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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
A/Buzzard/Denmark/6370/06
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
Map