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Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner.
Gregory, Devon A; Wieberg, Chris G; Wenzel, Jeff; Lin, Chung-Ho; Johnson, Marc C.
  • Gregory DA; Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65201, USA.
  • Wieberg CG; Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO 65102, USA.
  • Wenzel J; Bureau of Environmental Epidemiology, Missouri Department of Health and Senior Services, Division of Community and Public Health, Jefferson City, MO 65102, USA.
  • Lin CH; Center for Agroforestry, School of Natural Resources, University of Missouri, Columbia, MO 65201, USA.
  • Johnson MC; Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65201, USA.
Viruses ; 13(8)2021 08 19.
Article in English | MEDLINE | ID: covidwho-1367919
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ABSTRACT
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Software / Sequence Analysis, RNA / High-Throughput Nucleotide Sequencing / Wastewater / Wastewater-Based Epidemiological Monitoring / SARS-CoV-2 Type of study: Observational study Topics: Variants Country/Region as subject: North America Language: English Year: 2021 Document Type: Article Affiliation country: V13081647

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Software / Sequence Analysis, RNA / High-Throughput Nucleotide Sequencing / Wastewater / Wastewater-Based Epidemiological Monitoring / SARS-CoV-2 Type of study: Observational study Topics: Variants Country/Region as subject: North America Language: English Year: 2021 Document Type: Article Affiliation country: V13081647