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

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.