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Novel Under 10 Flu Cases In United States Approach 100%
Recombinomics Commentary 14:00
December 25, 2011

The latest novel influenza case, (3M – A/West Virginia/07/2011), reported in the CDC’s December 23 early release MMWR, increases the frequency of novel sequences to 89% for cases for United States patients this season, and 100% for cases since October 3, 2011.  Moreover, none of the recent cases (in Iowa, Minnesota, West Virginia) were linked to swine, all were linked to confirmed or suspect clusters. 

The new MMWR release provides additional data on the failure of the newly approved CDC PCR, casts additional doubt on the “swine exposure” linkage for the cases identified in the off season (A/Indiana/08/2011, A/Pennsylvania/09/2011, A/Pennsylvania/10/2011, A/Pennsylvania/11/2011) or initial cases at the beginning of the 2011/2012 season (A/Maine/06/2011 and A/Main/07/2011).  The data highlight the need for sequence confirmation, which has led to requests for new samples from all states, and new guidance on case definitions, sample collection, and 24 hour reporting. 

Although the early release MMWR clearly signals the CDC acknowledgment that a pandemic has begun, the limited testing has kept this pandemic largely hidden since the first cases in July and August.  This pandemic has largely involved two different constellations of H3N2 triple reassortants in cases under the age of 10, but trH1N1 and trH1N2 cases have also been recently reported, and all 20 novel cases reported in 2010 or 2011 have had H1N1pdm09 E618D in PB1 or an H1N1pdm09 M gene

Thus, in one sense the alarming evolution leading to the explosion of novel cases is an extension of the 2009 pandemic, but the 20 cases involve five different constellations and three different serotypes, including four different serotypes reported in the past month.

Below are the US under 10 cases represented by the public sequences for the 2011/2012 season.

Novel cases in bold:

A/West Virginia/07/2011 3M trH3N2            12/07
A/West Virginia/06/2011 1F trH3N2             11/21
A/Iowa/09/2011                 2M H3N2pdm11 11/14
A/Iowa/08/2011                 1M H3N2pdm11 11/14
A/Iowa/07/2011                  3F H3N2pdm11 11/14
A/Minnesota/19/2011       1F trH1N2            11/04
A/Maine/07/2011               8M H3N2pdm11  10/24
A/Maine/06/2011               8M H3N2pdm11  10/10
A/Indiana/09/2011             1M H3N2               10/02

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