Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner.
Viruses
; 13(8)2021 08 19.
Article
in English
| MEDLINE | ID: covidwho-1367919
Preprint
This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
See preprint
This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
See preprint
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.
Keywords
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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