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Clustering H5N1 Clusters Raise Pandemic Concerns in Egypt
Recombinomics Commentary 07:40
April 20, 2009

The Directorate girl Manar Saad Ibrahim Zidan (18 months) from the village of Chaabas Amir Kulain confirmed the status of her disease

The above translation describes the 66th confirmed H5N1 case in Egypt, which is the third confirmed case in three days.  However, more alarming than the frequency is the fact that all three cases are members of clusters, and the six most recent confirmed cases form three distinct clusters.

The 66th case is a toddler from the Kellin district of Kafr el Sheikh as is case #64 (33F).  The village of Shabas Emeir is only a few miles from the town of Kellin (see updated map), suggesting the two members of the Kellin cluster are from a small geographic area.  The precise location of case #64 was not released, but it is possible that both cases are from Shabas Emeir and/or are related or have contact.  Since the disease onset dates are 8 days apart, contact between the two cases would strongly support transmission of H5N1 from case #64 to case #66.

Similarly, case #65 forms a Cairo cluster with case #63.  Both were admitted to the Ain Shams hospital in Cairo and treatment was delayed for both, suggesting they denied a poultry connection.  These two cases also appear to be a few miles apart at the northern edge of Cairo (see updated map).

The third is the Beheira cluster created by two cousins in  Kom Hamada.  The cousins were next door neighbors and developed symptoms four days apart, strong supporting the infection of one cousin by the other.

These three clusters involving the six most recent confirmed cases create a significant cause for concern.  A recent report described a relationship between a subset of H5N1 isoaltes in Egypt and season flu, H1N1, which is efficiently transmitted to humans.  This relationship was tightly linked to a 3 BP deletion, which creates S129del, which involves a position that interacts with the receptor binding domain.  Moreover, this deletion was in siblings in the Qena cluster in 2007 and the sibling sequences were identical. 

Recently a phyologenetic of the first two cases in 2009 in Egypt were released and the position of these isolates suggests they also have S129del.  If these and other 2009 isolates have this deletion, including the six cases that form clusters in 2009, there would be a genetic explanation of the more efficient transmission represented by the clustering.

The release of the2009 sequences from Egypt is long overdue.  NAMRU-3 has not relased any human or poultry from the 2008/2009 season.

In addition, the relationship between the two Kellin cluster members, including the distance between residences, would be useful.

The clustering of clusters demands more transparency and a much more aggressive testing of toddlers without poultry contact, as well as antibody levels in the suspect cases that were PCR negative.

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