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Paradigm Shift Intervention Monitoring
The recently released H1N1
sequences by the CDC at GISAID include one HA sequence from the
Chihuahua, Mexico outbreak. Like two of the earlier sequences
from the Chihuahua
clade, it contained D225N. However, the D225N was on a S186P
genetic background. Unlike the two earlier sequences which were
generated via direct sequencing of upper
respiratory tract samples, the CDC sequence, A/Mexico/1658/2011,
came from an isolate grown on mammalian cells. Recent egg
isolates had higher frequencies of D225N and/or Q226R, but the above
isolate did not involve isolation on eggs, indicating a high level of
D225N in the clinical sample
Prior detection of D225N in mammalian isolates has been rare, so the detection of D225N in three isolates from Chihuahua, Mexico is unusual (and anecdotal reports cite several additional D225N isolates collected prior to the Easter holiday). The detection of D225N o two co-circulating clades raises concerns that the high concentration of D225N in Chihuahua, Mexico may be contributing to jumping of D225N from one clade to another.
Moreover, in addition to the D225N in the three isolates from direct sequencing or mammalian sub-cloning, there may be additional changes that would be detected in egg isolates. Two of the Chihuahua sub-clade isolates from the United States, A/Pennsylvania/02/2011 and A/Maryland/04/2011 were wild type at positions 225 and 226 when isolated on mammalian cells, but both had Q226R in egg isolates, raising concerns that Chihuahua isolates have additional receptor binding domain changes which are associated with severe and fatal cases (but only detected in egg isolates).
The latest Pneumonia and Influenza tally (week24) for El Paso, Texas reveals 10 more deaths, another weekly record which raises the 11 week death toll to 137, which is likely linked to the outbreak in Juarez in Chihuahua, Mexico.
Sequence data on Chihuahua egg isolates would be useful.