Phylodynamics of avian influenza clade 2.2.1 H5N1 viruses in Egypt

• DOI: 10.1186/s12985-016-0477-7
• Publication Date: 2016-03-22T00:23:16Z
• Authors: Abdelsatar Arafa; Ihab El-Masry; Shereen Kholosy; Mohammed K. Hassan; Gwenaelle Dauphin; Juan Lubroth; Yilma J. Makonnen
• Keywords: Viral phylodynamics; Viral evolution; Reassortment

Highly pathogenic avian influenza (HPAI) viruses of the H5N1 subtype are widely distributed within poultry populations in Egypt and have caused multiple human infections. Linking epidemiological sequence data is important to understand transmission, persistence evolution virus. This work describes phylogenetic dynamics based on molecular characterization hemagglutinin (HA) gene isolates collected from February 2006 May 2014. Full-length HA sequences 368 were generated genetically analysed study their genetic evolution. They different species, production sectors, geographic locations Egypt. The Bayesian Markov Chain Monte Carlo (BMCMC) method was applied estimate evolutionary rates among virus clusters; additionally, an analysis selection pressures performed using Single Likelihood Ancestor Counting (SLAC) method. H5 2006–14 indicated presence one introduction classic clade (2.2.1) which two main subgroups originated, variant subgroup further subdivided into 2 sub-divisions (2.2.1.1 2.2.1.1a) endemic (2.2.1.2). 2.2.1.2 showed a high rate over period 6 years (6.9 × 10−3 sub/site/year) comparison 2.2.1.1a cluster (7.2 4 years). Those clusters under positive as they possess 5 distinct positively selected sites gene. mutations at 120, 154, 162 antigenic other (129∆, I151T) that occurred 2009–14 found be stable clade. Additionally, 13 groups HPAI identified amino acid cleavage site "EKRRKKR" became dominant pattern beginning 2013. Continuous has been observed all farming systems almost regions country. wide circulation carrying triple (120, 129∆, associated with increased binding affinity receptors alarming finding public health importance.