Recombinomics Commentary 21:30
November 15, 2012
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
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.