Journal Article

Continent-wide evolutionary trends of emerging SARS-CoV-2 variants: dynamic profiles from Alpha to Omicron

Dhama, Kuldeep, Lee, Sang-Soo, Chakraborty, Chiranjib, Sharma, Ashish Ranjan, Bhattacharya, Manojit

2022

Overview

The ongoing SARS-CoV-2 evolution process has generated several variants due to its continuous mutations, making pandemics more critical. The present study illustrates SARS-CoV-2 evolution and its emerging mutations in five directions. First, the significant mutations in the genome and S-glycoprotein were analyzed in different variants. Three linear models were developed with the regression line to depict the mutational load for S-glycoprotein, total genome excluding S-glycoprotein, and whole genome. Second, the continent-wide evolution of SARS-CoV-2 and its variants with their clades and divergence were evaluated. It showed the region-wise evolution of the SARS-CoV-2 variants and their clustering event. The major clades for each variant were identified. One example is clade 21K, a major clade of the Omicron variant. Third, lineage dynamics and comparison between SARS-CoV-2 lineages across different countries are also illustrated, demonstrating dominant variants in various countries over time. Fourth, gene-wise mutation patterns and genetic variability of SARS-CoV-2 variants across various countries are illustrated. High mutation patterns were found in the ORF10, ORF6, S, and low mutation pattern E genes. Finally, emerging AA point mutations (T478K, L452R, N501Y, S477N, E484A, Q498R, and Y505H), their frequencies, and country-wise occurrence were identified, and the highest event of two mutations (T478K and L452R) was observed.

• Publisher: Springer International Publishing,Springer Nature B.V
• Subject: Biomedical and Life Sciences / Cell Biology / Clustering / Comparative studies / COVID-19 / COVID-19 - epidemiology / COVID-19 - genetics / Divergence / Evolution / Genes / Genetic variability / Genetics / Genomes / Genomics / Geriatrics/Gerontology / Glycoproteins / Humans / Life Sciences / Lineage / Linear analysis / Molecular Medicine / Mutation / Mutation - genetics / Original / Original Article / Pandemics / Regression analysis / SARS-CoV-2 - genetics / Severe acute respiratory syndrome / Severe acute respiratory syndrome coronavirus 2 / Variants