COVID-19

Wastewater testing for SARS-CoV-2

Wastewater testing is making waves

There's growing evidence that successful detection of SARS-CoV-2 RNA in wastewater or natural sewage is a powerful surveillance tool to prevent a surge in COVID-19 infections, and specifically of new variants that are gaining ground in certain communities. Applying wastewater-based epidemiology could afford reduced pressure on the public health system to manageable levels and help make informed decisions for better and timely treatments or vaccines.

Testing sewage to halt a pandemic
Testing sewage to halt a pandemic
Despite the availability of vaccines, scientists continue to seek answers in the sewage to help public health agencies survey COVID-19 circulation on a mass – and affordable – scale. Read about one lab’s journey in CSIRO Land & Water, Australia, dating back to the early months of the pandemic in March 2020.
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Predicting future outbreaks
Predicting future outbreaks
COVID-19 forced innovation and improvisation in disease detection and surveillance. One of the most promising tools to emerge from the pandemic is wastewater-based epidemiology (WBE). And public health experts are excited about its potential to detect a range of pathogen-related infections in the future.
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Flushing out SARS-CoV-2 variants from wastewater using NGS
Flushing out SARS-CoV-2 variants from wastewater using NGS
Dr. Davida Smyth discusses how whole genome NGS helped her detect circulating SARS-CoV-2 variants and even reveal new mutations from wastewater samples.
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Wastewater monitoring – simply explained
Wastewater monitoring – simply explained
QIAGEN supports wastewater testing efforts with research tools spanning nucleic acid extraction, amplification and detection, overcoming some of the common challenges with the analytical protocols along the workflow. We thought of explaining them in a simple way!
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Wastewater surveillance webinars: SARS-CoV-2 and beyond
Wastewater surveillance webinars: SARS-CoV-2 and beyond
Together with the experts, we have delved a little deeper each time into the challenges, solutions and outlooks related to wastewater-based epidemiology through a series of webinars.
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Congratulations to the APHL 2022 best poster winner

Dr. Jyotisna Saxena at the Ohio Department of Health Laboratory focuses on the detection of SARS-CoV-2 in wastewater samples using QIAGEN methods for RNA extraction and dPCR.

Nothing goes to waste

While wastewater surveillance does not replace individual patient testing, it provides a community-level understanding of the prevalence of the disease and the increasing or declining level of the virus. The tool is intended to be used in municipal wastewater treatment plants or facilities such as nursing homes, student dormitories, quarantine facilities, prisons, and flights and cruise ships, wherever feces are flushed into wastewater systems.

Early warning sign
Early warning sign
Detect the virus several days before people show clinical symptoms or are infected but asymptomatic.
More cost-effective and less invasive
More cost-effective and less invasive
Verify the reliability of epidemiological trends calculated from diagnosed cases by sampling wastewater daily without having to individually test patients.
Complement clinical surveillance in low-resource settings
Complement clinical surveillance in low-resource settings
Collect data from people who lack access and awareness to healthcare, where testing and clinical surveillance capacities may be stretched.
Proactive prevention
Proactive prevention
Guide early mitigation strategies and reinforce public health measures to minimize transmission and increase clinical testing.

An evolving science

The advantages of monitoring coronaviruses in wastewater have convinced experts to call for comprehensive testing programs, but the testing methods differ widely, and there’s no consensus on best practices. One of the major challenges is the lack of an optimized and standardized sample processing workflow from sample collection to RNA detection. The efficiency of viral concentration methods, sampling variability, viral genome stability and the sensitivity of the detection assay are some of the factors to consider while designing a testing strategy. Due to the highly heterogeneous nature and presence of inhibitors, one must tailor methods selected at each step for use with wastewater and validate performance using appropriate controls.

Infographic showing wastewater testing flow
Workflow detecting SARS-CoV-2 RNA in wastewater

Recommended workflow solutions for reliable data

QIAGEN supports wastewater testing efforts with research tools spanning nucleic acid extraction, amplification and detection, overcoming some of the common challenges with the analytical protocols along the workflow.

Viral RNA extraction

Wastewater samples are inhibitory. The choice of viral RNA extraction kit is sample-dependent.

The following kits can be automated on the QIAcube instruments based on your speed and throughput requirements.

Viral RNA quantification

Accurate testing requires quantification methods specifically designed for wastewater samples. The QIAcuity OneStep Advanced Probe Kit has been developed and can be used in conjunction with the QIAcuity Digital PCR System and QIAcuity Nanoplates. The GT-Digital SARS-CoV-2 Wastewater Surveillance Assay For QIAcuity* comprises a molecular reagent kit containing all primers, probes and controls for wastewater surveillance of SARS-CoV-2 in compliance with the CDC Wastewater Surveillance Testing Method guidance for reporting to the National Wastewater Surveillance System (NWSS). Digital PCR can measure low concentrations of SARS-CoV-2 RNA present in wastewater with good precision and shows a good correlation with qPCR results. Moreover, digital PCR can accurately distinguish and quantify the variants resulting from the mutating virus in a sample and also provide an accurate measure of the copy number of both wild-type and variant genomes.

