In-silico analysis of Covid-19 genome sequences of Indian origin: Impact of mutations in identification of SARS-Co-V2

Mol Cell Probes. 2021 Aug;58:101748. doi: 10.1016/j.mcp.2021.101748. Epub 2021 Jun 16.


Covid-19 disease caused by SARS-CoV-2 is still being transmitted in developed and developing countries irrespective of healthcare setups. India with 1.3 billion people in the world is severely affected by Covid-19 with 11.3 million cases and 157 000 deaths so far. We have assessed the mismatches in WHO recommended rRT-PCR assays primer and probe binding regions against SARS-CoV-2 Indian genome sequences through in-silico bioinformatics analysis approach. Primers and probe sequences belonging to CN-CDC-ORF1ab from China and HKU-ORF1b from Hong Kong targeting ORF1ab gene while NIH-TH-N from Thailand, HKU-N from Hong Kong and US-CDCN-2 from USA targeting N genes displayed accurate matches (>98.3%) with the 2019 novel corona virus sequences from India. On the other hand, none of the genomic sequences displayed exact match with the primer/probe sequences belonging to Charité-ORF1b from Germany targeting ORF1ab gene. We think it will be worthwhile to release this information to the clinical and medical communities working in Indian Covid-19 frontline taskforce to tackle the recently emerging Covid-19 outbreaks as of March-2021.

Keywords: Covid-19; Indian SARS-CoV-2 genome sequences; Primer and probe mismatches; rRT-PCR.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • COVID-19 / diagnosis*
  • COVID-19 / epidemiology
  • COVID-19 / virology
  • Computer Simulation*
  • DNA Primers / genetics
  • DNA Probes / genetics
  • Disease Outbreaks
  • Genome, Viral / genetics*
  • Humans
  • India / epidemiology
  • Mutation*
  • Open Reading Frames / genetics
  • RNA, Viral / genetics*
  • Real-Time Polymerase Chain Reaction / methods
  • Reproducibility of Results
  • SARS-CoV-2 / genetics*
  • SARS-CoV-2 / physiology
  • Sensitivity and Specificity


  • DNA Primers
  • DNA Probes
  • RNA, Viral