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Tamiflu Resistant Novel H1N1 in Saskatchewan Raises Concerns
Recombinomics Commentary 19:41
July 8, 2009

This new influenza is an animal strain that has been circulating in swine populations in North America since 1997.

It has been combined with two genes from the H1N1 seasonal flu, said Dr. Frank Plummer, scientific director-general of the national microbiology laboratory in Winnipeg.

"We think because of the genetic sequence of the virus, we think it would be resistant to Tamiflu," he said.

The above comments on the novel H1N1 identified in farm workers in Saskatchewan indicate the novel virus has a contemporary H1 and N1 from the Brisbane/59 seasonal flu strain, which has H274Y (Tamiflu resistance) levels near 100%.  Although swine with human H1N1 has been described previously, this version has the oseltamivir resistance marker and is in a cluster of farm workers, two confirmed and one suspect case.  Since the surface genes are human, the novel virus should transmit human to human efficiently, and since the novel virus was noit found in the swine associated with the workers, it is likely that the workers were infected by other humans and the two confirmed cases may have infected the suspect case.

Since the serotype fo the virus is human H1N1, detection would be limited to H1N1 isoaltes which were sequenced.  Although the number of H1N1 sequences deposited at Genbank or GISAID were high in later 2008, there have been very few 2009 seasonal flu sequences deposited worldwide, and only a tiny fraction of deposits have come from Canada,  Moreover, the vast majority of Canadian isolates outside of Bristish Columbia are not even sero-typed.  Thus, the level of novel H1N1 with human surface genes is largely unknown.  Since the cases this far are limited to farm workers, spread may be limited.

However, the widespread presence of pandemic H1N1 may lead to better efficiencies in humans due to adaptations facilitated by seasonal flu or the novel flu.  Moreover, levels may increase in the fall, when influenza is more stable and more seasonal flu is in circulation.
Although the above description provides more detail for the novel isolates, prompt release of sequences fro all eight gene segments would be useful.

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