Journal Article

A rapid, cost-effective tailed amplicon method for sequencing SARS-CoV-2

Watson, Ray H. B., Grady, Patrick, Beckman, Kenneth B., Garbe, John, Nelson, Andrew, Daniel, Jerry, Auch, Benjamin, Yohe, Sophia, Gohl, Daryl M.

2020

Overview

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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Animal Genetics and Genomics / Benchmarking / Binding sites / Biomedical and Life Sciences / Coronaviruses / COVID-19 / COVID-19 - diagnosis / COVID-19 - epidemiology / COVID-19 - virology / COVID-19 Nucleic Acid Testing - methods / COVID-19 Nucleic Acid Testing - standards / Deoxyribonucleic acid / Disease transmission / DNA / DNA sequencing / Ebola virus / Eukaryote microbial genomics / Gene amplification / Genome sequencing / Genome, Viral - genetics / Genomes / Genomics / Health aspects / Humans / Life Sciences / Metagenomics / Methodology / Methodology Article / Methods / Microarrays / Microbial Genetics and Genomics / Molecular Epidemiology / Mutation / Next-generation sequencing / Nucleotide sequence / Nucleotide sequencing / Pandemics / Plant Genetics and Genomics / Proteomics / Public health / RNA, Viral - genetics / SARS-CoV-2 / SARS-CoV-2 - genetics / SARS-CoV-2 - isolation & purification / Sequence Analysis - methods / Sequence Analysis - standards / Severe acute respiratory syndrome coronavirus 2 / Viral diseases / Viral surveillance / Whole genome sequencing / Zika virus