# Characterisation of the First Complete Dengue Genome in Sierra Leone

## TL;DR

This paper reports the first complete dengue virus genome from Sierra Leone and explores its genetic relationships with other dengue strains.

## Contribution

The study provides the first complete DENV-2 genome from Sierra Leone and identifies its phylogenetic lineage and relationships.

## Key findings

- The Sierra Leone DENV-2 genome belongs to genotype II, lineage F.1.1.
- The genome is phylogenetically distinct from Indian and Réunion DENV-2 sequences.
- The genetic divergence suggests diversification in an under-sampled region rather than a recent import from South Asia.

## Abstract

Dengue is the leading mosquito-borne viral cause of human illness and death. More than four billion people globally are at risk of dengue virus (DENV) infection, and most infections are asymptomatic or present with a non-specific febrile illness. We characterise the first complete DENV-2 genome from Sierra Leone, recovered from a febrile adult who tested RT-PCR–positive. The sequence was identified as DENV-2 genotype II, lineage F.1.1. Phylogenetically, the Sierra Leone genome formed a well-supported sister lineage with a 2024 USA DENV-2 genome; both were nested within but clearly diverged from Indian DENV-2 sequences (2021–2022) and were distinct from the Réunion DENV-2 clade. The degree of genetic divergence was incompatible with a recent or direct import of a South Asian lineage and was more consistent with diversification in an under-sampled Indian Ocean/South Asia network or outside this region in Africa. With a single Sierra Leone genome, the source and extent of local transmission remain unresolved. These findings underscore the benefits of integrating differential diagnostics and genomics into routine care for febrile illness and sustaining regional arboviral surveillance.