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Novel Michigan H3N2v Case With PB1 E618D
Recombinomics Commentary 14:30
October 18, 2012

The CDC has released another series of H3N2v sequence from collections from cases in July, August, and early September, 2012, which increased the number of such public sets of sequences to 111.  All were closely related to prior sequences and were dominated by N2 sequences from the same lineage as the initial isolates from West Virginia in late 2011 (A/West Virginia/06/2011 and A/West Virginia/07/2011).  The sole exception in the latest sequences was A/Michigan/23/2012 (MI/23), which like two earlier sets of related sequences were also from Michigan (A/Michigan/19/2012, MI/19 and A/Michigan/20/2012, MI/20).

The N2 sequence of MI/23 exactly matched MI/20, and the MP sequence exactly matched MI/19 and MI/20.  Similarly, H3 was also identical in MI/19 and differed by 1 BP with MI/20.  Sequences from 3 of the 5 remaining internal genes also had similarities.  The PB1 was also closely related to the two earlier Michigan sequences and all three had E618D as was the PA sequences.  However, the NP gene was easily distinguished.  MI/23 was most closely related to June swine isolates from Ohio (
A/swine/Ohio/1/2012, A/swine/Ohio/6/2012, A/swine/Ohio/7/2012), which also had a PB1 with E618D and an N2 which was from the same lineage as the first 10 human H3N2v cases from 2011.  The earlier sequences from Michigan had an NP which was an exact match with 40 recent human sequences and had a single difference with 29 additional human sequences.  A single difference was also present in multiple swine sequences which matched the 2011 human cases, including an N2 match.

Thus, MI/23 did not share a common source with MI/19 and MI/20 even though all three sequences are from Michigan cases collected 2 days apart, and all three had an H1N1pdm09 M gene was well as PB1 E618D.  The presence of this combination in three Michigan cases involving at least 2 different sources is cause for concern.

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