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Recombination in PB2 Gene of H1N1 Canadian Swine 

Recombinomics Commentary

March 13, 2006

Swine H1N1 and H1N2 sequences were recently made available at GenBank.  These sequences were from a publication entitled “Identification of Human H1N2 and Human-Swine Reassortant H1N2 and H1N1 Influenza A Viruses among Pigs in Ontario, Canada (2003 to 2005)”.  The paper focuses on ressortment between swine and human genes resulting  in one swine isolate that has 8 human genes and several that have 1 human gene (PB1) and 7 swine genes.  Reassortment occurs when two viruses infect the same host and new constellations of reshuffled genes emerge.

However, when two virus infect the same host, recombination can also occur.  Analysis of the sequences at GenBank identifies a series of recombination events in the PB2 gene. One of the 2004 isolates, A/swine/Ontario/11112/04(H1N1), has an exact match with positions 728 through 1573 of the 1998 isolate, . A/Swine/North_Carolina/35922/98(H3N2). In contrast the two sequences differ at 31 positions within the first 711 positions.  This distribution indicates the Ontario/11112 PB2 gene is a recombinant that has acquire a significant portion of the PB2 gene from an sequence similar to the North Carolina 1998 sequence.

A more complete analysis of recombination is available for another Canadian swine isolate, A/swine/Ontario/53518/03)H1N1.  The first 541 PB2 positions are an exact match with A/swine/Alberta/56626/03.  Comparison of the remaining 1742 positions shows 295 differences.  Thus the majority of the 3’ position of Ontario/53518 significantly diverges from Alberta/56626.  However, the portion of the gene that diverges from Alberta/56626 is an exact match with A/Swine/Korea/CY02/02(H1N2).  Thus, Ontario/53518 PB2 is a recombinant gene that is an exact match with Alberta/56626 for the first 541 positions, and the an exact match with Korea/CY02 for the remainder of the gene.  In addition the divergent portion of Alberta/56626 contains an exact match between positions 981 and 1300 with A/Swine/Tennessee/24/77 (H1N1). Thus, although the H1N1′s were isolated 26 years, there are no differences in the 320 BP stretch in the middle of the gene.

The above examples provide clear evidence for recombination in the PB2 gene of recent H1N1 isolates from swine in Canada.  Exact matches with portions of the gene can be found in isolates collected 6 to 26 years earlier.  These data indicate the genes are not changing via random mutation, but instead change via recombination.

Although the above examples of recombination are striking, there is no mention of recombination n the peer reviewed publication describing these sequences.  Similarly, pronouncements by WHO and consultants indicate that H5N1 is evolving via random mutation.  They fail to comment or acknowledge recombination.

This limited analysis is of even greater concern because the sequences are sequestered in a private database, precluding evaluation of the new identified sequences.  Moreover, WHO is using these unpublished and unavailable sequences to select new candidate pandemic vaccine targets.

WHO is actively ignoring recombination. This limited analysis coupled with the sequestering of the most recent H5N1 is cause for concern. 

These sequences should be released immediately and analyzed for evidence of recombination, which can cover large portions of individual genes, as described above for PB2, but can also involve recombination involving sequence differences that involve a single nucleotide change.


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