Abstract
BackgroundThe 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.ResultsHere 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.ConclusionsThe tailed amplicon method we describe represents a cost-effective and highly scalable method for SARS-CoV-2 sequencing.
Highlights
The global COVID-19 pandemic has led to an urgent need for scalable methods for clinical diagnostics and viral tracking
By reoptimizing the pooling strategy for the tailed primers, we demonstrate that this tailed amplicon approach can achieve similar coverage to the untailed ARTIC v3 primers at equivalent sequencing depths
The approach we describe is similar to a tailed-amplicon method that we have used to process more than 150,000 microbiome samples in recent years in the University of Minnesota Genomics Center [14], and represents a highly scalable method for sequencing large numbers of SARS-CoV-2 genomes in a rapid and cost-effective manner
Summary
The global COVID-19 pandemic has led to an urgent need for scalable methods for clinical diagnostics and viral tracking. 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 the origin and spread of SARS-CoV-2 [7, 8], including the sequencing efforts by the Seattle flu study which provided early evidence of extensive undetected community transmission of SARS-CoV-2 in the Seattle area [9]
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