Qinghai H5N1 Sequences in Karo Cluster in Sumatra Indonesia
Recombinomics Commentary
June 26, 2006
The recent workshop in Jakarta on human H5N1 in Indonesia provide additional detail on genetic changes associated with the Karo cluster. The father of the nephew of the index case had fourteen genetic changes not found in the consensus sequence H5N1 isolates from of the cluster. All other isolates had zero or one change. The high number of changes suggest the polymorphisms were acquired by recombination.
The past histories if polymorphisms can be identified in the flu database at Los Alamos. This approach has identified Qinghai bird flu sequences in recent isolates from Bali. Although Qinghai isolates in Indonesia have not been identified, the presence of Qinghai sequences on an Indonesian H5N1 genetic background points toward prior acquisitions via recombination.
The full sequences of the Karo H5N1 have not been released. However, phylogenetic trees of HA1 and M indicate that the closest public sequence to the Karo cluster isolates is A/chicken/Dairi/BPPVI/2005(H5N1). Like the Karo cluster, this isolate has an HA cleavage site of RERRRKKR and the amantadine resistance M2 change of S31N. Identities with the wild type positions were used to identify the number system used to represents the polymorphisms. For HA the chicken H5N1 sequence matched the consensus Kao cluster sequence for the first six polymorphism, but differed fro the last three indicating differences between the chicken and Karo sequences or a numbering error in the table, so these three positions were not evaluated.
Two of the matching eleven polymorphisms. HA A512G and M G651A were found in Qinghai isolates as listed below. The M polymorphism was defined with an 18 BP downstream probe, as well as a 23 BP upstream probe The downstream probe identified a large number of matching human isolates. H3N2 matches primarily limited to recent isolates from Indonesia and Canterbury, while a broader distribution was seen in H1N1 isolates. Several health care workers who cared for H5N1 patients in Karo and Bandung developed flu-like symptoms and was had been identified as being H1N1 positive. Although the healthcare workers tested negative for H5N1 virus, test results for H5N1 antibodies have not been disclosed. The M polymorphism is also in Canadian swine that have evidence of extensive recombination and have a human PB1 gene,
The profiling of these polymorphisms raises concerns that H5N1 in Indonesia is acquiring Qinghai sequences. Almost all Qinghai isolates have PB2 E627K. The only published exception is A/duck/Kurgan/08/2005(H5N1). Two of the human isolates in Indonesia, A/IDN/06/2005(H5N1) and A/IDN/321H/2006(H5N1) have E627K.
The rapid evolution of H5N1 in the Karo cluster and acquisition of Qinghai and human polymorphisms is cause fro concern.
HA A512G
DQ447199 A/chicken/Egypt/960N3-004/2006 2006 H5N1
DQ676834 A/chicken/Krasnodar/01/2006 2006 H5N1
DQ406728 A/chicken/Nigeria/641/2006 2006 H5N1
DQ515984 A/Cygnus olor/Czech Republic/5170/2006 2006 H5N1
DQ435200 A/domestic cat/Iraq/820/2006 2006 H5N1
DQ435201 A/domestic goose/Iraq/812/2006 2006 H5N1
DQ659113 A/duck/Niger/914/2006 2006 H5N1
DQ464377 A/Egypt/2782-NAMRU3/2006 2006 H5N1
DQ435202 A/Iraq/207-NAMRU3/2006 2006 H5N1
