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Azerbaijan H5N1 Sequences Fly Into Indonesia
Recombinomics Commentary

August 28, 2006

H5N1 bird flu sequences, A/Azerbaijan/006-207/2006(H5N1), from a prior patient in Azerbaijan were released at Los Alamos.  Seven of the eight gene segments were deposited on the public side of the database.  These sequences had a limited number of “new” polymorphisms which were shared with a subset of Qinghai sequences.  Azaerbaijan and the sequences from a swan in Italy were shared in six of the seven genes.  Polymorphisms were also frequently shares with the 2006 Tuva isolate, including polymorphisms in PA, which were not shared with the Italian sequence.

However, several of the Azerbaijan polymorphisms were also found in sequences from Indonesia, including PA and NA sequences in H5N1 from Karo cluster (see below).  These newly released sequences provide additional evidence for the presence of Qinghai sequences in Indonesia.

The mounting evidence of Qinghai sequences on an Indonesian background indicates that the Indonesian H5N1 genes are acquiring these polymorphisms via recombination.  These acquisitions are increasing the genetic diversity in H5N1 in Indonesia.  Similar changes are also happening in Fujian and Clade 1 sequences, which are creating additional problems for the generation of a pandemic vaccine because of limited cross-reactivity.  Recently, the WHO announced the availability of vaccine targets representing 3 sub-clades of Clade 2.  All three sub-clades have been identified in fatal human cases.

Most of the human H5N1’s isolated in Indonesia do not match avian sequences from domestic poultry.  The presence of Qinghai polymorphisms in Indonesian isolates suggest wild birds are bring in new sequences.  The sequences may also be present in a mammalian reservoir, because many of the novel polymorphisms are also not found in wild bird sequences.

The increasing detection of Qinghai sand other novel sequences in the Indonesian sequence database indicates a more aggressive program should be launched to increase the H5N1 survellance in additional hosts including humans without poultry exposure, other mammals, and wild bird birds.

Qinghai isolates are in black bold, while mammalian Indonesian isolates are in red bold.

