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Emergence of H1N1 Chihuahua Subclade In The United States

Recombinomics Commentary 16:40
April 24, 2011

The CDC recently released US 2011 H1N1 sequences at GISAID.  Included were five HA sequences (A/Maryland/04/2011, A/Oregon/03/2011, A/Pennsylvania/02/2011, A/Texas/07/2011,and A/Utah/08/2011) that were virtually identical to the eight Chihuahua sub-clade HA sequences at Genbank (A/Mexico/InDRE2222/2011, A/Mexico/InDRE2200/2011, A/Mexico/InDRE2197/2011, A/Mexico/InDRE2195/2011, A/Mexico/InDRE2192/2011) that matched the three isolates (A/Mexico/InDRE1947/2011, A/Mexico/InDRE1946/2011, A/Mexico/InDRE1945/2011) released earlier.

However, in addition to the 13 closely related sequences above, the Air Force had released additional sequences which had the Chihuahua genetic backbone (A/Arizona/AF21768/2011, A/Florida/AF21771/2011, A/New Jersey/AF21791/2011, A/North Carolina/AF21796/2011, A/South Carolina/AF21803/2011), and two of these isolates were from patients who had been vaccinated, raising serious doubts on the utility of vaccination campaigns in Mexico.

In addition to the above sequences, the CDC 2011 releases included additional isolates (A/North Carolina/03/2011, A/Vermont/04/2011, A/Massachusetts/06/2011, A/Maine/03/2011, A/New York/02/2011, A/Wisconsin/02/2011) which were virtually identical to the Air Force sequences and therefore should become more dominant as the flu season in the northern hemisphere winds down and the flu season in the southern hemisphere begins.

Recent reports from El Paso identify a dramatic spike in Pneumonia and Influenza deaths in El Paso in weeks 14 and 15, and one of the early deaths in Juarez was a El Paso resident.  Moreover, in week 14 there was a dramatic spike in influenza-like illness (ILI) in southeastern Juarez, suggesting this sub-clade is now rapidly spreading in Juarez and El Paso.

Release HA sequences from severe and fatal cases in Chihuahua have D225N in collections from the upper respiratory tract and anecdotal reports indicate additional examples of D225N in severe and fatal cases have been identified, raising concerns that infections with high concentrations of D225N will lead to a higher frequency of severe and fatal cases.

Release of HA sequences with D225N would be useful.
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