Phylodynamics of avian influenza clade 2.2.1 H5N1 viruses in Egypt

作者：Abdel-Satar Arafa, Ihab El Masry, SHEREEN G. KHOLOSY, Mohammed Khaled Hassan, Gwenae͏̈lle Dauphin, Juan Lubroth, Yilma J. Makonnen · 发表于：Virology Journal · 年份：2016 · DOI：10.1186/s12985-016-0477-7 · 被引用次数：60 · 研究领域：Influenza Virus Research Studies、Identification and Quantification in Food、Genomics and Phylogenetic Studies

BACKGROUND: 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 the epidemiological and sequence data is important to understand the transmission, persistence and evolution of the virus. This work describes the phylogenetic dynamics of H5N1 based on molecular characterization of the hemagglutinin (HA) gene of isolates collected from February 2006 to May 2014. METHODS: Full-length HA sequences of 368 H5N1 viruses were generated and were genetically analysed to study their genetic evolution. They were collected from different poultry species, production sectors, and geographic locations in Egypt. The Bayesian Markov Chain Monte Carlo (BMCMC) method was applied to estimate the evolutionary rates among different virus clusters; additionally, an analysis of selection pressures in the HA gene was performed using the Single Likelihood Ancestor Counting (SLAC) method. RESULTS: The phylogenetic analysis of the H5 gene from 2006-14 indicated the presence of one virus introduction of the classic clade (2.2.1) from which two main subgroups were originated, the variant subgroup which was further subdivided into 2 sub-divisions (2.2.1.1 and 2.2.1.1a) and the endemic subgroup (2.2.1.2). The clade 2.2.1.2 showed a high evolution rate over a period of 6 years (6.9 × 10(-3) sub/site/year) in comparison to the 2.2.1.1a variant cluster (7.2 × 10(-3) over a period of 4 ye...