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H1N1v Case In Ontario Canada
Recombinomics Commentary 16:00
September 25, 2012

Dr. Arlene King says the man is confirmed as having been infected with an H1N1 variant (H1N1v) influenza virus.

King says the man, who is not being identified, is being treated and closely monitored in a hospital in southwestern Ontario.

The above comments describe the first H1N1v case in Canada this year.  The genetic relationship between this isolate and the 2012 US isolate, A/Missouri/12/2012, is unclear, as is the presence of an H1N1pdm09 M gene.  In the US, the H1N1v isolate from 2011, A/Wisconsin/28/2011, and the above 2012 isolate have an H1N1pdm09 M gene, as did the four H1N2v cases (including A/Minnesota/12/2012, A/Minnesota/13/2012, A/Minnesota/14/2012 which are virtually identical to each other).  Similarly, the 306 H3N2v cases in 2012 also had an H1N1pdm09 M gene and all of the 58 public sequences have an N2 gene which matches the novel N2 seen in the sequences linked to the West Virginia day care center in late 2011 (A/West Virginia/06/2011 and A/West Virginia/07/2011).  Moreover, all other variants in the US in 2010 and 2011 (6 H3N2v cases in 2011 and 1 H1N2v case in 2011) had a PB1 with E610D, which is present in all H1N1pdm09 sequences.  Thus, it is likely that the Ontario isolate also has an H1N1pdm09 M gene or PB1 with E618D.

The Ontario cases creates an unprecedented situation involving three variant sub-clades (in addition to H1N1pdm09) co-circulation in North America.  In 2011 the three sub-clade were co-circulating at the end of the year, but there was only one H1N1v and H1N2v case.  In 2012 there are currently 306 H3N2v, 4 H1N2v, and 2 H1N1v cases and all US cases have an H1N1pdm09M gene.

Release of the sequences from the Ontario case would be useful.

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