Chicken H5N1 Related to Gharbiya Cluster in Egypt
Recombinomics Commentary
April 5, 2007
H5N1 HA avian sequences from Egypt generated by US NAMRU-3 became available today at Genbank and Los Alamos. Included was A/chicken/Egypt/1892N3-HK49/2007. As noted in the submission sheet, the isolate was from Gharbiya. It was collected in February, 2007 and both the HA and NA are closely related to the sequences from the Gharbiya cluster, A/Egypt/14724-NAMRU3/2006 and A/Egypt/14725-NAMRU3/2006. However, the chicken sequence is a mixture, with mixed signals at several positions.
As shown at the NCASM meeting (slide 53), the position encoding M230I is a mixture, coding for the wild type M as well as I. The HA sequence also has V223I, a receptor binding change present in a bar-headed goose from Mongolia, as well as Shantou geese. This change was also found in H5N1 infected patients in Vietnam. Additional synonymous changes found in the chicken and patients from Gharbiya include G82A and C1477T.
In addition, the poultry sequence has several matches with the NA sequence (slide 54) from the Gharbiya cluster, including M29I, which is also in the Shantou geese, and V34I. Synonymous changes found in the four sequences from the Gharbiya cluster, and the Gharbiya chicken, are C818T, A826A, and G995A (also present as a mixture).
Although the chicken sequence did not have N294S, the polymorphism associated with oseltamivir (Tamiflu) resistance, the mixed signals in the chicken sequence suggest that N294S may be present, but below the detection level. Therefore plaque purification of this isolate would be useful.
The presence of the Gharbiya cluster-releated sequences in a chicken in Gharbiya in February, 2007 is cause for concern. Thus far, the Gharbiya sequence has been limited to cluster members, who died in December, 2006. However, the presence of the related sequence in poultry in February, 2007 raises questions about the presence of N294S in birds in Egypt and neighboring countries.
Plaque purification of the chicken isolate, and additional testing of H5N1 infected poultry in the region, would be useful.
Media sources
Phylogenetic Trees