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Widespread Swine H3N2v Matches With Human US Cases
Recombinomics Commentary 03:30
July 27, 2012

Iowa State University in association with the USDA swine surveillance program has released a series of sets (HA, NA.MP) of swine sequences which significantly increase the number of matches with the 2011 and 2012 human cases.

Prior to these recently released sequences there were 7 sets of sequences from five swine infections.  The first example was from a pig in New York, A/swine/NY/A01104005/2011 , which was from a September 17, 2011 collection.  A second September sample, A/swine/Iowa/A01202640/2011, was subsequently released, which was followed by sequences from three swine infections in Illinois (A/swine/Illinois/A00857138a/2011, A/swine/Illinois/A00857300/2011, A/swine/Illinois/A00857304a/2012) as seen in the chronological list below. 

The newly released sequences included 3 Iowa isolates (A/swine/Iowa/A01202529/2011, A/swine/Iowa/A01202530/2011, A/swine/Iowa/A01202573/2011) collected prior to the New York sample, but all were collected after the detection of the human case from Indiana collected in late July, 2011.

In addition to these three earlier sequences, the recent sequences include 4 June isolates from Ohio (A/swine/Ohio/1/2012,  A/swine/Ohio/6/2012 ,  A/swine/Ohio/7/2012, A/swine/Ohio/9/2012), as well as 4 May isolates from Iowa and Indiana (A/swine/Iowa/A01203503/2012, A/swine/Indiana/A01203509/2012, A/swine/Indiana/A01203521/2012, A/swine/Indiana/A01203522/2012).  One of the Iowa sequences (A/swine/Indiana/A01203509/2012) and a February 13, 2012 isolate from North Carolina (A/swine/North Carolina/A01203272/2012) match the two most recent cases in West Virginia, as well as the first 2012 case (from Utah), which have an N2 found in H3N2 swine.  The other isolates matched the earlier cases from 2011, which have an N2 found in H1N2 swine.

This discordance between the sequences in swine and those in humans suggests that most of the human cases are not due to swine exposure.
However, the recently described cases from  the LaPorte County Fair in Indiana are linked to symptomatic swine which are infected with closely related H3N2 suggesting that these cases in contrast to earlier cases are linked to contact with symptomatic swine.

The increase in matches in recent collections in Iowa, Ohio, and Indiana, raises concerns that the number of human cases linked to symptomatic swine will dramatically increase in the upcoming weeks.

A/swine/Iowa/A01202529/2011                     8/22/11
A/swine/Iowa/A01202530/2011                     8/22/11
A/swine/Iowa/A01202573/2011                     9/07/11
A/swine/NY/A01104005/2011                        9/13/11 
A/swine/Iowa/A01202878/2011                     9/17/11
A/swine/Iowa/A01202879/2011                     9/17/11
A/swine/Indiana/A01202621/2011                9/28/11
A/swine/Iowa/A01202639/2011                     9/30/11
A/swine/Iowa/A01202640/2011                     9/30/11
A/swine/Illinois/A00857138a/2011              10/20/11 
A/swine/Illinois/A00857300/2011                11/28/11 
A/swine/Illinois/A01202978/2011                12/16/11
A/swine/Illinois/A00857304a/2012                1/05/12  
A/swine/Ohio/A01203186/2012                     1/24/12
A/swine/North Carolina/A01203272/2012+  2/13/12
A/swine/Illinois/A00857318a/2012*               2/23/12
A/swine/Indiana/A01203372/2012                 4/03/12
A/swine/Iowa/A01203503/2012                      5/09/12
A/swine/Indiana/A01203509/2012+               5/09/12
A/swine/Indiana/A01203521/2012                 5/15/12
A/swine/Indiana/A01203522/2012                 5/15/12
A/swine/Ohio/1/2012                                            6/12
A/swine/Ohio/6/2012                                            6/12
A/swine/Ohio/7/2012                                            6/12
A/swine/Ohio/9/2012                                            6/12

+ N2 matches WV/UT cases
*  H1N1pdm09 NP

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