Using Time-Structured Data to Estimate Evolutionary Rates of Double-Stranded DNA Viruses

Abstract

Double-stranded (ds) DNA viruses are often described as evolving through long-term codivergent associations with their hosts, a pattern that is expected to be associated with low rates of nucleotide substitution. However, the hypothesis of codivergence between dsDNA viruses and their hosts has rarely been rigorously tested, even though the vast majority of nucleotide substitution rate estimates for dsDNA viruses are based upon this assumption. It is therefore important to estimate the evolutionary rates of dsDNA viruses independent of the assumption of host-virus codivergence. Here, we explore the use of temporally structured sequence data within a Bayesian framework to estimate the evolutionary rates for seven human dsDNA viruses, including variola virus (VARV) (the causative agent of smallpox) and herpes simplex virus-1. Our analyses reveal that although the VARV genome is likely to evolve at a rate of approximately 1 x 10(-5) substitutions/site/year and hence approaching that of many RNA viruses, the evolutionary rates of many other dsDNA viruses remain problematic to estimate. Synthetic data sets were constructed to inform our interpretation of the substitution rates estimated for these dsDNA viruses and the analysis of these demonstrated that given a sequence data set of appropriate length and sampling depth, it is possible to use time-structured analyses to estimate the substitution rates of many dsDNA viruses independently from the assumption of host-virus codivergence. Finally, the discovery that some dsDNA viruses may evolve at rates approaching those of RNA viruses has important implications for our understanding of the long-term evolutionary history and emergence potential of this major group of viruses.

Global phylogeography and evolution of chelonid fibropapilloma-associated herpesvirus

“…Moreover, our findings are consistent with recent studies supporting the suggestion that the evolutionary rates of some dsDNA viruses are comparable to those of RNA and ssDNA viruses (Babkin & Shchelkunov, 2008;Firth et al, 2010;Hughes et al, 2010).…”

“…The analyses revealed that the DNA polymerase, UL34 and UL18 genes of CFPHV were already under purifying selection with an overall ratio of non-synonymous to synonymous substitutions (d N /d S ) of 0.17, 0.24 and 0.28, respectively, and only the glycoprotein B gene had an overall d N /d S of~1, indicative of no significant selective pressure. Moreover, our findings are consistent with recent studies supporting the suggestion that the evolutionary rates of some dsDNA viruses are comparable to those of RNA and ssDNA viruses (Babkin & Shchelkunov, 2008;Firth et al, 2010;Hughes et al, 2010).Substitution rates of viruses are a complex product of the underlying mutation rate, generation time, effective population size and fitness (Duffy et al, 2008). Factors such as changing environments, high transmission rates and high replication rates can inflate virus evolutionary rates (Duffy et al, 2008;Firth et al, 2010;Hughes et al, 2010).…”

“…They also used the rise of the Isthmus of Panama (3.1-3.5 mya) to separate the Florida and Hawaii lineages, and estimated, independent of host-linked evolution, that the two most divergent virus clades separated 7.9-8.9 mya. In both cases, they concluded that CFPHV has been associated with sea turtles for millions of years (Herbst et al, 2004).Although it is widely accepted that herpesviruses codiverge with their hosts, this assumption is seldom tested (Duffy et al, 2008;Firth et al, 2010). Adding temporal information from heterochronous sequences (i.e.…”

Evidence of Muller’s ratchet in herpes simplex virus type 1

“…How genetic variability affects DNA viruses as compared to RNA viruses is a critical, pertinent question in evolutionary virology (Domingo et al, 2001a, b;Firth et al, 2010). Drake compared several cellular and viral DNAs and concluded that they all displayed a mean rate of 0.003 mutations introduced per genome and round of replication (Drake, 1991), and that the value for HSV-1 was comparable to that for other DNA-based genomes (Drake & Hwang, 2005).…”

Characterization of the Repeat Sequences of Varicella-Zoster Virus

“…VZV genome has been noted to be highly conserved (4~7). The herpesviruses in that the natural mutation rate was estimated to range between 10 -6 and 10 -7 substitution/ site/year (8,9), while that of herpes simplex virus type 1 ranged between 10 -4 and 10 -5 substitution/site/year (7,9).…”