Codon usage polymorphism in SARS-2 CoV protein coding sequences

Abstract

Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2), which occurred in December of 2019, causes a severe acute respiratory illness, and has spread around the world. To reveal and understand genome expression mechanisms and evolution, we analyzed the codon usage (CU) pattern of SARS-CoV-2. CU refers to differences in the frequency of synonymous codons occurrence during protein translation. Multiple sequence alignment of different types SARS CoV 2 coding sequences (ORFs) has been performed in order to reveal if there is specificity of CU for different proteins types within viral genome during pandemic. We analyzed around 66000 complete SARS-CoV-2 isolates and around 770000 coding sequences (ORFs) divided into main 12 protein groups. Protein coding sequences in each group were aligned against corresponding ORF from referent SARS-CoV-2 genome (NC_045512.2) using Clustal Omega. Aligned ORFs were analyzed for changing frequencies of G, A, T and C nucleotides at the first, second and third codon position, as well as their influence to CU. Results obtained are illustrated on around 64000 Spike surface glycoproteins sequences.