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Rapid H1N1 Evolution In Mexico Raises Pandemic Concerns
Recombinomics Commentary 18:30
March 31, 2011

The virus has experienced a multiple mutation

The official said that so far it is a probable theory in which the human influenza virus has mutated or have features of two different viruses

The above translation describing the H1N1 in Mexico increases concerns that the circulating virus is a sub-clade that has evolved away from the pandemic H1N1 which was initially reported 2 years ago (the first confirmed cases in the United States were identified with samples collected on March 30, 2009 and April 1, 2009).  In addition to the cases in southern California, Mexico was reporting fatal atypical pneumonia cases that were poorly characterized, in part because the H1N1 was of swine origin and failed to react with sub-typing reagents directed at human flu sequences.

This year there have also been problems with lab confirmation.  The index case (26M) died with swine flu symptoms, but H1N1 was not confirmed. In contrast, his partner (33M) also died with swine flu symptoms, but H1N1 was confirmed.  These difficulties can be due to an evolved H1N1 which reacts poorly with reagents directed against earlier H1N1 isolates.

Recently the USDA released sequences from a series of swine isolates from Costa Rica.  These were pandemic H1N1 sequences, but had significant evolution away from the sequences commonly found in human cases.  The Costa Rica sequences had a number of changes flanking the receptor binding position at position 190 and would likely evade immune responses to earlier infections or vaccinations.  The Costa Rica had a large number of synonymous and non-synonymous changes, which could have reduced the sensitivity of testing reagents leading to false negatives as seen in the index case.

Moreover, a high percentage of reported cases have died or have been hospitalized, raising concerns that the current H1N1 circulating in Mexico is more virulent than earlier sub-clades.
The comments translated above suggest that initial sequencing on severe and fatal cases has been completed.

Release of these sequences is overdue.

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