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Spread of Chihuahua Novel H1N1 Across the United States

Recombinomics Commentary 20:00
April 16, 2011

The CDC has released a series of 2011 H1N1 sequences at GISAID, which includes a subset that is closely related to the sequences from Chihuahua, Mexico.  In addition, The instituto de Diagnostico y Referencia Epidemiologicos has released partial HA sequence from 8 additional isolates in Chihuahua, Mexico, which includes five isolates (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.

All eight of the above sequences from Mexico have the rare marker, K149N, as well as a rare synonymous marker, T462A, and the eight sequence above are the only sequences at Genbank with both markers.  These two markers were also found in five sequences at GISAID (A/Maryland/04/2011, A/Oregon/03/2011, A/Pennsylvania/02/2011, A/Texas/07/2011,and A/Utah/08/2011) demonstrating the close relationship between the dominant sub-clade in Chihuahua and the five sequences in the United States.  Moreover, full sequences of two of the US isolates (PA/02 and MD/04) were released, demonstrating the absence of reassortment.  The eight gene segments in these two isolates were closely related to an earlier full sequence (A/Texas/03/2010).

In addition MD/04 had H274Y, signaling Tamiflu resistance.  Moreover, the recent sequences confirm the presence of the novel sub-clade in Texas.

The two markers exclusively shared between the eight sequences from Chihuahua and the five sequences from the US signal a rapid emergence and evolution of this novel sub-clade.  All 13 sequences were from samples collected in 2011, and 2 of the 8 sequences from Chihuahua had D225N, in samples collected from the upper respiratory tract, signaling efficient transmission, and raising concerns that this novel sub-clade will spread worldwide and produce a high frequency of severe and fatal cases.

Anecdotal reports cite closely related sequences in South America, where cases are beginning to increase, in advance of the flu season in the southern hemisphere.

The rapid spread of the novel sub-clade, with frequently detected D225N in samples from the upper respiratory tract, continues to increase pandemic concerns.

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