ArticleEvolutionary bioinformatics online2018
Evolution of Synonymous Codon Usage Bias in West African and Central African Strains of Monkeypox Virus.
Article in Evolutionary bioinformatics online, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 32 citations in OpenAlex.
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- Insights into the Evolution and Host Adaptation of the Monkeypox Virus from a Codon Usage Perspective: Focus on the Ongoing 2022 Outbreak.International journal of molecular sciences · 2023Article
- The role of APOBEC3-induced mutations in the differential evolution of monkeypox virus.Virus evolution · 2023Article
- An overview on monkeypox virus: Pathogenesis, transmission, host interaction and therapeutics.Frontiers in cellular and infection microbiology · 2023Review
- Evolution, epidemiology, geographical distribution, and mutational landscape of newly emerging monkeypox virus.GeroScience · 2022Article
- Monkeypox: An emerging zoonotic pathogen.World journal of virology · 2022Review
- Analysis of codon usage bias of WRKY transcription factors in Helianthus annuus.BMC genomic data · 2022Article
- Analysis of codon usage bias of lumpy skin disease virus causing livestock infection.Frontiers in veterinary science · 2022Article
- Evolution of codon usage inFrontiers in veterinary science · 2022Article
- Genome-wide analysis of codon usage in sesame (Heliyon · 2022Article
- Strategies and Patterns of Codon Bias in Molluscum Contagiosum Virus.Pathogens (Basel, Switzerland) · 2021Article
- A comparative genomics-based study of positive strand RNA viruses emphasizing on SARS-CoV-2 utilizing dinucleotide signature, codon usage and codon context analyses.Gene reports · 2021Article
- Analysis of codon usage bias of classical swine fever virus.Veterinary world · 2021Article
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- Machine learning using intrinsic genomic signatures for rapid classification of novel pathogens: COVID-19 case study.PloS one · 2020Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The evolution of bias in synonymous codon usage in chosen monkeypox viral genomes and the factors influencing its diversification have not been reported so far. In this study, various trends associated with synonymous codon usage in chosen monkeypox viral genomes were investigated, and the results are reported. Identification of factors that influence codon usage in chosen monkeypox viral genomes was done using various codon usage indices, such as the relative synonymous codon usage, the effective number of codons, and the codon adaptation index. The Spearman rank correlation analysis and a correspondence analysis were used for correlating various factors with codon usage. The results revealed that mutational pressure due to compositional constraints, gene expression level, and selection at the codon level for utilization of putative optimal codons are major factors influencing synonymous codon usage bias in monkeypox viral genomes. A cluster analysis of relative synonymous codon usage values revealed a grouping of more virulent strains as one major cluster (Central African strains) and a grouping of less virulent strains (West African strains) as another major cluster, indicating a relationship between virulence and synonymous codon usage bias. This study concluded that a balance between the mutational pressure acting at the base composition level and the selection pressure acting at the amino acid level frames synonymous codon usage bias in the chosen monkeypox viruses. The natural selection from the host does not seem to have influenced the synonymous codon usage bias in the analyzed monkeypox viral genomes.
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