ARTICLE | doi:10.20944/preprints202305.1027.v1
Subject: Biology And Life Sciences, Virology Keywords: Highly pathogenic avian influenza; H5N1/H9N2 reassortant virus; Nigeria
Online: 15 May 2023 (10:38:06 CEST)
In 2021, amidst the COVID-19 pandemic and global food insecurity, the Nigerian poultry sector was yet exposed to highly pathogenic avian influenza (HPAI) virus and its economic challenges. Between 2021 and 2022, HPAI caused 467 outbreaks reported in 31 of the 37 administrative regions in Nigeria. In this study, we characterized the genome of 97 influenza A viruses of the subtypes H5N1, H5N2 and H5N8 identified in different agro-ecological zones and farms during the 2021-2022 epidemic. The phylogenetic analysis of the HA genes showed widespread distribution of the H5Nx clade 220.127.116.11b and similarity with the HPAI H5Nx viruses detected in Europe since late 2020. Topology of the phylogenetic trees indicates the occurrence of several independent introductions of the virus into the country followed by a regional evolution of the virus most probably linked to its persistent circulation in West African territories. An additional evidence of the evolutionary potential of HPAI viruses circulating in this region is the identification in this study of a putative H5N1/H9N2 reassortant virus in a mixed-species commercial poultry farm. Our data confirm Nigeria as a crucial hotspot for HPAI virus introduction from the Eurasian territories and reveal a dynamic pattern of avian influenza virus evolution within the Nigerian poultry population.