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Novel H1N1 in Saskatchewan Raises Pandemic Concerns
Recombinomics Commentary 13:46
July 8, 2009

A new strain of H1N1 flu sickened at least two workers at a pig farm in Saskatchewan, Canadian health officials said. Tests found the strain is different from the pandemic swine flu circulating the globe.

The two people recovered from mild illness, and a third case is under investigation, according to a government statement. Pigs from the farm tested positive for a common version of swine flu and didn't carry the new human version found in the workers.

The above comments raise serious concerns about the novel H1N1 virus in Saskatchewan, Canada.  Media reports remain sketchy, but the new virus appears to have human H1 and N1, although it remains unclear if these are acquisitions from contemporary season flu (Brisbane/59 clade 2B with H274Y tamiflu resistance on N1), or earlier versions circa 2007 or 2003, which have been described previously in H1N1 swine isolates.

Similarly, the constellation of the other six gene segments remains murky.  The pandemic H1N1 has a human PB1, avian PA and PB2, and a swine origin for the remaining three gene segments.  This combination has also been seen in other swine isolates, so the relatedness of the remaining six gene segments remain unclear.  However, above constellation is likely, since the remain genes have been described as swine triple reassortants.

The release of full sequences from isolates of the workers would address the uncertainties noted above.

However, there are additional issues raised but not fully answered in initial media reports.  If the influenza from the swine do not match the human isolates, the origin remains open, and of course other humans would represent a likely source.  Isolation of swine H1N1 from humans is not uncommon, but usually a matching sequence is found in swine linked to the patients.  Similarly, initial reports do not give disease onset dates, raising concerns that one or both of the confirmed cases infected the suspect case.

These unanswered questions raise concerns of yet another swine H1N1 that has jumped to humans and is transmitting H2H.

More details on the cases, as well as publication of the sequences of all eight gene segments would be useful.

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