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Review
. 2021 Jul 30;43(2):845-867.
doi: 10.3390/cimb43020061.

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

Goldin John  1 , Nikhil Shri Sahajpal  1 , Ashis K Mondal  1 , Sudha Ananth  1 , Colin Williams  1 , Alka Chaubey  1   2 , Amyn M Rojiani  3 , Ravindra Kolhe  1
Affiliations
Review

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

Goldin John et al. Curr Issues Mol Biol. .

Abstract

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.

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Conflict of interest statement

The authors declare no conflict of interest. RK has received honoraria, travel funding, and research support from Illumina, Asuragen, QIAGEN, PerkinElmer Inc.,Bioanano Genomics Inc. and BMS. AC is salaried employee at Bionano Genomics Inc.

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