Swine Sequences in H5 Wild Birds in British Columbia
Recombinomics Commentary
July 19, 2006
The HA sequence of A/mallard/BC/317/2005(H5N2) has been released. This isolate was obtained via an expanded banding project by the Canadian Cooperative Wildlife Health Centre. Last year the agency reported that H5 had been found in live healthy wild birds throughout southern Canada. A remarkable 24% of the birds tested in British Columbia were H5 positive. The latest breakdown by species indicates bird flu was detected in 1165/2657 of the mallards tested and H5 was detected in 187/811. The update report by region indicates H5 was detected in 167/380 birds tested in British Columbia.
Analysis of the above sequence indicates it has a HA cleavage site consistent with low path H5. However, analysis of individual polymorphisms indicates the H5 has acquired two tandem polymorphisms, C1367T and C1377T.
Other isolates in the Los Alamos flu database having these two polymorphisms are listed below. The only H5 or avian isolate in the list is the H5N1 sequence from British Columbia. All other isolates are mammalian H1 isolates, including recent isolates from Canadian swine as well as a fatal human case in Maryland
The most extensive homology is identified with a 25 bp probe which identifies the recent isolate A/swine/Ontario/11112/2004(H1N1), which was among a group of Canadian swine showing both extensive recombination as well as extreme conservation of sequences. As noted below, the 25 bp probe identifies A/Wilson-Smith/33 and A/WSN/33, the first human flu isolate as well as its neurotropic derivative.
The acquisition of these polymorphisms in a health wild bird population is cause for concern. Recent data from Prince Edward Island suggests the Qinghai strain of H5N1 has already entered North America. Recombination between low path H5 and high path H5N1 is common and provides a mechanism for acquisition of these mammalian polymorphisms by the Qinghai strain of H5N1 bird flu.
The initial H5N1 human isolates from Vietnam and Thailand had acquired a number of mammalian polymorphisms that were not found in other H5N1’s. The acquisition of swine polymorphisms in H5 in wild birds in Canada, and presumably the United States, is cause for concern.
DQ826532 A/mallard/BC/373/2005 2005 H5N2
DQ280250 A/swine/Ontario/11112/04 2004 H1N1
DQ447187 A/swine/Taiwan/CO935/2004 2004 H1N2
DQ431990 A/swine/Taiwan/CO935/2004 2004 H1N2
DQ280203 A/swine/Alberta/56626/03 2003 H1N1
DQ280195 A/swine/Ontario/57561/03 2003 H1N1
AY129156 A/Swine/Korea/CY02/02 2002 H1N2
AY233393 A/Duck/NC/91347/01 2001 H1N2
DQ058215 A/swine/Guangdong/2/01 2001 H1N1
AF455682 A/Swine/Illinois/100084/01 2001 H1N2
AF455681 A/Swine/Illinois/100085A/01 2001 H1N2
AF455679 A/Swine/Iowa/930/01 2001 H1N2
AY060050 A/Swine/MN/16419/01 2001 H1N2
AY060048 A/Swine/MN/23124-S/01 2001 H1N2
AY060047 A/Swine/MN/23124-T/01 2001 H1N2
AY060051 A/Swine/MN/34893/01 2001 H1N2
AF455677 A/Swine/North Carolina/93523/01 2001 H1N2
AF455676 A/Swine/North Carolina/98225/01 2001 H1N2
AF455675 A/Swine/Ohio/891/01 2001 H1N2
AF455680 A/Swine/Indiana/P12439/00 2000 H1N2
AF455678 A/Swine/Minnesota/55551/00 2000 H1N2
AF250124 A/Swine/Indiana/9K035/99 1999 H1N2
AF222035 A/Swine/Wisconsin/458/98 1998 H1N1
AF222036 A/Swine/Wisconsin/464/98 1998 H1N1
AF222026 A/Swine/Wisconsin/125/97 1997 H1N1
AF222027 A/Swine/Wisconsin/136/97 1997 H1N1
AF222032 A/Swine/Wisconsin/235/97 1997 H1N1
AF222033 A/Swine/Wisconsin/238/97 1997 H1N1
U53162 A/Wisconsin/4754/94 1994 H1N1
U53163 A/Wisconsin/4755/94 1994 H1N1
S67220 A/Swine/Nebraska/1/92 1992 H1N1
L09063 A/Swine/Nebraska/1/92 1992 H1
L24362 A/Maryland/12/91 1991 H1N1
U46783 A/Swine/Beijing/47/91 1991 H1N1
U11857 A/Swine/St-Hyacinthe/106/91 1991 H1
M81707 A/Swine/Indiana/1726/88 1988 H1N1
AF082042 A/Duck/Potsdam/1402-6/86 1986 H5N2
DQ508905 A/Wilson-Smith/1933 1933 H1N1
J02176 A/WSN/33 1933 H1N1
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