12/30,USA,H5N2
>KP739410,A/guinea fowl/Washington/41613-1/2014,2014/12/16,USA,H5N8
>KP307981,A/gyrfalcon/Washington/41088-6/2014,2014/12/08,USA,H5N8
>KP307954,A/turkey/BC/FAV10/2014,2014/12/02,Canada,H5N2
>KP739394,A/turkey/Washington/61-22/2014,2014/12/30,USA,H5N2

all have segments 1,4,7 from Asian H5N1
3 groups:
3 are similar to the Asian H5N8 (and thus also similar to each other)
the 5 H5N2 are similar to each other
plus the H5N1

mutation table:
http://magictour.free.fr/h5n8nei4.l5
[table updated,2015/02/24, added the Am.index]

these 9 have a base of 10,13,10,12,6,7,0,0 mutations in the 8 segments
from the (Korean) H5N8-index. This forms my American-H5-index for now.
Of these 8,-,7,9,-,6,0,0 are shared with the Taiwan sequences,
so they are pretty much related and probably share a common ancester
in Summer or fall 2014. It's still unclear how it came to America,
what locations and species were involved. Alaska is a possibility.

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

so far it looks as if there was just one introduction of H5N8 into
America , which I call the "American H5-index", which is a hypothetical,
calculated flu-H5N8-sequence.

Here are the differences from the American H5-index in the 8 segments
for the 9 available genomes :

a:host
b:US-State/Canadian Province
c:collection date
d:differences(1 digit per segment)
e:sum of differences
f:differences estimated including reassorted segments

Code: 
 a b c d e f
--------------------------------
TK,WA,2014/12/30,3-54--11=14,23
DK,WA,2014/12/30,3-46--12=16,26
CK,WA,2014/12/30,4-45--12=16,26
GF,WA,2014/12/16,12431010=12,12
CK,OR,2014/12/16,12431010=12,12
TK,BC,2014/12/02,1-42--02=09,15
NP,WA,2014/12/08,2-22--00=06,10
GY,WA,2014/12/08,00431210=11,11
TE,WA,2014/12/29,3--73-1-=18,37


Code: 
 a  b          c        d  e  f
--------------------------------
TK,WA,2014/12/30,3-54--11=14,23
DK,WA,2014/12/30,3-46--12=16,26
CK,WA,2014/12/30,4-45--12=16,26
GF,WA,2014/12/16,12431010=12,12
CK,OR,2014/12/16,12431010=12,12
TK,BC,2014/12/02,1-42--02=09,15
NP,WA,2014/12/08,2-22--00=06,10
GY,WA,2014/12/08,00431210=11,11
TE,WA,2014/12/29,3--73-1-=18,37



The American index, has 58 differences/mutations from the Korean index,
acquired in 10-11 months. (Normal is ~40-50 mutations per year for H5N1).

Then we have these additional mutations above in only 1-3 months !


(still no European H5N8 sequences at genbank after more than 3 months)

-------------------edit 2015/02/26-----------------
10 genomes now, the new H5N8 from guinea-fowl in Oregon, 2014/12/16 is identical
to the guinea fowl from WA, which was already identical to the chicken from OR
---edit again----
well, these are no new sequences, they just changed the State from
Washington to Oregon in the old sequence:
http://www.ncbi.nlm.nih.gov/nuccore/...port=girevhist
{Washington is North of Oregon, close to the Canadian border}
-------------------------------------------
 
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