Phylogenetic analysis of 2015-2016 Nigerian highly pathogenic avian influenza (HPAI) H5N1 viruses

Abstract

Highly pathogenic avian influenza (HPAI), characterize by sudden onset and excessively high mortality, was first reported in Nigeria in 2006 and again in 2015 to date with devastating economic consequences. The complete genomes of 100 isolates collected between 2015 and 2016, covering 16 states and the Federal Capital Territory, were analysed to provide a better understanding of the genetic characteristic and evolution of the current H5N1 viruses circulating in Nigeria. The complete genomes of 100 H5N1 viruses collected from January 2015 to June 2016 in Nigerian poultry were sequenced and submitted to the GenBank database. The deduced amino acid sequence (PQRERRRKR* GLF) at the HA cleavage sites is characteristic of an HPAI virus strain, but possesses an amino acid deletion at position 345 compared to clade 2.2 viruses previously reported in Nigeria. The topology of the phylogenetic tree of the HA gene demonstrated that all the viruses analyzed fall within clade 2.3.2.1c and cluster with H5N1 viruses identified since 2014 in Asia, the Middle East, East Europe and other West African countries including Niger, Ghana, Burkina Faso and Ivory Coast. Specific amino acid signatures were also considered in defining sub-groups observed within this clade. The Nigerian viruses collected in 2015 are dispersed throughout the tree, indicating the possible occurrence of multiple independent introductions or the evolution of the virus into multiple genetic groups.