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Early Flu Season Start in North America
Recombinomics Commentary 19:23
September 24, 2010

The Middlesex-London Health Unit says there's an outbreak of influenza A at a London, Ont., long-term care facility.

Two residents have tested positive for the virus, and several other residents and staff members are also experiencing flu-like symptoms.

The above comments describe an influenza A outbreak in a long term care facility in Canada.  This outbreak is likely cause by a rapidly resurging and evolving H3N2.  In August the CDC issued an H3N2 alert based on two outbreaks in eastern Iowa.  The HA sequence from that outbreak was a Perth/16 clade that was similar to H3N2 sequences from late 2009 / early 2010.  However, two additional sequences (A/Pennsylvania/02/2010 and A/Kansas/06/2010) contained a number of additional changes, including I230V. 

I230 is present in all three seasonal flus (H3N2, H1N1 and influenza B).  230V has been seen in vaccine resistant H5N1 in Egypt.  Those initial sequences were followed by another series, largely collected between May and June, which confirmed that this sub-clade was spreading worldwide.

The sub-clade formed two branches.  One had isolates from Cambodia, Australia, and the US (A/Alabama/05/2010 and A/Kansas/06/2010), while the larger branch had isolates from Hong Kong and Chile.  This larger branch has produced a more evolved H3N2, which was represented in 10 sequences released yesterday, which had S199A.  These isolates were from Colombia, Panama, Dominican Republic, Barbados, Mexico, and the US.  The high concentration of new isolates in this sub-clades suggests it will become dominant in North America and lead to significant infections in the elderly.

The above early outbreaks suggest that this newly emerging sub-clade will produce a dramatic rise in deaths in the over 65 population, in contrast to last season, which was dominated by pandemic H1N1 infections and fatalities in those under 65.

The Week 37 pneumonia and influenza deaths in the US spiked higher (to 6.87%)compared to 5.92% last week or 6.07% in Week 37 in 2009.  This level is well above the epidemic threshhold for Week 37.  Traditionally, the flu season in the northern hemisphere begins with week 40 and peaks in early weeks of the following calendar year.

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