An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India

Viruses. 2021 May 17;13(5):925. doi: 10.3390/v13050925.


The number of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) cases is increasing in India. This study looks upon the geographic distribution of the virus clades and variants circulating in different parts of India between January and August 2020. The NPS/OPS from representative positive cases from different states and union territories in India were collected every month through the VRDLs in the country and analyzed using next-generation sequencing. Epidemiological analysis of the 689 SARS-CoV-2 clinical samples revealed GH and GR to be the predominant clades circulating in different states in India. The northern part of India largely reported the 'GH' clade, whereas the southern part reported the 'GR', with a few exceptions. These sequences also revealed the presence of single independent mutations-E484Q and N440K-from Maharashtra (first observed in March 2020) and Southern Indian States (first observed in May 2020), respectively. Furthermore, this study indicates that the SARS-CoV-2 variant (VOC, VUI, variant of high consequence and double mutant) was not observed during the early phase of virus transmission (January-August). This increased number of variations observed within a short timeframe across the globe suggests virus evolution, which can be a step towards enhanced host adaptation.

Keywords: India; NGS; SARS-CoV-2; clades; epidemiology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • COVID-19 / epidemiology*
  • COVID-19 / genetics
  • Female
  • Genome, Viral / genetics
  • Genomics / methods
  • High-Throughput Nucleotide Sequencing / methods
  • Humans
  • India / epidemiology
  • Male
  • Middle Aged
  • Mutation / genetics
  • Phylogeny
  • Phylogeography / methods*
  • SARS-CoV-2 / genetics*
  • SARS-CoV-2 / pathogenicity