Characterising Genetic Diversity in Cassava Brown Streak Virus

Abstract

Plant viruses represent a significant threat to food security for many global populations. Cassava Brown Streak Virus (CBSV) causes immense damage to cassava crops in Eastern, Central and Southern Africa. The eradication of CBSV is a difficult challenge, as it has been shown to be fast-evolving and it is transmitted by flying insects that are ubiquitous in cassava growing regions. In this paper we demonstrate the ability of two new developments in bioinformatics that can be used to increase our understanding of CBSV and ultimately inform strategies for its combat. We reconstruct the phylogeny of 29 whole-genome virus isolates using the GHOST model. This phylogeny identifies three distinct clades among the viruses and highlights a section of the genomes that is highly influential in their divergence. We also perform Multiple Correspondence Analysis on the alignment which is consistent in recovering the three clades, and offers insight on the significance of the influence of a variety of external variables on the evolution of the viruses. Knowledge and information from this analysis will be used as a base on which to formulate sustainable Cassava Brown Streak Disease (CBSD) management strategies in Africa.