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Updated: Nov 4, 2025
18:10
Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
Published on: June 16, 2011
29.8K
Comparative analysis of human coronaviruses focusing on nucleotide variability and synonymous codon usage patterns
Jayanta Kumar Das1, Swarup Roy2
1Department of Pediatrics, Johns Hopkins University School of Medicine, MD, USA.
Genomics
|May 21, 2021
Summary
This study analyzes protein-coding sequences of seven human coronaviruses (HCoVs), revealing nucleotide variability and codon usage patterns. Findings suggest SARS-CoV-2 evolution is linked to specific dinucleotide pairs and codon biases, with phylogenetic analysis placing it near pangolin and cat CoVs.
Area of Science:
- Virology
- Molecular Evolution
- Bioinformatics
Background:
- The COVID-19 pandemic highlights the need to understand SARS-CoV-2 evolutionary origins.
- Human coronaviruses (HCoVs) exhibit diverse evolutionary trajectories and host adaptations.
- Nucleotide sequence variability and codon usage patterns are key indicators of viral evolution.
Purpose of the Study:
- To conduct a comprehensive quantitative analysis of protein-coding sequences from seven HCoVs.
- To decipher nucleotide sequence variability and codon usage patterns among HCoVs.
- To understand the evolutionary relationships and adaptation mechanisms of SARS-CoV-2.
Main Methods:
- Quantitative analysis of protein-coding sequences from seven HCoVs.
- Analysis of nucleotide sequence variability, dinucleotide relative abundance (odds ratio), and GC/CT/CG dinucleotide pair frequencies.
- Calculation of Relative Synonymous Codon Usage (RSCU) and Effective Number of Codons (ENC) to assess codon usage bias.
- Phylogenetic analysis using RSCU scores to construct a dendrogram and comparative phylogenetic studies.
Main Results:
- High abundance of GC and CT dinucleotide pairs and low abundance of CG pairs observed, potentially influencing viral evolution.
- Significant variability in GC content at the third codon position across HCoVs.
- RSCU values correlated with specific amino acid groups (aliphatic, hydroxyl, cyclic, charged, sulfur-containing).
- Phylogenetic analysis positioned SARS-CoV-2 close to pangolin and cat CoVs.
- SARS-CoV-2 showed lower codon usage bias and similar codon adaptability compared to SARS-CoV and MERS-CoV, with mutational bias potentially driving variations.
Conclusions:
- Codon usage patterns and nucleotide composition provide insights into HCoV evolution and host adaptation.
- SARS-CoV-2 shares evolutionary proximity with pangolin and feline CoVs.
- Mutational biases play a role in shaping codon usage variation among coronaviruses.
- Comparative analysis of codon adaptability reveals distinct patterns among different CoVs.
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