DQ458992 A/mallard/Bavaria/1/2006 2006 H5N1
DQ449031 A/mallard/Italy/332/2006 2006 H5N1
ISDN133105 A/Turkey/15/2006 2006 H5N1
ISDN133356 A/Turkey/651242/06 2006 H5N1
ISDN133364 A/Turkey/65596/06 2006 H5N1
AB233319 A/bar-headed goose/Mongolia/1/05 2005 H5N1
DQ320898 A/chicken/Guangxi/604/2005 2005 H5N1
DQ449632 A/chicken/Kurgan/05/2005 2005 H5N1
DQ323672 A/chicken/Kurgan/3/2005 2005 H5N1
DQ389158 A/Cygnus olor/Astrakhan/Ast05-2-1/2005 2005 H5N1
DQ434889 A/Cygnus olor/Astrakhan/Ast05-2-10/2005 2005 H5N1
DQ343502 A/Cygnus olor/Astrakhan/Ast05-2-2/2005 2005 H5N1
DQ358746 A/Cygnus olor/Astrakhan/Ast05-2-3/2005 2005 H5N1
DQ363918 A/Cygnus olor/Astrakhan/Ast05-2-4/2005 2005 H5N1
DQ365004 A/Cygnus olor/Astrakhan/Ast05-2-5/2005 2005 H5N1
DQ364996 A/Cygnus olor/Astrakhan/Ast05-2-6/2005 2005 H5N1
DQ363923 A/Cygnus olor/Astrakhan/Ast05-2-7/2005 2005 H5N1
DQ399540 A/Cygnus olor/Astrakhan/Ast05-2-8/2005 2005 H5N1
DQ399547 A/Cygnus olor/Astrakhan/Ast05-2-9/2005 2005 H5N1
DQ320899 A/duck/Guangxi/793/2005 2005 H5N1
DQ449640 A/duck/Kurgan/08/2005 2005 H5N1
DQ676840 A/goose/Krasnoozerka/627/2005 2005 H5N1
DQ320897 A/quail/Guangxi/575/2005 2005 H5N1
DQ320137 A/swan/Astrakhan/1/2005 2005 H5N1
ISDN129523 A/turkey/Turkey/1/05 2005 H5N1
DQ407519 A/turkey/Turkey/1/2005 2005 H5N1
AB233320 A/whooper swan/Mongolia/3/05 2005 H5N1
AB233321 A/whooper swan/Mongolia/4/05 2005 H5N1
AB233322 A/whooper swan/Mongolia/6/05 2005 H5N1
ISDN140936 A/Whooping swan/Mongolia/244/2005 2005 H5N1
DQ659326 A/Whooping swan/Mongolia/244/2005 2005 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
AY651345 A/Gf/Hong Kong/38/2002 2002 H5N1
AY575880 A/pheasant/Hong Kong/675.14/02 2002 H5N1
AY651348 A/SCk/Hong Kong/YU100/2002 2002 H5N1
M18450 A/Duck/Ireland/113/83 1983 H5N8
M G651A downstream probe
DQ676835 A/chicken/Krasnodar/01/2006 2006 H5N1
DQ529297 A/chicken/Nigeria/641/2006 2006 H5N1
DQ533580 A/Cygnus olor/Italy/742/2006 2006 H5N1
ISDN136480 A/Turkey/12/2006 2006 H5N1
ISDN133372 A/Turkey/15/06 2006 H5N1
ISDN133357 A/Turkey/651242/06 2006 H5N1
ISDN133365 A/Turkey/65596/06 2006 H5N1
AB239305 A/bar-headed goose/Mongolia/1/05 2005 H5N1
DQ237951 A/bar-headed goose/Qinghai/0510/05 2005 H5N1
DQ095641 A/Bar-headed Goose/Qinghai/12/05 2005 H5N1
DQ095637 A/Bar-headed Goose/Qinghai/5/05 2005 H5N1
DQ095632 A/Bar-headed Goose/Qinghai/59/05 2005 H5N1
DQ095635 A/Bar-headed Goose/Qinghai/60/05 2005 H5N1
DQ095638 A/Bar-headed Goose/Qinghai/61/05 2005 H5N1
DQ095640 A/Bar-headed Goose/Qinghai/62/05 2005 H5N1
DQ095642 A/Bar-headed Goose/Qinghai/65/05 2005 H5N1
DQ095643 A/Bar-headed Goose/Qinghai/67/05 2005 H5N1
DQ095633 A/Bar-headed Goose/Qinghai/68/05 2005 H5N1
DQ095639 A/Bar-headed Goose/Qinghai/75/05 2005 H5N1
DQ100566 A/black-headed goose/Qinghai/1/2005 2005 H5N1
DQ100567 A/black-headed goose/Qinghai/2/2005 2005 H5N1
DQ100568 A/black-headed gull/Qinghai/1/2005 2005 H5N1
DQ095636 A/Brown-headed Gull/Qinghai/3/05 2005 H5N1
DQ676839 A/chicken/Dovolnoe/03/2005 2005 H5N1
DQ320942 A/chicken/Fujian/1042/2005 2005 H5N1
DQ320964 A/chicken/Guangxi/604/2005 2005 H5N1
DQ449633 A/chicken/Kurgan/05/2005 2005 H5N1
DQ323678 A/chicken/Kurgan/3/2005 2005 H5N1
DQ095646 A/Chicken/Shantou/810/05 2005 H5N1
DQ394576 A/Cygnus olor/Astrakhan/Ast05-2-1/2005 2005 H5N1
DQ434888 A/Cygnus olor/Astrakhan/Ast05-2-10/2005 2005 H5N1
