A(H9N2) avian influenza virus in Côte d’Ivoire : molecular evidence from poultry and environmental sources, 2024–2025

Avian influenza A(H9N2) viruses are low-pathogenic but have zoonotic potential and are expanding geographically in Africa. In West Africa, molecular data are limited, particularly in Côte d’Ivoire, where information on circulation in poultry and environmental reservoirs is scarce. This study investigated the presence, molecular characteristics, and phylogenetic relationships of avian influenza A(H9N2) viruses in poultry and environmental samples from the Abidjan District in 2024–2025. Between December 2024 and February 2025, 193 samples were collected from 12 poultry farms and 11 live bird markets, including cloacal swabs, environmental surface swabs, drinking water, wastewater, and bioaerosols. Viral RNA was screened by real-time RT-PCR targeting the matrix gene; positive samples were sequenced by Oxford Nanopore MinION to determine subtypes and clades. Hemagglutinin (HA) gene sequences were analysed phylogenetically using maximum likelihood with reference strains from GISAID and GenBank. Influenza A RNA was detected in 44/193 samples (22.8%), with Ct values ranging from 18 to 35. Of these, 29 samples had Ct values ≤ 30 and were sequenced ; subtype analysis identified 21 as influenza A(H9N2) viruses. Influenza A(H9N2) viruses predominated in farms and was detected in both poultry and environmental samples, including drinking water and cloacal swabs, indicating active shedding and environmental contamination. Phylogenetic analysis showed that Ivorian influenza A(H9N2) viruses clustered within the G1 lineage, forming a monophyletic group with low divergence and close relationships to West African strains from Ghana, Mauritania, Benin, and Nigeria, whereas North African, Middle Eastern, and Asian strains formed separate clusters. This first molecular evidence of active influenza A(H9N2) viruses circulation in Côte d’Ivoire highlights a West African circulation dynamic likely facilitated by trade and live bird markets. Continuous genomic surveillance integrating environmental and animal monitoring under a One Health framework is essential to mitigate public health risks.