Wastewater Surveillance using Digital PCR | Thermo Fisher Scientific

dPCR enables quantitative detection of environmental DNA and RNA

Environmental surveillance and wastewater-based epidemiology are used to monitor public health threats by testing for specific environmental DNA (eDNA) and RNA (eRNA). Because such targets are often found at low concentration, detection requries sensitive analytical tools. The QuantStudio Absolute Q Digital PCR System enables absolute quantification of low-level targets while helping overcome common challenges with environmental samples:

	High tolerance to PCR inhibitors—reaction partitioning improves resistance to PCR inhibitors that can accumulate during concentration of dilute environmental samples
	Minimal sample waste—with our microfluidic array plate dPCR technology, less than 5% of input becomes dead volume, helping ensure low-level target data is captured, not lost
	Fast results—a simple workflow, minimal hands-on time, and fast time to answer enables rapid responses to questions of public health

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SARS-CoV-2 wastewater surveillance and tracking using digital PCR

Because individuals infected with SARS-CoV-2 shed detectable viral RNA, wastewater surveillance is an effective tool to identify and track SARS-CoV-2 outbreaks. Tracking SARS-CoV-2 in community wastewater enables early detection to help track spread, capture emerging mutations, and rapidly inform public health policies

Learn how other researchers have used the QuantStudio Absolute Q Digital PCR System in their SARs-COV-2 wastewater surveillance efforts:

Webinar: National Wastewater Surveillance System based on COVID-19 in a digital PCR application

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Webinar: Applications of multiplex digital PCR: Monitoring wastewater for SARS-CoV-2 and measuring bacterial gene expression

Dr. Joan L. Slonczewski of Kenyon College describes using the QuantStudio Absolute Q dPCR System and SARS-CoV-2 Wastewater Surveillance kit to monitor and measure SARS-CoV-2 RNA in community wastewater.

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Podcast: Tales of a pandemic PhD (Episode 1)

Dr. Sarah Philo of the University of Notre Dame Wastewater Surveillance for SARS-CoV-2 and Emerging Public Health Threats Research Coordination Network talks about using both qPCR and dPCR to detect and quantify SARS-CoV-2 and antimicrobial resistance genes in wastewater..

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Other applications of dPCR in environmental surveillance and testing

With proven utility for SARS-CoV-2 wastewater surveillance, researchers are expanding the applications of digital PCR in environmental and wastewater testing.

Geomicrobiologist Dr. Brandi Kiel Reese studies microbes in extreme environments, including those buried within the sediment under the sea floor. In this video, see how digital PCR enables Dr. Reese to accurately and precisely study rare samples with low biomass, detecting genes down to a single copy, and learn how other researchers have used the QuantStudio Absolute Q Digital PCR System for environmental surveillance.

Webinar: Environmental testing using the QuantStudio Absolute Q dPCR System

Join Dr. Karolina Setyowati as she will introduce the utility of digital PCR with robust multiplexing capabilities for researching pathogens present in environmental samples. She will also showcase how the QuantStudio Absolute Q dPCR system can efficiently detect multiple pathogens such as poliovirus, monkeypox (mpox), influenza A (FluA), influenza B (FluB), respiratory syncytial virus (RSV) and SARS-CoV-2 as well as enteric bacteria strains.

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Webinar: Beyond SARS-CoV-2, application of Absolute Q digital PCR system for waterborne pathogens

Dr. Huiyun Wu of the Tulane University School of Public Health and Tropical Medicine talks about using digital PCR to detect waterborne pathogens from the U.S. Environmental Protection Agency's (EPA) Contaminant Candidate List (CCL4) in environmental samples.

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Podcast: Avoiding the itch with digital PCR (Episode 3)

Dr. Patrick Hanington of the School of Public Health at the University of Alberta discusses how dPCR is advancing his team’s work in monitoring public and recreational waters for parasites, including schistosomes, which cause swimmer’s itch.