DQ359692 A/Cygnus olor/Astrakhan/Ast05-2-2/2005 2005 H5N1
DQ358739 A/Cygnus olor/Astrakhan/Ast05-2-3/2005 2005 H5N1
DQ363925 A/Cygnus olor/Astrakhan/Ast05-2-4/2005 2005 H5N1
DQ365009 A/Cygnus olor/Astrakhan/Ast05-2-5/2005 2005 H5N1
DQ365002 A/Cygnus olor/Astrakhan/Ast05-2-6/2005 2005 H5N1
DQ363928 A/Cygnus olor/Astrakhan/Ast05-2-7/2005 2005 H5N1
DQ399542 A/Cygnus olor/Astrakhan/Ast05-2-8/2005 2005 H5N1
DQ400912 A/Cygnus olor/Astrakhan/Ast05-2-9/2005 2005 H5N1
DQ320941 A/duck/Fujian/897/2005 2005 H5N1
DQ320965 A/duck/Guangxi/793/2005 2005 H5N1
DQ320967 A/duck/Guangzhou/20/2005 2005 H5N1
DQ449641 A/duck/Kurgan/08/2005 2005 H5N1
DQ234078 A/duck/Novosibirsk/56/2005 2005 H5N1
DQ320988 A/Environment/Qinghai/31/2005 2005 H5N1
DQ095648 A/Goose/Shantou/1621/05 2005 H5N1
DQ320981 A/goose/Shantou/2216/2005 2005 H5N1
DQ100569 A/great black-headed gull/Qinghai/1/2005 2005 H5N1
DQ095634 A/Great Black-headed Gull/Qinghai/2/05 2005 H5N1
DQ234077 A/grebe/Novosibirsk/29/2005 2005 H5N1
DQ320982 A/migratory duck/Jiangxi/1653/2005 2005 H5N1
DQ320983 A/migratory duck/Jiangxi/1657/2005 2005 H5N1
DQ320984 A/migratory duck/Jiangxi/1701/2005 2005 H5N1
DQ095647 A/Quail/Shantou/911/05 2005 H5N1
ISDN129521 A/turkey/Turkey/1/05 2005 H5N1
AB239312 A/whooper swan/Mongolia/3/05 2005 H5N1
AB239319 A/whooper swan/Mongolia/4/05 2005 H5N1
AB239326 A/whooper swan/Mongolia/6/05 2005 H5N1
AB212651 A/blow fly/Kyoto/93/2004 2004 H5N1
AY950238 A/chicken/Henan/210/2004 2004 H5N1
AB189048 A/chicken/Kyoto/3/2004 2004 H5N1
AB188819 A/chicken/Oita/8/2004 2004 H5N1
ISDN49085 A/Chicken/Yamaguchi/7/2004 2004 H5N1
AB166865 A/chicken/Yamaguchi/7/2004 2004 H5N1
AB189056 A/crow/Kyoto/53/2004 2004 H5N1
AB189064 A/crow/Osaka/102/2004 2004 H5N1
AY651412 A/peregrine falcon/Hong Kong/D0028/2004 2004 H5N1
AY790306 A/swine/Korea/S452/2004 2004 H9N2
DQ280252 A/swine/Ontario/11112/04 2004 H1N1
DQ280244 A/swine/Ontario/23866/04 2004 H1N1
DQ280234 A/swine/Ontario/48235/04 2004 H1N2
DQ280210 A/swine/Ontario/55383/04 2004 H1N2
AY676047 A/chicken/Korea/ES/03 2003 H5N1
ISDN45748 A/Chicken/Korea/es/2003 2003 H5N1
AY800234 A/chicken/Korea/S1/2003 2003 H9N2
AY862622 A/chicken/Korea/S18/03 2003 H9N2
AY862615 A/chicken/Korea/S4/03 2003 H9N2
DQ107517 A/chicken/Korea/S4/2003 2003 H9N2
AY862616 A/chicken/Korea/S5/03 2003 H9N2
AY862623 A/chicken/Korea/S6/03 2003 H3N2
AY862628 A/dove/Korea/S11/03 2003 H3N2
AY862619 A/dove/Korea/S14/03 2003 H9N2
AY676048 A/duck/Korea/ESD1/03 2003 H5N1
AY862627 A/duck/Korea/S10/03 2003 H3N2
AY862618 A/duck/Korea/S13/03 2003 H9N2
AY862624 A/duck/Korea/S7/03 2003 H3N2
AY862625 A/duck/Korea/S8/03 2003 H3N2
AY862626 A/duck/Korea/S9/03 2003 H3N2
AY862614 A/silky chicken/Korea/S3/03 2003 H9N2
DQ280220 A/swine/Ontario/53518/03 2003 H1N1
AY363579 A/swine/Hong Kong/1144/02 2002 H3N2
AY363580 A/swine/Hong Kong/1197/02 2002 H3N2
AY585391 A/duck/Shanghai/08/2001 2001 H5N1
AY363578 A/swine/Hong Kong/9745/01 2001 H3N2
AY684906 A/black-headed gull/Netherlands/1/00 2000 H13N8
AF523499 A/Duck/Shantou/1588/00 2000 H9N1
AF523500 A/Duck/Shantou/2030/00 2000 H9N1
AY363576 A/swine/Hong Kong/7982/00 2000 H3N2
AY684907 A/black-headed gull/Sweden/1/99 1999 H13N6
AY684908 A/black-headed gull/Sweden/2/99 1999 H16N3
AY684909 A/black-headed gull/Sweden/5/99 1999 H16N3
AF508692 A/Chicken/Korea/99029/99 1999 H9N2
