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. 2025 Jun 25;14(2):100001.
doi: 10.5501/wjv.v14.i2.100001.

Alpha to JN.1 variants: SARS-CoV-2 genomic analysis unfolding its various lineages/sublineages evolved in Chhattisgarh, India from 2020 to 2024

Pushpendra Singh  1 , Ruchi Khare  1 , Kuldeep Sharma  1 , Anudita Bhargava  1 , Sanjay Singh Negi  2
Affiliations

Alpha to JN.1 variants: SARS-CoV-2 genomic analysis unfolding its various lineages/sublineages evolved in Chhattisgarh, India from 2020 to 2024

Pushpendra Singh et al. World J Virol. .

Abstract

Background: The evolutionary mutational changes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) since its emergence in Chhattisgarh, India in 2020 have warranted the need for the characterization of every lineage/sublineage that has evolved until February 2024.

Aim: To unravel the evolutionary pathway of SARS-CoV-2 in Chhattisgarh from 2020 to February 2024.

Methods: A total of 635 coronavirus disease 2019 cases obtained between 2020 and February 2024 were investigated by whole genome sequencing.

Results: Whole genome sequencing analysis identified the evolution of SARS-CoV-2 into seventeen lineages from 2020 to 2024. SARS-CoV-2 initially emerged in Chhattisgarh in its Alpha (B.1.1.7) variant in 2020. Thereafter, it continuously underwent periodical mutational changes in the spike gene to further differentiate into various lineages/sublineages, viz., Kappa, Delta, BA.1, and BA.2 in 2021; the Omicron lineage (BA.5, BA.2.12.1, BA.2.75, BQ.1, and XBB) in 2022; the new Omicron lineage (XBB.1.5, XBB.1.16, XBB.1.9.1, and XBB.2.3) in 2023; and finally to JN.1 in January and February 2024. The predominant lineages over these 4 years were BA.1.1.7 (Alpha) in 2020, B.1.617.2 (Delta) in the period between 2021 and mid-2022, B.1.1.529 (Omicron) in late 2022 to 2023, and Omicron-JN.1 in early 2024. The presently circulating JN.1 lineage was observed harboring exclusive predominant mutations of E4554K, A570V, P621A, and P1143 L with 99% prevalence.

Conclusion: SARS-CoV-2 from 2020 to 2024 has evolved into 17 lineages/sublineages in Chhattisgarh. The presently circulating JN.1 harbored 40 mutations, especially E554K, A570V, P621S, and P1143 L, capacitating the virus with features of host cell entry, stability, replication, rapid transmissibility, and crucial immune evasion. Therefore, earlier immunity from either vaccination or prior infection may not protect against the current lineage and increases the possibility of future outbreaks. Thus, the periodical genomic surveillance of SARS-CoV-2 is essential for the genomic blueprint of the circulating virus, which may help in updating the vaccine strain and various basic research for developing appropriate therapeutics and diagnostics.

Keywords: 2020 to 2024; Genomic surveillance; Genomic variants; JN.1 variant; SARS-CoV-2.

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Conflict of interest statement

Conflict-of-interest statement: The authors have no conflicts of interest regarding the publication of this article.

Figures

Figure 1
Figure 1
Results of 635 whole genome sequencing samples. A: District detail of 635 whole genome sequencing cases; B: Year-wise male and female whole genome sequencing cases from 2020 to 2024. COVID-19: Coronavirus disease 2019.
Figure 2
Figure 2
Severe acute respiratory syndrome coronavirus 2 variants identified in Chhattisgarh between 2020 to 2024. VOC: Variants of concern; SARS-CoV-2: Severe acute respiratory syndrome coronavirus 2.
Figure 3
Figure 3
Circulation of different variants of severe acute respiratory syndrome coronavirus 2 in Chhattisgarh with detailed demographic appearance of JN.1 variant in various districts.
Figure 4
Figure 4
Circular phylogenetic tree representing whole genome sequencing of 635 strains from Chhattisgarh.
Figure 5
Figure 5
The three-dimensional structure and mutations in the spike protein of severe acute respiratory syndrome coronavirus 2 detected in different lineages.
Figure 6
Figure 6
Mutations of > 90% prevalence across four lineages.
See this image and copyright information in PMC

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