Full Genome Sequence of a Recombinant H5N1 Influenza Virus from a Condor in Southern China

[Gert van der Hoek]

Full Genome Sequence of a Recombinant H5N1 Influenza Virus from a Condor in Southern China

Peirong Jiao, Runyu Yuan, Yafen Song, Liangmeng Wei, Tao Ren, Ming Liao and Kaijian Luo
+ Author Affiliations

MOA Key Laboratory for Animal Vaccine Development, Key Laboratory of Zoonoses Control and Prevention of Guangdong, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China


ABSTRACT

In this study, we report the first genomic information on an H5N1 avian influenza virus (AIV) isolated from a condor in Guangdong Province in southern China in 2003. Full genome sequencing and phylogenetic analyses show that it is a recombinant virus containing genome segments derived from the Eurasia and North America gene pools. This will be useful for analyses of the evolution of H5N1 AIV in southern China.

GENOME ANNOUNCEMENT

H5N1 highly pathogenic avian influenza (HPAI) is caused by H5N1 influenza A virus, which can result in serious systemic or respiratory diseases in birds. H5N1 avian influenza viruses (AIV) have been reported to be transmitted from wild birds to domestic poultry and various mammalian species (1). In 1996, the H5N1 HPAI virus (A/Goose/Guangdong/1/1996) was first isolated from a sick goose in southern China (2, 9).

In 1997, the transmission of H5N1 viruses to humans had caused the deaths of 6 of 18 infected persons in southern China (3, 8). Since 2003, H5N1 HPAI viruses which had developed a high degree antigenic variation began to spread and caused serious outbreaks in more than 60 countries of Asia, Europe, and Africa, not only resulting in the destruction of hundreds of millions of poultry but also causing serious infection and death of humans. Therefore, H5N1 AIVs are zoonotic agents recognized as a continuing threat to both the poultry industry and human public health.

Here, a H5N1 influenza virus (A/Condor/Guangdong/139/2003 [GD139]) was isolated from a sick condor in southern China in 2003. To investigate more information about this recombinant virus, we determined the complete genomic sequence with an ABI 3730 genetic analyzer using the Sanger method, which is based on DNA fragments amplified by PCR with a previous primer (5). Sequence fragments were assembled using Sequencher 5.0. The 8 genome segments of the virus encode 10 proteins (PB2, PB1, PA, HA, NP, NA, M1, M2, NS1, and NS2) with lengths of 759, 757, 716, 568, 498, 449, 252, 97, 225, and 121 amino acids, respectively. There are 20- and 5-amino-acid deletions in NA and NS1, respectively. The GD139 virus has a series of basic amino acids at the cleavage site of the HA (RRKKR) that is characteristic of HPAI viruses. The receptor-binding pocket of HA1 retains the amino acid residues Q226 and G228 (H3 numbering), which preferentially bind to the avian influenza virus receptor (4). The PB2 protein has E and D at positions 627 and 701, which are characteristic of the avian influenza virus (6, 7).

Phylogenetic analysis of GD139 revealed that the HA and NA genes belong to the Eurasia gene pool (A/Hong Kong/213/2003 [H5N1]-like virus) and share 99% and 94.7% nucleotide identity with HK213-like virus, respectively.

The internal genes showed that PB1, PA, NP, M, and NS genes also belong to the Eurasia gene pool and exhibit more than 99%, 96%, 99% and 99% sequence identity to HK213-like virus, respectively. However, the PB2 gene belongs to the North America gene pool and has 94% sequence identity with the A/Pheasant/NJ/9804570/1998(H5N2) virus.

Thus, GD139 virus is a recombinant virus between the Eurasia gene pool and the North America gene pool which has rarely been reported in southern China.

The genomic information on this H5N1 natural recombinant virus from a condor will be helpful for analyses of the evolution of H5N1 AIV in southern China.

Nucleotide sequence accession numbers.

The genome sequences of A/Condor/Guangdong/139/2003 (H5N1) have been deposited in GenBank under accession numbers JQ966928 to JQ966935.

http://jvi.asm.org/content/86/14/7722.full

[gsgs]

Re: Full Genome Sequence of a Recombinant H5N1 Influenza Virus from a Condor in Southern China

not yet available

http://www.ncbi.nlm.nih.gov/nuccore/JQ966928
GenBank: 387965751

This record has not yet been released. Please contact info@ncbi.nlm.nih.gov with the publication details if the accession has been published.

