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H1N1/N2 Swine / Human Reassortants Raise Pandemic Concerns
Recombinomics Commentary 02:48
October 31, 2010

The recently released sequences of swine H1 reassortants in Argentina have raised concerns for new pandemic H1 sequences arising at multiple locations including the United States and Canada.  The two isolates from Argentina involved pandemic H1N1 swapping out the North American swine H1 and the European swine N1 for seasonal H1N1 or H1N2 sequences from 2003.  The Argentine sequences were isolated 7 months apart and in two adjacent provinces (Buenos Aires and Santa Fe), but had the same general constellation of genes (the swapping of the swine H and N for human H and N that had been maintained in swine).

The H1 from H1N1 isolate (A/swine/Argentina/CIP051-BsAs76/2009) was most closely related to a giant anteater sequences from Tennessee (A/giant anteater/Tennessee/UTCVM07-733/2007), while the H1N2 isolate (A/swine/Argentina/CIP051-StaFeN2/2010) was related to Canadian sequences isolated as early as 2003 (A/swine/Ontario/52156/03) and as recently as a United States sequence in 2010 (A/swine/Minnesota/03000/2010).

Prior to the 2009 pandemic, the number of public swine sequences from the Americas south of the United States were virtually non-existent.  Subsequently, pandemic sequences in swine or turkeys were released, including swine sequences from Argentina.  The recent ressortants demonstrate that North American swine sequences originating in humans in 2003 were also circulating in South America.  The similar constellation of genes in swine in Argentina suggest that similar reassortants are circulating in the United States and Canada based on the similar human sequences maintained in swine in both countries.
The detection of the swine reassortants in humans is largely dependent on sequencing or antigen characterization of H1 infections. 

Since the H and N in the above reassortants have a human origin, the routine serotyping of human H1 isolates would not distinguish between contemporary human H1 seasonal flu and the swine reassortants described above.  Although seasonal H1 was largely replaced by pandemic H1N1 last season, low numbers of seasonal H1 isolates are being reported this season in the United States and antigenic characterization or sequencing of these isolates has been limited. 

The latest CDC report (week 42) does not include antigenic characterization of any seasonal H1N1 and does not acknowledge the detection this season.  However, the week 42 report from Pennsylvania indicates that one of the three H1 isolates was seasonal H1.  In contrast, most other state reports fail to give serotype data because many positives are determined by the rapid test which does not determine serotypes.  This lack of serotyping in the US and worldwide would limit the detection of a new H1 pandemic with human H1 maintained in swine.

This lack of testing in the US and worldwide remains a cause for concern.

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