HA polymorphism  

ISDN140054  A/Azerbaijan/006-207/2006   2006  H5N1  
DQ435201  A/domestic goose/Iraq/812/2006    2006  H5N1  
ISDN187437  A/Indonesia/569H/2006    2006  H5N1  
ISDN183706  A/Indonesia/CDC623/2006   2006  H5N1  
ISDN183714  A/Indonesia/CDC623E/2006  2006  H5N1  
ISDN183722  A/Indonesia/CDC624/2006   2006  H5N1  
ISDN183730  A/Indonesia/CDC624E/2006  2006  H5N1  
DQ320876  A/chicken/Fujian/1042/2005  2005  H5N1  
DQ343150  A/chicken/Hebei/326/2005    2005  H5N1  
ISDN124038  A/Chicken/Viet Nam/NCVD09/2005  2005  H5N1  
AM183673  A/chicken/Vietnam/P78/05    2005  H5  
DQ320875  A/duck/Fujian/897/2005    2005  H5N1  
DQ320901  A/duck/Guangzhou/20/2005  2005  H5N1  
AM183676  A/duck/Vietnam/AG40-O2/05  2005  H5  
DQ095628  A/Goose/Shantou/1621/05    2005  H5N1  
DQ320915  A/goose/Shantou/2216/2005 2005  H5N1  
ISDN130912  A/Indonesia/195H/2005    2005  H5N1  
DQ320916  A/migratory duck/Jiangxi/1653/2005  2005  H5N1  
DQ320917  A/migratory duck/Jiangxi/1657/2005  2005  H5N1  
DQ320918  A/migratory duck/Jiangxi/1701/2005  2005  H5N1  
AY741213  A/blackbird/Hunan/1/2004    2004  H5N1  
DQ320893  A/chicken/Guangxi/2439/2004   2004  H5N1  
DQ080022  A/chicken/Henan/01/2004    2004  H5N1  
AY950230  A/chicken/Henan/1/2004    2004  H5N1  
AY950232  A/chicken/Henan/12/2004   2004  H5N1  
AY950233  A/chicken/Henan/13/2004   2004  H5N1  
AY950234  A/chicken/Henan/16/2004   2004  H5N1  
AY950231  A/chicken/Henan/210/2004  2004  H5N1  
ISDN48972  A/Chicken/Hu bei/14/2004   2004  H5N1  
AY684706  A/chicken/Hubei/327/2004    2004  H5N1  
AY770079  A/chicken/Hubei/489/2004    2004  H5N1  
AY653200  A/chicken/Jilin/9/2004    2004  H5N1  
AY830774  A/chicken/Macheng/2004    2004  H5N1  
DQ767725  A/chicken/Shandong/K01/2004   2004  H5N1  
AY623430  A/chicken/Yichang/lung-1/04   2004  H5N1  
AY651322  A/Dk/Indonesia/MS/2004    2004  H5N1  
DQ320883  A/duck/Guangxi/1311/2004  2004  H5N1  
DQ320884  A/duck/Guangxi/1378/2004  2004  H5N1  
DQ320885  A/duck/Guangxi/1586/2004  2004  H5N1  
DQ320886  A/duck/Guangxi/1681/2004  2004  H5N1  
DQ320887  A/duck/Guangxi/1793/2004  2004  H5N1  
DQ320890  A/duck/Guangxi/2291/2004  2004  H5N1  
DQ320892  A/duck/Guangxi/2396/2004  2004  H5N1  
DQ320879  A/duck/Guangxi/668/2004   2004  H5N1  
AB241624  A/duck/Hokkaido/101/04   2004  H5N3  
AB241625  A/duck/Hokkaido/193/04    2004  H5N3  
AB241626  A/duck/Hokkaido/299/04    2004  H5N3  
AY854190  A/duck/Shandong/093/2004  2004  H5N1  
AY639405  A/goose/China/F3/2004    2004  H5N1  
DQ320881  A/goose/Guangxi/1097/2004    2004  H5N1  
DQ320882  A/goose/Guangxi/1198/2004    2004  H5N1  
DQ320888  A/goose/Guangxi/1832/2004    2004  H5N1  
DQ320889  A/goose/Guangxi/2112/2004    2004  H5N1  
DQ320891  A/goose/Guangxi/2383/2004    2004  H5N1  
DQ320880  A/goose/Guangxi/914/2004    2004  H5N1  
DQ836043  A/goose/Huadong/220/2004    2004  H5N1  
AY651362  A/peregrine falcon/Hong Kong/D0028/2004  2004  H5N1  
AY950236  A/swan/Guangxi/307/2004   2004  H5N1  
AY741215  A/tree sparrow/Henan/1/2004   2004  H5N1  
AY741217  A/tree sparrow/Henan/2/2004   2004  H5N1  
AY741219  A/tree sparrow/Henan/3/2004   2004  H5N1  
AY741221  A/tree sparrow/Henan/4/2004   2004  H5N1  
AY950235  A/wild duck/Guangdong/314/2004   2004  H5N1  
AY651373  A/black headed gull/Hong Kong/12.1/2003   2003  H5N1  
DQ211925  A/chicken/luohuo/3/03    2003  H5N1  
ISDN40326  A/Chicken/Viet Nam/Ncvd8/2003    2003  H5N1  
AY651355  A/Ck/Hong Kong/WF157/2003    2003  H5N1  
AY651323  A/Ck/Indonesia/2A/2003    2003  H5N1  
