One of the largest studies of the highly pathogenic H5N1 virus genetic sequences from poultry and wild birds has found 39 distinct substitutions with the possible ability to increase the pandemic potential of the virus.
The US-based group looked at 925 viral samples of H5N1 from Egypt collected between 2005-2015. Egypt has been the epicentre of human H5N1 infections, with more confirmed cases than any other country. H5N1 has a high human fatality rate but is not yet well-adapted to human hosts.
Until now, there has never been any spatial analyses of key substitutions (KS) in Egypt. The researchers aligned protein sequences to the viral samples and scanned for KS. They geocoded isolates using dasymetric mapping and then carried out geospatial hot spot analyses to identify spatial clusters of high KS detection rates.
The results found that of the 39 distinct KS detected in the wild, a total of 17 had not previously been reported in Egypt.
Detection rates varied by viral protein with most KS observed in the surface hemagglutinin (HA) and neuraminidase (NS1) protein as well as the interior non-structural 1 (NS1) protein. The most frequently detected KS were associated with increased viral binding to mammalian cells and virulence.
Samples with high overall detection rates of KS exhibited statistically significant spatial clustering in 2 governorates in the northwestern Nile Delta, Alexandria and Beheira.
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The research, published in BMC Infectious Diseases, concluded that KS provides a possible mechanism by which avian influenza H5N1 could evolve into a pandemic candidate.
With numerous KS circulating in Egypt, and non-random spatial clustering of KS detection rates, these findings suggest the need for increased surveillance in these areas, say the authors, led by Professor Sean Young, of the Department of Environmental and Occupational Health, University of Arkansas.