Novel Cleavage Site in Southern Egyptian H5N1 Cases
Recombinomics Commentary
March 31, 2007
US NAMRU-3 generated HA and NA sequences for the confirmed cases eartlier this week. The HA sequence for the third patient from Aswan (3F), A/Egypt/2616/NAMRU-3/2007 and Menia (5M), A/Egypt/2620/NAMRU-3 had the Mongolian HA cleavage site, GERRRRKR, as seen in the two earlier cases from Aswan (10F and 2M) (A/Egypt/2321/NAMRU-3/2007 and A/Egypt/2331), while the HA sequence from Qena (6F), A/Egypt/2621-NAMRU-3/2007, has the 3 BP deletion seen previously in the isolates from Beni Suef, A/Egypt/0636-NAMRU-3/2007 and Fayyoum, A/Egypt/1394/NAMRU-3/2007.
Similarly the NA sequences from all three isolates were similar to the previously described four isolates from central and southern Egypt. However, the new sequences showed the same segregation pattern as the HA sequences, indicating the differences were due to recombination and not reassortment in the HA and NA sequences.
The matches suggest that the infection from the two groups of patients are coming from common sources.
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