AY651367  A/Dk/ST/4003/2003    2003  H5N1  
DQ320914  A/duck/Shantou/4610/2003    2003  H5N1  
AB212280  A/duck/Yokohama/aq10/2003   2003  H5N1  
AY747609  A/swine/Fujian/1/2003    2003  H5N1  
AY646424  A/swine/Shandong/2/03    2003  H5N1  
DQ023145  A/chicken/China/1/02    2002  H5N1  
DQ343152  A/chicken/Hebei/108/02  2002  H5N1  
AY575875  A/chicken/Hong Kong/31.4/02   2002  H5N1  
AY575879  A/chicken/Hong Kong/409.1/02  2002  H5N1  
AY575876  A/chicken/Hong Kong/61.9/02   2002  H5N1  
AY575878  A/chicken/Hong Kong/96.1/02   2002  H5N1  
AY575877  A/chicken/Hong Kong/YU777/02  2002  H5N1  
DQ320927  A/chicken/Hong Kongi/86.3/2002   2002  H5N1  
DQ211924  A/chicken/zhoukou/2/02   2002  H5N1  
AY651346  A/Ck/Hong Kong/31.2/2002   2002  H5N1  
AY651350  A/Ck/Hong Kong/3176.3/2002   2002  H5N1  
AY651347  A/Ck/Hong Kong/37.4/2002   2002  H5N1  
AY651349  A/Ck/Hong Kong/YU22/2002   2002  H5N1  
AJ632268  A/duck/France/02166/2002   2002  H5N3  
AY585357  A/duck/Fujian/01/2002   2002  H5N1  
AY585358  A/duck/Fujian/13/2002   2002  H5N1  
AY585362  A/duck/Guangdong/22/2002   2002  H5N1  
AY585366  A/duck/Guangxi/53/2002    2002  H5N1  
AY585368  A/duck/Shanghai/35/2002   2002  H5N1  
AY585369  A/duck/Shanghai/37/2002   2002  H5N1  
ISDN38689  A/Duck/Viet Nam/Ncvd1/2002   2002  H5N1  
AY651345  A/Gf/Hong Kong/38/2002    2002  H5N1  
AY995885  A/mallard/Sweden/21/02    2002  H5N2  
AY995895  A/mallard/Sweden/58/02    2002  H5N3  
AY995896  A/mallard/Sweden/64/02    2002  H5N2  
AY575880  A/pheasant/Hong Kong/675.14/02    2002  H5N1  
AY651348  A/SCk/Hong Kong/YU100/2002   2002  H5N1  
AY651352  A/teal/China/2978.1/2002    2002  H5N1  
DQ343151  A/chicken/Hebei/718/2001    2001  H5N1  
AY075027  A/Chicken/Hong Kong/317.5/2001   2001  H5N1  
AF509025  A/Chicken/Hong Kong/715.5/01    2001  H5N1  
AF509026  A/Chicken/Hong Kong/822.1/01    2001  H5N1  
AF509027  A/Chicken/Hong Kong/829.2/01    2001  H5N1  
AF509028  A/Chicken/Hong Kong/830.2/01    2001  H5N1  
AF509029  A/Chicken/Hong Kong/858.3/01    2001  H5N1  
AF509030  A/Chicken/Hong Kong/867.1/01    2001  H5N1  
AF509032  A/Chicken/Hong Kong/873.3/01    2001  H5N1  
AF509033  A/Chicken/Hong Kong/876.1/01    2001  H5N1  
AF509031  A/Chicken/Hong Kong/879.1/01    2001  H5N1  
AF509034  A/Chicken/Hong Kong/891.1/01    2001  H5N1  
AF509035  A/Chicken/Hong Kong/893.2/01    2001  H5N1  
AY221524  A/Chicken/Hong Kong/FY150/01    2001  H5N1  
AF509019  A/Chicken/Hong Kong/FY150/01   2001  H5N1  
AY221523  A/Chicken/Hong Kong/FY150/01-MB5  2001  H5N1  
AF509016  A/Chicken/Hong Kong/FY77/01  2001  H5N1  
AY221522  A/Chicken/Hong Kong/NT873.3/01 2001  H5N1  
AY221521  A/Chicken/Hong Kong/NT873.3/01-MB    2001  H5N1  
AF509024  A/Chicken/Hong Kong/SF219/01    2001  H5N1  
AY221529  A/Chicken/Hong Kong/YU562/01    2001  H5N1  
AF509017  A/Chicken/Hong Kong/YU562/01    2001  H5N1  
AF509018  A/Chicken/Hong Kong/YU563/01    2001  H5N1  
AY221528  A/Chicken/Hong Kong/YU822.2/01  2001  H5N1  
AY221527  A/Chicken/Hong Kong/YU822.2/01-MB    2001  H5N1  
DQ003215  A/chicken/Jiande/1218/2001   2001  H5N1  
AF468837  A/Duck/Anyang/AVL-1/2001    2001  H5N1  
AY585372  A/duck/Fujian/17/2001    2001  H5N1  
AY585360  A/duck/Guangdong/01/2001   2001  H5N1  
AY585364  A/duck/Guangxi/22/2001    2001  H5N1  
AY585375  A/duck/Guangxi/50/2001    2001  H5N1  
AY075033  A/Duck/Hong Kong/380.5/2001  2001  H5N1  
AF509038  A/Duck/Hong Kong/573.4/01    2001  H5N1  
AF509039  A/Duck/Hong Kong/646.3/01    2001  H5N1  
