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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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