A rapid, cost-effective tailed amplicon method for sequencing SARS-CoV-2
- PDF / 1,824,216 Bytes
- 10 Pages / 595.276 x 790.866 pts Page_size
- 40 Downloads / 152 Views
METHODOLOGY ARTICLE
Open Access
A rapid, cost-effective tailed amplicon method for sequencing SARS-CoV-2 Daryl M. Gohl1,2* , John Garbe1, Patrick Grady1, Jerry Daniel1, Ray H. B. Watson1, Benjamin Auch1, Andrew Nelson3, Sophia Yohe3 and Kenneth B. Beckman1
Abstract Background: The global COVID-19 pandemic has led to an urgent need for scalable methods for clinical diagnostics and viral tracking. Next generation sequencing technologies have enabled large-scale genomic surveillance of SARS-CoV-2 as thousands of isolates are being sequenced around the world and deposited in public data repositories. A number of methods using both short- and long-read technologies are currently being applied for SARS-CoV-2 sequencing, including amplicon approaches, metagenomic methods, and sequence capture or enrichment methods. Given the small genome size, the ability to sequence SARS-CoV-2 at scale is limited by the cost and labor associated with making sequencing libraries. Results: Here we describe a low-cost, streamlined, all amplicon-based method for sequencing SARS-CoV-2, which bypasses costly and time-consuming library preparation steps. We benchmark this tailed amplicon method against both the ARTIC amplicon protocol and sequence capture approaches and show that an optimized tailed amplicon approach achieves comparable amplicon balance, coverage metrics, and variant calls to the ARTIC v3 approach. Conclusions: The tailed amplicon method we describe represents a cost-effective and highly scalable method for SARS-CoV-2 sequencing. Keywords: COVID-19, SARS-CoV-2, Genome sequencing, Viral surveillance
Background The global COVID-19 pandemic has necessitated a massive public health response which has included implementation of society-wide distancing measures to limit viral transmission, the rapid development of qRT-PCR, antigen, and antibody diagnostic tests, as well as a world-wide research effort of unprecedented scope and speed. Next generation sequencing technologies (NGS) have recently enabled large-scale genomic surveillance of infectious diseases. Sequencing-based genomic surveillance has been applied to both endemic disease, such as seasonal influenza [1], and to emerging disease outbreaks such as Zika and Ebola [2–4]. * Correspondence: [email protected] 1 University of Minnesota Genomics Center, Minneapolis, MN 55455, USA 2 Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA Full list of author information is available at the end of the article
As of Novemeber 2020, over 225,000 SARS-CoV-2 genome sequences have been deposited in public repositories such as NCBI and GISAID [5, 6]. Several large-scale consortia in the UK (COG-UK: COVID-19 Genomics UK), Canada (CanCOGeN: Canadian COVID Genomics Network), and the United States (CDC SPHERES: SARS-CoV2 Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance) have begun coordinated efforts to sequence large numbers of SARS-CoV-2 genomes. Such genomic surveillance has already enabled insights into th
Data Loading...
