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A rapid, cost-effective tailed amplicon method for sequencing SARS-CoV-2.
BMC Genomics. 2020 Dec 04; 21(1):863.BG

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.

Authors+Show Affiliations

University of Minnesota Genomics Center, Minneapolis, MN, 55455, USA. dmgohl@umn.edu. Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, 55455, USA. dmgohl@umn.edu.University of Minnesota Genomics Center, Minneapolis, MN, 55455, USA.University of Minnesota Genomics Center, Minneapolis, MN, 55455, USA.University of Minnesota Genomics Center, Minneapolis, MN, 55455, USA.University of Minnesota Genomics Center, Minneapolis, MN, 55455, USA.University of Minnesota Genomics Center, Minneapolis, MN, 55455, USA.Department of Lab Medicine and Pathology, Division of Molecular Pathology and Genomics, University of Minnesota, Minneapolis, MN, 55455, USA.Department of Lab Medicine and Pathology, Division of Molecular Pathology and Genomics, University of Minnesota, Minneapolis, MN, 55455, USA.University of Minnesota Genomics Center, Minneapolis, MN, 55455, USA.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

33276717

Citation

Gohl, Daryl M., et al. "A Rapid, Cost-effective Tailed Amplicon Method for Sequencing SARS-CoV-2." BMC Genomics, vol. 21, no. 1, 2020, p. 863.
Gohl DM, Garbe J, Grady P, et al. A rapid, cost-effective tailed amplicon method for sequencing SARS-CoV-2. BMC Genomics. 2020;21(1):863.
Gohl, D. M., Garbe, J., Grady, P., Daniel, J., Watson, R. H. B., Auch, B., Nelson, A., Yohe, S., & Beckman, K. B. (2020). A rapid, cost-effective tailed amplicon method for sequencing SARS-CoV-2. BMC Genomics, 21(1), 863. https://doi.org/10.1186/s12864-020-07283-6
Gohl DM, et al. A Rapid, Cost-effective Tailed Amplicon Method for Sequencing SARS-CoV-2. BMC Genomics. 2020 Dec 4;21(1):863. PubMed PMID: 33276717.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A rapid, cost-effective tailed amplicon method for sequencing SARS-CoV-2. AU - Gohl,Daryl M, AU - Garbe,John, AU - Grady,Patrick, AU - Daniel,Jerry, AU - Watson,Ray H B, AU - Auch,Benjamin, AU - Nelson,Andrew, AU - Yohe,Sophia, AU - Beckman,Kenneth B, Y1 - 2020/12/04/ PY - 2020/05/15/received PY - 2020/11/25/accepted PY - 2020/12/5/entrez PY - 2020/12/6/pubmed PY - 2020/12/23/medline KW - COVID-19 KW - Genome sequencing KW - SARS-CoV-2 KW - Viral surveillance SP - 863 EP - 863 JF - BMC genomics JO - BMC Genomics VL - 21 IS - 1 N2 - 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. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/33276717/A_rapid_cost_effective_tailed_amplicon_method_for_sequencing_SARS_CoV_2_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-07283-6 DB - PRIME DP - Unbound Medicine ER -