Application of Next-Generation Sequencing Technology in Covid-19 and future pandemic preparedness

Author: Abhilash Kumar Tripathi, Department of Chemical and Biological Engineering

Mentor: Dr. Rajesh Kumar Sani, Department of Chemical and Biological Engineering

Next-generation sequencing (NGS) is an effective technology to identify new coronavirus strains and other pathogens without prior knowledge of organisms. NGS can be used to predict the possibility of community transmissions by examining the pathogen transmission networks in a locality. This research focuses on reviewing available literature on the applications of NGS technology in viral genome sequencing. Literature review suggests that the genomic information obtained from NGS data has been critical towards supporting public health and epidemiology. NGS data has allowed researchers and public health officials to quickly develop and implement solutions to combat COVID-19 pandemic. In our view, NGS based genomic surveillance will be an integral part of tracing SARS-CoV-2 and any future pandemic transmission. It would support major decision-making protocols such as lockdowns and travel restrictions. However, one alarming fact about Covid-19 genome is its instability, and therefore its genome undergoes mutations. These mutations occur over time and can lead to the emergence of new variants that may have different characteristics and can be more lethal. NGS helps in identifying such variants, monitor how it changes over time, understand how these changes affect the characteristics of the virus. This information can be used to predict how these variants might impact public health. Our aim through this review is to bring clarity to the rapidly growing body of NGS technologies and its applications in studying viral genome. In addition to reviewing literature, this review will also discuss the various types of NGS methods (shotgun metagenomics, amplicon sequencing, and target enrichment sequencing) currently being used to study COVID-19 genome. We will highlight the importance of each of these methods in clinical surveillance of any future pandemic. We believe this review will serve as a resource guide for scientists, physicians, students and the public at large.