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Viral Mutations

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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...

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Related Experiment Video

Updated: Dec 19, 2025

Precise Phage Mutagenesis with NgTET-Assisted CRISPR-Cas Systems

Precise Phage Mutagenesis with NgTET-Assisted CRISPR-Cas Systems

Published on: October 14, 2025

CpG-creating mutations are costly in many human viruses.

Victoria R Caudill^1,2, Sarina Qin^1,3, Ryan Winstead¹

¹Department of Biology, San Francisco State University, San Francisco, CA USA.

Evolutionary Ecology

|June 9, 2020

Summary

This summary is machine-generated.

CpG sites, rare in viral genomes, are costly mutations. This study analyzed viral mutation data, finding CpG sites are generally disadvantageous for most viruses, offering insights into viral evolution.

Keywords:

CpG sites Fitness costs Mutations Viruses

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Area of Science:

Virology
Genomics
Evolutionary Biology

Background:

Mutations are central to viral genome evolution, with varying impacts (beneficial, neutral, deleterious).
CpG sites (cytosine followed by guanine) are notably rare in eukaryotic and viral genomes.
Methylation-driven mutation is a proposed reason for CpG rarity in eukaryotes, but less is understood for viruses.

Purpose of the Study:

To investigate the evolutionary cost of CpG-creating mutations in diverse viral genomes.
To determine if the higher cost of CpG-creating mutations observed in HIV extends to other viruses.

Main Methods:

Analysis of allele frequencies of mutations across various viral strains, subtypes, and genes.
Utilized existing viral genomic data from Genbank, HIV Databases, and Virus Pathogen Resource.
Compared the frequency and impact of CpG-creating mutations versus non-CpG-creating mutations.

Main Results:

CpG sites were found to be costly for the majority of viruses analyzed.
The findings support the hypothesis that CpG sites represent a mutational burden in viral populations.
This cost likely influences viral genome composition and evolutionary trajectories.

Conclusions:

CpG sites impose a significant evolutionary cost on most viruses.
Understanding this cost provides critical insights into viral adaptation and evolution.
The rarity of CpG sites is a conserved feature across many viral systems due to mutational constraints.