AJ293925 A/Hong Kong/1774/99 1999 H3N2
AJ316047 A/swine/Cotes d'Armor/1482/99 1999 H1N1
AJ316051 A/swine/Cotes d'Armor/604/99 1999 H1N2
AY363573 A/swine/Hong Kong/5190/99 1999 H3N2
AY363574 A/swine/Hong Kong/5200/99 1999 H3N2
AY363575 A/swine/Hong Kong/5212/99 1999 H3N2
AJ316053 A/swine/Italy/1654-1/99 1999 H1N2
AJ316052 A/swine/Italy/1521/98 1998 H1N2
AJ293938 A/swine/Italy/1553-2/98 1998 H3N2
AF250493 A/Duck/Hong Kong/P151/97 1997 H3N8
AF250487 A/Duck/Hong Kong/P169/97 1997 H3N8
AJ316049 A/swine/Cotes d'Armor/790/97 1997 H1N2
AF156468 A/Chicken/Korea/25232-96006/96 1996 H9N2
AF156467 A/Chicken/Korea/38349-p96323/96 1996 H9N2
AF203788 A/Chicken/Korea/MS96/96 1996 H9N2
DQ102483 A/swine/Bakum/5/95 1995 H1N1
AF213916 A/Swine/Italy/25823/94 1994 H3N2
AJ316060 A/swine/Scotland/410440/94 1994 H1N2
Z46439 A/swine/Schleswig-Holstein/1/93 1993 H1N1
AJ311509 A/Swine/Belgium/220/92 1992 H3N2
Z26861 A/Swine/Germany/8533/91 1991 H1N1
AF188004 A/Swine/Quebec/5393/91 1991 H1N1
Z26859 A/turkey/Germany/3/91 1991 H1N1
Z26860 A/oystercatcher/Germany/87 1987 H1N1
M63525 A/Swine/Netherlands/12/85 1985 H1N1
AJ311508 A/swine/Cotes d'Armor/3633/84 1984 H3N2
AJ316059 A/swine/Finistere/2899/82 1982 H1N1
M55478 A/Swine/Germany/2/81 1981 H1N1
Z26862 A/Swine/Netherlands/25/80 1980 H1N1
upstream probe
AB259772 A/Aichi/104/2006 2006 H3N2
AB259773 A/Aichi/108/2006 2006 H3N2
AB259745 A/Aichi/122/2006 2006 H3N2
AB259768 A/Aichi/14/2006 2006 H3N2
AB259769 A/Aichi/173/2006 2006 H3N2
AB259770 A/Aichi/19/2006 2006 H3N2
AB259743 A/Aichi/211/2006 2006 H3N2
AB259747 A/Aichi/7/2006 2006 H3N2
AB259771 A/Aichi/80/2006 2006 H3N2
AB259746 A/Aichi/9/2006 2006 H3N2
DQ676835 A/chicken/Krasnodar/01/2006 2006 H5N1
DQ676831 A/chicken/Mahachkala/05/2006 2006 H5N1
DQ529297 A/chicken/Nigeria/641/2006 2006 H5N1
DQ533580 A/Cygnus olor/Italy/742/2006 2006 H5N1
ISDN136480 A/Turkey/12/2006 2006 H5N1
ISDN133372 A/Turkey/15/06 2006 H5N1
ISDN133357 A/Turkey/651242/06 2006 H5N1
ISDN133365 A/Turkey/65596/06 2006 H5N1
AB259751 A/Aichi/165/2005 2005 H3N2
AB259750 A/Aichi/174/2005 2005 H3N2
AB259767 A/Aichi/185/2005 2005 H3N2
AB259749 A/Aichi/188/2005 2005 H3N2
AB259748 A/Aichi/197/2005 2005 H3N2
AB239305 A/bar-headed goose/Mongolia/1/05 2005 H5N1
DQ237951 A/bar-headed goose/Qinghai/0510/05 2005 H5N1
DQ095641 A/Bar-headed Goose/Qinghai/12/05 2005 H5N1
DQ095637 A/Bar-headed Goose/Qinghai/5/05 2005 H5N1
DQ095632 A/Bar-headed Goose/Qinghai/59/05 2005 H5N1
DQ095635 A/Bar-headed Goose/Qinghai/60/05 2005 H5N1
DQ095638 A/Bar-headed Goose/Qinghai/61/05 2005 H5N1
DQ095640 A/Bar-headed Goose/Qinghai/62/05 2005 H5N1
DQ095642 A/Bar-headed Goose/Qinghai/65/05 2005 H5N1
DQ095643 A/Bar-headed Goose/Qinghai/67/05 2005 H5N1
DQ095633 A/Bar-headed Goose/Qinghai/68/05 2005 H5N1
DQ095639 A/Bar-headed Goose/Qinghai/75/05 2005 H5N1
DQ100566 A/black-headed goose/Qinghai/1/2005 2005 H5N1
DQ100567 A/black-headed goose/Qinghai/2/2005 2005 H5N1
DQ100568 A/black-headed gull/Qinghai/1/2005 2005 H5N1
DQ095636 A/Brown-headed Gull/Qinghai/3/05 2005 H5N1
CY009933 A/Canterbury/125/2005 2005 H3N2
CY008076 A/Canterbury/129/2005 2005 H3N2
CY008084 A/Canterbury/166/2005 2005 H3N2
CY008341 A/Canterbury/20/2005 2005 H3N2
CY008565 A/Canterbury/205/2005 2005 H3N2
CY008092 A/Canterbury/206/2005 2005 H3N2
