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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
Map