AY585370  A/duck/Shanghai/08/2001    2001  H5N1  
AY585367  A/duck/Shanghai/13/2001    2001  H5N1  
AY585376  A/duck/Shanghai/38/2001    2001  H5N1  
AF509036  A/Goose/Hong Kong/76.1/01  2001  H5N1  
AF509037  A/Goose/Hong Kong/ww100/01 2001  H5N1  
ISDN38260  A/Goose/Viet Nam/113/2001 2001  H5N1  
ISDN38261  A/Goose/Viet Nam/324/2001 2001  H5N1  
AF509020  A/Pheasant/Hong Kong/FY155/01   2001  H5N1  
AY221526  A/Pheasant/Hong Kong/FY155/01    2001  H5N1  
AY221525  A/Pheasant/Hong Kong/FY155/01-MB   2001  H5N1  
AF509023  A/Pigeon/Hong Kong/SF215/01    2001  H5N1  
AF509022  A/Quail/Hong Kong/SF203/01    2001  H5N1  
AF509021  A/Silky Chicken/Hong Kong/SF189/01    2001  H5N1  
AY747617  A/swine/Fujian/F1/2001    2001  H5N1  
AY585359  A/duck/Fujian/19/2000    2000  H5N1  
AY585373  A/duck/Guangdong/07/2000    2000  H5N1  
AY585361  A/duck/Guangdong/12/2000    2000  H5N1  
AY585374  A/duck/Guangdong/40/2000    2000  H5N1  
AY059481  A/Duck/Hong Kong/2986.1/2000    2000  H5N1  
AY059476  A/Duck/Hong Kong/ww381/2000    2000  H5N1  
AY059477  A/Duck/Hong Kong/ww382/2000    2000  H5N1  
AY059478  A/Duck/Hong Kong/ww461/2000    2000  H5N1  
AY059479  A/Duck/Hong Kong/ww487/2000    2000  H5N1  
AF501234  A/duck/Shanghai/1/2000  2000  H5  
AF501235  A/duck/Shanghai/1/2000   2000  H5  
AY585371  A/duck/Zhejiang/15/2000  2000  H5N1  
AY585377  A/duck/Zhejiang/52/2000  2000  H5N1  
AY075030  A/Goose/Hong Kong/3014.5/2000    2000  H5N1  
AY059482  A/Goose/Hong Kong/3014.8/2000    2000  H5N1  
AF398417  A/Goose/Hong Kong/385.3/2000    2000  H5N1  
AF398418  A/Goose/Hong Kong/385.5/2000    2000  H5N1  
AY059474  A/Goose/Hong Kong/ww26/2000    2000  H5N1  
AY059475  A/Goose/Hong Kong/ww28/2000    2000  H5N1  
AY059480  A/Goose/Hong Kong/ww491/2000   2000  H5N1  
DQ201829  A/Goose/Huadong/1/2000    2000  H5N1  
AY585363  A/duck/Guangxi/07/1999   1999  H5N1  
AF216737  A/Environment/Hong Kong/437-10/99   1999  H5N1  
AF216713  A/Environment/Hong Kong/437-4/99    1999  H5N1  
AF216721  A/Environment/Hong Kong/437-6/99    1999  H5N1  
AF216729  A/Environment/Hong Kong/437-8/99    1999  H5N1  
DQ092869  A/Pekin duck/Singapore/F59/04/98   1998  H5N2  
AF046100  A/Chicken/Hong Kong/915/97    1997  H5N1  
AF194992  A/Chicken/Italy/9097/97    1997  H5N9  
AF098543  A/Duck/Hong Kong/p46/97    1997  H5N1  
ISDN49024  A/duck/Singapore/3/97    1997  H5N3  
AF303057  A/duck/Singapore/Q-F119-3/97    1997  H5N3  
AF364334  A/Goose/Guangdong/3/97    1997  H5N1  
AF098545  A/Goose/Hong Kong/w355/97    1997  H5N1  
AF036356  A/Hong Kong/156/97    1997  H5N1  
AF046088  A/Hong Kong/156/97    1997  H5N1  
AF084279  A/Hong Kong/481/97    1997  H5N1  
AF046096  A/Hong Kong/481/97   1997  H5N1  
AF046098  A/Hong Kong/482/97    1997  H5N1  
AF084281  A/Hong Kong/486/97    1997  H5N1  
AF102671  A/Hong Kong/486/97    1997  H5N1  
AF102672  A/Hong Kong/488/97    1997  H5N1  
AF102675  A/Hong Kong/507/97    1997  H5N1  
AF102673  A/Hong Kong/516/97   1997  H5N1  
AF098546  A/Silky Chicken/Hong Kong/p17/97    1997  H5N1  
AF148678  A/goose/Guangdong/1/96    1996  H5N1  
AF144305  A/Goose/Guangdong/1/96    1996  H5N1  
AB241616  A/swan/Hokkaido/4/96    1996  H5N3  
AB241617  A/swan/Hokkaido/51/96   1996  H5N3  
AB241618  A/swan/Hokkaido/67/96  1996  H5N3  
AF082042  A/Duck/Potsdam/1402-6/86 1986  H5N2  
AF290443  A/Duck/Ho Chi Minh/14/78   1978  H5N3  
CY005575  A/duck/Hong Kong/342/1978  1978  H5N2  
AF082038  A/Duck/Hong Kong/205/77    1977  H5N3 
PB2 polymorphism

