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Article

Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner

1
Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65201, USA
2
Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO 65102, USA
3
Bureau of Environmental Epidemiology, Missouri Department of Health and Senior Services, Division of Community and Public Health, Jefferson City, MO 65102, USA
4
Center for Agroforestry, School of Natural Resources, University of Missouri, Columbia, MO 65201, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Oliver Schildgen
Viruses 2021, 13(8), 1647; https://doi.org/10.3390/v13081647
Received: 23 June 2021 / Revised: 11 August 2021 / Accepted: 17 August 2021 / Published: 19 August 2021
(This article belongs to the Section SARS-CoV-2 and COVID-19)
Sequencing Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from wastewater has become a useful tool in monitoring the spread of viral variants. Approaches to this task have been varied, relying on differing sequencing methods and computational analyses. We used a novel computation workflow based on amplicon sequencing of SARS-CoV-2 spike domains in order to track viral populations in wastewater. As part of this workflow, we developed a program, SAM Refiner, that has a variety of outputs, including novel variant reporting as well as functions designed to remove polymerase chain reaction (PCR) generated chimeric sequences. With these methods, we were able to track viral population dynamics over time. We report here on the emergence of two variants of concern, B.1.1.7 (Alpha) and P.1 (Gamma), and their displacement of the D614G B.1 variant in a Missouri sewershed. View Full-Text
Keywords: coronavirus; wastewater; metagenomics; molecular epidemiology coronavirus; wastewater; metagenomics; molecular epidemiology
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MDPI and ACS Style

Gregory, D.A.; Wieberg, C.G.; Wenzel, J.; Lin, C.-H.; Johnson, M.C. Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner. Viruses 2021, 13, 1647. https://doi.org/10.3390/v13081647

AMA Style

Gregory DA, Wieberg CG, Wenzel J, Lin C-H, Johnson MC. Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner. Viruses. 2021; 13(8):1647. https://doi.org/10.3390/v13081647

Chicago/Turabian Style

Gregory, Devon A., Chris G. Wieberg, Jeff Wenzel, Chung-Ho Lin, and Marc C. Johnson. 2021. "Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner" Viruses 13, no. 8: 1647. https://doi.org/10.3390/v13081647

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