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. 2022 Jan:97:105175.
doi: 10.1016/j.meegid.2021.105175. Epub 2021 Dec 3.

Codon usage divergence in Delta variants (B.1.617.2) of SARS-CoV-2

Gun Li  1 , Liang Zhang  2 , Pei Xue  2
Affiliations

Codon usage divergence in Delta variants (B.1.617.2) of SARS-CoV-2

Gun Li et al. Infect Genet Evol. 2022 Jan.

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spreads all over the world and brings great harm to humans in many countries. Many new SARS-CoV-2 variants appeared during its transmission. In the present study, the Delta variants (B.1.617.2) of SARS-CoV-2, which have appeared in many countries, were considered for analysis. In order to evaluate the evolutionary divergence of the Delta variants(B.1.617.2), the codon usage divergence in Delta variants (B.1.617.2) of SARS-CoV-2 was compared to that of the SARS-CoV-2 genomes emerged before June 2020. All Delta variants (B.1.617.2) and 350 early genomes of SARS-CoV-2 in the NCBI database were downloaded. Codon usage pattern including the basic composition, the GC ratio of the third position (GC3) and the first two positions (GC12) in codons, overall GC contents, the effective number of codons (ENC), the codon bias index (CBI), the relative synonymous codon usage (RSCU) values, etc., of all concerned important gene sequences were all calculated. Codon usage divergence of them was calculated via summing their standard deviations. The results suggested that base compositions in both Delta variants (B.1.617.2) of SARS-CoV-2 and the early SARS-CoV-2 genomes were similar to each other. However, the internal codon usage divergence for most genes in Delta variants (B.1.617.2) was significantly wider than that of SARS-CoV-2. The RSCU values were further used to explore the synonymous and non-synonymous mutations in the sequences of the Delta variants (B.1.617.2), and the results showed the synonymous mutations are more obvious than the non-synonymous in the concerned sequences. The related codon usage divergence analysis is helpful for further study on the adaptability and disease prognosis of the SARS-CoV-2 variants.

Keywords: Biodiversity; Codon usage divergence; Delta variants (B.1.617.2); Gene evolution; SARS-CoV-2.

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Conflict of interest statement

The author declares that there is no conflict of interests.

Figures

Fig. 1
Fig. 1
Codon usage divergence in different sequences in both SARS-CoV-2 genomes and in the Delta variants (B.1.617.2) of SARS-CoV-2.
Fig. 2
Fig. 2
Changes of proportion in protein via amino acids ratio, revealing the non-synonymous codon changes in Delta variants (B.1.617.2).
See this image and copyright information in PMC

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