Overwhelming mutations or SNPs of SARS-CoV-2: A point of caution

Abstract

The morbidity of SARS-CoV-2 (COVID-19) is reaching 3 Million landmark causing and a serious public health concern globally and it is enigmatic how several antiviral and antibody treatments were not effective in the different period across the globe. With the drastic increasing number of positive cases around the world WHO raised the importance in the assessment of the risk of spread and understanding genetic modifications that could have occurred in the SARS-CoV-2. Using all available deep sequencing data of complete genome from all over the world (NCBI repository), we identified several hundreds of point mutations or SNPs in SARS-CoV-2 all across the genome. This could be the cause for the constant change and differed virulence with an increase in mortality and morbidity. Among the 12 different countries (one sequence from each country) with complete genome sequencing data, we noted the 47 key point mutations or SNPs located along the entire genome that might have impact in the virulence and response to different antivirals against SARS-CoV-2. In this regard, key viral proteins of spike glycoprotein, Nsp1, RdRp and the ORF8 region got heavily mutated within these 3 months via person-to-person passage. We also discuss what could be the possible cause of this rapid mutation in the SARS-CoV-2.

Keywords: COVID-19; Coronavirus; Evolution; Genome; Sequence.

Fig. 1

(A) Phylogenetic tree showing the evolution of SARS-CoV-2 from the initial origin China (2020/01/17). The tree represents the mutations or SNPs that resulted in the evolution of current SARS-CoV-2 in the last three months. Individual countries are colored in as shown in the color key. (B) Position and number of SNPs across are the genome is denoted with bar graph. (C) The key mutations with change in amino acid observed across the whole genome of 12 countries are listed and highlighted in red lines. Enlarged view showing the mutations occurred in spike glycoprotein. (D) Bar graph depicting the number of mutations and position is complete genome.