-------------------------
ATM I'm not aware of other examples of American avian PB2 in China
can we trust it ?

what do condors eat, how far do they fly

[Laidback Al]

Re: Full Genome Sequence of a Recombinant H5N1 Influenza Virus from a Condor in Southern China

-------------------------
ATM I'm not aware of other examples of American PB2 in China
can we trust it ?

Can someone comment on the implications of this sample which was collected in 2003.

[gsgs]

Re: Full Genome Sequence of a Recombinant H5N1 Influenza Virus from a Condor in Southern China

I was a bit sloppy,lazy ...
well, I delayed my analysis, waiting for the sequences to be available

first I meant "avian" PB2, in humans, swine there is lots of continent-mixing
And it's not specific to PB2, although PB2 is the segment with
avian-flu-continents separated since the longest time.
In fact, I couldn't even reasonably estimate the date of the most recent
common ancestor of Eurasian and American avian PB2 when I last tried.
Probably they are separated since >100 years.
While the most recent common ancestor in segments 2,3 (PB1,PA)
of Eurasian and American avian flu was ~ in the 50s, AFAIR

I had a table here: (Feb.2010)
http://www.flutrackers.com/forum/sho...48&postcount=1

the 2nd table had the types in the continents (from flugenome.org)

the American avian PB2 would be type "1C" , this line
OF - 1: 2, , 1, , , , 209, 5, , 5, 892,
showed one such American avian PB2 in Eurasia, I'll check later what it was.





maybe I can make a better,more actual table later ...



PB2 was reported to be from American H5N2, we had outbreaks of H5N2
in American poultry, so maybe the condor got a sick chicken.
But there were no reports about American H5N2 in poultry in Eurasia.

If these segments would start to mix now, I'd expect new viruses
forming, enhanced evolution, strains with increased pandemic potential
and maybe (reassorted) H5N1 or H9N2 in the Americas

wasn't it this intercontinental mixing that created the pandemics 1918,1957,1968 ?
New rare avian segments of unclear continental origin jumping to humans

[gsgs]

Re: Full Genome Sequence of a Recombinant H5N1 Influenza Virus from a Condor in Southern China

7257 avian PB2s , genbank Jan. 2012

a:continent (1=Africa,2=Asia,3=Europe,4=North America,5=Oceania,6=South America)
b:flugenome.org - type (computed with 12-subsequences count)
c:count

 a  b c 
-----------
 1 1C,3
 1 1G,16
 1 1K,206

 2 1A,1
 2 1C,11
 2 1F,1
 2 1G,1104
 2 1J,6
 2 1K,1931
 2 1L,24
 2 47D,1

 3 1C,1
 3 1F,7
 3 1G,292
 3 1H,10
 3 1J,12
 3 1K,155
 3 1L,1

 4 1A,1
 4 1B,7
 4 1C,3283
 4 1G,14
 4 1H,1
 4 1J,21
 4 1K,10

 5 1C,1
 5 1G,35
 5 1I,11
 5 1J,8
 5 1K,69

 6 1C,3
 6 1E,11

avian PB2s in unusual continents
--------------------------------------

1C,,>A/Ck/Egypt/Q1182/2010,2010//,H5N1,Egypt, 1 
1C,,>A/Dk/Egypt/053/2005,2005/02/05,H6N2,Egypt, 1 
1C,,>A/whiskered tern/Egypt/04/2004,2004/12/05,H6N2,Egypt, 1 

