Relative synonymous codon usage of ORF1ab in SARS-CoV-2 and SARS-CoV

Abstract

Background: COVID-19, as a novel coronavirus disease caused by new coronavirus SARS-CoV-2, spreads all over the world, and brings harm to human in many countries. Humans suffered a lot from both SARS-CoV-2 now and by SARS-CoV in the year 2003. It is important to understand the differences and the relationships between these two types of viruses.

Objective: To compare relative synonymous codon usage of ORF1ab gene in SARS-CoV-2 and SARS-CoV, relative synonymous codon usage of their genomes are studied in this paper from the bioinformatics perspective.

Methods: The ORF1ab gene, which is an important non-structural polyprotein coding gene and now used for nucleic acid detection markers in many measurement method, in both SARS-CoV-2 (30 strains) and SARS-CoV (20 strains) are considered to be the research object in the present paper. The relative synonymous codon usage values of the ORF1ab gene are calculated to characterize the differences and the evolutionary characteristics among 50 strains.

Results: There is a significant difference between SARS-CoV and SARS-CoV-2 when the relative synonymous codon usage value of ORF1ab genes is concerned. The results suggest that codon usage pattern of SARS-CoV is more similar to human than that of the SARS-CoV-2, and that the inner difference in SARS-CoV-2 strains is larger than that of SARS-CoV, which denote the larger diversity exits in the SARS-CoV-2 virus.

Conclusion: These results show that the relative synonymous codon usage values in the coronavirus could be used for further research on their evolutionary phenomenon.

Keywords: COVID-19; Codon usage pattern; Coronavirus; Gene evolution; Relative synonymous codon usage; SARS-CoV; SARS-CoV-2.

Fig. 1

A Overall RSCU for ORF1ab of 20 SARS-CoV genomes, and B Overall RSCU for ORF1ab of 30 SARS-CoV-2 genomes. Red bars denote the codons, such as the GUG, UCA, CCA, ACA, UAA, AGA, AGG and GGA, with high RSCU values (more than 1.5) and could be regarded as the abundant codons, and the blue bars in the figure denote the less-abundant codons. All ORF1ab genes of 50 coronavirus select UAA as the stop codon, so the RSCU value of UAA is 3 (color figure online)

Fig. 2

Third-base usage frequency for ORF1ab of SARS-CoV-2 and SARS-CoV

Fig. 3

A Heat map of RSCU values of 50 ORF1ab coronavirus genes separately, and B The difference the mean RSCU values between SARS-CoV and SARS-CoV-2

Fig. 4

A Distance between overall codon usage pattern of coronavirus and human, and B phylogenetic tree of coronavirus genomes