H5N1 Evolution in Egypt
Recombinomics Commentary 03:22
January 1, 2008
Jabbour said the high fatality rate in the recent cases was likely due to a delay in diagnosis after patients and their family members denied exposure to infected birds.
"All of the new cases have exposure to sick or dead backyard birds. ... The problem is the delay in reporting that they have been exposed," he said. Patients are most likely to survive if they start treatment with Tamiflu early after symptoms occur.
The above explanation for the high current case fatality rate in Egypt, like many comments of the H5N1 evolution, is most viable in the absence of data. However, the data for last season suggest that much of the difference between the high case fatality rate at the beginning of the season, when the first seven cases died, and the case fatality rate for the remainder of the season, when only one of the seventeen confirmed case died, could be explained by newly acquired polymorphisms that were associated with fatal cases.
Egypt offers an ideal situation for rapid evolution. It lies at the intersection of two major flyways and has the large Nile Delta, which offers the opportunity for co-infections. The population of Egypt is concentrated in the Nile Delta and along the Nile River. The backyard poultry can mix with the wild birds, increasing opportunities for additional co-infections in domestic poultry.
Egypt reported 922 outbreaks in OIE reports beginning in early 2006. H5N1 was widespread then and affected large commercial farms as well as backyard holdings (see satellite maps here here here here here), In 2006, the sequence data from H5N1 linked to these outbreaks was relatively homogeneous. Samples had polymorphisms that traced upstream to Europe and downstream to west Africa, as well as markers that were regionally localized to Egypt, Israel, Gaza, and Djibouti.
After a lull over the summer, H5N1 infections were again reported in the fall of 2007. Both bird and human sequences had the same series of polymorphisms identified in the earlier isolates. However, the sequences were more genetically diverse and had many additional regional markers. One of the markers from northern isolates was M230I, a polymorphism found in all human seasonal flu isolates (H1N1, H3N2, influenza B). This marker was associated with fatal cases. All cases with M230I died, and M230I was in five of the seven fatal cases.
Other regional markers were found in isolates from southern Egypt. These cases were mild and were not linked to any fatalities. The reported cases in the spring were much more common than the cases in the fall.
This season, the H5N1 infections combine the properties seen in the previous season. The reported cases are frequent, as was seen in the spring, but the infections also produce a high case fatality rate, as seen in the prior fall.
This combination creates pandemic concerns.
Release of sequences from patients and birds would be useful.
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