1J,,>A/Mongolian gull/Mongolia/401/2007,2007/08/28,H13N6,Mongolia, 2 
1J,,>A/Mongolian gull/Mongolia/405/2007,2007/08/28,H13N6,Mongolia, 2 
1C,,>A/aquatic bird/Korea/CN20/2009,2009/11/,H6N1,South Korea, 2 
1L,,>A/Ck/Bali/UT2091/2005,2005//,H5N1,Indonesia, 2 
1L,,>A/Ck/Bali/UT2092/2005,2005//,H5N1,Indonesia, 2 
1L,,>A/Ck/Banten/UT6025/2006,2006/10/,H5N1,Indonesia, 2 
1L,,>A/Ck/East Java/UT6017/2006,2006/11/,H5N1,Indonesia, 2 
1L,,>A/Ck/East Java/UT6020/2006,2006/11/,H5N1,Indonesia, 2 
1L,,>A/Ck/East Java/UT6021/2006,2006/11/,H5N1,Indonesia, 2 
1L,,>A/Ck/East Java/UT6023/2006,2006/11/,H5N1,Indonesia, 2 
1L,,>A/Ck/East Java/UT6044/2007,2007/03/,H5N1,Indonesia, 2 
1L,,>A/Ck/East Java/UT6045/2007,2007/03/,H5N1,Indonesia, 2 
1L,,>A/Ck/Gunung Kidal/BBVW/2005,2005//,H5N1,Indonesia, 2 
1F,,>A/Ck/Hebei/1/2002,2002//,H7N2,China, 2 
1C,,>A/Ck/Ibaraki/1/2005,2005//,H5N2,Japan, 2 
1L,,>A/Ck/Indonesia/CDC24/2005,2005/10/04,H5N1,Indonesia, 2 
1L,,>A/Ck/Indonesia/CDC25/2005,2005/10/04,H5N1,Indonesia, 2 
1L,,>A/Ck/Magetan/BBVW/2005,2005//,H5N1,Indonesia, 2 
1C,,>A/Ck/Pakistan/1369-CR2/1995,1995//,H7N3,Pakistan, 2 
1C,,>A/Ck/Pakistan/447/1995,1995//,H7N3,Pakistan, 2 
1L,,>A/Ck/South Kalimantan/UT6028/2006,2006/11/,H5N1,Indonesia, 2 
1L,,>A/Ck/South Kalimantan/UT6029/2006,2006/11/,H5N1,Indonesia, 2 
1L,,>A/Ck/Sulawesi Selatan/UT2093/2005,2005//,H5N1,Indonesia, 2 
1L,,>A/Ck/Sulawesi Selatan/UT2094/2005,2005//,H5N1,Indonesia, 2 
1L,,>A/Ck/Wajo/BBVM/2005,2005//,H5N1,Indonesia, 2 
1L,,>A/Ck/Yogjakarta/BBVet-IX/2004,2004//,H5N1,Indonesia, 2 
1C,,>A/Dk/Hokkaido/107/01,2001//,H2N3,Japan, 2 
1J,,>A/Dk/HK/175/77,1977//,H6N1,HK, 2 
1C,,>A/Dk/Korea/U5-2/2007,2007/05/03,H3N8,South Korea, 2 
1L,,>A/Dk/Parepare/BBVM/2005,2005//,H5N1,Indonesia, 2 
1C,,>A/Dk/Shantou/83/2000,2000//,H6N2,China, 2 
1L,,>A/Dk/Vietnam/OIE-4039/2010,2010/10/,H6N2,Viet Nam, 2 
1J,,>A/Gs/HK/23/1978,1978//,H5N3,HK, 2 
1J,,>A/Gs/HK/23/1978,1978//,H5N3,HK, 2 
1J,,>A/herring gull/Mongolia/454/2008,2008/09/,H13N8,Mongolia, 2 
1C,,>A/mallard Dk/Korea/LBM347/2007,2007/03/,H3N8,South Korea, 2 
1C,,>A/mallard Dk/Korea/LBM397/2007,2007/03/,H3N2,South Korea, 2 
1A,,>A/Qa/Nanchang/12-340/2000,2000//,H1N1,China, 2 
1L,,>A/Qa/Yogjakarta/BBVet-IX/2004,2004//,H5N1,Indonesia, 2 
1L,,>A/Qa/Yogjakarta/UT1023/2004,2004/01/15,H5N1,Indonesia, 2 
1L,,>A/Qa/Yogjakarta/UT1075/2004,2004/05/25,H5N1,Indonesia, 2 
1C,,>A/shorebird/Korea/S82/2006,2006//,H9N2,South Korea, 2 
1C,,>A/wild Dk/Korea/7-D19/2005,2005/11/04,H4N6,South Korea, 2 

