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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    

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