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H5N1 From Danish Buzzard Similar to Astrakhan Swan 

Recombinomics Commentary

March 20, 2006

The rapid disclosure of H5N1 bird flu sequences in Denmark was announced in a recent ProMed commentary.  The sequences were available for download and the traffic quickly exceeded the download quota for site.  These sequences are now available at an alternate site.  The transparency and prompt posting of sequences of all eight genes of H5N1 from a buzzard (_Buteo buteo_) by the Danish Institute for Food and Veterinary Research (DFVF) and Statens Seruminstitut (SSI) is to be commended.

As indicated in the ProMed commentary, there was significant relatedness with the Astrakhan sequences from mute swans.  Ten sequences are publicly available and form two clades.  The Danish sequences shares several polymorphisms with A/Cygnus olor/Astrakhan/Ast05-2-3/2005 (H5N1), which constitutes the smaller clade.  However, as shown below, some buzzard polymorphisms are specifically found in all of the Astrakhan sequences.  Although other Qinghai isolates do not share these specific sequences, they are shared by a discrete number of other isolates.  Listed below is an example where the polymorphism, PB2 A261G, is almost exclusively found in North American isolates.  Another buzzard PB2 polymorphism, C1605A, is found in a number of Asian sequences, but more recently is also found in swine sequences in Canada, which was conserved since 1977.  However, in contrast with the swine sequences which acquired long stretches of polymorphisms, the buzzard sequence identity is limited to a single polymorphism.  The acquisition of individual polymorphisms on a Qinghai genetic background has been noted in many of the Qinghai sequences, suggesting these acquisitions are recent and due to recombination.

PB2 A261G

   DQ389161  A/Cygnus olor/Astrakhan/Ast05-2-1/2005   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   
   CY004405   A/shorebird/Delaware/101/2004                  2004  H5N7   
   CY004983   A/shorebird/Delaware/75/2004                    2004  H5N7   
   AY651721   A/Viet Nam/3062/2004                                  2004  H5N1   
   CY004359   A/mallard/Alberta/209/2003                          2003  H10N7   
   AY619954   A/Swine/Saskatchewan/18789/02               2002  H1N1   
   AF457705   A/chicken/California/139/01                          2001  H6N2   
   AF457681   A/chicken/California/6643/01                       2001  H6N2   
   AY585518   A/duck/Shanghai/08/2001                             2001  H5N1   
   CY004709   A/mallard/Alberta/156/2001                          2001  H3N8   
   CY005249   A/pintail/Alberta/202/2000                             2000  H10N7   
   CY005371   A/ruddy turnstone/Delaware/97/2000           2000  H12N5   
   AY633179   A/mallard/Alberta/199/99                               1999  H3N6   
   AY633379   A/pintail/Alberta/37/99                                    1999  H3N8   
   AY497099   A/chicken/Aguascalientes/124-3705/98       1998  H5N2   
   AY497100   A/Chicken/Puebla/231-5284/98                    1998  H5N2   
   CY003975   A/mallard/Alberta/205/1998                           1998  H2N3   
   AY633203   A/mallard/Alberta/205/98                                1998  H2N3   
   CY003983   A/mallard/Alberta/226/1998                           1998  H2N3   
   AY633235   A/mallard/Alberta/226/98                                1998  H2N3   
   CY005844   A/chicken/Chis/15224/1997                           1997  H5N2   
   CY004273   A/mallard/Alberta/206/1996                           1996  H6N8   
   AY633211   A/Mallard/Alberta/206/96                                1996  H6N8   
   AY497101   A/Chicken/Puebla/28159-474/95                  1995  H5N2   
   CY004545   A/blue-winged teal/Alberta/141/1992            1992  H1N4   
   CY004201   A/blue-winged teal/Alberta/69/1985              1985  H6N2   
   CY004193   A/mallard duck/Alberta/10/1985                    1985  H6N2   
   CY005113   A/mallard duck/Alberta/98/1985                    1985  H6N2   
   AY633315   A/mallard/Alberta/98/85                                  1985  H6N2   
   CY004217   A/pintail duck/Alberta/111/1985                    1985  H6N2   
   AY633323   A/pintail/Alberta/113/85                                  1985  H6N2   
   CY004412   A/ruddy turnstone/New Jersey/65/1985        1985  H7N3   
   CY004225   A/shoveler/Alberta/114/1985                         1985  H6N2   
   CY005638   A/duck/Hong Kong/784/1979                         1979  H9N2   
   CY004634   A/mallard duck/Alberta/1012/1979                1979  H3N4   
   CY004497   A/mallard duck/Alberta/965/1979                  1979  H1N1   
   CY005043   A/pintail duck/Alberta/121/1979                     1979  H7N8   
   CY005038   A/blue-winged teal/Alberta/221/1978            1978  H7N2  
PB2 C1605A

