H5N1 Bird Flu in Djibouti Simlar to Isolates from Egypt
Recombinomics Commentary
July 11, 2006
The H5N1 HA sequences from a human case in Djibouti, A/Djibouti/5691NAMRU3/2006(H5N1) has been released. As expected, te sequence was a Qinghai sequence which had acquired a series of new polymorphisms. These polymorphisms demonstrate the evolution of H5N1 ad allow the isolates to be grouped and analyzed. The partial 1311 BP sequence has 14 such changes and 11 of them are also found in a chicken and human isolate from nearby Egypt, A/chicken/Egypt/960N3-004/2006 and A/Egypt/2782-NAMRU3/2006, respectively, demonstrating significant evolution from the H5N1 sequences from Qinghai Lake in China and Novosibirsk in Russia. Six or seven of the 11 changes are also found in isolates from Italy, A/mallard/italy/332/2006 and A/Cygnus olor/Czech Republic/5170/2006.
These relationships indicate the H5N1 sequences are acquiring new polymorphisms via recombination with other Qinghai sequences in the area.
A recent presentation at the meeting on H5N1 and wild birds included phylogenetic trees of H5N1 in Europe. These trees have an increasing number of branches for these Qinghai isolates. Recently two groups of isolates from Lagos, Nigeria were described, which differ from each other and isolates in northern Nigeria and southern Niger. These four distinct groupings of H5N1 in Nigeria differed from the Egypt/Djoubi isolates, but it is likely that representatives from this latest grouping also migrated to Nigeria, where sequence data is just beginning to emerge.
The phylogenetic trees and newly emerging sequence data clearly show rapid diversification of Qinghai sequences throughout Europe, the Middle East, and Africa, raising concerns over cross-reactivity of pandemic vaccines and new problems in the fall after more recombination in wintering sites southern Siberia and northern Mongolia.
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Phylogenetic Trees