A genomic landscape of haplotype diversity and signatures of phylogeographic distribution in zaire ebolavirus during the 2014 EVD epidemic.

Abstract

The Ebola virus (EBOV) disease epidemic from 2013 to 2015 is the largest in history, affecting multiple countries in West Africa. Genome sequencing of EBOV has re‐ vealed extensive genetic variation and mutation rate. The evolution and the varia‐ tions among genotypes of EBOV observed remain low, which suggests that the viral haplotypes may be common in this transmission. To address this hypothesis, we investigated the genomic portrait of haplotype diversity in EBOV from 1976 to the 2014 outbreaks. We obtained 176 haplotypes in 305 gene-coding sequences of EBOV and found that the Hap8 in multiple viral haplotypes is the major epidemic lineage in the 2014 Sierra Leone outbreak. The phylogeographic analysis of EBOV transmission in Sierra Leone during 2014 outbreaks indicated that the genetic flow in EBOV was no more likely to occur within or without populations and the correlation between genetic and geographical distance is not significant. Our study first detected the diversity of viral haplotypes with systematic calculation of phylogeographic distribution in EBOV. This observation highlighted how Ebola virus is substantially different in virulence or transmissibility in comparison to the virus lineages associated with 2014 outbreaks in Sierra Leone, which provides a clue to understand the 2014 EBOV spreading. Keywords: Ebolavirus, Genome sequencing, Evolutionary, Haplotype diversity, Phy‐ logeographic distribution