Singh P, Khare R, Sharma K, Bhargava A, Negi SS. Alpha to JN.1 variants: SARS-CoV-2 genomic analysis unfolding its various lineages/sublineages evolved in Chhattisgarh, India from 2020 to 2024. World J Virol 2025; 14(2): 100001 [DOI: 10.5501/wjv.v14.i2.100001]
Corresponding Author of This Article
Sanjay Singh Negi, PhD, Professor, Department of Microbiology, All India Institute of Medical Sciences, Tatibandh, GE Road, Raipur 492099, Chhattīsgarh, India. negidr@aiimsraipur.edu.in
Research Domain of This Article
Virology
Article-Type of This Article
Basic Study
Open-Access Policy of This Article
This article is an open-access article which was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/4.0/
Pushpendra Singh, Ruchi Khare, Kuldeep Sharma, Anudita Bhargava, Sanjay Singh Negi, Department of Microbiology, All India Institute of Medical Sciences, Raipur 492099, Chhattīsgarh, India
Author contributions: Negi SS, Singh P, Sharma K, and Bhargava A were responsible for conceptualization and contributed to the design and implementation of the research; Singh P, Khare R, and Negi SS were responsible for methodology and writing of the original draft; Sharma K, Negi SS, and Singh P were responsible for bioinformatics software analysis; Negi SS and Bhargava A were responsible for supervision and analyzed the data along with resources for the study; Singh P, Sharma K, and Khare R performed all experiments; All authors read and agreed to the published version of the manuscript, and the corresponding author had final responsibility for the decision to submit for publication.
Institutional review board statement: The submitted study was approved both from institutional ethical and research committee, AIIMS, Raipur (IEC/AIIMS/RPR/1453/2021).
Conflict-of-interest statement: The authors have no conflicts of interest regarding the publication of this article.
Data sharing statement: All genome sequences and associated metadata in this dataset are published in GISAID’s EpiCoV database. To view the contributors of each individual sequence with details such as accession number, virus name, collection date, originating lab and submitting lab and the list of authors, visit 10.55876/gis8.240227op (GISAID Identifier: EPI_SET_240227op).
Open Access: This article is an open-access article that was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution NonCommercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: https://creativecommons.org/Licenses/by-nc/4.0/
Corresponding author: Sanjay Singh Negi, PhD, Professor, Department of Microbiology, All India Institute of Medical Sciences, Tatibandh, GE Road, Raipur 492099, Chhattīsgarh, India. negidr@aiimsraipur.edu.in
Received: August 5, 2024 Revised: December 30, 2024 Accepted: January 23, 2025 Published online: June 25, 2025 Processing time: 322 Days and 1 Hours
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.
Core Tip: Chhattisgarh, a central state of India is still being affected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease 2019 infection in humans, even in 2024 after four years from the time of its first emergence in April, 2020. No specific report giving details of each and every variant with their mutational pattern evolved over these four years is available. This study has provided insight of evolutionary journey underwent by the virus to unravel SARS-CoV-2 Lineages circulating predominantly in Chhattisgarh at different time period along with genomic pattern of crucial mutations and their effect. The details of circulating lineages with their prevalence rate and mutational pattern would help the researchers and policy makers to update the vaccine strain for persisting its effectivity against new variants or providing baseline data for developing new therapeutics.
