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Minnesota trH1N2 Delayed Detection
Recombinomics Commentary 11:00
December 16, 2011

The Minnesota case, with the unrelated virus, is still under investigation, Finelli said. The child had no contact with pigs, but may have been in contact with a sick child a day or two before becoming ill.

The above comments describe the trH1N2 case from Minnesota, which as identified from an isolate from a November 4, 2011 collection.  The child (listed as female by the CDC) developed symptoms on October 30 and the sample was tested using the CDC PCR kit during routine surveillance.  Therefore, confirmation of trH1N2 was more than a month after disease onset.

Consequently, the symptomatic contact was not detected, and epidemiological investigates were compromised by the month delay between disease onset and trH1N2 confirmation.

Thus, the ability of the PCR detection kit to detect trH1N2 in samples is unclear and low levels of H1N2 may contribute to the mild nature of the infant’s infection.  The sequence (from an isolate) was released by the CDC at GISAID on December 9, 2011, and was received by the Minnesota Department of Health as an isolate, as noted by Aaron DeVries, Medical Epidemiologist for the Minnesota Department of Health.

The full sequence clearly demonstrated the relationship between the trH1N2 isolate and trH3N2 sequences from 2010 cases.  The six internal genes matched the lineages of A/Pennsylvania/40/2010 and A/Wisconsin/12/2010, which included PB1 E618D, which was in the first confirmed human trH3N2 in the United States, A/Kansas/13/2009, as well as all six human cases in 2010.  PB1 E618D is common in swine, other than infections with the H1N1pdm09 PB1 gene.  The human trH3N2 cases, like the trH1N2 case above, have a PB1 that traces back to the 2007 Huron County fair.  The only swine with PB1 E618D on the 2007 genetic background are Pennsylvania swine sequences that evolved from the human sequence, A/Pennsylvania/14/20101, or Minnesota swine sequences that evolved from the human sequence, A/Minnesota/11/2010.

All 2011 trH3N2 human cases have exchanged the PB1 and M gene from the 2010 human cases for a PB1 and M gene found in the recently released Ohio swine H1N2 sequences.  The first ten isolates (H3N2pdm11) also have the N2 from the above parental strain, while the most recent trH3N2 sequence, A/West Virginia/06/2011 has another N2, which is commonly found in trH3N2 swine.  However, the N2 in human 2010 and 2011 cases lnks back to human H3N2 sequences from 2003.
Thus, all 18 human novel cases in 2010 and 2011 either have PB1 with the H1N1pdm09 E618D or the M gene from H1N1pdm09 and these sequences are readily distinguished from swine sequences.

Moreover the five most recent novel influenza cases represent three different, but related constellations, from cases in Iowa, West Virginia, and Minnesota, with no known swine exposure.

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