Genomic Evidence for a Novel Introduction and Intra-host Diversity of DENV-2 in Dar es Salaam, Tanzania

Abstract

Dengue virus (DENV) poses a growing risk in Tanzania, yet its diversity in mosquitoes is poorly understood. Using Nanopore sequencing, we recovered full coding sequences from six DENV-2 positive mosquito pools collected in Dar es Salaam outside outbreak periods. Phylogenetic analysis placed the sequences in a distinct monophyletic clade within genotype II, separate from strains linked to Tanzanias 2014 outbreak. Instead, they clustered with Asian lineages, showing closest relatedness to DENV-2 from Kenya (2013) and India (2014), with divergence estimated around 2010. Variant profiling identified 212 low-frequency intra-host variants, largely nonsynonymous changes in NS3 and NS5. These results suggest an unrecognized introduction of genotype II now circulating silently in local mosquito populations. Our findings highlight the value of genomic surveillance in vectors for early detection of arboviral threats, even when human cases are absent.