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Astrakhan Mute Swan H5N1 Acquisition of American Sequences

Recombinomics Commentary

February 26, 2006

The availability of all eight genes from six isolates from Astrakhan allows for analysis of newly acquired polymorphisms.  The consensus sequence of the Astrakhan isolates have 8 major polymorphisms which are in 5 or 6 isolates and not in other Qinghai H5N1 sequences.

Two of these polymorphisms have been found in human H1N1 sequences.  The polymorphism described below is similar to the two PB2 polymorphisms that are found in isolates from North America.  The PB1 polymorphism is also found in recent North American isolates.  The two H5N7 isolates from Alberta also have the two polymorphisms in PB2, making it a likely source.  These data suggest that the polymorphism were acquired via recombination from the same North American host.

The polymorphism is C1539T and was screened using a 25 BP probe.  All of the isolates below have an exact match in their PB1 gene and this polymorphism has an unusual history.  It was first reported in the 1957 H2N2 pandemic strain.  In 1968 it was then found in the H3N2 pandemic strain.  It remained in human isolates until 1976 when it was detected in H3 bird isolates.  It has been in a wide variety of bird sero-types, but almost all isolates were from North America, including the swine isolates.

Now the polymorphism is in 5 of the 6 Astrakhan H5N1 isolates.  These same isolates have picked up a number of  current human polymorphism including two from H1N1 and two from H3N2 isolates. 

The acquisition of human isolates are cause for concern. 

The three North American polymorphisms found in the 2004 H5N7 isolates from Delaware suggest the H5N1 has already migrated t North America.