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Explore digital PCR assays

Representative data

dPCR inhibitor tolerance. dPCR results remain consistent across all bile levels (0.1–2 mg/mL), showing no impact from inhibitors. Figures B and D: qPCR results are compromised, with higher Cqs at the lowest bile concentration (0.1 mg/mL) and no quantification at 1 mg/mL and above.

Digital PCR for improved inhibitor tolerance

The QuantStudio Absolute Q dPCR System demonstrates exceptional tolerance to PCR inhibitors compared to qPCR. In this study, purified samples were spiked with varying concentrations of bile, a common inhibitor in wastewater.

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Easy implementation of a predesigned TaqMan Assay on dPCR. TaqMan catalog assay Vi07922890_po was tested with synthetic targets representing one of the three poliovirus serotypes or a No Template Control (NTC) on the QuantStudio Absolute Q dPCR System using the Absolute Q 1-step RT-dPCR Master Mix. Blue dots represent chambers called positive for amplification, and gray dots represent chambers called negative for amplification based on the threshold cutoff value indicated by the horizontal black line.

Viral pathogen quantification

Monitoring wastewater for viral pathogens is crucial for public health, providing early warning signs of potential outbreaks and helping allow for timely interventions.

Poliovirus remains an important target for wastewater surveillance, especially in regions where it has not been eradicated or where the oral polio vaccine is still in use. Adapting existing assays to dPCR can help with surveillance of important pathogens with high sensitivity and precision.

Enteric bacteria detection by dPCR. Targets include Shiga-toxin producing Escherichia coli (STEC), Campylobacter jejuni, Campylobacter coli, Campylobacter upsaliensis, Salmonella spp., and Shigella spp./enteroinvasive Escherichia coli (EIEC). The TrueMark panel successfully detected all four targets on the QuantStudio Absolute Q dPCR System across various sample concentrations using the Universal DNA Digital PCR Master Mix.

Enteric pathogen detection using multiplex assays for enteric bacteria detection

Expand your wastewater surveillance with by multiplex assays for enteric bacteria detection by dPCR. Here the TrueMark Enteric Bacterial Select Panel I was used to detect key bacterial pathogens at varying concentrations.

Digital PCR assays and kits for wastewater and environmental surveillance

TaqMan Assays for digital PCR

Our TaqMan probe-based technology is now making digital PCR (dPCR) simple with ready-to-use assays supporting a broad range of pathogen targets. Explore this extensive portfolio of pre-designed assays by using the search bar below.

Absolute Q SARS-CoV-2 Wastewater Surveillance Kit

The Applied Biosystems Absolute Q SARS-CoV-2 Wastewater Surveillance Kit contains a triplex dPCR assay designed for simultaneous high-resolution detection and quantification of the SARS-CoV-2 N1 and N2 gene regions alongside pepper mild mottle virus, a common human fecal normalization target.

Simple workflow—includes pre-mixed assays and Absolute Q 1-step RT-dPCR Master Mix for easy setup
Fast results—absolute quantification of targets in less than two hours, including reaction preparation and data collection
Multiplexing flexibility—the triplex assay leaves a fourth red dye channel free to enable multiplexing with a custom assay
Dependability—analyze your data with confidence using verified assays backed by a performance guarantee*

Bar graph depicting concentration of SARS-CoV-2 RNA in wastewater

Figure 1. Accurate target detection from wastewater samples. Wastewater samples spiked with varying levels of SARS-CoV-2 were extracted using the MagMAX Wastewater Ultra Nucleic Acid Isolation Kit with Virus Enrichment on the KingFisher Flex system and tested using the Absolute Q dPCR SARS-CoV-2 Wastewater Surveillance Kit. The concentration of each region of the SARS-CoV-2 N gene is expressed relative to the concentration of PMMoV in the same sample (per million copies). Concentrations shown are means of four technical replicates.