CY008381 A/Canterbury/220/2005 2005 H3N2
CY008581 A/Canterbury/233/2005 2005 H3N2
CY008389 A/Canterbury/234/2005 2005 H3N2
CY008405 A/Canterbury/236/2005 2005 H3N2
CY008413 A/Canterbury/237/2005 2005 H3N2
CY008421 A/Canterbury/238/2005 2005 H3N2
CY008044 A/Canterbury/24/2005 2005 H3N2
CY008429 A/Canterbury/242/2005 2005 H3N2
CY008637 A/Canterbury/258/2005 2005 H3N2
CY008108 A/Canterbury/259/2005 2005 H3N2
CY009029 A/Canterbury/26/2005 2005 H3N2
CY008052 A/Canterbury/29/2005 2005 H3N2
CY007964 A/Canterbury/33/2005 2005 H3N2
CY009037 A/Canterbury/34/2005 2005 H3N2
DQ676839 A/chicken/Dovolnoe/03/2005 2005 H5N1
DQ320942 A/chicken/Fujian/1042/2005 2005 H5N1
DQ320964 A/chicken/Guangxi/604/2005 2005 H5N1
DQ449633 A/chicken/Kurgan/05/2005 2005 H5N1
DQ323678 A/chicken/Kurgan/3/2005 2005 H5N1
DQ095646 A/Chicken/Shantou/810/05 2005 H5N1
DQ394576 A/Cygnus olor/Astrakhan/Ast05-2-1/2005 2005 H5N1
DQ434888 A/Cygnus olor/Astrakhan/Ast05-2-10/200 2005 H5N1
DQ359692 A/Cygnus olor/Astrakhan/Ast05-2-2/2005 2005 H5N1
DQ363925 A/Cygnus olor/Astrakhan/Ast05-2-4/2005 2005 H5N1
DQ365009 A/Cygnus olor/Astrakhan/Ast05-2-5/2005 2005 H5N1
DQ365002 A/Cygnus olor/Astrakhan/Ast05-2-6/2005 2005 H5N1
DQ363928 A/Cygnus olor/Astrakhan/Ast05-2-7/2005 2005 H5N1
DQ399542 A/Cygnus olor/Astrakhan/Ast05-2-8/2005 2005 H5N1
DQ400912 A/Cygnus olor/Astrakhan/Ast05-2-9/2005 2005 H5N1
DQ320941 A/duck/Fujian/897/2005 2005 H5N1
DQ320965 A/duck/Guangxi/793/2005 2005 H5N1
DQ320967 A/duck/Guangzhou/20/2005 2005 H5N1
DQ449641 A/duck/Kurgan/08/2005 2005 H5N1
DQ234078 A/duck/Novosibirsk/56/2005 2005 H5N1
DQ320988 A/Environment/Qinghai/31/2005 2005 H5N1
DQ095648 A/Goose/Shantou/1621/05 2005 H5N1
DQ320981 A/goose/Shantou/2216/2005 2005 H5N1
DQ100569 A/great black-headed gull/Qinghai/1/2005 2005 H5N1
DQ095634 A/Great Black-headed Gull/Qinghai/2/05 2005 H5N1
DQ234077 A/grebe/Novosibirsk/29/2005 2005 H5N1
DQ320982 A/migratory duck/Jiangxi/1653/2005 2005 H5N1
DQ320983 A/migratory duck/Jiangxi/1657/2005 2005 H5N1
DQ320984 A/migratory duck/Jiangxi/1701/2005 2005 H5N1
DQ095647 A/Quail/Shantou/911/05 2005 H5N1
ISDN141893 A/Taiwan/482/2005 2005 H3N2
ISDN141892 A/Taiwan/518/2005 2005 H3N2
ISDN129521 A/turkey/Turkey/1/05 2005 H5N1
AB239312 A/whooper swan/Mongolia/3/05 2005 H5N1
AB239319 A/whooper swan/Mongolia/4/05 2005 H5N1
AB239326 A/whooper swan/Mongolia/6/05 2005 H5N1
AB212651 A/blow fly/Kyoto/93/2004 2004 H5N1
CY007468 A/Canterbury/106/2004 2004 H1N1
AB189048 A/chicken/Kyoto/3/2004 2004 H5N1
AB188819 A/chicken/Oita/8/2004 2004 H5N1
ISDN49085 A/Chicken/Yamaguchi/7/2004 2004 H5N1
AB166865 A/chicken/Yamaguchi/7/2004 2004 H5N1
AB189056 A/crow/Kyoto/53/2004 2004 H5N1
AB189064 A/crow/Osaka/102/2004 2004 H5N1
AY651412 A/peregrine falcon/Hong Kong/D0028/20042004 H5N1
CY004444 A/shorebird/Delaware/68/2004 2004 H13N9
DQ280252 A/swine/Ontario/11112/04 2004 H1N1
AY676047 A/chicken/Korea/ES/03 2003 H5N1
ISDN45748 A/Chicken/Korea/es/2003 2003 H5N1
AY862622 A/chicken/Korea/S18/03 2003 H9N2
AY862615 A/chicken/Korea/S4/03 2003 H9N2
AY862623 A/chicken/Korea/S6/03 2003 H3N2
AY862628 A/dove/Korea/S11/03 2003 H3N2
AY676048 A/duck/Korea/ESD1/03 2003 H5N1
AY862627 A/duck/Korea/S10/03 2003 H3N2
AY862618 A/duck/Korea/S13/03 2003 H9N2
AY862624 A/duck/Korea/S7/03 2003 H3N2
AY862625 A/duck/Korea/S8/03 2003 H3N2
AY862626 A/duck/Korea/S9/03 2003 H3N2
