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

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.

Detection of clade 2.3.4.4 highly pathogenic avian influenza H5 viruses in healthy wild birds in the Hadeji‐Nguru wetland, Nigeria 2022

“…In a recent report on the diversity and evolution of highly pathogenic avian influenza in Nigeria, 36 2023 confirm the detection of H5N1, H5N2, and H5N8 of the clade 2.3.4.4b in commercial poultry farms across different states in Nigeria. Comparison of the H5Nx viruses of the clade 2.3.4.4b viruses detected and characterized in poultry in this study 36 revealed that these poultry viruses are genetically distinct from the ones identified in Hadejia Nguru wetland. The adduced reasons for this genetic divergence can include the inadequate/limited surveillance activities for HPAI in wild birds in wetlands across the country.…”

“…This implies that as these birds migrate from one continent to another, they can transmit the virus to the resident aquatic birds, which can then further disseminate the virus across the region. In a recent report on the diversity and evolution of highly pathogenic avian influenza in Nigeria, 36 2023 confirm the detection of H5N1, H5N2, and H5N8 of the clade 2.3.4.4b in commercial poultry farms across different states in Nigeria. Comparison of the H5Nx viruses of the clade 2.3.4.4b viruses detected and characterized in poultry in this study 36 revealed that these poultry viruses are genetically distinct from the ones identified in Hadejia Nguru wetland.…”

“…This implies that as these birds migrate from one continent to another, they can transmit the virus to the resident aquatic birds, which can then further disseminate the virus across the region. In a recent report on the diversity and evolution of highly pathogenic avian influenza in Nigeria, 36 Plateau, and the upper Orashi forests in Rivers state. 54,55 We, therefore, recommend sustained risk-based surveillance for AIV in wild birds for early detection, early warning alert for the poultry industry, disease mitigation, and control.…”

“…Whole‐genome sequences were obtained for 17 H5N1 viruses identified in wild birds in Nigerian wetlands. Analysis of the hemagglutinin (HA) gene segment confirms the presence of a cleavage site motif typical of the HPAI viruses (KRRKR*GLF) and shows that the HPAI H5N1 viruses from wild birds (Figure 3) belong to clade 2.3.4.4b but cluster separately from the H5N1 viruses, which have been circulating in the Nigerian poultry population since early 2021 36 . Specifically, the viruses identified in wild birds form two distinct groups in all the phylogenetic trees provisionally named here A and B groups (Figure 2 and Figures S1–S7).…”

“…Analysis of the hemagglutinin (HA) gene segment confirms the presence of a cleavage site motif typical of the HPAI viruses (KRRKR*GLF) and shows that the HPAI H5N1 viruses from wild birds (Figure 3) belong to clade 2.3.4.4b but cluster separately from the H5N1 viruses, which have been circulating in the Nigerian poultry population since early 2021. 36 Specifically, the viruses identified in wild birds form two distinct groups in all the phylogenetic trees provisionally named here A and B groups (Figure 2 and Figures S1-S7). Most of the viruses detected in wild birds in the Hadejia-Nguru wetlands cluster together in group B with viruses identified in wild and domestic birds in Senegal in December 2020- 3).…”