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2011 Human trH3N2 Constellation Absent In US Swine
Recombinomics Commentary 14:30
October 26, 2011

CDC has confirmed the fifth case of human infection with a swine–origin influenza A (H3N2) virus that carries the M gene from the 2009 H1N1 virus. This virus was first detected in a child in Indiana in July. Subsequently three additional cases of human infection with swine–origin influenza A (H3N2) viruses carrying the same genetic change were detected in Pennsylvania. Though rare, human infections with swine–origin influenza viruses can occur, usually after close contact with infected swine.

The above comments are from the latest (October 21,2011) “Have You Heard?” report, and assumes that the linkage between human trH3N2 and swine is due to transmission from swine to humans, instead of testing of out of season flu cases for trH3N2 if there is a swine contact.  The heavy bias toward testing of such cases has increased due to the CDC request in the early release MMWR (September 2, 2011), when samples of cases with swine linkage were requested, instead of cases from children in general.  This absence of testing in children is also evident in the FluView reports for the final 10 weeks of the 2010/2011 flu season (weeks 30-39) where 67 of the 107 influenza A positive cases were not sub-typed.

However, in addition to the heavy bias in trH3N2 testing, which is not available at state labs, the absence of the above constellation of flu genes in US swine also cast serious doubt on the CDC statements on the relationship between close contact with swine and human trH3N2 cases.

The 2009 pandemic has led to an increase in swine surveillance in US swine by the USDA, as well as several academic institutions.  This surveillance has produced public sequences from 11 trH3N2 swine isolates, as well as 25 from 2010 including 19 collected after October 24, 2010 (see list below), and none have the constellation of flu genes found in all 5 human isolates, as cited above.

Moreover, the 2011 human trH3N2 sequences are linked to the 2010 human trH3N2.  In 2010 the human cases clustered, which most isolates sharing most gene segments.  This human adaptation has led to the 2011 identities, where all 8 gene segments in all 5 human cases match each other.

Thus, the CDC should distribute trH3N2 PCR testing kits to the state labs, so a true distribution of human trH3N2 can be determined.

2011 US swine trH3N2 isolates
A/swine/Nebraska/A01049937/2011          05-05
A/swine/Minnesota/A01049936/2011         05-03
A/swine/Texas/A01049914/2011                 04-28
A/swine/Texas/A01049915/2011                 04-28
A/swine/Iowa/A01049750/2011                    03-28
A/swine/Indiana/A01049744/2011               03-23
A/swine/Indiana/A01049745/2011               03-23
A/swine/Indiana/A01049653/2011               03-08
A/swine/Texas/A01049555/2011                 02-14
A/swine/Texas/A01049556/2011                 02-14
A/swine/North Carolina/A01049436/2011  01-19

2010 US swine trH3N2 isolates (since Oct 24)
A/swine/Minnesota/A01049346/2010         12-29
A/swine/Iowa/A01049317/2010                   12-22
A/swine/Iowa/A01049254/2010                   12-09
A/swine/Pennsylvania/A01049256/2010    12-07
A/swine/Nebraska/A01049235/2010          12-07
A/swine/Iowa/A01049185/2010                   12-01
A/swine/Iowa/A01049160/2010                   11-30
A/swine/Iowa/A01049113/2010                   11-22
A/swine/Iowa/A0109112/2010                     11-22
A/swine/Indiana/A01049124/2010              11-19
A/swine/Indiana/A0109091/2010                 11-18
A/swine/Iowa/A01049035/2010                   11-16
A/swine/Iowa/A01049034/2010                   11-16
A/swine/Iowa/A0109032/2010                     11-16
A/swine/Iowa/A0109031/2010                     11-16
A/swine/Pennsylvania/602170-3/2010        10-25
A/swine/Pennsylvania/602170-1/2010        10-25
A/swine/Pennsylvania/602170-4/2010        10-25
A/swine/Pennsylvania/602170-2/2010        10-25

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