High Rates of Evolution and Pervasive Purifying Selection in Coat Protein Gene of Cassava Brown Streak Virus

Cassava brown streak viruses (Cassava brown streak virus [CBSV] and Uganda cassava brown streak virus [UCBSV]) are extremely damaging plant pathogens, affecting the sustainability of cassava production in Africa. However, little is known about the rate at which the viruses evolve, the timescale of their epidemiological history, and how much adaptive change the viruses are experiencing. This information is central to understanding the evolutionary dynamics of the viruses, which in turn has major implications on virus’ ability to emerge in new host species and resist RNAi approaches for control. We present here the rates of evolution determined from most important gene in CBSV’s pathogenicity, the coat protein (CP). We analysed the evolutionary dynamics of the viral gene and our Bayesian coalescent approach using BEAST revealed that the CBSV CP is the fastest evolving among studied potyviruses, with a mean rate of 1.72 x 10^-3 nucleotide substitutions per site per year (95% Highest Posterior Density, 1.22 – 2.0 x 10^-3 s/s/y). This rate indicates that the most recent common ancestor of CBSV existed 100 years before present (95% HPD, between years 1881-1949). Finally, the study documented pervasive evidence of purifying selection in the CBSV CP gene, but highlighted two sites that are undergoing diversifying selection, indicating CBSV has been adapting over the last two decades.