Clinical Report: A Multilevel Molecular Monitoring System for Dengue in Senegal

Overview

This observational study established and evaluated a tiered molecular surveillance framework linking arbovirus screening with rapid dengue serotyping and genomic epidemiology across 4 regions of Senegal.

Background

DENV, ZIKV, and CHIKV can co-circulate and produce overlapping clinical syndromes that complicate diagnosis and surveillance. Arboviral transmission in Africa remains under-recognized and underreported, while limited laboratory infrastructure and fragmented surveillance constrain outbreak detection and genomic characterization. The study evaluated a workflow integrating scalable molecular screening with targeted sequencing.

Data Highlights

Key Findings

• Multiplex RT-qPCR provided evidence of concurrent DENV, ZIKV, and CHIKV circulation among the sampled population.

• Among 43 individually tested samples from Touba, DENV was detected in 20.9%, ZIKV in 9.3%, and CHIKV in 11.6%.

• Among 108 pooled tests, DENV was detected in 18.5%, ZIKV in 5.6%, and CHIKV in 10.2%; these pool-level results do not represent individual prevalence.

• RT-RPA was completely concordant with RT-qPCR within the tested subset and identified DENV-2 in all serotyped positive samples.

• Targeted amplicon sequencing recovered near-complete DENV-2 genomes from 14 of 18 RT-RPA-positive samples, compared with sufficient genomic coverage in 8 using metagenomic sequencing.

• Recovered sequences clustered within DENV-2 genotype II, lineage II-F.1.1, with phylogenetic findings consistent with recent emergence or introduction followed by rapid expansion.

• Metagenomic sequencing detected Plasmodium falciparum reads in 3 samples despite negative routine malaria rapid tests.

Clinical Implications

The tiered workflow connected broad molecular screening with rapid dengue serotyping and targeted genomic analysis. This approach may improve surveillance efficiency by prioritizing positive specimens for resource-intensive sequencing. However, the study evaluated surveillance rather than clinical management, and it did not demonstrate improved treatment decisions, outbreak control, or patient outcomes.

Conclusion

The study documented concurrent DENV, ZIKV, and CHIKV circulation and characterized a recently expanding DENV-2 lineage in Senegal. Combining individual or pooled RT-qPCR screening, RT-RPA serotyping, and targeted sequencing provided a potentially scalable framework for linking arbovirus detection with genomic epidemiology in resource-limited settings. Pooled testing, the short surveillance period, and sequencing limited to DENV-2 constrain interpretation.

Related Resources & Content

A Tiered Molecular Surveillance Framework Linking Rapid Dengue Detection to Genomic Epidemiology in Senegal — Gaye A, Vaidya V, Toure M, et al. International Journal of Infectious Diseases. 2026;171:109009. doi:10.1016/j.ijid.2026.109009.