Human adenovirus 5 strain:5 Genome sequencing and assembly

Rates of spontaneous mutation play a central role in the ability of viruses to evolve, infect new hosts, evade immunity and become drug-resistant. Contrarily to RNA viruses, few mutation rate estimates have been obtained for DNA viruses, because the relatively low mutation rate of DNA viruses implies that new mutations typically fall below the detection limit of Sanger and standard next-generation sequencing. Here, we have used a recently developed high-fidelity deep sequencing technique (Duplex Sequencing) to score spontaneous mutations in human adenovirus 5 under conditions of minimal selection. Based on >200 single-base spontaneous mutations detected throughout the entire viral genome, we infer an average mutation rate of 1.3 × 10–7 per base per cell infection cycle. This value is similar to those of other, large double-stranded DNA viruses, but an order of magnitude lower than those of single-stranded DNA viruses, and suggests the action of post-replicative repair. The mutation rate did not vary strongly along the adenovirus genome, but we found several sources of mutation rate heterogeneity. First, two regions mapping to transcription units L3 and E1B-IVa2 were significantly depleted for mutations. Second, several point insertions/deletions located within low-complexity sequence contexts appeared recurrently, suggesting mutational hotspots. Third, mutation probability was increased at CpG dinucleotides. Our findings suggest that host factors influence the distribution of spontaneous mutations in human adenoviruses and, potentially, other DNA viruses that replicate in the cell nucleus.