The Evolution of Highly Pathogenic Avian Influenza A (H5) in Poultry in Nigeria, 2021-2022

Viruses. 2023 Jun 17;15(6):1387. doi: 10.3390/v15061387.

Abstract

In 2021, amidst the COVID-19 pandemic and global food insecurity, the Nigerian poultry sector was exposed to the 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 genomes of 97 influenza A viruses of the subtypes H5N1, H5N2, and H5N8, which were identified in different agro-ecological zones and farms during the 2021-2022 epidemic. The phylogenetic analysis of the HA genes showed a widespread distribution of the H5Nx clade 2.3.4.4b and similarity with the HPAI H5Nx viruses that have been detected in Europe since late 2020. The topology of the phylogenetic trees indicated the occurrence of several independent introductions of the virus into the country, followed by a regional evolution of the virus that was most probably linked to its persistent circulation in West African territories. Additional evidence of the evolutionary potential of the 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.

Keywords: H5N1/H9N2 reassortant virus; Nigeria; highly pathogenic avian influenza.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Birds
  • COVID-19* / epidemiology
  • Humans
  • Influenza A Virus, H5N1 Subtype* / genetics
  • Influenza A Virus, H5N2 Subtype* / genetics
  • Influenza A Virus, H9N2 Subtype* / genetics
  • Influenza in Birds* / epidemiology
  • Influenza, Human* / epidemiology
  • Nigeria / epidemiology
  • Pandemics
  • Phylogeny
  • Poultry
  • Poultry Diseases* / epidemiology

Grants and funding

Partial support for this work was provided by the United Nations Food and Agriculture Organization (UN-FAO) with funding from USAID under the OSRO/GLO/507/USA project within the “Global Health Security Agenda” (GHSA) program. The work was partially funded by the Italian Ministry of Health—Ricerca Corrente IZSVE IZS VE 10/19 RC “Sequenziamento di terza generazione: sviluppo di strategie innovative per l’identificazione e la caratterizzazione di virus prioritari per il settore avicolo”. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.