Molecular Epidemiology of Dengue and Chikungunya Viruses Co-circulation in Urban Communities in Abeokuta, Ogun State

Dengue virus (DENV) and chikungunya virus (CHIKV) are co-transmitted by Aedes mosquitoes and share overlapping clinical presentations, leading to frequent misdiagnosis in settings with limited laboratory capacity. Both viruses have been detected in Nigeria, but data on their simultaneous urban co-circulation are scarce. This study investigated the molecular epidemiology of DENV and CHIKV co-circulation in febrile patients in urban Abeokuta, Ogun State, Southwest Nigeria. Serum samples from 110 febrile outpatients testing negative for malaria were collected. Viral RNA extraction and singleplex RT-PCR were performed for DENV (using serotype-specific primers) and CHIKV (targeting the E1 gene). NS1 antigen ELISA was used as a supplementary DENV screening tool. DENV was detected in 18.2% and CHIKV in 14.5% of tested samples. Co-detection of both viruses in the same patient was confirmed in 3.6% of cases, representing the first molecular documentation of DENV/CHIKV co-infection in Abeokuta. DENV-2 and DENV-3 were the dominant serotypes, while CHIKV sequences clustered with the East Central South African genotype. The study highlights the complexity of arboviral febrile illness in Southwest Nigeria and the need for multiplexed diagnostics. Keywords: dengue, chikungunya, co-infection, RT-PCR, Abeokuta.