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Withheld Novel H1N1 Sequences Raise Pandemic Concerns

Recombinomics Commentary 02:05
April 4, 2011

The recently released sequences from Chihuahua, Mexico identify an emerging sub-clade that appears to have spread throughout Mexico, Venezuela, and multiple countries in Central and South America.  This new sub-clade is associated with a high frequency of severe and fatal cases, which may be linked to the D225N found in the fatal case (but not the two other sequences from Chihuahua).

This sub-clade was circulating in the spring is 2010 in Galicia, Spain, and was also in a few additional sequences (from Cape Town, A/CapeTown/29/2010 and El Salvador, A/El Salvador/798/2010).  This sub-clade was also seen in 2011 sequences from the United States (A/Arizona/AF21768/2011, A/Florida/AF21771/2011, A/New Jersey/AF21791/2011, A/North Carolina/AF21796/2011, A/South Carolina/AF21803/2011).  These recent sequences were released by the Air Force as part of their surveillance program of military personnel and dependents.  

However, the distribution of this sub-clade in the United States in 2011 is not well understood because the CDC has withheld its collection of 2011 sequences from the United States.  Its last release of pH1N1 from the US was February 2, 2011 and was largely composed of sequences from samples collected in 2010.

In the past 9 weeks, the US pneumonia and influenza death rate has been at or above the epidemic threshold.  Reports of atypical pneumonia and a high hospitalization and death rate linked to the sub-clade in Chihuahua has raised concerns that this sub-clade has contributed to the high P&I rate reported in the United States and the sub-clade may emerge as a significant problem.  Some of the Chihuahua cases were epidemiologically linked to travel from New Mexico and Texas, increasing concerns that this sub-clade may be emerging in the United States also and may be considerably more common and widespread than represented by the Air Force samples, which did not include any sequences from Texas or New Mexico.

The CDC should release its 2011 H1N1 sequences and the Air Force should release 2011 H1N1 sequences from Texas, where the program is based (Brooks AFB).

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