A tiered molecular surveillance framework linking rapid dengue detection to genomic epidemiology in Senegal

Arboviral surveillance in Africa is limited by fragmented diagnostic capacity and insufficient integration of molecular detection with genomic epidemiology, particularly in settings where dengue (DENV), Zika (ZIKV), and chikungunya (CHIKV) viruses co-circulate and present with overlapping clinical syndromes.

We conducted a molecular surveillance study across multiple regions in Senegal, including samples collected from 367 individuals with febrile or nonfebrile illness. A tiered workflow was implemented using multiplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) screening for DENV, ZIKV, and CHIKV, performed on a combination of individually tested samples (n = 43) and pooled samples (three individuals per pool). DENV RT-qPCR-positive samples were further characterized by RT recombinase polymerase amplification (RT-RPA) serotyping and genomic sequencing.

Multiplex RT-qPCR revealed concurrent circulation of multiple arboviruses. Among individually tested samples, positivity rates were 20.9% (9/43) for DENV, 9.3% (4/43) for ZIKV, and 11.6% (5/43) for CHIKV. In pooled screening across all sites (108 pools), positivity rates were 18.5% for DENV (20/108), 5.6% for ZIKV (6/108), and 10.2% for CHIKV (11/108), indicating widespread arboviral transmission. DENV-1-4 serotyping by RT-RPA demonstrated complete concordance with RT-qPCR and identified exclusive circulation of DENV-2, enabling triage of samples for downstream genomic sequencing. Amplicon-based sequencing substantially improved genome recovery compared with metagenomic sequencing, yielding near-complete genomes in 77.8% (14/18) of RT-RPA-positive samples. Phylogenetic analyzes demonstrated that all sequences clustered within the DENV-2 cosmopolitan genotype (genotype II), lineage II-F.1.1, closely related to recent strains from West Africa and Asia. Time-resolved reconstruction suggested recent emergence (∼2022-2023) and rapid expansion, consistent with ongoing transmission and regional dissemination.

These findings demonstrate co-circulation of DENV, ZIKV, and CHIKV in Senegal and provide evidence of recent expansion of DENV-2 within a globally connected transmission network. A tiered strategy integrating pooled molecular screening with RT-RPA triage and genomic sequencing offers a scalable framework for arboviral surveillance in resource-limited settings.