1F,,>A/Ck/Italy/5945/95,1995//,H3N2,Italy, 3 
1J,,>A/black-headed gull/Netherlands/1/00,2000//,H13N8,Netherlands, 3 
1J,,>A/black-headed gull/Sweden/1/1999,1999//,H13N6,Sweden, 3 
1J,,>A/black-headed gull/Sweden/1/2005,2005//,H13N8,Sweden, 3 
1J,,>A/black-headed gull/Sweden/2/99,1999//,H16N3,Sweden, 3 
1J,,>A/black-headed gull/Sweden/5/99,1999//,H16N3,Sweden, 3 
1J,,>A/blackhead gull/Astrakhan/1421/1979,1979//,H13N6,Russia, 3 
1J,,>A/blackhead gull/Astrakhan/44/1988,1988//,H13N6,Russia, 3 
1J,,>A/blackhead gull/Astrakhan/458/1985,1985//,H13N6,Russia, 3 
1J,,>A/blackhead gull/Astrakhan/65/1983,1983//,H13N6,Russia, 3 
1H,,>A/Ck/Brescia/1902,1902//,H7N7,Italy, 3 
1H,,>A/Ck/Brescia/1902,1902//,H7N7,Italy, 3 
1H,,>A/Ck/FPV/Rostock/1934,1934//,H7N1,Germany, 3 
1H,,>A/Ck/Germany/1934,1934//,H7N1,Germany, 3 
1H,,>A/Ck/Rostock/45/1934,1934//,H7N1,Germany, 3 
1H,,>A/Ck/Rostock/45/1934,1934//,H7N1,Germany, 3 
1H,,>A/Ck/Rostock/8/1934,1934//,H7N1,Germany, 3 
1H,,>A/Ck/Rostock/8/1934,1934//,H7N1,Germany, 3 
1F,,>A/Dk/Germany/1215/1973,1973//,H2N3,Germany, 3 
1L,,>A/Dk/IT/701/2005,2005//,H10N7,Italy, 3 
1J,,>A/Dk/Siberia/272/1998,1998//,H13N6,Russia, 3 
1J,,>A/Dk/Siberia/272PF/1998,1998//,H13N6,Russia, 3 
1H,,>A/fowl/Dobson/1927,1927//,H7N7,United Kingdom, 3 
1H,,>A/fowl/Weybridge,1934//,H7N7,United Kingdom, 3 
1C,,>A/guillemot/Sweden/3/00,2000//,H6N2,Sweden, 3 
1J,,>A/gull/Astrakhan/227/1984,1984//,H13N6,Russia, 3 
1F,,>A/Tk/England/N28/1973,1973//,H5N2,United Kingdom, 3 
1F,,>A/Tk/England/N28/1973,1973//,H5N2,United Kingdom, 3 
1F,,>A/Tk/England/N28/73,1973//,H5N2,United Kingdom, 3 
1F,,>A/Tk/France/05016/2005,2005/01/,H1N1,France, 3 
1F,,>A/Tk/France/05045/2005,2005/01/,H1N2,France, 3 

