Abstract
BackgroundHighly 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.MethodsFull-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.ResultsThe 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 years). Those two clusters are under positive selection as they possess 5 distinct positively selected sites in the HA gene. The mutations at 120, 154, and 162 HA antigenic sites and the other two mutations (129∆, I151T) that occurred from 2009–14 were found to be stable in the 2.2.1.2 clade. Additionally, 13 groups of H5N1 HPAI viruses were identified based on their amino acid sequences at the cleavage site and “EKRRKKR” became the dominant pattern beginning in 2013.ConclusionsContinuous evolution of H5N1 HPAI viruses in Egypt has been observed in all poultry farming and production systems in almost all regions of the country. The wide circulation of the 2.2.1.2 clade carrying triple mutations (120, 129∆, I151T) associated with increased binding affinity to human receptors is an alarming finding of public health importance.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-016-0477-7) contains supplementary material, which is available to authorized users.
Highlights
Pathogenic avian influenza (HPAI) viruses of the H5N1 subtype are widely distributed within poultry populations in Egypt and have caused multiple human infections
The classic group of clade 2.2.1 that was introduced into Egypt in 2006 remained stable through 2009 and represented the original viruses known at that time
In 2008, the classic viruses evolved into a new clade 2.2.1.2 due to gradual accumulation of genetic mutations in the HA protein, and was the dominant cluster between 2009 and 2014 in both the household and commercial poultry sectors irrespective of their vaccination status (Figs. 1 and 2)
Summary
Pathogenic avian influenza (HPAI) viruses of the H5N1 subtype are widely distributed within poultry populations in Egypt and have caused multiple human infections. Point mutations can introduce small changes known as genetic drift which mainly occurs because the virus polymerase lacks the proofreading property. These changes are thought to be selected by pressures that force the virus to mutate. The H5N1 viruses spread from Asia to Europe and to Africa, becoming endemic in poultry in parts of Asia and Egypt with frequent transmission to humans. In Egypt, the H5N1 HPAI virus (clade 2.2) was first reported in poultry in February 2006. The majority of viruses derived from vaccinated poultry in commercial farms belonged to the 2.2.1.1 clade of variant viruses [4,5,6]
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