Genomic surveillance of dengue virus in Benin

Dengue is a widespread viral infection transmitted from mosquitoes to humans, mainly in tropical and subtropical climates. In Benin, only dengue virus (DENV) serotype 2 infection has been previously described in humans. This study aimed to investigate DENV infection and serotypes in suspected patients. Plasma samples from 464 patients attending health centers in February 2023 with clinical symptoms and suspected for dengue infection were included, and analyzed for DENV by real time quantitative Polymerase Chain Reaction (Dengue Altona 3.0 kit). PCR positives samples were further characterized by whole genome sequencing and phylogenetic analysis to identify the circulating DENV serotype. The RT-qPCR results showed that four patients (D6, D23, D28, D44) were positive with the cycle threshold values less than 40 (31.3, 34.7, 14.7 and 14.3) respectively. Full-length DENV sequences were obtained for D6, D28 and D44. One patient (D6) was infected with DENV-1 serotype, and the two others (D28 and D44) were positive for DENV-3. Phylogenetic analysis shows that the new DENV-1 sequence is close to those obtained in Burkina Faso in 2022 and Nigeria in 2023, and the two DENV-3 sequences form a separate cluster with sequences obtained in Burkina Faso in 2022. We showed for the first time, the presence of dengue serotype 1 and serotype 3 infection in Benin. These results send a strong signal to health authorities and show that arbovirus surveillance efforts must be integrated into pathogen monitoring programs. •Dengue sequencing capacity in Benin.•Circulation of DENV-1 and DENV-3 sequences in humans in Benin.•Serotype 1 sequence is close to recent sequences from Burkina Faso and Nigeria.•Serotype 3 sequences are close to recent sequences from Burkina Faso.