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.

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 2.3.4.4b 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.

Newcastle disease (ND) is a highly infectious viral disease of birds caused by the Newcastle disease virus (NDV) and it has been reported in domestic birds in Nigeria. Waterfowls and village poultry in live bird markets (LBM) acts as reservoirs, potentially reintroducing the virus to commercial poultry. This study aims at molecular and serological detection of NDV at live bird markets in Plateau State, Nigeria. A cross sectional analysis involved 309 pooled cloacal and tracheal swabs over three months were analyzed by reverse transcriptase polymerase chain reaction (RT-PCR), RT-qPCR, virus isolation and haemagglutination and haemagglutination-inhibition test (HA &HI). Virus isolation was attempted in 9 to 11 days old specific antibody negative (SAN) embryonated chicken eggs and fifteen samples showed haemagglutination. Subsequent tests confimed nine of these as NDV positive through haemagglutination and haemagglutination inhibition (HI) tests. ConventionalRT-PCR and RT-qPCR further validated five of the nine NDV positive isolates. The phylogenetic analysis of partial F gene nucleotide sequences revealed that all three isolates belonged to class II genotype XIV.2_XIVb. This finding underscores the persistent threat of NDV to local poultry, necessitating comprehensive virological surveillance to understand, isolate and characterize the virus in Nigeria. Therefore, monitoring for emerging lineages and sub-lineages in Nigeria birds is crucial for safeguarding commercial poultry production.

Newcastle disease (ND) is a highly infectious viral disease of birds caused by the Newcastle disease virus (NDV) and it has been reported in domestic birds in Nigeria. Waterfowls and village poultry in live bird markets (LBM) acts as reservoirs, potentially reintroducing the virus to commercial poultry. This study aims at molecular and serological detection of NDV at live bird markets in Plateau State, Nigeria. A cross sectional analysis involved 309 pooled cloacal and tracheal swabs over three months were analyzed by reverse transcriptase polymerase chain reaction (RT-PCR), RT-qPCR, virus isolation and haemagglutination and haemagglutinationinhibition test (HA &HI). Virus isolation was attempted in 9 to 11 days old specific antibody negative (SAN) embryonated chicken eggs and fifteen samples showed haemagglutination. Subsequent tests confimed nine of these as NDV positive through haemagglutination and haemagglutination inhibition (HI) tests. Conventional RT-PCR and RT-qPCR further validated five of the nine NDV positive isolates. The phylogenetic analysis of partial F gene nucleotide sequences revealed that all three isolates belonged to class II genotype XIV.2_XIVb. This finding underscores the persistent threat of NDV to local poultry, necessitating comprehensive virological surveillance to understand, isolate and characterize the virus in Nigeria. Therefore, monitoring for emerging lineages and sub-lineages in Nigeria birds is crucial for safeguarding commercial poultry production.