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WSN/33 Recombination and Reassortment in Swine in Korea

Recombinomics Commentary
December 12, 2004

I believe that the National Veterinary Research and Quarantine Service in South Korea is working on confirming the swine sequences that were recently placed on deposit at GenBank.  I expect the sequencing to be fully confirmed and the service will be quite shocked by the result.  They will probably focus on reassortment, which will generate cause for concern.  At a very gross level, they will clearly see evidence for reassortment between WSN/33 a human virus derived from WS/33 the first human influenza virus ever isolated (in 1933) as well as a H9N2 avian virus, most closely related to avian H9N2 isolated from a chicken in 2003 and a  swine in 2004.  The six sequences with human genes have 7, 5, 4, or 3 WSN/33 genes, demonstrating extensive reassortment.  The H1N1 isolates will be all human except for PB2.  However other isolates will have PB2 from avian recombined with PB2 from human, which will make recombination obvious to even the most skeptical.  There is also additional recombination in NA between the avian genes (involving two fairly closely related H9N2 viruses found in Korea).

This data will sound alarm bells for several reasons.  The two H1N1 isolates should be quite infectious in humans because 7 of the 8 genes are from WSN/33, a human H1N1 virus and the swine isolates have the H1N1 human genes.  Since the H1N1 genes from 1933 are quite different than 2004, this isolate can be a major problem in its own right.  However, the human flu vaccine uses A/PR/8/34 as the background for the 6 gene products not on the surface and since it is from 1934, these internal genes have a fair amount of homology with WSN/33.  However, the virus is clearly recombining and reassorting, so it could also reassort with H5N1 to produce an H1N1 with H5N1 internal genes or it could recombine, placing an H1N1 receptor binding sequence on an H5N1 virus.

The high frequency of reassortment and recombination in the 6 swine isolates will ring many alarm bells, and confirmation should come soon.

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