PS 52-195 - Molecular Epidemiology and Phylogeography of Dengue II Virus in Kenya

Background/Question/Methods

Dengue is a mosquito-transmitted viral infection that poses a significant public health risk, particularly in developing countries. The causative agent, dengue virus (DENV), is an arbovirus whose geographic range covers 128 countries across tropical and subtropical regions of the world, making it the most common human mosquito-transmitted viral disease. Despite the increasing burden of dengue in Kenya, the influences of the virus’ evolution, and their interplay with population and global-level factors in determining spread, have not been examined. The objective of this study is to assess the genetic structure of circulating dengue virus and evaluate the extent of gene flow across Kenya as well as migration from outside Kenya. Viral RNA was isolated from blood samples collected from a cohort of acutely ill patients recruited from 4 clinical sites in western and coastal Kenya between 2014 to 2018. High sensitivity reverse transcriptase PCR was conducted to test for the presence of dengue virus. Viral genomic material obtained from DENV positive samples was enriched using a multiplex, tiled-amplicon enrichment protocol with custom primers and complete viral genomes for phylogenetic analysis were obtained via next generation sequencing.

Results/Conclusions

7,563 total patients were recruited into the acutely ill cohort between 2014 and 2018. Of the 2,547 blood samples available for analysis from the study biobank to date, 256 samples were tested for viral presence, and 32 had enough dengue virus genomic material to allow sequencing. Preliminary viral sequencing results suggests the circulation of the genotype-II lineage of dengue-II virus. Phylogeographic models suggest frequent importation of dengue-II virus into Kenya from South-East Asia via the coastal port of Mombasa. Mombasa further acts as a landing point for importations into the rest of Kenya and Western Africa. The results also identified an additional single lineage found to have been circulating in the region since at least 1980. Dengue-II disease dynamics in the East Africa region are strongly tied to dengue-II dynamics in East and South-East Asia, with frequent gene flow between the two regions. These frequent importations, in addition to some local circulation, contribute to disease dynamics in the region. The evolutionary characteristics of infectious agents like dengue virus drive disease dynamics, and modern advances in genomics and computation allow researchers to model these evolutionary and disease dynamics.