ISDN140030  A/Azerbaijan/006-207/2006    2006  H5N1  
DQ529292  A/chicken/Nigeria/641/2006  2006  H5N1  
DQ533586  A/Cygnus olor/Italy/742/2006    2006  H5N1  
DQ852607  A/grebe/Tyva/Tyv06-2/06    2006  H5N1  
ISDN133322  A/Indonesia/283H/2006    2006  H5N1  
ISDN133329  A/Indonesia/286H/2006    2006  H5N1  
ISDN133103  A/Turkey/12/2006    2006  H5N1  
ISDN133377  A/Turkey/15/06   2006  H5N1  
ISDN133363  A/Turkey/651242/06    2006  H5N1  
ISDN133371  A/Turkey/65596/06   2006  H5N1  
AB264769  A/whooper swan/Mongolia/2/06    2006  H5N1  
AB239300  A/bar-headed goose/Mongolia/1/05    2005  H5N1  
DQ237956  A/bar-headed goose/Qinghai/0510/05  2005  H5N1  
DQ095761  A/Bar-headed Goose/Qinghai/12/05    2005  H5N1  
DQ095757  A/Bar-headed Goose/Qinghai/5/05    2005  H5N1  
DQ095752  A/Bar-headed Goose/Qinghai/59/05   2005  H5N1  
DQ095755  A/Bar-headed Goose/Qinghai/60/05   2005  H5N1  
DQ095758  A/Bar-headed Goose/Qinghai/61/05   2005  H5N1  
DQ095760  A/Bar-headed Goose/Qinghai/62/05   2005  H5N1  
DQ095762  A/Bar-headed Goose/Qinghai/65/05   2005  H5N1  
DQ095763  A/Bar-headed Goose/Qinghai/67/05   2005  H5N1  
DQ095753  A/Bar-headed Goose/Qinghai/68/05   2005  H5N1  
DQ095759  A/Bar-headed Goose/Qinghai/75/05   2005  H5N1  
DQ100542  A/black-headed goose/Qinghai/1/2005   2005  H5N1  
DQ100543  A/black-headed goose/Qinghai/2/2005   2005  H5N1  
DQ100544  A/black-headed gull/Qinghai/1/2005    2005  H5N1  
DQ095756  A/Brown-headed Gull/Qinghai/3/05    2005  H5N1  
DQ650670  A/chicken/Crimea/08/2005    2005  H5N1  
DQ320810  A/chicken/Fujian/1042/2005   2005  H5N1  
DQ320832  A/chicken/Guangxi/604/2005   2005  H5N1  
DQ449639  A/chicken/Kurgan/05/2005    2005  H5N1  
DQ323675  A/chicken/Kurgan/3/2005   2005  H5N1  
DQ095766  A/Chicken/Shantou/810/05   2005  H5N1  
DQ840518  A/chicken/Tula/Russia/Oct-5/2005    2005  H5N1  
DQ492887  A/chicken/Vietnam/393/2005    2005  H5N1  
DQ389161  A/Cygnus olor/Astrakhan/Ast05-2-1/2005  2005  H5N1  
DQ434890  A/Cygnus olor/Astrakhan/Ast05-2-10/2005  2005  H5N1  
DQ343506  A/Cygnus olor/Astrakhan/Ast05-2-2/2005    2005  H5N1  
DQ358750  A/Cygnus olor/Astrakhan/Ast05-2-3/2005    2005  H5N1  
DQ363916  A/Cygnus olor/Astrakhan/Ast05-2-4/2005    2005  H5N1  
DQ365011  A/Cygnus olor/Astrakhan/Ast05-2-5/2005    2005  H5N1  
DQ365001  A/Cygnus olor/Astrakhan/Ast05-2-6/2005    2005  H5N1  
DQ363921  A/Cygnus olor/Astrakhan/Ast05-2-7/2005    2005  H5N1  
DQ386305  A/Cygnus olor/Astrakhan/Ast05-2-8/2005    2005  H5N1  
DQ399543  A/Cygnus olor/Astrakhan/Ast05-2-9/2005   2005  H5N1  
DQ320809  A/duck/Fujian/897/2005   2005  H5N1  
DQ320833  A/duck/Guangxi/793/2005  2005  H5N1  
DQ320835  A/duck/Guangzhou/20/2005    2005  H5N1  
DQ449647  A/duck/Kurgan/08/2005    2005  H5N1  
DQ864713  A/duck/Novosibirsk/02/05    2005  H5N1  
DQ232608  A/duck/Novosibirsk/56/2005  2005  H5N1  
DQ320856  A/Environment/Qinghai/31/2005    2005  H5N1  
DQ095768  A/Goose/Shantou/1621/05   2005  H5N1  
DQ320849  A/goose/Shantou/2216/2005   2005  H5N1  
DQ100545  A/great black-headed gull/Qinghai/1/2005  2005  H5N1  
DQ095754  A/Great Black-headed Gull/Qinghai/2/05    2005  H5N1  
DQ232607  A/grebe/Novosibirsk/29/2005    2005  H5N1  
DQ320850  A/migratory duck/Jiangxi/1653/2005   2005  H5N1  
DQ320851  A/migratory duck/Jiangxi/1657/2005   2005  H5N1  
DQ320852  A/migratory duck/Jiangxi/1701/2005   2005  H5N1  
DQ095767  A/Quail/Shantou/911/05   2005  H5N1  
DQ840532  A/swan/Astrakhan/Russia/Nov-2/2005   2005  H5N1  
ISDN129518  A/turkey/Turkey/1/05    2005  H5N1 

