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Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses.
Ke-Jia Shan1,2, Changcheng Wu3, Xiaolu Tang1
1State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China.
Genomics, Proteomics & Bioinformatics
|June 11, 2024
Summary
The 2022 monkeypox virus (mpox virus, MPXV) outbreak showed accelerated evolution and changes in codon usage. MPXV uses non-preferred codons, which may correlate with reduced fatality rates.
Area of Science:
- Virology
- Evolutionary Biology
- Genomics
Background:
- The 2022 monkeypox virus (mpox virus, MPXV) epidemic presented a significant public health challenge.
- Understanding the evolutionary dynamics of MPXV is crucial for managing outbreaks.
Purpose of the Study:
- To investigate the evolutionary patterns of protein sequences and codon usage in MPXV.
- To identify evolutionary mechanisms driving MPXV during the 2022 outbreak.
Main Methods:
- Analysis of protein sequence evolution and selection pressures.
- Codon Usage Bias (CUB) analysis using the Codon Adaptation Index (CAI).
- Examination of epistasis between amino acid substitutions.
Main Results:
- Positive selection was detected in the OPG027 gene within the MPXV Clade I lineage.
- Accelerated protein sequence evolution was observed in MPXV variants from the 2022 outbreak.
- MPXV exhibited a tendency to use non-preferred codons compared to human genes, with CAI decreasing over time and varying across clades (Clade I > IIa > IIb-A > IIb-B).
- Strong epistasis was found between amino acid substitutions in different genes.
Conclusions:
- MPXV evolution is characterized by positive selection, accelerated protein evolution, and significant epistasis.
- The observed deoptimization of codon usage in MPXV may be linked to reduced fatality rates, though further research is needed to confirm causality.
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