Molecular Characterization and Genomic Surveillance of SARS-CoV-2 Lineages in Central India

Viruses. 2024 Oct 14;16(10):1608. doi: 10.3390/v16101608.

Abstract

Since the first reported case of COVID-19 in December 2019, several SARS-CoV-2 variants have evolved, and some of them have shown higher transmissibility, becoming the prevalent strains. Genomic epidemiological investigations into strains from different time points, including the early stages of the pandemic, are very crucial for understanding the evolution and transmission patterns. Using whole-genome sequences, our study describes the early landscape of SARS-CoV-2 variants in central India retrospectively (including the first known occurrence of SARS-CoV-2 in Madhya Pradesh). We performed amplicon-based whole-genome sequencing of randomly selected SARS-CoV-2 isolates (n = 38) collected between 2020 and 2022 at state level VRDL, ICMR-NIRTH, Jabalpur, from 11899 RT-qPCR-positive samples. We observed the presence of five lineages, namely B.1, B.1.1, B.1.36.8, B.1.195, and B.6, in 19 genomes from the first wave cases and variants of concern (VOCs) lineages, i.e., B.1.617.2 (Delta) and BA.2.10 (Omicron) in the second wave cases. There was a shift in mutational pattern in the spike protein coding region of SRAS-CoV-2 strains from the second wave in contrast to the first wave. In the first wave of infections, we observed variations in the ORF1Ab region, and with the emergence of Delta lineages, the D614G mutation associated with an increase in infectivity became a prominent change. We have identified five immune escape variants in the S gene, P681R, P681H, L452R, Q57H, and N501Y, in the isolates collected during the second wave. Furthermore, these genomes were compared with 2160 complete genome sequences reported from central India that encompass 109 different SARS-CoV-2 lineages. Among them, VOC lineages Delta (28.93%) and Omicron (56.11%) were circulating predominantly in this region. This study provides useful insights into the genetic diversity of SARS-CoV-2 strains over the initial course of the COVID-19 pandemic in central India.

Keywords: COVID-19; SARS-CoV-2; genetic diversity; phylogenetic tree; transmission; whole-genome sequencing.

MeSH terms

  • COVID-19* / epidemiology
  • COVID-19* / transmission
  • COVID-19* / virology
  • Genome, Viral*
  • Genomics / methods
  • Humans
  • India / epidemiology
  • Mutation
  • Phylogeny*
  • Retrospective Studies
  • SARS-CoV-2* / classification
  • SARS-CoV-2* / genetics
  • SARS-CoV-2* / isolation & purification
  • Spike Glycoprotein, Coronavirus / genetics
  • Whole Genome Sequencing*

Substances

  • Spike Glycoprotein, Coronavirus

Supplementary concepts

  • SARS-CoV-2 variants

Grants and funding

The study has been carried out with the support of Indian Council of Medical Research (ICMR) and the Department of Health Research (DHR, grant number DHR/VDL/04/2018). The Laboratory and staff of P.S. is supported by LRI Netherlands (Grant number 708.20.09), R2STOP Canada, DBT (Ramalingaswami Fellowship Grant), DHR and ICMR. Infrastructure and funding support from ICMR are also gratefully acknowledged. P.D. and M.S. are recipients of Senior Research Fellowship and Research Associateship, respectively, from ICMR.