Next-Generation Sequencing (NGS) in COVID-19: A Tool for SARS-CoV-2 Diagnosis, Monitoring New Strains and Phylodynamic Modeling in Molecular Epidemiology

Curr Issues Mol Biol. 2021 Jul 30;43(2):845-867. doi: 10.3390/cimb43020061.


This review discusses the current testing methodologies for COVID-19 diagnosis and explores next-generation sequencing (NGS) technology for the detection of SARS-CoV-2 and monitoring phylogenetic evolution in the current COVID-19 pandemic. The review addresses the development, fundamentals, assay quality control and bioinformatics processing of the NGS data. This article provides a comprehensive review of the obstacles and opportunities facing the application of NGS technologies for the diagnosis, surveillance, and study of SARS-CoV-2 and other infectious diseases. Further, we have contemplated the opportunities and challenges inherent in the adoption of NGS technology as a diagnostic test with real-world examples of its utility in the fight against COVID-19.

Keywords: COVID-19; challenges; diagnostic assay; next-generation sequencing.

Publication types

  • Review

MeSH terms

  • COVID-19 / diagnosis
  • COVID-19 / epidemiology
  • COVID-19 / genetics
  • COVID-19 / virology*
  • Computational Biology / methods
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Molecular Epidemiology / methods
  • Pandemics
  • Phylogeny
  • SARS-CoV-2 / genetics*
  • SARS-CoV-2 / isolation & purification