1K,,>A/American black Dk/Washington/699/1978,1978//,H3N8,USA, 4 
1G,,>A/Pekin robin/CA/30412/1994,1994//,H7N1,USA, 4 
1G,,>A/Steller's eider/Alaska/44222-192/2006,2006/09/06,H3N3,USA, 4 
1G,,>A/arctic tern/Alaska/300/1975,1975//,H5N3,USA, 4 
1B,,>A/Ck/NY/21665-73/1998,1998//,H1N1,USA, 4 
1G,,>A/Ck/PA/298101-4/2004,2004//,H2N2,USA, 4 
1B,,>A/Ck/PA/35154/1991,1991//,H1N1,USA, 4 
1G,,>A/Ck/Pennsylvania/Sg-00426/2004,2004//,H2N2,USA, 4 
1G,,>A/Ck/Pennsylvania/Sg-00427/2004,2004//,H2N2,USA, 4 
1K,,>A/common murre/Alaska/44085-165/2006,2006/06/08,H11N9,USA, 4 
1K,,>A/common murre/Alaska/44089-066/2006,2006/06/08,H10N2,USA, 4 
1A,,>A/Dk/Ontario/05/00,2000//,H3N2,Canada, 4 
1K,,>A/Dk/Washington/4954/1983,1983//,H3N8,USA, 4 
1G,,>A/emu/NY/12716/1994,1994//,H5N9,USA, 4 
1H,,>A/fowl/Dobson/1927,1927//,H7N7,USA, 4 
1J,,>A/great black-backed gull/Newfoundland/296/2008,2008/10/21,H13N2,Canada, 4 
1J,,>A/gull/Maryland/704/1977,1977//,H13N6,USA, 4 
1J,,>A/gull/Maryland/704/1977,1977/09/22,H13N6,USA, 4 
1J,,>A/gull/Maryland/704/1977,1977/06/11,H13N6,USA, 4 
1J,,>A/gull/Minnesota/945/1980,1980/08/25,H13N6,USA, 4 
1J,,>A/herring gull/DE/475/1986,1986/06/01,H13N2,USA, 4 
1J,,>A/herring gull/DE/665/1988,1988/05/16,H4N6,USA, 4 
1J,,>A/herring gull/Delaware/712/1988,1988/05/16,H16N3,USA, 4 
1J,,>A/herring gull/NJ/782/1986,1986/05/12,H13N2,USA, 4 
1J,,>A/herring gull/New Jersey/780/86,1986/05/12,H1N3,USA, 4 
1J,,>A/laughing gull/Delaware Bay/2838/1987,1987/06/12,H13N2,USA, 4 
1J,,>A/laughing gull/Delaware Bay/2838/1987,1987/05/19,H13N2,USA, 4 
1J,,>A/laughing gull/New Jersey/Sg-00485/2008,2008/05/15,H13N9,USA, 4 
1J,,>A/laughing gull/New Jersey/Sg-00559/2008,2008/05/28,H13N9,USA, 4 
1J,,>A/laughing gull/New Jersey/Sg-00568/2008,2008/05/28,H13N9,USA, 4 
1G,,>A/northern pintail/Alaska/44204-108/2006,2006/10/12,H3N1,USA, 4 
1G,,>A/northern pintail/Alaska/44340-010/2007,2007/09/16,H6N2,USA, 4 
1G,,>A/ruddy turnstone/Delaware/24/1990,1990/05/09,mixed,USA, 4 
1G,,>A/ruddy turnstone/New Jersey/138/1990,1990/05/26,H3N6,USA, 4 
1G,,>A/ruddy turnstone/New Jersey/260/1990,1990/05/27,H3N6,USA, 4 
1G,,>A/ruddy turnstone/New Jersey/47/1985,1985//,H4N6,USA, 4 
1G,,>A/semi-palmated sandpiper/New Jersey/237/1990,1990/05/26,H3N6,USA, 4 
1J,,>A/shorebird/DE/68/2004,2004/05/17,H13N9,USA, 4 
1J,,>A/shorebird/Delaware/168/06,2006//,H16N3,USA, 4 
1J,,>A/shorebird/Delaware/195/2006,2006/05/22,H16N3,USA, 4 
1J,,>A/shorebird/Delaware/221/2006,2006/05/22,H13N9,USA, 4 
1J,,>A/shorebird/Delaware/224/2006,2006/05/22,H13N9,USA, 4 
1K,,>A/softbill/CA/33445-158/1992,1992//,H7N1,USA, 4 
1K,,>A/softbill/CA/33445-136/1992,1992//,H7N1,USA, 4 
1K,,>A/thick-billed murre/Alaska/44085-090/2006,2006/06/05,H11N9,USA, 4 
1K,,>A/thick-billed murre/Alaska/44085-108/2006,2006/06/07,H1N9,USA, 4 
1K,,>A/thick-billed murre/Alaska/44086-095/2006,2006/05/27,H11N9,USA, 4 
1K,,>A/thick-billed murre/Alaska/44088-059/2006,2006/05/30,H11N9,USA, 4 
1B,,>A/Tk/IA/10271-3/1990,1990//,H1N1,USA, 4 
1B,,>A/Tk/IA/21089-3/1992,1992//,H1N1,USA, 4 
1B,,>A/Tk/Kansas/4880/1980,1980//,H1N1,USA, 4 
1J,,>A/Tk/Minnesota/1012/1990,1990/11/26,H13N2,USA, 4 
1B,,>A/Tk/NC/17026/1988,1988//,H1N1,USA, 4 
1B,,>A/Tk/NC/19762/1988,1988//,H1N1,USA, 4 