CY002985 A/New York/221/2003 2003 H1N1
CY002681 A/New York/222/2003 2003 H1N1
CY002689 A/New York/223/2003 2003 H1N1
CY002537 A/New York/227/2003 2003 H1N1
CY003297 A/New York/228/2003 2003 H1N1
CY002625 A/New York/230/2003 2003 H1N1
CY003377 A/New York/292/2003 2003 H1N1
CY003385 A/New York/293/2003 2003 H1N1
CY002705 A/New York/348/2003 2003 H1N1
CY006428 A/New York/350/2003 2003 H1N1
CY002809 A/New York/399/2003 2003 H1N1
CY008525 A/New York/483/2003 2003 H1N1
CY008997 A/New York/484/2003 2003 H1N1
CY003689 A/New York/486/2003 2003 H1N1
CY006916 A/New York/488/2003 2003 H1N1
CY006668 A/New York/493/2003 2003 H1N1
CY003705 A/New York/496/2003 2003 H1N1
AY862614 A/silky chicken/Korea/S3/03 2003 H9N2
AY303652 A/chicken/Chile/176822/02 2002 H7N3
AY303653 A/chicken/Chile/4322/02 2002 H7N3
AY303654 A/chicken/Chile/4957/02 2002 H7N3
AY303655 A/chicken/Chile/4968/02 2002 H7N3
AY303656 A/chicken/Chile/4977/02 2002 H7N3
CY000418 A/New York/103/2002 2002 H3N2
CY000114 A/New York/110/2002 2002 H3N2
CY001334 A/New York/118/2002 2002 H3N2
CY001198 A/New York/122/2002 2002 H3N2
CY001945 A/New York/126/2002 2002 H3N2
CY000426 A/New York/128/2002 2002 H3N2
CY002529 A/New York/220/2002 2002 H1N1
CY003305 A/New York/291/2002 2002 H1N1
CY003105 A/New York/404/2002 2002 H3N2
CY003137 A/New York/409/2002 2002 H3N2
CY003161 A/New York/412/2002 2002 H3N2
CY003193 A/New York/416/2002 2002 H3N2
CY006676 A/New York/494/2002 2002 H1N1
CY001302 A/New York/75/2002 2002 H3N2
CY000402 A/New York/89/2002 2002 H3N2
CY000926 A/New York/93/2002 2002 H3N2
DQ249267 A/Taiwan/2984/2002 2002 H1N1
AY303657 A/turkey/Chile/4418/02 2002 H7N3
CY010397 A/Canterbury/01/2001 2001 H1N1
CY009861 A/Canterbury/08/2001 2001 H1N1
CY010477 A/Canterbury/106/2001 2001 H1N1
CY010309 A/Canterbury/119/2001 2001 H1N1
CY010317 A/Canterbury/125/2001 2001 H1N1
CY010325 A/Canterbury/126/2001 2001 H1N1
CY010333 A/Canterbury/139/2001 2001 H1N1
CY010341 A/Canterbury/144/2001 2001 H1N1
CY011089 A/Canterbury/152/2001 2001 H1N1
CY009981 A/Canterbury/153/2001 2001 H1N1
CY010349 A/Canterbury/155/2001 2001 H1N1
CY009877 A/Canterbury/16/2001 2001 H1N1
CY010149 A/Canterbury/17/2001 2001 H1N1
CY010157 A/Canterbury/19/2001 2001 H1N1
CY010765 A/Canterbury/20/2001 2001 H1N1
CY010165 A/Canterbury/21/2001 2001 H1N1
CY010773 A/Canterbury/22/2001 2001 H1N1
CY010173 A/Canterbury/23/2001 2001 H1N1
CY010181 A/Canterbury/24/2001 2001 H1N1
CY010189 A/Canterbury/25/2001 2001 H1N1
CY010197 A/Canterbury/27/2001 2001 H1N1
CY010205 A/Canterbury/29/2001 2001 H1N1
CY010213 A/Canterbury/30/2001 2001 H1N1
CY010221 A/Canterbury/34/2001 2001 H1N1
CY010229 A/Canterbury/35/2001 2001 H1N1
CY010237 A/Canterbury/40/2001 2001 H1N1
CY009885 A/Canterbury/41/2001 2001 H1N1
CY010781 A/Canterbury/42/2001 2001 H1N1
CY010245 A/Canterbury/45/2001 2001 H1N1
CY010253 A/Canterbury/47/2001 2001 H1N1
CY010261 A/Canterbury/48/2001 2001 H1N1
CY010413 A/Canterbury/51/2001 2001 H1N1
CY010269 A/Canterbury/53/2001 2001 H1N1
CY010557 A/Canterbury/54/2001 2001 H1N1
CY010277 A/Canterbury/58/2001 2001 H1N1
CY011081 A/Canterbury/60/2001 2001 H1N1
CY010421 A/Canterbury/63/2001 2001 H1N1
CY010285 A/Canterbury/64/2001 2001 H1N1
CY010429 A/Canterbury/65/2001 2001 H1N1
CY009957 A/Canterbury/66/2001 2001 H1N1
CY010437 A/Canterbury/68/2001 2001 H1N1
