RT Journal Article
SR Electronic
T1 SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.06.06.138339
DO 10.1101/2020.06.06.138339
A1 Divinlal Harilal
A1 Sathishkumar Ramaswamy
A1 Tom Loney
A1 Hanan Al Suwaidi
A1 Hamda Khansaheb
A1 Abdulmajeed Alkhaja
A1 Rupa Varghese
A1 Zulfa Deesi
A1 Norbert Nowotny
A1 Alawi Alsheikh-Ali
A1 Ahmad Abou Tayoun
YR 2020
UL http://biorxiv.org/content/early/2020/06/18/2020.06.06.138339.abstract
AB Background With the gradual reopening of economies and resumption of social life, robust surveillance mechanisms should be implemented to control the ongoing COVID-19 pandemic. Unlike RT-qPCR, 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 and cost considerations of cWGS should be addressed before it can be widely implemented.Methods We 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 cost-effectiveness. 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.Results We 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 99% of the sequencing reads mapped to the viral genome compared to an average of 0.63% 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 SARS-CoV-2 genome sequences can be used to determine their possible origin through phylogenetic analysis including other viral strains.Conclusions SARS-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.Competing Interest StatementThe authors have declared no competing interest.