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Confirmed H5N1 Case in Egypt
Recombinomics Commentary
October 10, 2006

The woman, 39-year-old Hanan Aboul Magd of the Nile Delta province of Gharbiya, has been in hospital since October 4 and has been treated with the drug Tamiflu, state news agency MENA said.

The woman was on a respirator but her condition was stable

MENA reported that the newly infected woman had raised a flock of 11 ducks from her home north of the Egyptian capital. Two became sick and died, and she then slaughtered the rest before she was hospitalized.

Chickens on rooftops may be particularly susceptible to catching the virus from infected migrant birds, which fly along the densely populated Nile valley during migration, experts have suggested.

The above confirmation of the first human H5N1 bird flu case this season in Africa is not unexpected.  Recently Egypt reported new H5N1 infections in birds in several locations, and birds should be migrating into the area. The Ukraine has also reported recent H5N1 outbreaks as has Sudan..

Last season H5N1 infections were reported in Romania and Turkey in October.  Although H5N1 had migrated into Europe, the Middle East, and Africa, most countries, including Egypt, did not report H5N1 until human fatalities were confirmed in Turkey in January of this year.  Those reports were followed by acknowledgement of H5N1 in many countries in the region.

This year, most countries are again failing to detect or report H5N1 migration into the area.  This lack of transparency is cause for concern.

Similarly, the sequences from most of the H5N1 in Europe have been withheld by Weybridge, who presented in May 2006 a phylogenetic tree of approximately 80 isolates from Europe in early 2006.  They have only released one bird sequence, from a turkey isolated in October, 2005 as well as five human sequences (4 from Turkey and 1 from Azerbaijan).  Although Weybridge has indicated they will release the sequences, they have hoarded the data for 8-12 months.

The sequences are critical for identification of the evolution of tehse isolates via recombination.  Full sequences from the Capua lab are being released through the NIAID Influenza Sequencing program.  It facilities like Weybridge do not have the resources for timely sequencing and release of the data, turning the samples over to NIAID would be appropriate.  NIAID generates sequences at no charge, but sequences are made public instead of placing the data into the private WHO database.

Bejing Genomics Institute is releasing full sequences of H5N1 isolates China.  These sequences clearly demonstrate the evolution of H5N1 via recombination, which is also seen in the recent Qinghai sequences.  In the past examples of recombination has been hampered because most of the H5N1 sequences from Hong Kong and China generated by Hong Kong University and St Jude have been partial sequences.  These sequences should also be completed or turned over to NIAID so a full data set can be generated to map out a more complete picture of the H5N1 evolution by recombination.

The scandalous lack of full sequences in H5N1 isolates should be corrected.

Resources are now available to rectify these sequencing shortfalls.


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