Recombinomics Commentary
“We got the message, disturbing information on the paging system of the World Health Organization that in the U.S. for two people the virus H3N2” told Interfax “the head of Rospotrebnadzor, chief state sanitary doctor Gennady Onishchenko. “This mutation Influenza swine origin”, – said Gennady Onishchenko.

The above translation is from another Russian report on the WHO paging alert. These reports suggest that the two cases in the US are current. The Pennsylvania cases (46M) is noted in the week 44 MMWR report which is available today because tomorrow is a holiday. The confirmation of the Illinois case (7 mo old child) may have come too late for today’s MMWR release. If both cases are current, then it is likely that an H3N2 pandemic has begun.

Swine H3N2 cases in humans are rare and difficult to detect because swine H3N2 triple reassortants have human seasonal H3 and N2, so standard testing (influenza A or sub-typing) would not distinguish swine H3N2 from seasonal H3N2. Sequence analysis on the other six genes would identify the avian and swine flu genes.

A year ago a novel H3N2 cases in Iowa was identified, but it was not reported until January, 2010. The 2010 MMWR first reported a novel H3N2 in the week 23 report, which was likely in reference to the Iowa case. Two unrelated cases of novel H3N2 at the same time would be without precedence, which is why a swine H3N2 pandemic is likely if both cases are current.

These cases may be linked to the pH1N1 pandemic, because it also involves swine triple reassortants and is now widespread in humans and swine. Recently released sequences in Argentina and Thailand are examples of pH1N1 swapping out H and N swine genes. In Argentina the swine H1 and N1 were swapped for human H1 and N1 from 2003, which is widespread in swine populations in North and South America. In Thailand the pandemic N1 was swapped for a swine N1 circulating in Thailand. Moreover, the pH1N1 MP gene recombined with the Thai swine MP gene to produce a novel recombinant. Shorter regions also recombined to generate rapid genetic drift.

The novel H3N2 in Pennsylvania and Illinois may be examples where the H1 and N1 are swapped for H3 and N2 from swine (representing older seasonal flu sequences) or humans (representing currently circulating seasonal H3N2).

Pandemic H1N1 is from a constellation that initially had H and N represented by human H3 and N2 from the 1990’s. Thus, the widespread presence of pandemic H1N1 in humans and swine allows for many new combinations which can easily transmit in humans. Thus, the human / swine influenza axis is far more common and interactive, which will produce many combinations with pandemic potential. Continued:

•  Because of the weather increased respiratory illnesses (Link)

•  Some cases of influenza A and B in Ile-de-France and PACA (Link)

•  WHO Warns Georgian Experts About Swine Flu Mutation (Link)

•  Low pathogen avian influenza detected in Germany (Link)

•  Nasal vaccine for H1N1 selling too rapidly for FDA’s comfort (Link)

Saudi Arabia
•  ProMED: Health Hazards, Human, Animal – Worldwide: Hajj (Link)

•  In Zaporozhye boarding a strange flu outbreak (translated) (Link)

United States
•  Flu outbreak causes Penguins to recall forward Conner (Link)

•  AZ: Health officials report ‘sporadic’ flu activity (Link)

•  CIDRAP: European findings show westward spread of H5N1 avian flu strain (Link) Abstract (Link)

•  Flu shots safe for pregnant women, study finds (Link)
•  Influenza (13): World Health Organization Update (Link)
•  Scientists Explore 1510 Influenza Pandemic and Lessons Learned (Link) Abstract (Link)

•  Recombinomics: H1N1 Evolution In Thailand Raises Pandemic Concerns (Link)
•  H3N2 Triple Reassortants in Pennsylvania and Illinois Patients (Link)

•  Recombinomics: Novel H3N2 Cases In United States Raise Pandemic (Link)