1J,,>A/Pacific black Dk/Western Australia/4045/1980,1980//,H6N5,Australia, 5 
1J,,>A/Pacific black Dk/Western Australia/4045/1980,1980//,H6N5,Australia, 5 
1J,,>A/Ck/Victoria/1976,1976/01/,H7N7,Australia, 5 
1J,,>A/Dk/Australia/749/1980,1980//,H1N1,Australia, 5 
1J,,>A/Dk/Victoria/23/1981,1981//,H1N1,Australia, 5 
1J,,>A/Dk/Victoria/2a/1980,1980//,H1N1,Australia, 5 
1J,,>A/Dk/Victoria/2b/1980,1980//,H1N1,Australia, 5 
1I,,>A/red-necked stint/Australia/4189/1980,1980/10/25,H4N8,Australia, 5 
1I,,>A/red-necked stint/Australia/4500/1980,1980/12/06,H3N8,Australia, 5 
1I,,>A/red-necked stint/Australia/5745/1981,1981/03/05,H12N9,Australia, 5 
1I,,>A/red-necked stint/Bunbury/4500/1980,1980/06/12,H3N8,Australia, 5 
1I,,>A/red-necked stint/Western Australia/4094/1984,1984//,H4N8,Australia, 5 
1I,,>A/red-necked stint/Western Australia/4126/1980,1980//,H4N8,Australia, 5 
1I,,>A/red-necked stint/Western Australia/4188/1984,1984//,H4N8,Australia, 5 
1I,,>A/red-necked stint/Western Australia/4915/1984,1984//,H3N8,Australia, 5 
1I,,>A/red-necked stint/Western Australia/4923/1983,1983//,H3N8,Australia, 5 
1I,,>A/red-necked stint/Western Australia/5745/1982,1982/03/30,H12N9,Australia, 5 
1I,,>A/red-necked stint/Western Australia/5745/1982,1982//,H12N9,Australia, 5 
1J,,>A/silver gull/Tasmania/062/2006,2006//,H13N6,Australia, 5 
1C,,>A/Tk/Ontario/6118/1967,1967//,H8N4,Australia, 5 

1C,,>A/Ck/Chile/184240-5/2002,2002//,H7N3,Chile, 6 
1C,,>A/semi-palmated sandpiper/Brazil/43/1990,1990/04/18,H2N1,Brazil, 6 
1C,,>A/Tk/Chile/28317-6504-3/2009,2009/08/17,H1N1,Chile, 6

North American avian PB2s ("1C") in other continents
--------------------------------------

1C,,>A/Ck/Egypt/Q1182/2010,2010//,H5N1,Egypt, 1 
1C,,>A/Dk/Egypt/053/2005,2005/02/05,H6N2,Egypt, 1 
1C,,>A/whiskered tern/Egypt/04/2004,2004/12/05,H6N2,Egypt, 1 

1C,,>A/aquatic bird/Korea/CN20/2009,2009/11/,H6N1,South Korea, 2 
1C,,>A/Ck/Ibaraki/1/2005,2005//,H5N2,Japan, 2 
1C,,>A/Ck/Pakistan/1369-CR2/1995,1995//,H7N3,Pakistan, 2 
1C,,>A/Ck/Pakistan/447/1995,1995//,H7N3,Pakistan, 2 
1C,,>A/Dk/Hokkaido/107/01,2001//,H2N3,Japan, 2 
1C,,>A/Dk/Korea/U5-2/2007,2007/05/03,H3N8,South Korea, 2 
1C,,>A/Dk/Shantou/83/2000,2000//,H6N2,China, 2 
1C,,>A/mallard Dk/Korea/LBM347/2007,2007/03/,H3N8,South Korea, 2 
1C,,>A/mallard Dk/Korea/LBM397/2007,2007/03/,H3N2,South Korea, 2 
1C,,>A/shorebird/Korea/S82/2006,2006//,H9N2,South Korea, 2 
1C,,>A/wild Dk/Korea/7-D19/2005,2005/11/04,H4N6,South Korea, 2 

