Phylodynamic Investigation of Yellow Fever Virus Sheds New Insight on Geographic Dispersal Across Africa

Molecular epidemiology has shown the presence of four genotypes circulating across Africa, a paucity of data exists regarding phylogeography of the African Yellow fever (YF) genotypes. The need to fill this gap with spatiotemporal data from continuous YF outbreaks in Africa conceptualized this study; which aims to investigate the most recent transmission events and directional spread of yellow fever virus (YFV) using updated genomic sequence data.

Yellow fever sequence data was utilized along with epidemiologic data from outbreaks in Africa, to analyze the case/fatality distribution and genetic diversity. Phylodynamic and phylogeographic were utilized to investigate ancestral history, virus population dynamics, and geographic dispersal of yellow fever across Africa.

There was a sharp increase in laboratory confirmed cases after year 2015, with Nigeria and the Democratic Republic of Congo having the highest numbers of cases. Phylogeny of the YF genotypes followed a previously reported pattern with distinct geographic clustering. Historical dispersal of YFV was discovered to have occurred from West into Central/East Africa, with recent introductions occurring in West Africa.

We have shown the continuous circulation of YF in Africa, with distinct genotype distributions within the west and central African sub-regions. We have also shown the potential contribution of African genotypes, in the historical dispersal of yellow fever. We advocate for expanded and integrated molecular surveillance of YFV and other Arboviruses in Africa.