Related Experiment Video
Updated: Jun 14, 2026
18:10
Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
Published on: June 16, 2011
Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses.
Cadhla Firth1, Andrew Kitchen, Beth Shapiro
1Department of Biology, The Pennsylvania State University, USA. cbf2118@columbia.edu
Molecular Biology and Evolution
|April 6, 2010
Summary
Double-stranded DNA viruses may evolve faster than previously assumed, challenging long-held theories of host-virus codivergence. New methods using time-structured data allow for more accurate evolutionary rate estimations, revealing potential for rapid viral evolution.
Area of Science:
- Virology
- Evolutionary Biology
- Genomics
Background:
- Double-stranded DNA (dsDNA) viruses are typically considered to evolve slowly due to long-term codivergence with hosts.
- Estimates of dsDNA virus evolutionary rates often rely on the unverified assumption of host-virus codivergence.
Purpose of the Study:
- To estimate dsDNA virus evolutionary rates independently of the host-virus codivergence assumption.
- To investigate the evolutionary dynamics of human dsDNA viruses using time-structured sequence data.
Main Methods:
- Bayesian phylogenetic analysis of temporally structured sequence data.
- Estimation of nucleotide substitution rates for seven human dsDNA viruses, including variola virus (VARV) and herpes simplex virus-1.
- Utilized synthetic datasets to validate the methodology for estimating evolutionary rates.
Main Results:
- Variola virus (VARV) exhibits an evolutionary rate of approximately 1 x 10^-5 substitutions/site/year, comparable to many RNA viruses.
- Estimating evolutionary rates for many other dsDNA viruses remains challenging.
- Time-structured analyses can accurately estimate dsDNA virus substitution rates with sufficient data length and sampling depth.
Conclusions:
- Some dsDNA viruses may evolve at rates approaching those of RNA viruses.
- This finding has significant implications for understanding the evolutionary history and emergence potential of dsDNA viruses.
- The study demonstrates a robust method for estimating viral evolutionary rates independent of host codivergence.
Related Concept Videos
01:26Size and Structure of Viral Genomes
Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
02:54Evolutionary Relationships through Genome Comparisons
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
02:05Gene Evolution - Fast or Slow?
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
02:05Gene Evolution - Fast or Slow?
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
00:36Viral Mutations
A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material for adaptive...
01:29Viruses with RNA Genomes
RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...