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LaPorte Human and Swine H3N2v Do Not Match
Recombinomics Commentary 23:55
September 5, 2012

Additionally, all respiratory specimens collected from a sample of 12 swine at the fair were positive for influenza A (H3N2) virus. The specimens were forwarded to the National Veterinary Services Laboratories of the U.S. Department of Agriculture for additional testing. Preliminary genetic analysis has shown a very high level of similarity between the gene sequences of H3N2v viruses from humans and the H3N2 viruses from swine.

The above comments are from the CDC MMWR describing the H3N2v positive swine at the LaPorte County Fair.  Today the USDA released the first set (HA, NA, MP) of sequences from one of the above swine,
A/swine/Indiana/A00968380/2012 (collected on July 18, two days after the collection of samples from the first four confirmed cases).

As noted above the sequences matched the novel sub-clade identified in all recent 43 sets of H3N2v sequences, as well as the first 2012 set of sequences, A/Utah/10/2012, and the last two isolates in 2011 (A/West Virginia/06/2012 and A/West Virginia/07/2012).  However, the 43 recent sets of sequences (collected in July and August) defined clear clusters of human sequences within the novel sub-clade.

Isolates were obtained from two of the LaPorte cases, A/Indina/07/2012 and A/Indiana/09/2012, which generated full sequences for all 8 gene segments, and all positives were identical in both isolates.  Similarly, partial sequences from the other two cases, A/Indiana/06/2012 and A/Indiana/08/2012, also exactly matched the full sequences.  These identities were due to clonal expansion from a common source.

However, the common source was not the LaPorte swine H3N2v described above.  Each of the three segments were distinct from the human sequences.  One novel change in the LaPorte NA sequences is N234D, which abolishes the glycosylation site.  Although this change is recent (the Hawaii, A/Hawaii/03/2012 and earlier Iowa swine, A/swine/Indiana/A01203509/2012, are identical to the LaPorte NA sequence in all positions except A700G, which codes for N234D), it is also in the Butler County sequences (A/Ohio/13/2012, A/Ohio/14/2012, A/Ohio/15/2012, A/Ohio/16/2012, A/Ohio/17/2012, A/Ohio/18/2012, A/Ohio/20/2012, A/Ohio/24/2012), which are closely related to each other, but distinct from the LaPorte sequence.  However, this change is not present in the LaPorte swine sequences.

Thus, although the swine H3N2v was likely present in fair attendees, it did not cause the first four confirmed infections.  Moreover, the match with the novel H3N2v that has been found in all 2012 human cases, was likely due to an attendee infecting the LaPorte swine, since this sub-clade is common in humans, but has only been reported in two swine  samples collected prior to the LaPorte Fair,  Similarly, the sub-clade identified in the first 2011 human cases is widespread in swine including April/May isolates from Indiana (A/swine/Indiana/A01203372/2012, A/swine/Indiana/A01203521/2012, A/swine/Indiana/A01203522/2012) or June isolates from Ohio (A/swine/Ohio/1/2012, A/swine/Ohio/6/2012, A/swine/Ohio/7/2012, A/swine/Ohio/9/2012), yet have cause no reported human cases in 2012.

Thus, the H3N2v in the LaPorte swine is likely due to human to swine transmission.

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