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2013 Human and Swine H3N2v Sequence Discordance
Recombinomics Commentary 23:45
August 15, 2013

The USDA released the first July, 2013 H3N2v sequences (H3, N2, and MP from Ohio and Minnesota), and the sequences matched the sequences from 2012 human cases.  The July sequences were similar to earlier 2013 swine H3N2v sequences.  A/swine/Ohio/A01351573/2013 (collected July 10) was closely related to swine sequences such as A/swine/Ohio/A01349485/2013, and the USDA released a full set of sequences from this earlier isolates confirming matches with all 8 gene segments from the 2012 human cases.  Virtually identical H3 sequences were seen in 2013 collections on March 29, 22, 22, 12, 12 (A/swine/Ohio/A01349615/2013, A/swine/Ohio/A01349495/2013, A/swine/Ohio/A01349485/2013, A/swine/Ohio/A01349305/2013, A/swine/Ohio/A01349302/2013, respectively), but no human H3N2v cases have been reported in Ohio in 2013. 

The only Ohio resident with confirmed H3N2 in 2013 had visited a agricultural fair in northwestern Virginia just prior to disease onset. 

Similarly no cases have been reported in Minnesota this year although the July 11 isolate, A/swine/Minnesota/A01351603/2013, also matched 2012 human cases.

In contrast to the frequent detection of 2013 swine matches with 2012 human cases, only one swine sequence, A/swine/Illinois/A01432795/2013, isolated in June is closely related to the 2013 human cases, which all have a closely related H3 which has either N145K or K145R (the Illinois swine has N145K).  Thus, there is significant discordance between swine sequences, where there is just one closely related to the human sequences, while all 16 human cases in 2012 are closely related even though they are linked to fairs and farms in Indiana, Virginia, and Illinois.

Moreover, the three most recent human cases (A/Ohio/05/2013, A/Illinois/03/2013, and A/Indiana/11/2013) all have an H1N1pdm09 PA gene segment (as well as an M gene segments) which is identical in the isolates from Illinois and Indiana and are virtually identical to the sequence from Virginia (diagnosed and confirmed in Ohio).

This discordance again suggests that humans are infecting swine, which is why the human sequences share changes that are rarely found in swine collections made prior to the fair season.

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