OmaraI/rvfv-evolution-africa

This repository contains outputs, analysis code and workflow supporting the manuscript: Evolutionary dynamics and molecular adaptation of Rift Valley fever virus across human and non-human outbreaks in Africa: #### Manuscript:**“Evolutionary dynamics and molecular adaptation of Rift Valley fever virus across human and non-human outbreaks in Africa (1944-2022)”** --- #### Project Overview Rift Valley fever virus (RVFV) is an emerging zoonotic pathogen with a broad host range and significant public health and veterinary impact across Africa. This study performed the first continental wide analysis integrating: - Identification of Protein coding mutations - Comparative genomic diversity (Human,livestock, wildlife & vectors) - Time-scaled phylogenetics to study transmission bottlenecks - Ancestral state reconstruction - Codon level selection pressure analysis - Spatiotemporal distribution of adaptive mutations --- This repository contains reproducible scripts, workflows and outputs from the study. #### Results The analyses identify seven nonsynonymous mutations, adaptive codons and host-specific selection signals that shape RVFV evolution across Africa (1944-2022) --- #### Pipeline used in this manuscript The procedure for installation and usage was obtained from Juma et al, github.com and other custom scripts used are available in this repo.