PB1 polymorphism

ISDN140037  A/Azerbaijan/006-207/2006    2006  H5N1  
DQ533585  A/Cygnus olor/Italy/742/2006  2006  H5N1  
ISDN183245  A/Feline/Indonesia/CDC1/2006    2006  H5N1  
DQ852606  A/grebe/Tyva/Tyv06-2/06   2006  H5N1  
ISDN133330  A/Indonesia/283H/2006   2006  H5N1  
ISDN133331  A/Indonesia/286H/2006   2006  H5N1  
ISDN138754  A/Indonesia/292H/2006   2006  H5N1  
ISDN136855  A/Indonesia/304H/2006   2006  H5N1  
ISDN140816  A/Indonesia/534H/2006   2006  H5N1  
ISDN140912  A/Indonesia/535H/2006   2006  H5N1  
ISDN140913  A/Indonesia/536H/2006   2006  H5N1  
ISDN140824  A/Indonesia/538H/2006   2006  H5N1  
ISDN140932  A/Indonesia/542H/2006   2006  H5N1  
ISDN187427  A/Indonesia/546bH/2006  2006  H5N1  
ISDN140914  A/Indonesia/546H/2006   2006  H5N1  
ISDN185504  A/Indonesia/560H/2006   2006  H5N1  
ISDN187435  A/Indonesia/567H/2006   2006  H5N1  
ISDN187451  A/Indonesia/583H/2006   2006  H5N1  
ISDN187459  A/Indonesia/604H/2006   2006  H5N1  
ISDN183265  A/Indonesia/CDC326/2006  2006  H5N1  
ISDN183268  A/Indonesia/CDC326N/2006  2006  H5N1  
ISDN183272  A/Indonesia/CDC326N2/2006   2006  H5N1  
ISDN183274  A/Indonesia/CDC326T/2006    2006  H5N1  
ISDN183278  A/Indonesia/CDC329/2006    2006  H5N1  
ISDN183280  A/Indonesia/CDC357/2006    2006  H5N1  
ISDN181363  A/Indonesia/CDC523/2006    2006  H5N1  
ISDN183303  A/Indonesia/CDC523E/2006   2006  H5N1  
ISDN183311  A/Indonesia/CDC523T/2006  2006  H5N1  
ISDN183319  A/Indonesia/CDC582/2006    2006  H5N1  
ISDN140833  A/Indonesia/CDC594/06    2006  H5N1  
ISDN140841  A/Indonesia/CDC595/06    2006  H5N1  
ISDN140849  A/Indonesia/CDC596/06    2006  H5N1  
ISDN140857  A/Indonesia/CDC597/06    2006  H5N1  
ISDN140864  A/Indonesia/CDC599/06    2006  H5N1  
ISDN183780  A/Indonesia/CDC599N/2006    2006  H5N1  
ISDN183700  A/Indonesia/CDC610/2006    2006  H5N1  
ISDN183740  A/Indonesia/CDC625/2006   2006  H5N1  
SDN183772  A/Indonesia/CDC625L/2006  2006  H5N1  
ISDN183748  A/Indonesia/CDC634/2006    2006  H5N1  
ISDN183756  A/Indonesia/CDC634P/2006   2006  H5N1  
ISDN183764  A/Indonesia/CDC634T/2006   2006  H5N1  
ISDN207106  A/Indonesia/CDC644/2006  2006  H5N1  
ISDN207098  A/Indonesia/CDC644T/2006   2006  H5N1  
ISDN204135  A/Indonesia/CDC669/2006    2006  H5N1  
ISDN204143  A/Indonesia/CDC669P/2006   2006  H5N1  
ISDN204151  A/Indonesia/CDC699/2006    2006  H5N1  
AB264770  A/whooper swan/Mongolia/2/06  2006  H5N1  
DQ493367  A/chicken/Dairi/BPPVI/2005    2005  H5N1  
DQ493368  A/chicken/Deli Serdang/BPPVI/2005   2005  H5N1  
DQ351875  A/chicken/Hebei/326/2005    2005  H5N1  
DQ321305  A/chicken/Hunan/999/2005    2005  H5N1  
