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2011 Human H5N1 Sequence Indentities In Egypt
Recombinomics Commentary 16:45
February 25, 2012

Although Egypt has the second highest number of confirmed H5N1 cases in the world (161), as well as the most since 2009 (110), it has been almost two years since any human sequences were released by NAMRU-3.  The most recent human sequence is from A/Egypt/N04434/2010, which was from a March 31, 2010 collection.  NAMRU-3 release of human H5N1 sequence data has become increasingly less transparent since they became a WHO regional center.  Similarly, the US CDC, another WHO regional center, has failed to release H5N1 sequences from cases in Egypt, even though NAMRU-3 routinely sends samples to the CDC.

However, since both agencies are WHO regional centers, the withheld sequences are used to create clade 2.2 phylogenetic trees used in WHO updates of vaccine targets.  The latest WHO update includes eleven 2011 isolates from human cases in Egypt.  The phylogenetic analysis demonstrates a cluster for three of the 2011 isolates from early 2011.  However, the two most recent isolates on the tree, A/Egypt/11126/2011 and A/Egypt/11470/2011, have sequences which are identical, even though the sample numbers indicate they were collected weeks apart near the end of 2011, supporting human to human transmission.

The above two sequences are a concern because they form a branch with no poultry isolates and the length of the branch stem signals multiple changes, yet the two human sequences are identical.

The WHO tree only has 11 of the 39 confirmed human cases in 2011, so it is unclear if this cluster is larger than the above two cases, or if there are closely related avian sequences, which is why the full set of 2011/2012 sequences should be immediately released by the CDC or NAMRU-3, who clearly have much more data than is indicated on the tree in the WHO update.

This lack of transparency, which follows the NSABB request to censor the latest H5N1 transmission papers, continues to increase pandemic concerns and remain a hazard to the world's health.

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