Detection of flaviviruses in mosquitoes from a livestock farm in Ibadan, Nigeria

Orthoflaviviruses constitute a diverse genus within the Flaviviridae family, comprising over 70 enveloped, single-stranded positive-sense RNA viruses that pose significant global health threats. Yellow fever virus (YFV) remains a significant public health concern in Nigeria, with suboptimal vaccination coverage and a persistent risk of transmission. Understanding the circulation of local orthoflaviviruses in mosquito vectors is crucial for disease surveillance and prevention strategies. Adult female mosquitoes were collected from the University of Ibadan’s dairy and teaching farms between June and August 2022 using stationary human-bait catches and miniature light traps. Mosquitoes were morphologically identified, pooled by species and collection site, and screened for orthoflaviviruses using hemi-nested reverse transcription PCR targeting the NS5 gene. Positive samples were sequenced and phylogenetic analysis was carried out. A total of 600 mosquitoes, representing six species from three genera, were collected, with Aedes aegypti predominating (60.67%). Of 22 mosquito pools tested, three were positive for orthoflaviviruses. Yellow fever virus was detected in one pool of 37 A. aegypti specimens, whilst insect-specific flaviviruses were identified in two other pools of the same mosquito genus. Phylogenetic analysis placed the YFV isolate within the West African genotype, consistent with genotypic affiliation to West African reference strains; however, fine-scale clustering inferences are limited by the short (~ 220 bp) NS5 fragment used. This study provides molecular evidence of orthoflavivirus nucleic acid in mosquito populations at a peri-agricultural site in Ibadan, Nigeria. The detection of YFV RNA in a single A. aegypti pool, at a minimum infection rate of 5.49 per 1000 specimens (95% CI: 1.34–19.95), is consistent with low-level vector-associated viral presence and warrants continued entomological and virological surveillance. These findings do not independently establish active transmission cycles or quantifiable human risk, but highlight the need for integrated virological and serological monitoring at human–animal–environment interfaces.