Journal
VIRUSES-BASEL
Volume 13, Issue 8, Pages -Publisher
MDPI
DOI: 10.3390/v13081647
Keywords
coronavirus; wastewater; metagenomics; molecular epidemiology
Categories
Funding
- Missouri Department of Health and Senior Services (DHSS)
- Centers for Disease control
- National Institute on Drug Abuse of the National Institutes of Health [U01DA053893-01]
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Sequencing SARS-CoV-2 from wastewater is an effective tool for monitoring viral variants, and a novel computational workflow was developed to track viral populations in a Missouri sewershed, identifying two variants of concern.
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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