Molecular Detection and Genetic Characterization of H9N2 Avian Influenza Virus in Laying Hen and Broiler Farms in Dakar and Thiès Regions, Senegal.

Avian influenza, particularly the low pathogenic H9N2 subtype, is a major challenge to poultry and public health in Senegal. As important as it is, little is known about the occurrence and genetic characteristics of the H9N2 detected within the country's poultry farms. This study was therefore carried out to assess the occurrence and the molecular characteristics of H9N2 avian influenza virus strains in broiler and layer farms of the Dakar and Thiès regions. Throughout a period of 16 months, a cross-sectional survey was undertaken, collecting 390 tracheal and cloacal swabs from 39 chicken farms that reported respiratory disease. Viral RNA was isolated and analysed using real-time RT-PCR followed by viral isolation and hemagglutinin gene sequencing on positive samples. Phylogenetic analysis was performed to determine genetic associations with regional strains. Overall, the prevalence was 9.2% across 87 pools made from 390 swabs, with broiler chickens showing a high prevalence of 19.4% and layer hens a low prevalence of 2.0%. The majority of the positive farms were located in the Thiès region, which accounted for 6 out of the 8 positive farms. Phylogenetic analysis revealed that the circulating strain belonged to the G1 lineage and was closely related to Moroccan strains, indicating likely regional spread through poultry trade. The strains did not possess any molecular markers of increased virulence or zoonotic potential. These findings confirm the endemicity of H9N2 in Senegal's important poultry-producing regions and raise the need for targeted surveillance and improved biosecurity to avoid outbreaks and preserve public health.