Related Experiment Video
Updated: Oct 8, 2025
18:10
Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
Published on: June 16, 2011
29.7K
Distinct codon usage bias evolutionary patterns between weakly and strongly virulent respiratory viruses.
1Department of Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.
Iscience
|January 3, 2022
Summary
Weakly virulent respiratory viruses show codon usage bias (CUB) similarities in nonstructural genes with humans, while highly virulent ones match in structural genes. This reveals distinct CUB evolutionary patterns linked to viral virulence.
Area of Science:
- Virology
- Molecular Evolution
- Genomics
Background:
- Human respiratory viruses exhibit a wide spectrum of virulence, from mild to life-threatening.
- The impact of virulence on the molecular evolution and specific evolutionary patterns of these viruses is not well understood.
Purpose of the Study:
- To investigate the relationship between viral virulence and codon usage bias (CUB) in human respiratory viruses.
- To compare the evolutionary patterns of CUB in weakly and strongly virulent viruses, including coronaviruses and SARS-CoV-2.
Main Methods:
- Comparative analysis of codon usage bias (CUB) in structural and nonstructural genes of respiratory viruses.
- Examination of CUB similarities between viral genes and human genomic sequences.
- Phylogenetic independent contrasts to assess the evolutionary divergence of viral CUB from human CUB, specifically for SARS-CoV-2.
Main Results:
- Weakly virulent viruses showed higher CUB similarity with humans in nonstructural genes.
- Strongly virulent viruses displayed greater CUB similarity with humans in structural genes.
- Coronaviruses demonstrated increased CUB similarity with humans in more virulent strains. SARS-CoV-2 showed divergence in CUB from humans.
Conclusions:
- Distinct evolutionary patterns of CUB exist between weakly and strongly virulent respiratory viruses.
- A novel interaction between codon usage bias and virulence in respiratory viruses has been identified.
- These findings contribute to understanding the molecular basis of viral virulence and evolution.
Related Concept Videos
00:36Viral Mutations
34.5K
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...
34.5K
02:28Leaky Scanning
5.3K
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R...
5.3K
01:29Viruses with RNA Genomes
197
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...
197
02:05Gene Evolution - Fast or Slow?
7.5K
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...
7.5K
01:26Size and Structure of Viral Genomes
208
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...
208
01:05Single Nucleotide Polymorphisms-SNPs
16.7K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
16.7K