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.

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.

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.

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.

Streamline your workflow
Need help with SARS-CoV-2 viral RNA detection in wastewater?
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."

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.”
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.”
In the news

*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 Contact your country representative for product availability details outside the United States and Canada. GT Molecular is The Molecular App Company™.