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Published on: January 28, 2019
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Codon usage of host-specific P genotypes (VP4) in group A rotavirus
Han Wu1, Bingzhe Li1, Ziping Miao2
1Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety (Fudan University), School of Public Health, Fudan University, Shanghai, 200032, China.
BMC Genomics
|July 16, 2022
Summary
Human rotavirus A (RVA) P genotypes exhibit strong codon usage bias driven by natural selection and mutation pressure. Porcine and zoonotic RVA P genotypes show similar biases, primarily influenced by natural selection, suggesting cross-species transmission potential.
Area of Science:
- Virology
- Genetics
- Evolutionary Biology
Background:
- Group A rotavirus (RVA) causes gastroenteritis globally in young children.
- RVA P genotypes, defined by VP4 sequences, infect humans and animals.
- Codon usage patterns of RVA P genotypes across hosts were previously unclear.
Purpose of the Study:
- To analyze codon usage patterns of host-specific RVA P genotypes.
- To investigate evolutionary and host adaptation insights from codon usage.
- To determine factors shaping codon usage bias in RVA P genotypes.
Main Methods:
- Comprehensive codon usage analysis of 233 RVA P genotype VP4 sequences.
- Calculation of nucleotide composition, relative synonymous codon usage (RSCU), and effective number of codons (ENC).
- Principal component analysis (PCA), ENC-plot, parity rule 2 plot, and neutrality plot analyses to assess codon usage patterns and driving forces.
Main Results:
- All RVA P genotypes preferred A/U nucleotides and codons ending in A/U.
- PCA revealed distinct codon usage patterns for human, porcine, and zoonotic RVA P genotypes, with overlap between porcine and zoonotic.
- Human RVA P genotypes showed stronger codon usage bias (lower ENC) than porcine and zoonotic genotypes.
- Natural selection was the predominant driver of codon usage bias, with mutation pressure also contributing to human genotypes.
Conclusions:
- Human RVA P genotypes exhibit significant codon usage bias due to natural selection and mutation pressure.
- Porcine and zoonotic RVA P genotypes share similar codon usage bias driven mainly by natural selection.
- Findings suggest potential for RVA cross-species transmission, highlighting the need for surveillance.
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