ArticleViruses2021
Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner.
Article in Viruses, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- SARS-CoV-2 wastewater genomic surveillance: approaches, challenges, and opportunities.Genome biology · 2026Review
- Unsupervised detection and fitness estimation of emerging SARS-CoV-2 variants: Application to wastewater samples (ANRS0160).PLoS computational biology · 2025Article
- A highly divergent cryptic SARS-CoV-2 lineage exhibits strong receptor binding and immune evasion.medRxiv : the preprint server for health sciences · 2025Article
- Early detection of emerging SARS-CoV-2 Variants from wastewater through genome sequencing and machine learning.Nature communications · 2025Article
- Detecting SARS-CoV-2 cryptic lineages using publicly available whole genome wastewater sequencing data.PLoS pathogens · 2025Article
- Environmental Dissemination of SARS-CoV-2: An Analysis Employing Crassphage and Next-Generation Sequencing Protocols.Food and environmental virology · 2025Article
- Revealing patterns of SARS-CoV-2 variant emergence and evolution using RBD amplicon sequencing of wastewater.The Journal of infection · 2024Article
- SWAMPy: simulating SARS-CoV-2 wastewater amplicon metagenomes.Bioinformatics (Oxford, England) · 2024Article
- Highly sensitive wastewater surveillance of SARS-CoV-2 variants by targeted next-generation amplicon sequencing provides early warning of incursion in Victoria, Australia.Applied and environmental microbiology · 2024Article
- RBD amplicon sequencing of wastewater reveals patterns of variant emergence and evolution.medRxiv : the preprint server for health sciences · 2024Article
- Environmental Surveillance of Flood Control Infrastructure Impacted by Unsheltered Individuals Leads to the Detection of SARS-CoV-2 and Novel Mutations in the Spike Gene.Environmental science & technology letters · 2024Article
- Tracing the origin of SARS-CoV-2 omicron-like spike sequences detected in an urban sewershed: a targeted, longitudinal surveillance study of a cryptic wastewater lineage.The Lancet. Microbe · 2024Article
- Omicron and Delta variant prevalence detection and identification during the fourth COVID-19 wave in Mexico using wastewater-based epidemiology.IJID regions · 2024Article
- Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data.GigaScience · 2024Article
- An interpretative review of the wastewater-based surveillance of the SARS-CoV-2: where do we stand on its presence and concern?Frontiers in microbiology · 2024Review
- Quantitatively assessing early detection strategies for mitigating COVID-19 and future pandemics.Nature communications · 2023Article
- Continued selection on cryptic SARS-CoV-2 observed in Missouri wastewater.PLoS pathogens · 2023Article
- Quantitatively assessing early detection strategies for mitigating COVID-19 and future pandemics.medRxiv : the preprint server for health sciences · 2023Article
- Wastewater surveillance uncovers regional diversity and dynamics of SARS-CoV-2 variants across nine states in the USA.The Science of the total environment · 2023Article
- Wastewater surveillance of SARS-CoV-2 genomic populations on a country-wide scale through targeted sequencing.PloS one · 2023Article
Corrections and comments
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Authors and funding
5 authors.
Funding
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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Registered trials
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