Analysis of Codon Usage and Nucleotide Bias in Severe Acute Respiratory Syndrome Coronavirus 2(SARS-CoV-2) Genes

SARS-CoV-2 has recently emerged as a virus that poses a significant public health concern. The genetic features concerning the codon usage of SARS-CoV-2 genes were analyzed by the relative synonymous codon usage, the relative strength of codon bias, the effective number of codons (ENC), the codon adaptation index, and neutrality plot. Compositional analysis indicated that G and C at the first and second codon positions significantly affect synonymous codon choices. The mutational bias toward A/U may confer a selective advantage. The results suggest that mutation, together with selection dynamics, may play an essential role in shaping the pattern of codon usages in SARS-CoV-2 genomes. Turning to the codon usage preference and codon pair association in the viral genome, some of the most preferentially used codon observed across the genome did not occur at similar magnitudes in all genes. The possible co-evolution of the virus and its adaptation to the animal host has been discussed based on the codon adaptation index and codon de-optimization index.