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1998 Hong Kong Swine M Gene in a 2003 Korean Chicken

Recombinomics Commentary
March 6 2005

>>  Molecular biologist and flu expert Ron Fouchier of Erasmus University Medical Center in Rotterdam, the Netherlands, says the sequences definitely contain WSN's genetic signature. But he says the fact that the six controversial isolates have varying numbers of WSN fragments points to lab contamination: "If this was an endemic pig virus, I'd expect all viruses to have the same WSN gene segments." <<

There is significant genetic variation in Korea.  A recent publication on bird flu in Korea in 2003 found H9N2, H3N2, and H6N1 subtypes.  However, within this population there was additional variation.  The 5' half of NP of A/chicken/Korea/S16/03 has been deposited at Genbank.  It is a recombinant between Korean and Hong Kong avian genes.  The recombinant contains sequences that differ from A/guineafowl/Hong Kong/NT184/03 by only 1 bp in the first 234 bp deposited at GenBank.

The relationship of this Korean isolate to Hong Kong isolates is also seen in the M gene.  The M gene of S16 exactly matches a 1998 H9N2 swine isolate from Hong Kong, A/swine/Hong Kong/9/98, and differs from another 1998 H9N2 swine isolate, A/swine/Hong Kong/10/98, by a single BP.

Thus, like the 2004 swine sequences at GenBank with WSN/33 and H9N2 Korean avian genes, at least one isolate from Korea in 2003 has both recombined and reassorted genes.  Yet, there has not been any indication that the sequence of a 1998 H9N2 Hong Kong swine M gene in a 2003 H9N2 Korean chicken isolate was a lab error.

Moreover, the finding creates a problem for current dogma on influenza evolution which states that genetic drift is due to replication errors by an influenza encoded polymerase that lacks a proof-reading function.  The amount of genetic drift each year in influenza genes is considerable, yet the 1998 swine virus in Hong Kong was able to faithfully replicate the M gene for five years without an error.  The M gene in a 2003 H9N2 isolate from a Korean chicken was an exact match with the 1998 swine sequence.

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