SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission

Abstract

These authors contributed equally to this work. Abstract BackgroundWith the gradual reopening of economies and resuming social life, robust surveillance mechanisms should be implemented to control the ongoing COVID-19 pandemic. Unlike RT-PCR, SARS-CoV-2 Whole Genome Sequencing (cWGS) has the added advantage of identifying cryptic origins of the virus, and the extent of community-based transmissions versus new viral introductions, which can in turn influence public health policy decisions.However, practical considerations of cWGS should be addressed before it can be widely implemented. MethodsWe performed shotgun transcriptome sequencing using RNA extracted from nasopharyngeal swabs of patients with COVID-19, and compared it to targeted SARS-CoV-2 full genome amplification and sequencing with respect to virus detection, scalability, and costeffectiveness. To track virus origin, we used open-source multiple sequence alignment and phylogenetic tools to compare the assembled SARS-CoV-2 genomes to publicly available sequences. ResultsWe show a significant improvement in whole genome sequencing data quality and viral detection using amplicon-based target enrichment of SARS-CoV-2. With enrichment, more than 95% of the sequencing reads mapped to the viral genome compared to an average of 0.7% without enrichment. Consequently, a dramatic increase in genome coverage was obtained using significantly less sequencing data, enabling higher scalability and significant cost reductions. We also demonstrate how this SARS-CoV-2 genome sequence can be used to determine its possible origin through phylogenetic analysis including other viral strains. ConclusionsSARS-CoV-2 whole genome sequencing is a practical, cost-effective, and powerful approach for population-based surveillance and control of viral transmission in the next phase of the COVID-19 pandemic.The COVID-19 pandemic continues to inflict devastating human life losses (1), and has enforced significant social changes and global economic shut downs (2). With the accumulating financial burdens and unemployment rates, several governments are sketching out plans for slowly re-opening the economy and reviving social life and economic activity.However, robust population-based surveillance systems are essential to track viral transmission during the re-opening process.While RT-PCR targeting SARS-CoV-2 can be effective in identifying infected individuals for isolation and contact tracing, it is not useful in determining which viral strains are circulating in the community: autochthonous versus imported ones, and -if imported -it is important to know the origin of the strains, which in turn influences public health policy decisions. In addition, super-spreader events are very important to identify as they can be influenced by the virus strain (3). SARS-CoV-2 whole genome sequencing (cWGS), on the other hand, can detect the virus and can delineate its origins through phylogenetic analysis (4, 5) in combination with other local and international viral strains, especially given the accu...

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