CY010445 A /Canterbury/69/2001 2001 H1N1
CY010453 A /Canterbury/70/2001 2001 H1N1
CY010461 A/ Canterbury/71/2001 2001 H1N1
CY010293 A/ Canterbury/72/2001 2001 H1N1
CY010301 A/ Canterbury/73/2001 2001 H1N1
CY009965 A/ Canterbury/74/2001 2001 H1N1
CY009973 A/ Canterbury/76/2001 2001 H1N1
CY010469 A/ Canterbury/79/2001 2001 H1N1
AY651428 A/Dk/ST/5048/2001 2001 H3N8
AY585391 A/ duck/Shanghai/08/2001 2001 H5N1
CY001953 A/New York/205/2001 2001 H1N1
CY002617 A/New York/208/2001 2001 H1N1
CY006420 A/New York/212/2001 2001 H1N1
CY010853 A/New York/235/2001 2001 H1N1
CY003001 A/New York/239/2001 2001 H1N1
CY003009 A/New York/241/2001 2001 H1N1
CY006356 A/New York/242/2001 2001 H1N1
CY003017 A/New York/246/2001 2001 H1N1
CY002569 A/New York/281/2001 2001 H1N1
CY003313 A/New York/302/2001 2001 H1N1
CY006364 A/New York/303/2001 2001 H1N1
CY003393 A/New York/305/2001 2001 H1N1
CY003401 A/New York/306/2001 2001 H1N1
CY002801 A/New York/308/2001 2001 H1N1
CY006876 A/New York/309/2001 2001 H1N1
CY002673 A/New York/310/2001 2001 H1N1
CY002697 A/New York/312/2001 2001 H1N1
CY003025 A/New York/341/2001 2001 H1N1
CY003321 A/New York/342/2001 2001 H1N1
CY002393 A/New York/343/2001 2001 H1N1
CY006780 A/New York/344/2001 2001 H1N1
CY002401 A/New York/345/2001 2001 H1N1
CY003329 A/New York/346/2001 2001 H1N1
CY003089 A/New York/402/2001 2001 H3N2
CY009237 A/New York/441/2001 2001 H1N1
CY003465 A/New York/442/2001 2001 H1N1
CY003473 A/New York/443/2001 2001 H1N1
CY003289 A/New York/444/2001 2001 H1N1
CY003834 A/New York/445/2001 2001 H1N1
CY003481 A/New York/446/2001 2001 H1N1
CY006172 A/New York/447/2001 2001 H1N1
CY009869 A/South Canterbury/15/2001 2001 H1N1
CY010357 A/South Canterbury/159/2001 2001 H1N1
CY011185 A/Waikato/10/2001 2001 H1N1
CY011193 A/Waikato/16/2001 2001 H1N1
CY011209 A/Waikato/18/2001 2001 H1N1
CY011201 A/Waikato/20/2001 2001 H1N1
CY011161 A/Waikato/4/2001 2001 H1N1
CY011233 A/Waikato/42/2001 2001 H1N1
CY011225 A/Waikato/51/2001 2001 H1N1
CY011169 A/Waikato/7/2001 2001 H1N1
CY011393 A/Waikato/80/2001 2001 H1N1
CY011153 A/Wellington/1/2001 2001 H1N1
CY011241 A/Wellington/28/2001 2001 H1N1
CY011177 A/Wellington/3/2001 2001 H1N1
CY011217 A/Wellington/9/2001 2001 H1N1
CY011073 A/West Coast/31/2001 2001 H1N1
CY010405 A/West Coast/33/2001 2001 H1N1
CY010133 A/Canterbury/100/2000 2000 H1N1
CY009757 A/Canterbury/23/2000 2000 H1N1
CY010101 A/Canterbury/27/2000 2000 H1N1
CY009189 A/Canterbury/28/2000 2000 H1N1
CY009181 A/Canterbury/30/2000 2000 H1N1
CY009221 A/Canterbury/32/2000 2000 H1N1
CY009213 A/Canterbury/33/2000 2000 H1N1
CY009229 A/Canterbury/34/2000 2000 H1N1
CY009197 A/Canterbury/36/2000 2000 H1N1
CY009533 A/Canterbury/37/2000 2000 H1N1
CY009829 A/Canterbury/41/2000 2000 H1N1
CY010093 A/Canterbury/43/2000 2000 H1N1
CY009541 A/Canterbury/5/2000 2000 H1N1
CY010109 A/Canterbury/51/2000 2000 H1N1
CY010125 A/Canterbury/54/2000 2000 H1N1
CY009845 A/Canterbury/57/2000 2000 H1N1
CY010117 A/Canterbury/58/2000 2000 H1N1
CY009821 A/Canterbury/60/2000 2000 H1N1
CY010389 A/Canterbury/63/2000 2000 H1N1
CY009549 A/Canterbury/65/2000 2000 H1N1
CY009765 A/Canterbury/7/2000 2000 H1N1
CY009789 A/Canterbury/76/2000 2000 H1N1
CY009813 A/Canterbury/78/2000 2000 H1N1
CY009797 A/Canterbury/79/2000 2000 H1N1
CY010381 A/Canterbury/8/2000 2000 H1N1
