Empirical estimates of the mutation rate for an alphabaculovirus

• Published in: PLoS genetics Vol. 18; no. 6; p. e1009806
• Main Authors: Boezen, Dieke, Ali, Ghulam, Wang, Manli, Wang, Xi, van der Werf, Wopke, Vlak, Just M, Zwart, Mark P
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.06.2022; Public Library of Science (PLoS)
• Subjects: Bias; Biology and Life Sciences; Cloning; Demography; DNA viruses; Estimates; Genes; Genomes; Mutation; Mutation rates; Population; Population genetics; Proofreading; RNA viruses; Supplies; Viruses
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1009806

Mutation rates are of key importance for understanding evolutionary processes and predicting their outcomes. Empirical mutation rate estimates are available for a number of RNA viruses, but few are available for DNA viruses, which tend to have larger genomes. Whilst some viruses have very high mutation rates, lower mutation rates are expected for viruses with large genomes to ensure genome integrity. Alphabaculoviruses are insect viruses with large genomes and often have high levels of polymorphism, suggesting high mutation rates despite evidence of proofreading activity by the replication machinery. Here, we report an empirical estimate of the mutation rate per base per strand copying (s/n/r) of Autographa californica multiple nucleopolyhedrovirus (AcMNPV). To avoid biases due to selection, we analyzed mutations that occurred in a stable, non-functional genomic insert after five serial passages in Spodoptera exigua larvae. Our results highlight that viral demography and the stringency of mutation calling affect mutation rate estimates, and that using a population genetic simulation model to make inferences can mitigate the impact of these processes on estimates of mutation rate. We estimated a mutation rate of μ = 1×10-7 s/n/r when applying the most stringent criteria for mutation calling, and estimates of up to μ = 5×10-7 s/n/r when relaxing these criteria. The rates at which different classes of mutations accumulate provide good evidence for neutrality of mutations occurring within the inserted region. We therefore present a robust approach for mutation rate estimation for viruses with stable genomes, and strong evidence of a much lower alphabaculovirus mutation rate than supposed based on the high levels of polymorphism observed.