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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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