   DQ343505  A/Cygnus olor/Astrakhan/Ast05-2-2/2005  2005  H5N1   
   DQ363915  A/Cygnus olor/Astrakhan/Ast05-2-4/2005  2005  H5N1   
   DQ365008  A/Cygnus olor/Astrakhan/Ast05-2-5/2005  2005  H5N1   
   DQ365000  A/Cygnus olor/Astrakhan/Ast05-2-6/2005  2005  H5N1   
   DQ363920  A/Cygnus olor/Astrakhan/Ast05-2-7/2005  2005  H5N1   
   AY849785  A/chicken/TX/298313/04                               2004  H5N2   
   CY004404  A/shorebird/Delaware/101/2004                  2004  H5N7   
   CY004288  A/shorebird/Delaware/12/2004                    2004  H6N8   
   CY005262  A/shorebird/Delaware/122/2004                  2004  H10N7   
   CY004982  A/shorebird/Delaware/75/2004                    2004  H5N7   
   CY004280  A/mallard/Alberta/154/2003                          2003  H6N5   
   CY004371  A/mallard/Alberta/245/2003                          2003  H11N9   
   CY005336  A/shorebird/Delaware/236/2003                  2003  H11N9   
   CY004331  A/mallard/Alberta/27/2001                            2001  H7N3   
   CY005097  A/mallard/Alberta/34/2001                            2001  H7N1   
   AY619971  A/Swine/Ontario/42729A/01                         2001  H3N3   
   AY619963  A/Swine/Ontario/K01477/01                         2001  H3N3   
   CY004938  A/pintail/Alberta/207/1999                            1999  H4N8   
   CY003950  A/mallard/Alberta/201/1996                          1996  H2N3   
   AF156424  A/Quail/Hong Kong/AF157/92                      1992  H9N2   
   CY004232  A/mallard duck/Alberta/155/1990                 1990  H6N3   
   CY004240  A/mallard duck/Alberta/191/1990                 1990  H6N3   
   CY004248  A/mallard duck/Alberta/253/1990                 1990  H6N3   
   CY005084  A/red knot/New Jersey/325/1989                 1989  H7N7   
   CY004566  A/herring gull/Delaware/712/1988                1988  H16N3   
   CY005386  A/laughing gull/Delaware/554/1988             1988  H13N3   
   CY005146  A/mallard duck/Alberta/321/1988                 1988  H9N2   
   CY005077  A/ruddy turnstone/Delaware/2378/1988      1988  H7N7   
   CY005296  A/ruddy turnstone/Delaware/637/1988        1988  H11N9   
   CY005070  A/laughing gull/Delaware/2838/1987           1987  H13N2   
   CY005001  A/mallard duck/Alberta/7/1987                      1987  H8N4   
   CY005291  A/ruddy turnstone/Delaware/2762/1987       1987  H11N2   
   CY005381  A/herring gull/Delaware/471/1986                 1986  H13N7   
   CY003928  A/laughing gull/New Jersey/798/1986           1986  H2N7   
   CY005426  A/sanderling/Delaware/1258/1986                1986  H6N6   
   CY004852  A/blue-winged teal/Alberta/562/1985            1985  H4N6   
   CY004200  A/blue-winged teal/Alberta/69/1985              1985  H6N2   
   CY005056  A/green-winged teal/Alberta/228/1985         1985  H7N3   
   CY004829  A/laughing gull/New Jersey/72/1985             1985  H4N9   
   CY004192  A/mallard duck/Alberta/10/1985                    1985  H6N2   
   CY004841  A/mallard duck/Alberta/25/1985                    1985  H4N6   
   CY003885  A/mallard duck/Alberta/376/1985                  1985  H2N3   
   CY005063  A/mallard duck/Alberta/435/1985                  1985  H7N3   
   CY004668  A/mallard duck/Alberta/525/1985                  1985  H3N8   
   CY005112  A/mallard duck/Alberta/98/1985                    1985  H6N2   
   CY004216  A/pintail duck/Alberta/111/1985                    1985  H6N2   
   CY005960  A/redhead duck/Alberta/116/1985                1985  H4N6   
   CY004391  A/ruddy turnstone/New Jersey/49/1985        1985  H4N9   
   CY004411  A/ruddy turnstone/New Jersey/65/1985        1985  H7N3   
   CY004224  A/shoveler/Alberta/114/1985                         1985  H6N2   
   CY005205  A/mallard duck/Alberta/40/1984                    1984 H10N6   
   CY005212  A/pintail duck/Alberta/584/1984                    1984  H10N6   
   CY005217  A/redhead duck/Alberta/767/1984                1984  H10N7   
   CY005349  A/mallard duck/Alberta/342/1983                  1983  H12N1   
   CY004337  A/mallard duck/Alberta/396/1983                  1983  H9N1   
   CY004648  A/mallard duck/Alberta/506/1983                  1983  H9N1   
   CY004816  A/mallard duck/Alberta/581/1983                  1983  H4N4   
   CY004655  A/mallard duck/Alberta/635/1983                  1983  H3N5   
   CY005104  A/mallard duck/Alberta/743/1983                  1983  H9N1   
   CY005279  A/mallard duck/Alberta/797/1983                  1983  H11N3   
   CY005342  A/pintail duck/Alberta/306/1983                    1983  H12N5   
   CY005269  A/redhead duck/Alberta/357/1983                1983  H11N9   
   CY004168  A/blue-winged teal/Alberta/266/1982            1982  H6N6   
   CY004184  A/blue-winged teal/Alberta/685/1982           1982  H6N4   
   CY004176  A/mallard duck/Alberta/289/1982                 1982  H6N6   
   CY004152  A/pintail duck/Alberta/189/1982                    1982  H6N6   
   CY004160  A/widgeon/Alberta/256/1982                         1982  H6N6   
   CY005901  A/duck/MN/1516/1981                                    1981  H5N2   
   CY005198  A/mallard duck/Alberta/742/1981                  1981  H10N1   
   CY005872  A/pigeon/MN/1407/1981                                1981  H1N1   
   CY004502  A/pintail duck/Alberta/631/1981                    1981  H1N5   
   CY005887  A/blue-winged teal/MN/993/1980                  1980  H6N6   
   CY004971  A/mallard duck/Alberta/645/1980                 1980  H5N2   
   CY005894  A/pheasant/MN/917/1980                             1980  H7N3   
   CY005049  A/pintail duck/Alberta/169/1980                   1980  H3N8   
   DQ266098 A/seal/Mass/1/80 (MA)                                  1980  H7N7   
   M25925      A/Turkey/Minnesota/833/80                          1980  H4N2   
   CY005912  A/turkey/MN/833/1980                                  1980  H4N2   
   CY004612  A/green-winged teal/Alberta/438/1979       1979  H3N8   
   CY004135  A/mallard duck/Alberta/1151/1979              1979  H6N9   
   CY004112  A/mallard duck/Alberta/564/1979                1979  H3N8   
   CY004127  A/mallard duck/Alberta/676/1979                 1979  H3N6   
   CY004141  A/pintail duck/Alberta/1298/1979                 1979  H6N9   
   CY004085  A/pintail duck/Alberta/1303/1979                 1979  H6N2   
   CY004488  A/pintail duck/Alberta/238/1979                    1979  H1N1   
   CY004619  A/pintail duck/Alberta/462/1979                    1979  H3N6   
   CY004624  A/pintail duck/Alberta/627/1979                    1979  H3N2   
   CY004017  A/blue-winged teal/Alberta/48/1978             1978  H6N5   
   CY005193  A/blue-winged teal/Alberta/778/1978          1978  H10N3   
   M25926      A/Mallard/New York/6750/78                        1978  H2N2   