DQ493352  A/chicken/Kulon Progo/BBVW/2005    2005  H5N1  
DQ493365  A/chicken/Simalanggang/BPPVI/2005  2005  H5N1  
DQ493369  A/chicken/Tarutung/BPPVI/2005   2005  H5N1  
DQ493366  A/chicken/Tebing Tinggi/BPPVI/2005    2005  H5N1  
DQ321306  A/duck/Hunan/1265/2005    2005  H5N1  
DQ321307  A/duck/Hunan/1608/2005    2005  H5N1  
DQ321308  A/duck/Hunan/1652/2005    2005  H5N1  
ISDN132412  A/Indonesia/239H/2005   2005  H5N1  
ISDN132420  A/Indonesia/245H/2005   2005  H5N1  
ISDN128032  A/Indonesia/6/2005    2005  H5N1  
ISDN183253  A/Indonesia/CDC287E/2005  2005  H5N1  
ISDN183256  A/Indonesia/CDC287T/2005  2005  H5N1  
ISDN183260  A/Indonesia/CDC292N/2005  2005  H5N1  
ISDN183264  A/Indonesia/CDC292T/2005  2005  H5N1  
DQ321316  A/migratory duck/Jiangxi/2300/2005    2005  H5N1  
AY737294  A/chicken/Guangdong/178/04    2004  H5N1  
AY737287  A/chicken/Guangdong/191/04    2004  H5N1  
DQ366328  A/chicken/Guangxi/12/2004    2004  H5N1  
AY684704  A/chicken/Hubei/327/2004    2004  H5N1  
AY770083  A/chicken/Hubei/489/2004    2004  H5N1  
AY653199  A/chicken/Jilin/9/2004    2004  H5N1  
AY651652  A/Dk/Indonesia/MS/2004    2004  H5N1  
DQ366336  A/duck/Guangxi/13/2004    2004  H5N1  
DQ321278  A/duck/Guangxi/1311/2004  2004  H5N1  
DQ321282  A/duck/Guangxi/1793/2004  2004  H5N1  
DQ321285  A/duck/Guangxi/2291/2004  2004  H5N1  
DQ321287  A/duck/Guangxi/2396/2004  2004  H5N1  
DQ321276  A/goose/Guangxi/1097/2004   2004  H5N1  
DQ321277  A/goose/Guangxi/1198/2004   2004  H5N1  
DQ321284  A/goose/Guangxi/2112/2004   2004  H5N1  
DQ321286  A/goose/Guangxi/2383/2004   2004  H5N1  
AY651694  A/peregrine falcon/Hong Kong/D0028/2004    2004  H5N1  
AY950278  A/swan/Guangxi/307/2004    2004  H5N1  
AY950277  A/wild duck/Guangdong/314/2004    2004  H5N1  
AY651651  A/Ck/Indonesia/BL/2003   2003  H5N1  
AY651653  A/Ck/Indonesia/PA/2003   2003  H5N1  
AY518366  A/duck/China/E319-2/03   2003  H5N1  
DQ321309  A/duck/Shantou/4610/2003   2003  H5N1  
AY576398  A/chicken/Hong Kong/31.4/02    2002  H5N1  
AY576400  A/chicken/Hong Kong/YU777/02   2002  H5N1  
AY651678  A/Ck/Hong Kong/37.4/2002    2002  H5N1  
AY585490  A/duck/Guangdong/22/2002    2002  H5N1  
AF509170  A/Chicken/Hong Kong/YU562/01   2001  H5N1  
AY221583  A/Chicken/Hong Kong/YU562/01   2001  H5N1  
AF509171  A/Chicken/Hong Kong/YU563/01   2001  H5N1  
AY221582  A/Chicken/Hong Kong/YU822.2/01    2001  H5N1  
AY221581  A/Chicken/Hong Kong/YU822.2/01-MB    2001  H5N1  
AY585485  A/duck/Fujian/17/2001    2001  H5N1  
AY585493  A/duck/Guangxi/22/2001   2001  H5N1  
AY585494  A/duck/Guangxi/35/2001   2001  H5N1  
AY585495  A/duck/Guangxi/50/2001   2001  H5N1 

