Evolution of Synonymous Codon Usage Bias in West African and Central African Strains of Monkeypox Virus - PubMed (original) (raw)

Evolution of Synonymous Codon Usage Bias in West African and Central African Strains of Monkeypox Virus

Sudeesh Karumathil et al. Evol Bioinform Online. 2018.

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.

Keywords: Monkeypox viruses (MPXV); mutational pressure; selection pressure; synonymous codon usage bias (SCUB).

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Conflict of interest statement

Declaration of conflicting interests:The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Figures

Figure 1.

Figure 1.

Mutational pressure versus selection pressure in MPXV genomes. ENC versus GC3 plots for (A) Congo-2003-358, (B) COP-58, (C) DRC Yandongi-1985, (D) Liberia-1970-184, (E) MPXV-WRAIR7-61, (F) Sierra Leone, (G) Sudan-2005-01, (H) USA-2003-039, (I) USA-2003-044, (J)V79-I-005, (K) Zaire-1979-005 (cr), (L) Zaire-1979-005, and (M) Zaire-96-I-16. ENC indicates effective number of codons; MPXV, monkeypox viruses.

Figure 2.

Figure 2.

Influence of GC in shaping SCUB in MPXV genomes. Neutrality plots for (A) Congo-2003-358, (B) COP-58, (C) DRC Yandongi-1985, (D) Liberia-1970-184, (E) MPXV-WRAIR7-61, (F) Sierra Leone, (G) Sudan-2005-01, (H) USA-2003-039, (I) USA-2003-044, (J)V79-I-005, (K) Zaire-1979-005 (cr), (L) Zaire-1979-005, and (M) Zaire-96-I-16. MPXV indicates monkeypox viruses; SCUB, synonymous codon usage bias.

Figure 3.

Figure 3.

Deviation from parity rule 2 in MPXV genomes. PR2 bias plots for (A) Congo-2003-358, (B) COP-58, (C) DRC Yandongi-1985, (D) Liberia-1970-184, (E) MPXV-WRAIR7-61, (F) Sierra Leone, (G) Sudan-2005-01, (H) USA-2003-039, (I) USA-2003-044, (J)V79-I-005, (K) Zaire-1979-005 (cr), (L) Zaire-1979-005, and (M) Zaire-96-I-16. MPXV indicates monkeypox viruses.

Figure 4.

Figure 4.

Relationship between synonymous codon usage bias and virulence. The cluster analysis grouped more virulent strains into one major cluster (upper cluster) and less virulent strains into another cluster (lower cluster). CAI indicates codon adaptation index; ENC, effective number of codons.

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