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

Abstract

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.

Ensitrelvir is effective against SARS-CoV-2 3CL protease mutants circulating globally

“…The antiviral activities of ensitrelvir were assessed using VeroE6T against nine SARS-CoV-2 variants, including six omicron variants, which have continuously emerged and circulated globally: omicron (BA1.1, BA.2, BA.2.75, BA.4, BA.5, and XE), mu (B.1.621), lambda (C.37), and theta (P.3) [ 16 ]. Ensitrelvir exhibited similar antiviral activities against all tested SARS-CoV-2 variants and EC 50 s were 0.22–0.57 μM ( Table 1 ).…”

Genetic features of SARS-CoV-2 Alpha, Delta, and Omicron variants and their association with the clinical severity of COVID-19 in Vietnam

“…Data from Weng et al [21] , Nikolaidis et al [22] , and Chakraborty et al . [23] have revealed the rate and type of mutation change among variants. We found several exclusive alterations in SARS-CoV-2 in this study; this is a transmission trait with a short viral life cycle that has been documented in several studies over the years.…”

Variant-specific deleterious mutations in the SARS-CoV-2 genome reveal immune responses and potentials for prophylactic vaccine development

“…Similar to other RNA viruses, SARS-CoV-2 is prone to mutations that produce new variants, creating difficulties in developing effective antiviral drugs and vaccines against this virus ( Ahmed et al, 2020 ; Jacobs et al, 2023 ; Sakib et al, 2021 ; Wang et al, 2020 ). Over 2 years, the SARS-CoV-2 virus has evolved through multiple new mutations and various genetic variants, such as Alpha (B.1.1.7) with seven, Beta (B.1.351) with nine, Gamma (P.1) with 12, Delta (B.1.6, B.1.6.2) with 17, Omicron (B.1.1.529) and Neocov variant with 32 new mutations in the spike protein gene ( Ahmed et al, 2021 ; Chakraborty et al, 2022a ; Chakraborty et al, 2022b ; Chakraborty et al, 2022c ; Chakraborty et al, 2022d ; Chakraborty et al, 2022e ). These variants have spread to various regions of the world, and among them, variants of concern (VOCs) such as Delta, Omicron, and their sub-lineages have caused significant risk to public health ( Hossain et al, 2021 ; Islam et al, 2021 , Islam et al, 2022a ).…”