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North American Polymorphisms in Mute Swan H5N1 in Astrakhan
Recombinomics Commentary
February 22, 2006
Detection of H5N1 in swans throughout Europe has raised concerns. Sequences from several recent mute swan H5N1 isolates from Astrakhan were placed on deposit at GenBank. In addition, many older isolates from North America dating back to the 1970's were also made available.
The mute swans had a number of polymorphisms that were not found in other H5N1 Qinghai strain isolates. A search of the database indicated some of these polymorphisms were found in North American isolates. Two such PB2 polymorphisms were found (G211A and A234G). A 25 nucleotide probe using the two mute swan polymorphisms and the intervening 23 nucleotides found exact matches in the isolates listed below. The isolates with the identical sequence represented a number of serotypes, but all were isolated from wild birds or chickens from North America. The isolates with matching sequence traced back to 1978.
The data support acquisition of these polymorphisms by recombination. These sequences were fixed in isolates from 1978 to 2004. The sequences were found in five of the six mute swan isolates (A234G was found in the seventh isolate).
The data indicate these polymorphisms had been circulating in wild birds in North America and were recently acquired by the recent mute swan isolates. These data suggest that H5N1 has circulated into North America previously, consistent with the H5N1 detected in western Europe. Birds in western Europe use the East Atlantic Flyway which goes into northern Siberia as well as northern Canada.
These data also indicate that the H5N1 that will soon be migrating north in the East Atlantic Flyway will be returning to North America and Western Europe.
These data raise additional surveillance issues. Although Canada identified a number of H5 serotypes from a n August banding program in southern Canada, H5N1 was not detected. Moreover the United States has failed to report detection HPAI or LPAI H5 in 2005 or 2006.
The failures are cause for concern as new H5N1 migrations will begin in a few months in Africa. There is no data on where the H5N1 in the United States is located. A number of bird die-offs have been reported, but there have been no reports of detected H5.
DQ343506 A/Cygnus olor/Astrakhan/Ast05-2-2/2005 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
CY004405 A/shorebird/Delaware/101/2004 2004 H5N7
CY004983 A/shorebird/Delaware/75/2004 2004 H5N7
CY004359 A/mallard/Alberta/209/2003 2003 H10N7
AF457705 A/chicken/California/139/01 2001 H6N2
AF457681 A/chicken/California/6643/01 2001 H6N2
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
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
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
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
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