QIAamp Viral RNA Mini Kit
diagnostics and clinical research sample processing
QIAamp Viral RNA Mini Kit
For isolation of viral RNA from cell-free body fluids
QIAcube Connect
dna rna purification instruments equipment
QIAcube Connect
For fully automated, spin-column-based nucleic acid extraction that you can manage from outside the lab using QIAsphere
QIAcube HT
instruments and automation nucleic acid purification
QIAcube HT
Instrument for automated mid- to high-throughput nucleic acid purification in 96-well format
Streamline your workflow
Need help with SARS-CoV-2 viral RNA detection in wastewater?
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Dr. Franz Durandet, President of I.A.G.E. in Montpellier, France

"In a trial run with the new, high-throughput QIAcuity Eight, we were able to detect new variants of SARS-CoV-2 in wastewater samples successfully. Our tests have proven that this fast and scalable technology from QIAGEN can provide a valuable addition to our environmental, biological testing services, which we will offer to our clients in the near future."

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Professor Brent A. French, University of Virginia
“Wastewater surveillance is a powerful tool for controlling the spread of pandemics such as COVID-19, and may prove useful for detecting pockets of resurgence as the pandemic subsides. However, such applications require exquisitely sensitive methods capable of detecting trace levels of viral genomes, and digital PCR shows promise for the timely and sensitive detection of SARS-CoV-2 genomes in community wastewater.”
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Dr. Warish Ahmed, Senior Research Scientist, CSIRO Land & Water
“If you monitor wastewater, you can potentially screen 10,000 people, 100,000 people, by analyzing one sample. As vaccines reduce the number of COVID-19 infections, it will become harder to detect in the wastewater, as the viral concentration will be very low. We believe digital PCR is going to increase the sensitivity at least five- to ten-fold.”
Microbiome sample preparation
Microbiome sample preparation
Find dedicated solutions that address the specific demands of complex matrices and their analysis workflows
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Real-time PCR
Real-time PCR
Exploit the gold standard in routine quantification because of its high sensitivity, accessibility and cost-effectiveness
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Digital PCR
Digital PCR
Go beyond the limits of real-time PCR for improved limit of detection, accuracy and direct absolute quantification
Discover digital
Next-generation sequencing
Next-generation sequencing

Benefit from high-throughput NGS solutions for reliable detection of emerging variants and associated mutations

See how
What is wastewater and why is wastewater-based epidemiology gaining importance?
Wastewater includes all the water from toilets carrying human waste, showers and baths, basins and sinks, and laundries. Their sources include businesses, hospitals, nursing homes, prisons, schools and universities, military bases, and transport vessels such as aircraft and cruise ships. Wastewater-based epidemiology (WBE) has previously been used to track infectious diseases like polio, hepatitis A and norovirus. The shed viruses are detectable in wastewater samples days before symptoms appear. Researchers can test these samples for specific viral genetic signatures without performing extensive sequencing, allowing clinicians and public health officials to monitor spread and take timely action to prevent outbreaks. It is also a simple, cost-effective strategy that can identify COVID-19 cases through non-invasive measures.
How does coronavirus get into wastewater?
The virus is shed in our poo and pee (fecal matter) that is flushed down the toilet or secreted from our hands or skin and passed down the basin or shower. It breaks into ‘viral fragments’ once in the wastewater system. Both asymptomatic or presymptomatic carriers may shed the virus days before they turn symptomatic and show up as positive cases in clinical swab testing.
How is SARS-CoV-2 detected in wastewater?
The sample is collected from a wastewater treatment plant or sewage. The sample containing viruses can be liquid wastewater, primary sludge or attached to water matrices. Depending on the starting volume, samples may require a concentration step. Concentrating wastewater samples can improve the detection of SARS-CoV-2 RNA. The sample then undergoes lysis followed by viral RNA extraction for analysis. Finally, the purified RNA is mixed with reagents and measured for SARS-CoV-2 using an RT-qPCR or RT-dPCR method. Each method can be performed as either a 1-step reaction, in which RT and PCR occur in the same reaction mixture or a 2-step reaction, in which RT and PCR are performed in separate, sequential reactions. Depending on the technique, it includes multiple controls for internal amplification and inhibitor assessment to generate reliable and accurate results.
References
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*The GT-Digital SARS-CoV-2 Wastewater Surveillance Assay For QIAcuity is currently available in the United  States and Canada and can be ordered at www.gtmolecular.com. Contact your country representative for product availability details outside the United States and Canada. GT Molecular is The Molecular App Company™.