Recombinomics Commentary April 22, 2009

“This virus is different, very different from that circulating in pigs. That was a red flag,” Finelli told WebMD and several other news organizations. “The other red flag is both cases appeared almost simultaneously, 100 miles apart.

The above comments leave little doubt that the H1N1 swine flu is being efficiently transmitted human to human in southern California.  The unique constellation of swine genes has not been reported previously and the two cases do not have swine contacts.  Moreover, family members had symptoms before and after the confirmed cases, indicating the H1N1 spread efficiently within each family.

However, none of the family members were tested because the H1N1 was mild and they recovered without treatment.  The two cases were identified through routine surveillance, but such identifications require sero-typing.  The swine sequences will test positive fro influenza A.  

Therefore the virus can silently spread, which resulted in two independent detections 100 miles apart – (Snip).  Specific locations within San Diego and Imperial countries have not been released, but (upcoming testing of classmates should lead to the identification of locations).

Although both cases recovered without hospitalization, the spread of the swine H1N1 in a human population is cause for concern. The virus can adapt and spread more efficiently. Moreover, co-infection of H1N1 swine flu and osletamivir resistant H1N1 season flu can lead to acquisition of H274Y by the swine flu via recombination or reassortment.  Swine H1N1 with human H1 and N1 have been reported.  Moreover, the swine flu can also infect swine and acquire more polymorphisms that could lead to increased virulence.

The 1918 pandemic strain has polymorphism from swine and human H1N1 in all eight gene segments.  Similar swapping of polymorphism in human co-infected with season and swine H1N1 can lead to rapid evolution.  Therefore, release of both sets of sequences, as well as new sequences, which will likely be detected in the near term in the United States and Mexico, would be useful.