                         A/Buzzard/Denmark/6370/06               2006  H5N1
   DQ280229  A/swine/Ontario/48235/04                     2004  H1N2   
   DQ280205  A/swine/Ontario/55383/04                     2004  H1N2   
   DQ226181  A/Ck/HK/CSW161/2003                        2003  H9N2   
   DQ226178  A/Ck/HK/YU463/2003                            2003  H9N2   
   DQ226179  A/Ck/HK/YU577/2003                            2003  H9N2   
   DQ226182  A/Gf/HK/NT101/2003                             2003  H9N2   
   DQ226180  A/SCk/HK/YU663/2003                         2003  H9N2   
   AY576386   A/chicken/Hong Kong/31.4/02              2002  H5N1   
   AY576390   A/chicken/Hong Kong/409.1/02            2002  H5N1   
   AY576389   A/chicken/Hong Kong/96.1/02              2002  H5N1   
   AY585511   A/duck/Guangdong/22/2002                 2002  H5N1   
   AY585520   A/duck/Shanghai/35/2002                     2002  H5N1   
   DQ064550  A/chicken/Guangdong/56/01                 2001  H9N2   
   DQ351870  A/chicken/Hebei/718/2001                    2001  H5N1   
   DQ064556  A/chicken/Heilongjiang/48/01                2001  H9N2   
   AF509152   A/Chicken/Hong Kong/715.5/01           2001  H5N1   
   AF509153   A/Chicken/Hong Kong/751.1/01           2001  H5N1   
   AF509154   A/Chicken/Hong Kong/822.1/01           2001  H5N1   
   AF509155   A/Chicken/Hong Kong/829.2/01           2001  H5N1   
   AF509156   A/Chicken/Hong Kong/830.2/01           2001  H5N1   
   AF509157   A/Chicken/Hong Kong/858.3/01           2001  H5N1   
   AF509158   A/Chicken/Hong Kong/866.3/01           2001  H5N1   
   AF509159   A/Chicken/Hong Kong/867.1/01           2001  H5N1   
   AF509161   A/Chicken/Hong Kong/873.3/01           2001  H5N1   
   AF509162   A/Chicken/Hong Kong/876.1/01           2001  H5N1   
   AF509160   A/Chicken/Hong Kong/879.1/01           2001  H5N1   
   AF509163   A/Chicken/Hong Kong/891.1/01           2001  H5N1   
   AF509164   A/Chicken/Hong Kong/893.2/01           2001  H5N1   
   AF509146   A/Chicken/Hong Kong/FY150/01          2001  H5N1   
   AY221587   A/Chicken/Hong Kong/FY150/01          2001  H5N1   
   AY221586   A/Chicken/Hong Kong/FY150/01-MB   2001  H5N1   
   AF509143   A/Chicken/Hong Kong/FY77/01             2001  H5N1   
   AY221585   A/Chicken/Hong Kong/NT873.3/01        2001  H5N1   
   AY221584   A/Chicken/Hong Kong/NT873.3/01-MB 2001  H5N1   
   AF509151   A/Chicken/Hong Kong/SF219/01           2001  H5N1   
   AF509144   A/Chicken/Hong Kong/YU562/01           2001  H5N1   
   AY221592   A/Chicken/Hong Kong/YU562/01           2001  H5N1   
   AF509145   A/Chicken/Hong Kong/YU563/01           2001  H5N1   
   AY221591   A/Chicken/Hong Kong/YU822.2/01        2001  H5N1   
   AY221590   A/Chicken/Hong Kong/YU822.2/01-MB 2001  H5N1   
   AY585506   A/duck/Fujian/17/2001                              2001  H5N1   
   AY585508   A/duck/Guangdong/01/2001                    2001  H5N1   
   AY585514   A/duck/Guangxi/22/2001                          2001  H5N1   
   AY585515   A/duck/Guangxi/35/2001                          2001  H5N1   
   AF509167   A/Duck/Hong Kong/573.4/01                   2001  H5N1   
   AF509168   A/Duck/Hong Kong/646.3/01                   2001  H5N1   
   AY585519   A/duck/Shanghai/13/2001                        2001  H5N1   
   AF523471   A/Duck/Shantou/1605/01                         2001  H9N2   
   AF509165   A/Goose/Hong Kong/76.1/01                  2001  H5N1   
   AF509147   A/Pheasant/Hong Kong/FY155/01         2001  H5N1   
   AY221589   A/Pheasant/Hong Kong/FY155/01          2001  H5N1   
   AY221588   A/Pheasant/Hong Kong/FY155/01-MB   2001  H5N1   
   AF509150   A/Pigeon/Hong Kong/SF215/01              2001  H5N1   
   AF509149   A/Quail/Hong Kong/SF203/01                 2001  H5N1   
   AF509148   A/Silky Chicken/Hong Kong/SF189/01   2001  H5N1   
   AY585512   A/duck/Guangdong/40/2000                     2000  H5N1   
   AY059525   A/Duck/Hong Kong/2986.1/2000             2000  H5N1   
   AF523472   A/Duck/Shantou/2102/00                          2000  H9N2   
   AY059529   A/Goose/Hong Kong/3014.8/2000          2000  H5N1   
   AY253750   A/Chicken/Shanghai/F/98                         1998  H9N2   
   CY005091   A/pintail/Alberta/129/1993                        1993  H10N1   
   CY004691   A/mallard/Alberta/129/1991                      1991  H3N6   
   CY005085   A/red knot/New Jersey/325/1989             1989  H7N7   
   M73513       A /Swine/Tennessee/24/77                        1977  H1N1   
   CY005831   A/turkey/Ontario/6118/1968                       1968  H8N4   
   AF156443   A/Turkey/California/189/66                         1966  H9N2   
   DQ067437  A/turkey/Wisconsin/66                                 1966  H9N2  


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