In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations

Eltayib H Ahmed-Abakur; Mohammad Fahad Ullah; Elmutuz H Elssaig; Tarig M S Alnour

doi:10.1016/j.sjbs.2022.02.030

In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations

Saudi J Biol Sci. 2022 May;29(5):3494-3501. doi: 10.1016/j.sjbs.2022.02.030. Epub 2022 Feb 25.

Authors

Eltayib H Ahmed-Abakur^{1

2}, Mohammad Fahad Ullah^{1

2}, Elmutuz H Elssaig^{1

2}, Tarig M S Alnour^{1

2

3}

Affiliations

¹ Department of Medical Laboratory Technology (FAMS), University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia.
² Prince Fahad Research Chair, University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia.
³ Faculty of Medical Laboratory Science, Department of Microbiology and Immunology, Alzaiem Alazhari University, Khartoum North 11111, Sudan.

Abstract

In-silico studies on SARS-CoV-2 genome are considered important to identify the significant pattern of variations and its possible effects on the structural and functional characteristics of the virus. The current study determined such genetic variations and their possible impact among SARS-CoV-2 variants isolated in India. A total of 546 SARS-CoV-2 genomic sequences (India) were retrieved from the gene bank (NCBI) and subjected to alignment against the Wuhan variant (NC_045512.2), the corresponding amino acid changes were analyzed using NCBI Protein-BLAST. These 546 variants revealed 841 mutations; most of these were non-synonymous 464/841 (55.1%), there was no identical variant compared to the original strain. All genes; coding and non-coding showed nucleotide changes, most of the structural genes showed frequent nonsynonymous mutations. The most affected genes were ORF1a/b followed by the S gene which showed 515/841 (61.2%) and 120/841 (14.3%) mutations, respectively. The most frequent non-synonymous mutation 486/546 (89.01%) occurred in the S gene (structural gene) at position 23,403 where A changed to G leading to the replacement of aspartic acid by glycine in position (D614G). Interestingly, four variants also showed deletion. The variants MT800923 and MT800925 showed 12 consecutive nucleotide deletion in position 21982-21993 resulting in 4 consecutive amino acid deletions that were leucine, glycine, valine, and tyrosine in positions 141, 142, 143, and 144 respectively. The present study exhibited a higher mutations rate per variant compared to other studies carried out in India.

Keywords: FAB1a/b; In-silico; Mutations, synonymous; Non-synonymous; S gene; SARS - CoV- 2.