PA Polymorphism

ISDN140044  A/Azerbaijan/006-207/2006    2006  H5N1  
DQ852603  A/grebe/Tyva/Tyv06-2/06    2006  H5N1  
ISDN140815  A/Indonesia/534H/2006   2006  H5N1  
ISDN140909  A/Indonesia/535H/2006    2006  H5N1  
ISDN140910  A/Indonesia/536H/2006    2006  H5N1  
ISDN140823  A/Indonesia/538H/2006    2006  H5N1  
ISDN187426  A/Indonesia/546bH/2006   2006  H5N1  
ISDN140911  A/Indonesia/546H/2006    2006  H5N1  
ISDN185502  A/Indonesia/560H/2006    2006  H5N1  
ISDN140834  A/Indonesia/CDC594/06    2006  H5N1  
ISDN140842  A/Indonesia/CDC595/06    2006  H5N1  
ISDN140850  A/Indonesia/CDC596/06    2006  H5N1  
ISDN140858  A/Indonesia/CDC597/06    2006  H5N1  
ISDN140865  A/Indonesia/CDC599/06    2006  H5N1  
ISDN183779  A/Indonesia/CDC599N/2006   2006  H5N1  
ISDN183739  A/Indonesia/CDC625/2006    2006  H5N1  
ISDN183771  A/Indonesia/CDC625L/2006   2006  H5N1  
AB263751  A/whooper swan/Mongolia/2/06  2006  H5N1  
DQ493280  A/chicken/Dairi/BPPVI/2005    2005  H5N1  
AY303660  A/chicken/Chile/176822/02    2002  H7N3  
AY303662  A/chicken/Chile/4322/02   2002  H7N3  
AY303661  A/chicken/Chile/4957/02    2002  H7N3  
AY497139  A/chicken/Aguascalientes/124-3705/98    1998  H5N2  
AY497140  A/Chicken/Puebla/231-5284/98   1998  H5N2  
AY210200  A/Canada/2/70    H3N2  
AY210196  A/England/878/69   1969  H3N2  
CY006304  A/Hong Kong/3/69   1969  H3N2 

NA polymorphism

ISDN140069  A/Azerbaijan/006-207/2006   2006  H5N1  
ISDN140812  A/Indonesia/534H/2006  2006  H5N1  
ISDN140900  A/Indonesia/535H/2006    2006  H5N1  
ISDN140901  A/Indonesia/536H/2006    2006  H5N1  
ISDN140820  A/Indonesia/538H/2006  2006  H5N1  
ISDN187423  A/Indonesia/546bH/2006   2006  H5N1  
ISDN140902  A/Indonesia/546H/2006    2006  H5N1  
ISDN185497  A/Indonesia/560H/2006    2006  H5N1  
ISDN140837  A/Indonesia/CDC594/06    2006  H5N1  
ISDN140845  A/Indonesia/CDC595/06   2006  H5N1  
ISDN140853  A/Indonesia/CDC596/06  2006  H5N1  
ISDN140861  A/Indonesia/CDC597/06    2006  H5N1  
ISDN140868  A/Indonesia/CDC599/06    2006  H5N1  
ISDN183784  A/Indonesia/CDC599N/2006   2006  H5N1  
ISDN183743  A/Indonesia/CDC625/2006    2006  H5N1  
ISDN183775  A/Indonesia/CDC625L/2006   2006  H5N1  
DQ493015  A/chicken/Dairi/BPPVI/2005   2005  H5N1  
DQ493016  A/chicken/Deli Serdang/BPPVI/2005    2005  H5N1  
DQ884461  A/chicken/Indonesia/77/2005   2005  H5N1  
ISDN187393  A/Chicken/Indonesia/Wates77/2005   2005  H5N1  
ISDN187396  A/Chicken/Indonesia/Wates83/2005   2005  H5N1  
DQ321059  A/chicken/Salatiga/BBVet-I/2005   2005  H5N1  
DQ493013  A/chicken/Simalanggang/BPPVI/2005    2005  H5N1  
DQ493017  A/chicken/Tarutung/BPPVI/2005    2005  H5N1  
DQ493014  A/chicken/Tebing Tinggi/BPPVI/2005    2005  H5N1  
DQ493012  A/chicken/Pangkalpinang/BPPV3/2004    2004  H5N1  
DQ493018  A/turkey/Kedaton/BPPV3/2004    2004  H5N1 

Media Sources

Phylogenetic Trees

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