1C,,>A/guillemot/Sweden/3/00,2000//,H6N2,Sweden, 3 

1C,,>A/Ck/Chile/184240-5/2002,2002//,H7N3,Chile, 6 
1C,,>A/semi-palmated sandpiper/Brazil/43/1990,1990/04/18,H2N1,Brazil, 6 
1C,,>A/Tk/Chile/28317-6504-3/2009,2009/08/17,H1N1,Chile, 6

some of the sequences are presumably partials
with unclear strain-assignment

>1.7bi      ,>1C         ,>1eNA         ,   958, 887, 860 ,     ,>A/Dk/Egypt/053/2005,2005/02/05,H6N2,Egypt
>1.7bi      ,>1C         ,>1eNA         ,   958, 887, 860 ,     ,>A/whiskered tern/Egypt/04/2004,2004/12/05,H6N2,Egypt

>1NA        ,>1.pNA_07   ,>1C           ,  1297,1165,1079 ,     ,>A/aquatic bird/Korea/CN20/2009,2009/11/,H6N1,South Korea
>1.52_02    ,>1.52_94    ,>1C           ,  1664,1102, 703 ,     ,>A/Ck/Ibaraki/1/2005,2005//,H5N2,Japan
>1.7bi      ,>1eNA       ,>1e63         ,   518, 477, 460 ,     ,>A/Ck/Pakistan/1369-CR2/1995,1995//,H7N3,Pakistan
>1.7bi      ,>1eNA       ,>1e63         ,   523, 482, 460 ,     ,>A/Ck/Pakistan/447/1995,1995//,H7N3,Pakistan
>1NA        ,>1C         ,>1.7bi        ,   328, 307, 247 ,     ,>A/Dk/Hokkaido/107/01,2001//,H2N3,Japan
>1NA        ,>1C         ,>1.7bi        ,  1415,1239,1137 ,     ,>A/Dk/Korea/U5-2/2007,2007/05/03,H3N8,South Korea
>1.pNA_75   ,>1C         ,>1eNA         ,  1505,1466,1412 ,     ,>A/Dk/Shantou/83/2000,2000//,H6N2,China
>1NA        ,>1C         ,>1.7bi        ,  1143,1015, 923 ,     ,>A/mallard Dk/Korea/LBM347/2007,2007/03/,H3N8,South Korea
>1NA        ,>1C         ,>1.7bi        ,  1110, 973, 888 ,     ,>A/mallard Dk/Korea/LBM397/2007,2007/03/,H3N2,South Korea
>1C         ,>1.7bi      ,>1eNA         ,   349, 331, 330 ,     ,>A/shorebird/Korea/S82/2006,2006//,H9N2,South Korea
>1NA        ,>1C         ,>1.pNA_75     ,  1376,1189,1089 ,     ,>A/wild Dk/Korea/7-D19/2005,2005/11/04,H4N6,South Korea

>13*        ,>13*5       ,>1Mx          ,  1597,1306,1256 ,     ,>A/guillemot/Sweden/3/00,2000//,H6N2,Sweden

>1.7bi      ,>1eNA       ,>1e63         ,   495, 454, 447 ,     ,>A/Ck/Chile/184240-5/2002,2002//,H7N3,Chile
>1C         ,>1.52_94    ,>1.pNA_75     ,  1163,1133,1042 ,     ,>A/semi-palmated sandpiper/Brazil/43/1990,1990/04/18,H2N1,Brazil

1.7bi : ancient strain, similar to 1918
1NA,1C : typical North American
1.52_02: North American H5N2 (2002)
1.pNA_75: don't know, North American from 1975
13*: US-triple reassortant swine (I think)


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

so we had one American H5N2 - PB2 in Asia before, the Ibaraki chicken from 2005

   0    0 2280  915 >A/Ck/Ibaraki/1/2005,2005//,H5N2,Japan
 228   52 2280 4336 >A/Ck/Guatemala/45511-5/2000,2000//,H5N2,Guatemala
 285   65 2280 4558 >A/Ck/Tabasco/234-8289/1998,1998//,H5N2,Mexico
 583  133 2280 4356 >A/Ck/Mexico/31381-7/1994,1994//,H5N2,Mexico
 622  142 2280 4077 >A/black Dk/Ohio/195/1990,1990//,mixed,USA
 723  165 2280 5079 >A/mallard/Alberta/140/1987,1987/08/13,H3N8,Canada
 728  166 2280 4930 >A/mallard Dk/Alberta/331/1985,1985/08/18,H3N6,Canada

the chicken could have been just imported, but a condor ?!