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2011 and 2009 H1N1 Similarities In Mexico Raise Concerns
Recombinomics Commentary 14:50
March 28, 2011

In an updated report on Sunday, the Ministry of Health reported that besides the four deaths from the H1N1 influenza in the state are seven people who are infected the virus, while eight others could also be carriers because of the atypical pneumonia that presented.
The above translation is from a report providing more detail on initial cases in Mexico.  All are under 65 years of age and in multiple locations in northern Mexico in the state of Chihuahua.  The cases are in addition to the four fatal cases, who were all between the ages of 24-35, which have strinking similarities with the 2009 outbreak in Mexico almost exactly 2 years ago.  At the time, seasonal flu levels were declining, and the outbreak of lethal atypical pneumonia in previously healthy young adults created significant concern.  These were H1N1 cases that were positive for influenza A, but negative for seasonal H3 or H1 because the H1N1 was of swine origin which failed to react with sub-typing reagent that targeted human influenza sequences.  Consequently, the cases were described as atypical pneumonia.  Similar influenza A positive cases were identified in southern Caliifornia in samples collected March 30 or April 1.  Sequencing of the cases identified swine triple reassortant viruses in cases that were over 100 miles apart and how no evidence of contact with each other or swine.
In the past 2 years H1N1 has spread worldwide and labs have reagents that can detect the swine H1N1 sequences.  However, the recent cases in northern Mexico were initially characterized as atypical pneumonia because of sub-typing difficulties, raising concerns that the H1N1 in the recent cases represents a more evolved sub-clade which is emerging now because of reduced competition from seasonal influenza.
Moreover, at least two of the fatalities were in traffic agents who were partners, indicating the H1N1 in that cluster was particularly virulent, killing two young adults (26M and 33M).  The H1N1 has spread rapidly, leading to alerts in Juarez, the state of Chihuahua, and the entire country.
These additional similarities between the 2009 and 2011 outbreaks require a rapid release of sequences from the cases in Mexico, as well as sequences from the United States.  The release of 2011 H1N1 sequences by the CDC has been delayed.  Last week 2011 H3N2 and influenza B sequences were released, but the last submission of H1N1 sequences was February 2, and the released sequences were largely from December, 2010 collections.
The relationship between the sequences in Mexico and Venezuela, and the in the United States is of interest, as are recent changes.  Swine sequences from the US and other countries worldwide include a broad array or reassortants which involve H1N1, H1N2, and H3N2 triple reassortants with segments from the pandemic H1N1 sub-clade. 

These newly formed genomes create additional threats since all 8 gene segments have a history of transmission in humans.

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