Paradigm Shift Intervention Monitoring
twitter
Commentary
Suspect H5N1
Cluster in Fayoum Egypt
Recombinomics Commentary 17:20
January 17, 2012
The above translation describes a suspect H5N1 cluster in Fayoum, Egypt. The index case (22F) has died with bird flu symptoms. Here brother (30M) is hospitalized, and any family member has symptoms.
This clusters follows a number of recent confirmed fatal cases in Egypt. The past three confirmed adult cases have died in December (42M Menofia Dec 22; 29M Dakahlia Dec 19; F Dakahlia Dec 3) and the November case was in critical condition and on a ventilator (31F Dakahlia Nov 16). The most recent child was the daughter of the Dakahlia case who died on Dec 3).
The high frequency of severe and fatal adult cases (all four of the most recent confirmed cases) is in marked contrast to cases in late 2009 /, early 2010, where almost all were young children who recovered, lowering the case fatality rate in Egypt to less than 10%. All of the earlier cases were clade G, which had a 3 base pair deletion (133del) and gave bioinformatic profiles similar to seasonal H1N1.
At that time a vaccine resistant H5N1 was identified in poultry, and no human cases have been reported. However, the last human H5N1 sequence from Egypt was from March of 2010, raising concerns that the severe and fatal adult cases reflect a host range expansion of the vaccine resistant sub-clade F to humans.
These concerns were increased by recently released sequences from 2010 poultry in Egypt, which were PB1 and PB2 recombinants which had acquired seasonal H1N1 and pandemic H1N1 gene sequences, as well as wild bird sequences which matched recent H3N2v, H1N2v, and H1N1v cases in the United States
Concerns have been increased further by a lack of transparency by NAMRU-3 regarding release of sequences. Three years ago NAMRU-3 promptly released sequences from the Gharbia cluster (largest confirmed cluster to date in Egypt), as well as fatal cases in early 2007 and milder cases in the spring of 2007. NAMRU-3 was then designated a WHO regional center, and release of sequences has slowed significantly. The lat series of sequences were in 2010, and included sequences from cases confirmed a year earlier.
However, the latest sequences are now almost 2 years old moving Egypt from the most transparent to the least transparent for human H5N1 sequences. Indonesia recently released full sequences for thye Bali cluster prior to official confirmation, and the same was done for a December fatal case in Shenzhen, China. In addition, sequences from 2011 fatal cases in Cambodia have been released.
In contrast, the sequences from Egypt have been withheld, even though the case fatality rate has increased dramatically, and the issues associated with the similarities between H5N1 clade G cases with seasonal H1N1 as well as the clade F vaccine resistance remains, while the recent internal gene sequences (especially PB1 and PB2) demand an immediate release of full sequences by NAMRU-3 and/or the US CDC.
Recombinomics
Presentations
Recombinomics
Publications
Recombinomics
Paper
at Nature Precedings