ArticleThe Science of the total environment2022
Direct comparison of RT-ddPCR and targeted amplicon sequencing for SARS-CoV-2 mutation monitoring in wastewater.
Article in The Science of the total environment, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 57 citations in OpenAlex.
- SARS-CoV-2 wastewater genomic surveillance: approaches, challenges, and opportunities.Genome biology · 2026Review
- A 1-year study on SARS-CoV-2 variant shifts in wastewater using dPCR: comparison with clinical and GISAID data.mSystems · 2025Article
- Article
- Diagnostic performance of allele-specific RT-qPCR and genomic sequencing in wastewater-based surveillance of SARS-CoV-2.Eco-Environment & Health · 2025Article
- RBD Amplicon Sequencing and Evolutionary Analysis of SARS-CoV-2 Variants from Wastewater Samples.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Revealing patterns of SARS-CoV-2 variant emergence and evolution using RBD amplicon sequencing of wastewater.The Journal of infection · 2024Article
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens.Nature communications · 2024Article
- Viruses in Wastewater-A Concern for Public Health and the Environment.Microorganisms · 2024Review
- RBD amplicon sequencing of wastewater reveals patterns of variant emergence and evolution.medRxiv : the preprint server for health sciences · 2024Article
- A scoping review of global SARS-CoV-2 wastewater-based epidemiology in light of COVID-19 pandemic.Heliyon · 2024Article
- Amplidiff: an optimized amplicon sequencing approach to estimating lineage abundances in viral metagenomes.BMC bioinformatics · 2024Article
- Comparison of Nanopore and Synthesis-Based Next-Generation Sequencing Platforms for SARS-CoV-2 Variant Monitoring in Wastewater.International journal of molecular sciences · 2023Article
- SARS-CoV-2 genomic surveillance in wastewater as a model for monitoring evolution of endemic viruses.Nature communications · 2023Article
- An improved method for determining frequency of multiple variants of SARS-CoV-2 in wastewater using qPCR assays.The Science of the total environment · 2023Article
- Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater.Nature communications · 2023Article
- Robust Performance of SARS-CoV-2 Whole-Genome Sequencing from Wastewater with a Nonselective Virus Concentration Method.ACS ES&T water · 2023Article
- Parallel deployment of passive and composite samplers for surveillance and variant profiling of SARS-CoV-2 in sewage.The Science of the total environment · 2023Article
- Wastewater surveillance of SARS-CoV-2 and influenza in preK-12 schools shows school, community, and citywide infections.Water research · 2023Article
- Rapid Assessment of SARS-CoV-2 Variant-Associated Mutations in Wastewater Using Real-Time RT-PCR.Microbiology spectrum · 2023Article
- From Alpha to Omicron BA.2: New digital RT-PCR approach and challenges for SARS-CoV-2 VOC monitoring and normalization of variant dynamics in wastewater.The Science of the total environment · 2022Article
Corrections and comments
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Authors and funding
16 authors at 2 institutions in 1 country.
Funding
Abstract
Over the course of the COVID-19 pandemic, variants of SARS-CoV-2 have emerged that are more contagious and more likely to cause breakthrough infections. Targeted amplicon sequencing approach is a gold standard for identification and analysis of variants. However, when applied to environmental samples such as wastewater, it remains unclear how sensitive this method is for detecting variant-associated mutations in environmental samples. Here we directly compare a targeted amplicon sequencing approach (using ARTIC v3; hereafter referred to as sequencing) with RT-ddPCR quantification for the detection of five mutations that are characteristic of variants of concern (VoCs) in wastewater samples. In total, 547 wastewater samples were analyzed using both methods in parallel. When we observed positive mutation detections by RT-ddPCR, 42.6% of the detection events were missed by sequencing, due to negative detection or the limited read coverage at the mutation position. Further, when sequencing reported negative or depth-limited mutation detections, 26.7% of those events were instead positive detections by RT-ddPCR, highlighting the relatively poor sensitivity of sequencing. No or weak associations were observed between quantitative measurements of target mutations determined by RT-ddPCR and sequencing. These findings caution the use of quantitative measurements of SARS-CoV-2 variants in wastewater samples determined solely based on sequencing.
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