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Pennsylvania trH3N2 Swine Have PB1 E618D
Recombinomics Commentary 15:50
February 11, 2011

The USDA has released sequences from the six internal genes from the Pennsylvania trH3N2 swine, A/swine/Pennsylvania/62170-1/2010 and A/swine/Pennsylvania/62170-3/2010 as well as two additional isolates, A/swine/Pennsylvania/62170-2/2010 and A/swine/Pennsylvania/62170-4/2010, which are closely related to each other and the human trH3N2 from Pennsylvania, A/Pennsylvania/14/2010, as expected from the previously released HA sequences.

Moreover, all four swine PB1 sequences have E618D, representing the first reported swine H3N2 isolates with this change.  The change is in 5 of the 6 public trH3N2 human sequences, including the four isolated in 2010.  It is a recent change and all swine or human trH3N2 isolates with this change have been isolate after the start of the 2009 pandemic.  Virtually all pH1N1 PB1 sequences also have E618D, suggesting it is a change linked to human adaptation of the swine pH1N1.

The presence of this change in the human trH3N2 sequences have raised concerns that it was acquired by recombination, and further acquisitions may increase the transmissibility of trH3N2 in humans.

This concern was increased by the recently released sequences from swine H1N2 sequences in South Dakota which have NA sequences very closely related to the human trH3N2 NA sequence from Pennsylvania (the Pennsylvania swine NA sequences have not been released), and have a pH1N1 MP gene segment.   This reassortant demonstrates the exchange of trH1N1 and trH3N2 genes in swine.  The presence of PB1 E618D in the South Dakota swine sequences is not known because only the HA, NA, and MP sequences were released.

Although the Pennsylvania swine PB1 sequences have E618D, the sequences are heterogeneous, indicating the trH3N2 has been circulating in the swine population, although the human case denies swine contact.

The presence of E618D as well as relatedness to the NA sequences in the reassortants in South Dakota continue to increase concerns for rapid evolution of tr genes in swine that can re-infect humans and produce more disease with increased severity.

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