Analysis and comparison of genetic variants and mutations of the novel coronavirus SARS-CoV-2

Abstract

We present an analysis and comparison study of genetic variants and mutations of about 1200 genomes of SARS-CoV-2 virus sampled across the first seven months of 2020. The study includes 12 sets of about 100 genomes each collected between January and September. We analyzed the mutations, mutation frequency and count trends over time, and genomes trends over time from January through September. We show that certain mutations in the SARS-CoV-2 genome are not occurring randomly as it has been commonly believed. This finding is in agreement with other recently published research in this domain. Therefore, this validates other findings in this direction. This study includes approximately 1000 genomes and was able to identify over 35 different mutations most of which are common to almost all genomes groups. Some mutations' ratios (frequency percentage) fluctuate over time to adapt the virus to various environmental factors, climate, and populations. One of the interesting findings in this paper is that the coding region, at the nucleotide level for NSP13 protein is relatively conserved compared with other protein regions in the ORF1ab gene which makes this protein a good candidate for developing drug targets and treatment for the COVID-19 disease. Although this outcome was already reported by other researchers, we corroborated their result with our work in a different approach and another experimental setting with almost one thousand complete genome sequences. We presented and discussed all these results and findings with tables of results and illustrating figures.

Keywords: 2019 H-CoV 2; Genetic variants; Novel coronavirus; SARS-CoV-2; SARS-CoV-2 genetic variants; SARS-CoV-2 genome.

Fig. 1

Structure of the SARS-CoV-2 genome in three different views: (a) basic illustration of the complete genome structure (b) illustration of coronavirus 2 isolate Wuhan-Hu-1, NC_045512 (complete genome 29,903 bp) as presented in the GenBank/NCBI https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2?report=graph (c) another view of the NC_045512.2 reference genome from NCBI showing all location of all genes. {Note: (b) and (c) are both courtesy of The US National Center for Biotechnology Information NCBI www.ncbi.nlm.nih.org.}

Fig. 2

This figure shows the divisions of the genome into genes/proteins and highlights the ORF1ab and Spike protein.

Fig. 3

Visualization of the genomic sequences showing the alignment and genetic variants. (a) This shows 23406A>G using NCBI msa viewer (this is the dataset S₅ (this is only partial view showing position 23354 to position 23463 with a sample of 30 genomes). (b) Visualization of the multiple sequence alignment (using Jalview tool). (c) S1c-100-genome (aligned with clustal msa)>>partial view with Jalview. Note: Y is C or T; R is A or G; W is A or T. Note: (a) is courtesy of the US National Center for Biotechnology Information NCBI. (b) and (c) are courtesy of Jalview tool (Waterhouse et al., n.d.): https://www.jalview.org/.

Fig. 4

Illustration of the percentage of five mutations in eight genomic sets (sets S₁…S₈) collected between 1 January and 31 May.