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Delays With trH1N2 Minnesota Case(s) Raise Concerns
Recombinomics Commentary 18:30
December 14, 2011

This latest case occurred in a Minnesota infant in October. The infant had no direct contact with swine and neither did anyone in his family. That means the case represents a mutation of the flu virus.

The above comments describe a trH1N2 case in Minnesota from October.  The CDC recently released trH1N2 sequences from a sample collected November 4, 2011 and labeled as from a female, while media reports describe the above infant as a male.  The Helen Branswell piece noted prior contact with a symptomatic child, suggesting there were two H1N2 cases in Minnesota.  However, the success in getting two cases confirmed, or the generation of two sets of sequences remains unclear.
The sequences at GISAID (which are not related to the 2007 trH1N2 case from Michigan) were from a cloned isolate, instead of a direct sequence, as had been done for the H3N2pdm11 cases from Indiana, Pennsylvania, and Maine, as well as the trH3N2 case from West Virginia. 

Thus, the absence of a direct sequence, and the delayed release of sequence of an isolate is remarkably similar to the circumstances surrounding the 2010 Pennsylvania case, A/Pennsylvania/40/2010, which was due to a September, 2010 infection that was not described in the November WHO alert.  Instead, it was announced on February 4, 2011 (week 4 FluView) and the sequence was not released until Sunday, April 17, 2011.  The sequence was important because it match the other September, 2010 case, A/Wisconsin/12/2010, signaling human transmission.

This year WHO issued an alert, following the confirmation of a cluster in Iowa that included three confirmed cases (Iowa/07/2011, Iowa/08/201, Iowa/09/2011).  In addition to the three confirmed case the MMWR also noted symptomatic relatives (brother and father of index case), who were not tested.  Like the Minnesota trH1N2 case, none of the Iowa confirmed or suspect cases had a know swine exposure, but there was no mention of the Minnesota case in the WHO announcement, even though the US should have notified WHO within 48 hours of lab confirmation, in accordance with IHR regulations, which should have been several weeks prior to the WHO announcement.

Thus, the reason for the delay in the announcement, as well as the status of the contact/sequences remains unclear.  The trH1N2 case is significant, because it is a reassortant between the same two parental sequence that produce the constellation and lineages seen in the first 10 confirmed H3N2pdm11 cases in 2011, and therefore represents a second version of the 2010 human sequences, while the recent case from West Virginia (A/West Virginia/06/2011) represents the third version in circulation in humans. 

The WHO has yet to comment on concerns related to co-circulation of three different novel sub-clades in patients with no swine contact.

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