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trH1N2 Matches With NA and MP H3N2pdm11
Recombinomics Commentary 14:0
December 08, 2011

The recently released trH1N2 sequences from a swine in Ohio confirmed that presence of the three gene segments (PB1, NA, MP) acquired by H3N2pdm11, were circulating in swine in 2010.  Earlier deposits from 2010 isolates from South Dakota had the NA and MP matches, but were missing the other internal genes.  The number of trH1N2 sequences with a H1N1pdm09 M gene is large and growing and a subset of sequences also have a match with NA lineage found in H3N2pdm11 (see list below).  In addition to the Ohio and South Dakota isolates, and 2010 Iowa sequence also matched, although the earliest collection date with NA and MP matches was the Ohio sequence, which was collected October 1 (the other isolates were from samples collected in November and December).

The sequence from the isolates listed below suggests the matching PB1 sequence was also widespread in swine in late 2010, when the trH3N2 cases were announced in the WHO page alert.  The two cases in the alert were A/Wisconsin/12/2010 and A/Pennsylvania14/2010), but a third isolate, A/Pennsylvania/40/2010, had not been disclosed at the time, in part due to a misdiagnosis as seasonal H3N2

The Pennsylvania and Wisconsin sequences matched each other and had the lineage for PB2, PA, HA, NP, and NS that emerged in 2011 in H3N2pdm11.  The other Pennsylvania isolate, A/Pennsylvania/14/2010, had the matching NA, but the Ohio sequence has the NA match, but also had the PB1 and MP match.

Thus, it is likely that H3N2pdm11 was generate well in advance of the first case in July 2011 (A/Indiana/08/2011), who had no swine contact.  Thus far the only public swine sequence with H3N2pdm11 is a New York isolate
A/swine/NY/A01104005/2011, from a sample collected September 13.

The absence of any swine H3N2pdm11 sequences prior to the first human cases in Indiana and Pennsylvania (A/Pennsylvania/09/2010, A/Pennsylvania/10/2011, A/Pennsylvania/11/2011) in spite of increase swine surveillance that has identified a series of trH3N2 swine isolates with the H1N1pdm09 M gene, which is also in a large series of trH1N2 sequences, including a subset with H3N2pdm11 NA strongly suggests that the ten cases with H3N2pdm11 represent widespread transmission in humans, which appears to be concentrated in patients under the age of 10.  In spite of the matches in the 10 cases, with 9 of the 10 being under the age of 10, there are only 3 such influenza A positive sequences in samples collected since July, which are not H3N2pdm11.

Enhanced surveillance of children under 10, including sequencing of influenza A positive samples is long overdue.

H1N2 With NA and MP H3N2pdm11
 A/swine/South Dakota/2/2010
 A/swine/South Dakota/3/2010
 A/swine/South Dakota/4/2010

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