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Commentary
Egypt H5N1 NA
Sequences Acquire H1N1pdm09 Polymorphisms
Recombinomics
Commentary 02:15
May 30, 2012
The National Laboratory for Veterinary Quality Control on Poultry Production in Egypt has released a series of 2011 NA sequences from birds in Egypt (see list here). As was seen for the recently released HA sequences, clade 2.2.1 G dominated recent poultry sequences, as was seen in the most recent human H5N1 sequences (although the most recent human sequences are from the spring of 2010). However, recent human H5N1 sequences in phylogenetic trees of the WHO update on pandemic vaccines has additional 2011 human sequences, all of which are clade 2.2.1 G.
Although the recent 2011 NA sequences are also in the 2.2.1 G sub-clade, the majority for a subclade that is dominated by 2011 sequences (see list below), which are closely related to two 2011 sequences from Israel (A/turkey/Jenin/341/2011 and A/harrier/Israel/531/2011). The most closely related human sequence is A/Egypt/N14604/2009.
Most of the newly acquired polymorphisms in these isolates are shared with H1N1pdm09, raising additional concerns that the H1N1pdm09 is providing polymorphisms for clade 2.2.1 G in addition to sequences found in 2010 clade 2.2.1 F PB1 and PB2 sequences.
Sequences from internal genes from 2011 and 2012 human and avian sequences in Egypt should be generated and released along with recent human HA and NA sequences withheld by NAMRU-3.
A/chicken/Egypt/1119AF/2011
A/quail/Egypt/1171SG/2011
A/chicken/Egypt/1118AF/2011
A/ostrich/Egypt/11139F/2011
A/ch/icken/Egypt/1155/2011
A/duck/Egypt/11106SF/2011
A/duck/Egypt/1110AF/2011
A/chicken/Egypt/1158SF/2011
A/duck/Egypt/1148SF/2011
A/chicken/Egypt/112AF/2011
A/goose/Egypt/1117SF/2011
A/duck/Egypt/1113SD/2011
A/chicken/Egypt/1113/2011
A/chicken/Egypt/1112/2011
A/chicken/Egypt/112SG/2011
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