CY009805 A/Canterbury/87/2000 2000 H1N1
CY009941 A/Canterbury/9/2000 2000 H1N1
CY010141 A/Canterbury/95/2000 2000 H1N1
AF523499 A/Duck/Shantou/1588/00 2000 H9N1
AF523500 A/Duck/Shantou/2030/00 2000 H9N1
CY002641 A/New York/233/2000 2000 H1N1
CY002649 A/New York/234/2000 2000 H1N1
CY005428 A/Quail/Nanchang/12-340/2000 2000 H1N1
AJ458304 A/Saudi Arabia/7971/2000 2000 H1N1
DQ021740 A/semi-palmated sandpiper/DE/2109/00 2000 H11N6
CY009773 A/South Canterbury/31/2000 2000 H1N1
CY009205 A/South Canterbury/35/2000 2000 H1N1
CY009781 A/South Canterbury/40/2000 2000 H1N1
CY009173 A/South Canterbury/50/2000 2000 H1N1
CY009837 A/South Canterbury/59/2000 2000 H1N1
CY010997 A/Wellington/2/2000 2000 H1N1
CY011005 A/Wellington/3/2000 2000 H1N1
CY011013 A/Wellington/5/2000 2000 H1N1
AF508692 A/Chicken/Korea/99029/99 1999 H9N2
DQ508860 A/New Caledonia/20/1999 1999 H1N1
ISDN139828 A/New Caledonia/20/99 1999 H1N1
AJ458301 A/New Caledonia/20/99 1999 H1N1
AF250493 A/Duck/Hong Kong/P151/97 1997 H3N8
AF250487 A/Duck/Hong Kong/P169/97 1997 H3N8
AF250484 A/Duck/Hong Kong/P185/97 1997 H3N8
AF073201 A/Turkey/Utah/24721-10/95 1995 H7N3
AF073204 A/Emu/Texas/39924/93 1993 H5N2
AY664429 A/ruddy turnstone/Delaware/34/93 1993 H2N1
AY664465 A/ruddy turnstone/Delaware/81/93 1993 H2N1
AF001677 A/Equine/LaPlata/1/88 1988 H3N8
DQ021729 A/mottled duck/LA/32M/87 1987 H6N2
Z26860 A/oystercatcher/Germany/87 1987 H1N1
CY005421 A/sanderling/Delaware/1258/1986 1986 H6N6
AY664436 A/sanderling/Delaware/1258/86 1986 H6N6
CY004838 A/mallard duck/Alberta/25/1985 1985 H4N6
CY004831 A/mallard duck/Alberta/630/1984 1984 H4N2
CY010957 A/Memphis/15/1983 1983 H1N1
CY005896 A/duck/MN/1516/1981 1981 H5N2
M63528 A/turkey/Minnesota/166/81 1981 H1N1
M63538 A/Gull/Massachusetts/26/80 1980 H13N6
M63527 A/turkey/Minnesota/833/80 1980 H4N2
CY005907 A/turkey/MN/833/1980 1980 H4N2
CY004798 A/blue-winged teal/Alberta/580/1979 1979 H4N2
CY004631 A/mallard duck/Alberta/1012/1979 1979 H3N4
CY004626 A/mallard duck/Alberta/663/1979 1979 H3N5
CY004988 A/pintail duck/Alberta/114/1979 1979 H8N4
CY004012 A/blue-winged teal/Alberta/48/1978 1978 H6N5
CY004784 A/mallard duck/Alberta/354/1978 1978 H4N2
CY004600 A/mallard duck/Alberta/712/1978 1978 H3N3
DQ107490 A/turkey/MN/511/78 1978 H9N2
CY004743 A/blue-winged teal/Alberta/243/1977 1977 H4N6
CY005016 A/blue-winged teal/Alberta/295/1977 1977 H7N3
CY004722 A/canvasback duck/Alberta/274/1977 1977 H4N6
AF001686 A/Equine/Newmarket/1/77 1977 H7N7
CY005033 A/gadwall duck/Alberta/291/1977 1977 H7N3
CY004729 A/gadwall duck/Alberta/53/1977 1977 H4N6
CY004593 A/mallard duck/Alberta/127/1977 1977 H1N1
CY004961 A/mallard duck/Alberta/291/1977 977 H4N1
CY004459 A/mallard duck/Alberta/42/1977 1977 H1N6
AY664426 A/mallard duck/Alberta/42/1977 1977 H1N6
CY004750 A/mallard/Alberta/300/1977 1977 H4N3
AY664480 A/mallard/Alberta/300/1977 1977 H4N3
CY003848 A/mallard/Alberta/77/1977 1977 H2N3
AY664425 A/mallard/Alberta/77/1977 1977 H2N3
CY004736 A/redhead duck/Alberta/74/1977 1977 H4N6
CY005023 A/widgeon/Alberta/284/1977 1977 H7N3
CY004310 A/mallard duck/Alberta/20/1976 1976 H4N6
CY004710 A/mallard duck/Alberta/26/1976 1976 H3N1
CY004290 A/mallard duck/Alberta/65/1976 1976 H1N1
AF073197 A/Turkey/Oregon/71 1971 H7N3
AF001674 A/Equine/Miami/63 1963 H3N8
Media Sources
Phylogenetic Trees