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Egypt H5N1 Matches In Fatal 2011 Cases Raise Concerns
Recombinomics Commentary 21:30
November 15, 2012

The CDC has released a series of H5N1 sequences from cases in Egypt.  Full sets of sequences were released for cases through the end of 2011.  The three most recent sets were from fatal cases who died in December, 2011.  The first case (F), A/Egypt/N11126/2011 was 24 weeks pregnant and developed symptoms on November 26 (which was also true for her young child, who was also H5N1 confirmed, but survived).  The mother died on December 3 (the sample was collected on December 1, when the mother was admitted) and was from Dakahlia Governorate.  The second fatal case (29M), A/Egypt/N11470/2011, was also from Dakahlia.  He developed symptoms on December 8 and died December 19 (the sample was collected on December 15, when he was admitted).  The third fatal case (42M), A/Egypt/N14976/2011, was from Menofia Governorate.  He developed symptoms on December 16, and died on December 22 (the sample was collected on December 21, when he was admitted).

Although the cases were from two distinct governorates, and from cases that developed symptoms more than three weeks apart, all three sequences were virtually identical.  Sequences for PA and NS were identical in all three patients.  Five other genes (PB2, HA, NP, NA, MP) where identical in the two male patients, and the female sequence had one nucleotide difference in each of the five genes.  The PB1 sequence was also closely related in all three cases and mapped on the same branch in phylogenetic analysis.

The near identity in all three cases (which would almost certainly be closely related to the child who was also H5N1 confirmed, raises concerns that H5N1 is evolving toward more efficient transmission in humans in Egypt.  The adaptations had been noted previously, since all recent human cases have been from the same sub-clade, which has the 3 BP deletion in HA.

More information on relationships between these three cases, as well as sequences from 2012 H5N1 cases would be useful.

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