Kayode, O.A., Edet, U.O., Olukayode, O.O. et al. Surveillance of zoonotic avian influenza viruses H5N1 and H9N2 in selected live bird markets in Northern Nigeria: public health implications. BMC Vet Res (2026)
Background
Avian influenza viruses (AIVs), including highly pathogenic H5N1 and low pathogenic H9N2, represent significant zoonotic threats. Both subtypes have been repeatedly introduced into Nigeria since their initial detection in West Africa in 2006 and 2017, respectively. This study aimed to investigate the current genetic diversity and spillover potential of these viruses through active surveillance in live bird markets (LBMs) in Hadejia and Kano, Nigeria, from March to November 2022.
Results
We sampled 219 birds, collecting two swabs per bird (438 swab specimens). A positive bird was defined as having at least one positive swab. At the bird level, highly pathogenic H5N1 was detected in 3/125 (2.4%) apparently healthy guinea fowl at Sabon Gari LBM in Kano. Notably, low pathogenic H9N2 was detected at a substantially higher prevalence, 10/94 (10.6%) in chickens at Hadejia LBM. Overall, 13/219 (5.9%) birds were positive for either H5N1 or H9N2. Phylogenetic and selection pressure analysis confirmed that the H9N2 viruses belong to the G1 lineage and harbor key mammalian adaptation signatures in the hemagglutinin (HA) gene, including S143T, S145T, and S121T, which are associated with increased affinity for human-like α2–6 sialic acid receptors. Phylogenetic analysis placed the H5N1 strain within clade 2.3.4.4b, showing close genetic relationships with viruses responsible for the 2021–2022 Nigerian epidemic and subsequent outbreaks in Niger in early 2023.
Conclusion
H5N1 and H9N2 were detected in different Nigerian live bird markets. Although these findings do not provide evidence of current co-circulation or reassortment, the detection of both subtypes within the broader LBM system, together with putative mammalian adaptation markers in H9N2, highlights a potential reassortment risk should these viruses later co-circulate within the same market and co-infect the same host. Continued genomic surveillance is therefore warranted to detect future viral convergence and emergent reassortant strains and to inform pandemic preparedness and control strategies.
Avian influenza viruses (AIVs), including highly pathogenic H5N1 and low pathogenic H9N2, represent significant zoonotic threats. Both subtypes have been repeatedly introduced into Nigeria since their initial detection in West Africa in 2006 and 2017, respectively. This study aimed to investigate the current genetic diversity and spillover potential of these viruses through active surveillance in live bird markets (LBMs) in Hadejia and Kano, Nigeria, from March to November 2022.
Results
We sampled 219 birds, collecting two swabs per bird (438 swab specimens). A positive bird was defined as having at least one positive swab. At the bird level, highly pathogenic H5N1 was detected in 3/125 (2.4%) apparently healthy guinea fowl at Sabon Gari LBM in Kano. Notably, low pathogenic H9N2 was detected at a substantially higher prevalence, 10/94 (10.6%) in chickens at Hadejia LBM. Overall, 13/219 (5.9%) birds were positive for either H5N1 or H9N2. Phylogenetic and selection pressure analysis confirmed that the H9N2 viruses belong to the G1 lineage and harbor key mammalian adaptation signatures in the hemagglutinin (HA) gene, including S143T, S145T, and S121T, which are associated with increased affinity for human-like α2–6 sialic acid receptors. Phylogenetic analysis placed the H5N1 strain within clade 2.3.4.4b, showing close genetic relationships with viruses responsible for the 2021–2022 Nigerian epidemic and subsequent outbreaks in Niger in early 2023.
Conclusion
H5N1 and H9N2 were detected in different Nigerian live bird markets. Although these findings do not provide evidence of current co-circulation or reassortment, the detection of both subtypes within the broader LBM system, together with putative mammalian adaptation markers in H9N2, highlights a potential reassortment risk should these viruses later co-circulate within the same market and co-infect the same host. Continued genomic surveillance is therefore warranted to detect future viral convergence and emergent reassortant strains and to inform pandemic preparedness and control strategies.
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