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

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

Clement Meseko  1 , Adelaide Milani  2 , Bitrus Inuwa  1 , Chinonyerem Chinyere  1 , Ismaila Shittu  1 , James Ahmed  1 , Edoardo Giussani  2 , Elisa Palumbo  2 , Bianca Zecchin  2 , Francesco Bonfante  2 , Silvia Maniero  2 , Angélique Angot  3 , Mamadou Niang  4 , Alice Fusaro  2 , Federica Gobbo  2 , Calogero Terregino  2 , Taiwo Olasoju  5 , Isabella Monne  2 , Maryam Muhammad  1
Affiliations

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

Clement Meseko et al. Viruses. .

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.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Map of Nigeria showing location and distribution of HPAI in Nigeria, 2021–2022.
Figure 2
Figure 2
Haemorrhages of organs and tissues caused by HPAI in Nigeria, 2021–2022.
Figure 3
Figure 3
Phylogenetic tree of the nucleotide sequence of the HA gene obtained with the Maximum Likelihood method by using IQ-TREE v.1.6.12. H5Nx Nigerian viruses analysed in this study are in bold. The orange box (Group-1) includes the 2021-2022 H5N1 (black) and the reassortant H5N2 (red) Nigerian viruses. The light blue box (Group-2) includes the H5N8 Nigerian viruses. The Ultra-fast bootstrap values higher than 80% are indicated next to the nodes. The ovals next to the tree show the genetic composition of the three different genotypes (H5N1, H5N8, and H5N2) characterized in Nigeria between 2021 and 2022. Horizontal bars within each oval represent the 8 gene segments, coloured according to their origin (orange: H5N1; light blue: H5N8; and red: H9N2).
See this image and copyright information in PMC

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