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Paradigm Shift Intervention Monitoring
The instituto de Diagnostico y Referencia Epidemiologicos has released partial HA sequence from 8 additional isolates in Chihuahua, Mexico bring the total number of recent HA sequences to 11. Five of the eight ((A/Mexico/InDRE2222/2011, A/Mexico/InDRE2200/2011, A/Mexico/InDRE2197/2011, A/Mexico/InDRE2195/2011, A/Mexico/InDRE2192/2011) were closely related to the three isolates (A/Mexico/InDRE1947/2011, A/Mexico/InDRE1946/2011, A/Mexico/InDRE1945/2011) released earlier., indicating this Chihuahua sub-clade is dominant in Chihuahua, Mexico. One of the five sequences had D225G and D225N, which is a combination that was frequently seen in autopsy lung samples from Ukraine in 2009.
The detection of D225N in 2 of 8 sequences from the Chihuahua sub-clade is striking because it is generally detected a frequencies lower than D225G, and much lower than D225E. In sequences recently released by the CDC, sequences very closely related to those in Mexico were found in five isolates that were spread across the country (MD, PA, TX, UT, OR) which were in addition to other related sequences released earlier from the Air Force, although 2011 H1N1 sequences from Brooks Air Force Base have not been released.
The above sequences confirm a rapid spread of this sub-clade. Anecdotal reports indicate a large series of sequences from Mexico with D225N have yet to be released. These additional sequences will confirm a high frequency of D225N in this sub-clade, which is unusual. None of the 2010 sequences at Genbank habe D225N, and the frequency is also low in sequences deposited at GISAID in 2010.
The levels of D225N are even more striking, because like the Chihuahua sequences already released, the H1N1 is from pharyngeal swabs (collected from the upper respiratory tract). The frequent detection of D225N in Ukraine was from autopsy lung samples (lower respiratory tract).
The presence of D225N in the upper respiratory tract may explain presentations with bloody noses, which was been stated in additional anecdotal reports. The D225N levels in the upper respiratory tract may explain the spread of fatal infections in the Juarez traffic department, which increased concerns that the novel sub-clade with D225N in the upper respiratory tract will lead to a higher frequency of severe and fatal cases.
Mexico has tried to stem the spread with vaccination “fences”, but isolation of the novel sub-clade from vaccinated hosts suggest such vaccination campaigns will have limited success.
Additional sequences from severe and fatal cases throughout North and South America would be useful.