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Illinois Swine H3N2v Matches Grant County Indiana Cases
Recombinomics Commentary 14:45
July 27, 2013

The early appearance of H3N2v clusters in Indiana has increased concerns over the status of similar sequences in swine.  The USDA has recently released sequences, and the most recent sequence (H3, N2, and MP from a June, 2013 collection), A/swine/Illinois/A01432795/2013, has N145K and is closely related to the human sequences linked to the Grant County Fair (see map).

Five sequences (A/Indiana/04/2013, A/Indiana/05/2013, A/Indiana/06/2013, A/Indiana/07/2013, A/Indiana/08/2013) were closely related to each other and human sequence from the 2012 outbreaks, but has also added H3 N145K, which was present in the Fujian strain which dominated the 2002/2003 season.  The season flu was virulent and the large number of adolescent deaths led to regulations requiring the reporting of all lab confirmed adolescent flu deaths in the United States.  The above human sequences were the first reported cases with N145K and the above swine sequence is the first sequence set closely related to the human sequences (Michigan swine sequence set, A/swine/Michigan/A01432678/2013, collected on May; or Iowa swine sets, A/swine/Iowa/A01432529/2013, collected in March, or A/swine/Indiana/A01432300/2013 collected in January) also have N145K and lineages matching the 2012 human cases, but are not as closely related to the 2013 human sequences as the Illinois swine).  Thus, the Illinois swine sequence raises concerns that sequences similar to the Indiana sequences will be found in human cases in Illinois.

However, the human sequences in Indiana have evolved further, leading to K145R, which was present in the sequences linked to the Hancock County fair (A/Indiana/14/2013, A/Indiana/15/2013, A/Indiana/16/2013, A/Indiana/17/2013, A/Indiana/18/2013).  K145R has not been reported in any of the swine sequences and raises concerns that H3N2v is adapting to humans, which could lead to a record number of cases in 2013.

This concern was increased by the report of the 13th case in Indiana, as well as the sequence of A/Indiana/10/2013, which also had K145R even though it was collected more than two weeks after the earlier sequences, and likely represents an independent outbreak (because the CDC generated a full set of original sequences).

The confirmation of H3N2v in an attendee of a Virginia County Fair (likely the Fauquire County Fair) which is the first case linked to a fair in Virginia.  This case (which was reported as an Ohio case since the attendee was an Ohio resident and the patient was H3N2v confirmed in Ohio), represent another earlier case, which also signals infections outside of Indiana.

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