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North Carolina Swine H3N2v Sequences Match 2012 Cases
Recombinomics Commentary 01:45
December 21, 2012

North Carolina ILI

The USDA has recently released various series of swine sequences including H3N2v.  In November, North Carolina matches with human H3N2v cases from 2012 were noted.  In the summer of 2012, there was an explosion of swine H3N2v cases which matched the human cases in 2012 that were largely linked to agricultural fairs.  The close sequence similarities between the human and swine sequences strongly supported interspecies transmission, which left open the distinct possibility that the swine at the fairs were infected by human attendees.

Prior to the summer cases, swine H3N2v sequences which matched the human sequences from late 2011 and early 2012 were rare.  Only two swine examples were noted, a February 13 isolate from North Carolina, A/swine/North Carolina/A01203272/2012, and a May 9 isolate from Indiana, A/swine/Indiana/A01203509/2012.  Both of these isolates had an N2 from a swine H3N2 lineage, in contrast to the vast majority of matching swine isolates, which had an N2 from a swine H1N2 lineage, which was present in the first 10 human cases in 2011.

The recent USDA sequences included a third swine match with the human 2012 cases, which was also from North Carolina, A/swine/North Carolina/A01300820/2012, which was not linked to agricultural fairs or human cases.  Moreover, it was closely related to the February isolate from North Carolina, indicating this sub-clade was common in North Carolina.  Similarly, a September isolate from North Carolina, A/swine/North Carolina/A01203801/2012, was also reported in November and also matched the human cases from 2012.

However, although three examples were reported in 2012 swine isolates from North Carolina, no human cases from North Carolina have been reported.  The absence of human cases from North Carolina may indicate that jumps from swine to human are rare of surveillance is lacking.  Most human cases of H3N2v are identified in the off season, due in part to the decline in seasonal H3N2 and an increase in surveillance for cases linked to swine exposure.

As seen in the above graph of ILI in North Carolina, the flu season of 2012/2013 has started early, and reports from the North Carolina website indicate the vast majority of flu isolates at this time are H3N2.  These high levels will decrease the likelihood of detection of H3N2v cases in the near term.

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