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Novel Swine H3 Human Cluster In Vietnam NOT
Recombinomics Commentary 16:45
February 9, 2012

The Heath Ministry has quoted sources from the Ho Chi Minh City Pasteur Institute confirming that a new kind of porcine flu virus, A/H3N1, has appeared, apparently a combination of the pig-related A/H1N1 and A/H3N2 flu viruses.

The medical sector has monitored 10 patients infected with the A/H3N2 virus with porcine origin, and found that three of them had not had direct contact with any diseased pigs.

Therefore, the sector has not ruled out the possibility of a mutation in the A/H3N2 strain which could lead to transmission between humans, instead of strictly from pigs to humans as previously.

CORRECTION:  The above information is strikingly similar to a December 7 Vietnam report on US H3N2v cases, including the Iowa cluster.  Thus , the report in the Vietnam media today appears to be a re-write of this old news.  Thefore, the discussion below of cases in Vietnam appears to be inappropriate at this time.

The above comments describe a novel H3 in patients in Vietnam.  It is unclear if the novel H3 is H3N2v or H3N1v, although it seems likely that the novel H3 is H3N2v with internal genes from H1N1pdm09.  There are 6 sets of public sequences from H3N2v in swine, isolated in 2010 (A/swine/Binh Duong/03_06/2010, A/swine/Binh Duong/03_08/2010, A/swine/Binh Duong/03_09/2010, A/swine/Binh Duong/03_10/2010, A/swine/Binh Duong/03_13/2010, A/swine/Binh Duong/03_14/2010).  All six isolates are closely related and have human H3 and N2 genes, with swine internal genes that are generally more closely related to H3N2v swine sequences in Asia (South Korea and Hong Kong).

However, Hong Kong has released 3 sets of sequences from Guangxi and Hong Kong (A/swine/Guangxi/NS2783/2010, A/swine/Hong Kong/2503/2011, A/swine/Hong Kong/NS2439/2011) , which have similar H3 and N2 human genes surrounding six internal genes from H1N1pdm09.  In the United States, all 12 of the H3N2v sequences in humans in 2011 have an H1N1pdm09 M gene.  Prior H3N2v cases in the United States have PB1 E618D, which is not in the swine isolates from Vietnam, but is in the new sequences from Hong Kong and China, since E618D is in virtually all H1N1pdm09 PB1 sequences.

Thus, it is likely that the novel H3 has acquired internal H1N1pdm09 genes, and the detection of 10 cases, including those without swine exposure, suggests that this H3N2v is efficiently transmitted.  The H3 is closely related to recent H3 sequences, including A/California/07/2004, in contrast to the H3 in the United States which is related to seasonal H3 from the mid-1990’s.  Consequently, D is at position 225 instead of G, which is in the United States cases. 

However, the movement of another constellation of H3N2v genes into the human population would likely fuel evolution via recombination and reassortment.

More information on the constellation of genes and release of sequences would be useful.

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