Since 2006, in Egypt, highly pathogenic avian influenza virus (HPAIV) H5N1 has established endemic status in poultry. Bayesian evolutionary analysis sampling trees suggested an introduction date in the third quarter of 2005. Evolutionary dynamics using Bayesian analysis showed that H5N1 viruses of clade 22.214.171.124 evolved at higher rates than those of clade 126.96.36.199. Bayesian skyline plot analysis of the HA gene of 840 and NA gene of 401 Egyptian H5N1 viruses from 2006-2015 identified two waves of viral population expansion correlating with the stepwise emergence of the 188.8.131.52 variant lineage in 2008 and with the newly emerging 184.108.40.206 cluster in late 2014. H5N1 infections in human hosts in 2014-2015 were statistically linked to a contemporary poultry outbreak.
Archives of Virology – Springer Journals
Published: Apr 11, 2016
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