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Silent Spread of D225N in Novel H1N1 in Chihuahua Mexico

Recombinomics Commentary 14:50
April 9, 2011

Two cities are primarily affected: Juarez and Chihuahua. Between March 22 and April 4, there have been 142 cumulative cases of ILI and severe acute respiratory infection (SARI) identified (24% of which were confirmed to be influenza A/H1N1 2009) and seven deaths (all adults, previously healthy, with the exception of one with COPD and one who was pregnant), of which six were confirmed to have influenza A/H1N1 2009. The Institute of Diagnosis and Epidemiological Reference (InDRE) of Mexico carried out genetic sequencing of the first three pandemic (H1N1) 2009 influenza cases (two fatal cases and one mild),.......
The above comments are from the Pan American Health Organization week 12 report describing the H1N1 outbreak in Juarez and Chihuahua, Mexico.  As noted previously, the seven fatalities were largely previously healthy young adults and the three sets of sequences at Genbank represent three of the first cases identified.  The above comments indicate two of the three samples were from fatal cases, which are likely to be 
A/Mexico/InDRE1945/2011 and A/Mexico/InDRE1946/2011.  These two sequences are virtually identical.  The only HA difference is the presence of D225N in Mexico/InDRE1945.  All three samples were collected from the upper respiratory tract (pharyngeal swabs) and it is likely that a low respiratory tract collection from the second fatal case would also yield D225N.  Moreover, the dates of collection and age of the patients (36M and 29M) combined with the close relationship at the nucleotide level suggests that both fatalities were from the traffic department in Juarez and signal transmission of a lethal H1N1 carrying D225N.

The "missing" D225N is similar to sequence data from the Duke Medical Center death cluster.  Four patients were infected with the same H1N1 which had H274Y in NA and a rare polymorphism in the HA, Y233H, and these markers were present in all four patients, who were on the same floor of the hospital.  Three of the four died within a day or two of each other.  The index case had D225G.  The second fatal case had D225N, while the thrid cases was wild type at position 225.  These differences are virtually certainly linked to the timing and location of the sample collected, and all four patients had both D225G and D225N.

Anecdotal reports suggest that the novel sub-clade in Chihuahua, Mexico is rapidly spreading in Mexico as well as Central and South America, raising serious pandemic concerns.  Media reports describe the appearance of H1N1 in San Pedro Sula, Honduras and
PAHO week 12 report notes seven severe acute respiratory infection deaths in the same area, which are likely due to the same novel sub-clade reported above for Chihuahua, Mexico, in addition to H1N1 outbreaks in Venezuela and El Salvador.

Moreover, anecdotal reports indicate D225N in the novel sub-clade is widespread in these countries.

Release of 2011 sequences from the United States as well as severe and fatal cases in Mexico, Central, and South America, would be useful.

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