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H1N1 D225G In Upper Respiratory Tract in Chihuahua Mexico

Recombinomics Commentary 19:25
April 14, 2011

The Laboratorio de Genoma de Patogenos,Instituo de Diagnostico y Referencia Epidemiologicos in Mexico has released eight more HA sequences from Chihuahua, Mexico.  Five of the eight sequences were the novel sub-clade, and one, A/Mexico/InDRE2195/2011, was a pharyngeal sample from a patient, (41M) who was likely a severe or fatal case, which had a mixture of D225G and D225N, as expected.  This combination was frequently detected in autopsy lung samples in Ukraine in late 2009, which demonstrated phylogenetic and geographic clustering.  However, these combinations were not detected in upper respiratory tract collections.

The detection of this combination in an upper respiratory tract sample signals transmission at a high concentration, which is supported by detection of D225N in an upper respiratory tract collection from a fatal case.  Anecdotal reports indicate D225N has been found in additional upper respiratory tract samples in Mexico and South America in isolates representing the same novel sub-clade.  The partial sequence from the above sample had the same series of synonymous (G386A, T462A, C681T) and non-synonymous (K149N, S165N, A189T) markers seen in the other novel sequences, with D225N and D225G appended onto this genetic background.  The presence of different combinations at position 225 (one sample in Ukraine had three markers, D225G, D225N, D225A), one the same background supports recombination, as does the presence of the same RBD changes in Chihuahua as seen in Ukraine.

Thus, in contrast to WHO claims that D225G did not cluster phylogenetically or geographically, the data out of Chihuahua, Mexico once again demonstrates that the WHO claims are false (which was also demonstrated by the detection of D225G and D225N in the Duke Medical center death cluster).

The presence of D225G and D225N in the upper respiratory tract may also explain anecdotal reports of patients with nose bleeds and breathing difficulties in Chihuahua and Nuevo Leon in northern Mexico and raises additional concerns that this novel sub-clade with D225N and D225G will produce a high frequency in severe and fatal cases.

The CDC has released 2011 sequences from the United States, and although the novel sub-clade was present, the recent sequences did not contain D225G or D225N, although an earlier novel sequence, A/Pennsylvania/07/2010) did have D225G.  The results from Chihuahua suggest that a more aggressive effort, including deep sequencing, may be required to get a true picture of the virulence of this sub-clade.

Sequences from countries in Central and South America would be useful.
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