   CY004748  A/blue-winged teal/Alberta/243/1977           1977  H4N6   
   CY004727  A/canvasback duck/Alberta/274/1977         1977  H4N6   
   CY004734  A/gadwall duck/Alberta/53/1977                   1977  H4N6   
   CY004775  A/mallard duck/Alberta/161/1977                 1977  H4N6   
   CY004464  A/mallard duck/Alberta/42/1977                   1977  H1N6   
   CY004472  A/mallard duck/Alberta/46/1977                   1977  H1N1   
   CY006769  A/Nanjing/49/77                                              1977  H3N2   
   AF251390  A/Swine/Colorado/1/77                                 1977  H3N2   
   CY004586  A/canvasback duck/Alberta/102/1976         1976  H3N6   
   CY006889  A/Memphis/103/76                                        1976  H3N2  
   CY008698  A/Memphis/106/76                                        1976  H3N2   
   CY008706  A/Memphis/108/76                                        1976  H3N2   
   CY006841  A/Memphis/110/76                                        1976  H3N2   
   CY006729  A/Memphis/137/76                                        1976  H3N2   
   CY006050  A/Beijing/39/75                                              1975  H3N2   
   CY003734  A/Hong Kong/43/75                                       1975  H3N2   
   CY003502  A/Hong Kong/14/74                                       1974  H3N2   
   CY006913  A/Hong Kong/49/74                                       1974  H3N2   
   CY006721  A/Memphis/101/74                                         1974  H3N2   
   CY006825  A/Memphis/102/74                                         1974  H3N2   
   CY006833  A/Memphis/103/74                                         1974  H3N2   
   M74899      A/Dunedin/4/73                                                1973  N2   
   CY003534  A/Hong Kong/11/73                                        1973  H3N2   
   CY006817  A/Memphis/3/73                                              1973  H3N2   
   AY210283  A/England/42/72                                              1972  H3N2   
   CY008682  A/Memphis/101/72                                          1972  H3N2   
   CY002102  A/Memphis/102/72                                          1972  H3N2   
   CY008466  A/Memphis/103/72                                          1972  H3N2   
   CY008690  A/Memphis/105/72                                          1972  H3N2   
   CY002750  A/Memphis/109/72                                          1972  H3N2   
   AY210284  A/Tokyo/31/72                                                  1972  H3N2   
   AY210280  A/Caracas/1/71                                                1971  H3N2   
   AY210281  A/Chiba/5/71                                                    1971  H3N2   
   CY006689  A/Hong Kong/46/71                                         1971  H3N2   
   CY002502  A/Memphis/1/71                                               1971  H3N2   
   CY006225  A/Memphis/2/71                                               1971  H3N2   
   AY210279  A/Taiwan/3/71                                                   1971  H3N2   
   AY210277  A/Canada/2/70                                                 1970  H3N2   
   AY210278  A/Queensland/7/70                                          1970  H3N2   
   AY210282  A/Taiwan/2/70                                                  1970  H3N2   
   AY210274  A/England/878/69                                            1969  H3N2   
   AJ564806  A/England/939/69                                            1969  H3N2   
   CY006305  A/Hong Kong/3/69                                           1969  H3N2   
   AY210275  A/Rio/6/69                                                         1969  H3N2   
   AY210276  A/Taiwan/1/69                                                   1969  H3N2   
   CY008162  A/Beijing/1/68                                                   1968  H3N2   
   AY210025  A/Berkeley/1/68                                                1968  H2N2   
   AF348172  A/Hong Kong/1/68                                            1968  H3N2   
   AF348173  A/Hong Kong/1/68 (isolate MA20c)               1968  H3N2   
   AY210273  A/HongKong/16/68                                           1968  H3N2   
   M25935      A/Korea/426/68                                                1968  H2N2   
   CY006217  A/Memphis/1/68                                               1968  H3N2   
   J02138       A/NT/60/68                                                        1968  H3N2   
   AY210271  A/Panama/1/68                                                1968  H3N2   
   AY210272  A/USSR/039/68                                               1968  H3N2   
   AY210024  A/Ann Arbor/7/67                                             1967  H2N2   
   AY210021  A/England/10/67                                              1967  H2N2   
   AY210022  A/Georgia/1/67                                                1967  H2N2   
   AY210023  A/Tokyo/3/67                                                    1967  H2N2   
   AY210019  A/California/1/66                                              1966  H2N2   
   AY210020  A/Panama/1/66                                                1966  H2N2   
   AY210016  A/Albany/1/65                                                   1965  H2N2   
   AY210017  A/Kumamoto/1/65                                            1965  H2N2   
   AY210018  A/Pittsburgh/2/65                                              1965  H2N2   
   AY210015  A/Murakami/4/64                                               1964  H2N2   
   CY005818  A/duck/Ukraine/1/1963                                     1963  H3N8   
   AY210014  A/Japan/170/62                                                 1962  H2N2   
   AY210013  A/Panama/1/61                                                  1961  H2N2   
   AY210012  A/Ann Arbor/6/60                                               1960  H2N2   
   M23972    A/Ann Arbor/6/60                                                1960  H2N2   
   AY210011  A/Victoria/15681/59                                        1959  H2N2   
   AY210010  A/Albany/6/58                                                   1958  H2N2   
   AY210008  A/Chile/13/57                                                    1957  H2N2   
   M81580    A/Leningrad/134/17/57                                      1957  H2N2   
   M81586    A/Leningrad/134/47/57                                      1957  H2N2   
   M81574    A/Leningrad/134/57                                            1957  H2N2   
   M25924    A/Singapore/1/57                                                1957  H2N2   
   AY210009  A/Singapore/1/57                                              1957  H2N2  


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