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

• Published in: Current issues in molecular biology Vol. 43; no. 2; pp. 845 - 867
• Main Authors: John, Goldin, Sahajpal, Nikhil Shri, Mondal, Ashis K., Ananth, Sudha, Williams, Colin, Chaubey, Alka, Rojiani, Amyn M., Kolhe, Ravindra
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI 30.07.2021; MDPI AG
• Subjects: challenges; Computational Biology - methods; COVID-19; COVID-19 - diagnosis; COVID-19 - epidemiology; COVID-19 - genetics; COVID-19 - virology; diagnostic assay; High-Throughput Nucleotide Sequencing - methods; Humans; Molecular Epidemiology - methods; next-generation sequencing; Pandemics; Phylogeny; Review; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; COVID-19; challenges; diagnostic assay; next-generation sequencing
• ISSN: 1467-3045; 1467-3037; 1467-3045
• 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.