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A rapid, cost-effective tailed amplicon method for sequencing SARS-CoV-2.
Daryl M Gohl1,2, John Garbe3, Patrick Grady3
1University of Minnesota Genomics Center, Minneapolis, MN, 55455, USA. dmgohl@umn.edu.
BMC Genomics
|December 5, 2020
Summary
A new, low-cost tailed amplicon method offers a scalable solution for sequencing SARS-CoV-2 (the virus that causes COVID-19), improving viral tracking and diagnostics.
Area of Science:
- Genomics
- Virology
- Molecular Biology
Background:
- The COVID-19 pandemic necessitates scalable diagnostic and viral tracking methods.
- Next-generation sequencing (NGS) enables large-scale genomic surveillance of SARS-CoV-2.
- Current SARS-CoV-2 sequencing methods face limitations due to costly library preparation.
Purpose of the Study:
- To introduce a cost-effective and streamlined method for SARS-CoV-2 sequencing.
- To bypass expensive and time-consuming library preparation steps.
- To provide a scalable solution for viral genomic surveillance.
Main Methods:
- Development of a low-cost, all amplicon-based sequencing method.
- Benchmarking the tailed amplicon method against ARTIC amplicon protocol and sequence capture.
- Optimization of the tailed amplicon approach for SARS-CoV-2 sequencing.
Main Results:
- The optimized tailed amplicon method achieves comparable amplicon balance to ARTIC v3.
- Equivalent coverage metrics were observed between the tailed amplicon and ARTIC v3 methods.
- The tailed amplicon approach demonstrated comparable variant calls to established methods.
Conclusions:
- The described tailed amplicon method is a cost-effective solution for SARS-CoV-2 sequencing.
- This method offers a highly scalable approach for viral sequencing.
- The method supports efficient clinical diagnostics and viral tracking.
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