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Swine H3N2v Matches With Current Human Cases
Recombinomics Commentary 23:55
July 25, 2012

Veterinary Diagnostic and Production Animal Medicine at Iowa State University have released of series of recent swine sequences closely related to the human H3N2v cases in 2011 and 2012.  Included were Iowa isolates from August 22, 2011 collections (A/swine/Iowa/A01202529/2011 and A/swine/Iowa/A01202530/2011) as well as September 7, 2011 (A/swine/Iowa/A01202573/2011) which were prior to the earliest previous collection on September 13, 2011 (A/swine/NY/A01104005/2011).  However, none were collected prior to the first human case in 2011 (A/Indiana/08/2011), which was collected in July, 2011.
The first 10 human H3N2v cases in 2011 matched the above isolates.  However, the most recent 2011 sequences  (A/West Virginia/06/2011 and A/West Virginia/07/2011) as well as the 2012 case (A/Utah/10/2012) had an N2 which was closely related to H3N2v swine, in contrast to the earlier isolates which had N2 sequences closely related to H1N2v swine.  One of the recently released swine sequences, A/swine/North Carolina/A01203272/2012, collected on February 13, 2012, matched the three most recent confirmed human cases.  However, as was seen for the swine sequences which matched the human cases, the swine isolate was collected after the matching human case raising concerns that  the detection of these swine isolates were driven by jumps from humans to swine.
The pattern of detection in humans prior to swine also was seen in the PB1 change E618D.  This change is present in all H1N1pdm09 sequences (human and swine) and was initially seen in H3N2v in the first human case (A/Kansas/13/2009) collected on July 27, 2009 and was subsequently found in all 6 confirmed human cases in 2010, including A/Minnesota/09/2010, which was collected in the spring of 2010 (May 27).  The ealiset swine isolate with E618D, other than H1N1pdm09 isolates was A/swine/Pennsylvania/057108-1/2010, collected on September 20, 2010.
The pattern of detection of isolates in humans prior to swine was also seen for H1N1pdm09.  The novel constellation of genes was not detected in any swine sample collected prior to the start of the 2009 pandemic.  However, spread in humans led to the detection of matches in swine worldwide (all continents other than Antarctica).
Today ISU released additional recent H3N2v swine sequences, including a second match, A/swine/Indiana/A01203509/2012 (collected May 9, 2012), with the recent human sequences.  However 13 of the 15 swine matches collected after the appearance of the human cases match the earlier 2011 cases.
This discordance increases concerns that the H3N2v is spreading in humans, followed by spread in swine.

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