SARS-CoV-2 / COVID-19 Wastewater Testing


Fast, sensitive, & reliable tests are critical to monitor the emergence COVID-19 and other diseases of concern to public health. Even when vaccines are available, new variants arise, requiring scientists and public health officials to continuously assess their impact on transmissibility, virulence, response to treatment, and the virus' ability to evade immune response. Identifying variants as soon as they appear is critical to protecting public health and informing public guidelines and policy.

  • Wastewater testing can help detect SARS-CoV-2 viral RNA shed in the stool of symptomatic and asymptomatic infected individuals, providing near real-time surveillance of SARS-CoV-2 viral spread at the community level.

  • In this webinar, a team of scientists from Colorado State University (CSU) describe their experiences building a successful wastewater surveillance system to monitor viral loads in wastewater.

Wastewater Surveillance with Droplet Digital PCR

Wastewater based epidemiology (WBE) has already been successfully used to track infectious diseases like polio, hepatitis A, and norovirus. The shed viruses are detectable in wastewater samples days before symptoms appear, providing information about infection within a community at many levels. WBE for detecting SARS-CoV-2 has recently been carried out in a range of countries, and a strong correlation has been found between the number of COVID-19 cases and SARS-CoV-2 gene concentration in wastewater, forming a basis for the epidemiological role of wastewater testing (Medema et al. 2020).

Droplet Digital PCR (ddPCR) overcomes many challenges associated with WBE and is a comprehensive, cost-effective, and highly sensitive way to detect specific variants of SARS-CoV-2 and other diseases in communities, allowing scientists and public health officials to monitor spread and take action. Using ddPCR for WBE has enabled scientists to detect virus up to 6 days before clinical testing with a sensitivity of 1 infected individual in 10,000. ddPCR can accurately discriminate and quantify multiple variants in a sample using a single-well test. Additionally, multiplexing using ddPCR is less prone to artifacts and has simpler data analysis compared to multiplexing with other technologies. As a result, ddPCR can give an accurate measure of the copy number of both wild-type and variant genomes.

>215 ...and growing
of individuals infected
with SARS-CoV-2
seek medical attention1
Detects virus
6 days4
before clinical testing
Detects 1
infected individual in 10,0005
Saves billions of
when combined
Wastewater surveillance detects SARS-CoV-2
Clinical testing detects SARS-CoV-2
Infected person
Contagious person
Symptomatic person
Clinical testing and results
Infected couple
Infected family
Infected group
Infected community
Wasterwater sampling from a university to track community spread of SARS-CoV-2
Water Sampling
Water sampling
Dorm Sample
Dormatory samples prepared for ddPCR detection of SARS-CoV-2 infections in wastewater
Wasterwater sampling from residential neighborhood to track community spread of SARS-CoV-2
Water Sampling
Water sampling
Community samples prepared for ddPCR detection of SARS-CoV-2 infections in wastewater
Wasterwater treatment facility
ddPCR Analysis
ddPCR instrument to detect community-level SARS-CoV-2 infections in wastewater
ddPCR detects community-level SARS-CoV-2 infections in wastewater
ddPCR plate

A recent study (Gonzalez 2020) used ddPCR to track SARS-CoV-2 viral shedding in weekly wastewater samples from nine wastewater treatment plants over several months. Increased wastewater SARS-CoV-2 RNA levels predicted increases in confirmed case numbers, highlighting the ability of ddPCR to identify local outbreaks before they occur.

In another study using ddPCR, SARS-CoV-2 RNA was detected in aircraft and cruise ship wastewater, illustrating that wastewater testing has the potential to aid clinical testing and contact tracing for disembarking passengers (Ahmed et el. 2020).

With the return to in-person education to college and university campuses, administrators will continue to face tough decisions on how to support a safe learning environment in future outbreaks. Campus WBE has demonstrated value as part of a comprehensive pandemic prevention plan. Academic laboratories can leverage wastewater testing to prevent future campus outbreaks.


Learn how scientists from around the world are monitoring the
community-level spread of SARS-CoV-2 through wastewater testing.


End-to-End Solution for SARS-CoV-2 Molecular Testing

With over 5,000+ peer-reviewed publications and thousands of placements worldwide, Bio-Rad’s Droplet Digital PCR is a proven molecular technology for the detection and quantitation of rare targets in complex backgrounds.

Wastewater Assays

SARS-CoV-2, N1, SARS-CoV-2 N2, and BRSV assays are formatted for wastewater testing and come in singleplex, duplex, or triplex formats. Bio-Rad’s Droplet Digital PCR Assays are designed for optimal ddPCR performance and manufactured to reduce the incidence of false positives.

System Feature Comparison

QX200 Manual System
QX200 Manual System
QX200 AutoDG System
QX200 AutoDG System
QX ONE System
QX ONE System
Hands-on Time
50 min
10 min
0 min
Sample Throughput
Number of Color Channels
Thermal Cycler

Benefits of Droplet Digital PCR for SARS-CoV-2 Molecular Testing

  • Absolute Quantification

    Directly count DNA molecules and eliminate standard curves

  • Inhibitor Tolerant

    End-point PCR uncouples quantification from amplification efficiency

  • High Sensitivity

    Partitioning allows for enrichment of rare targets

The PREvalence ddPCR SARS-CoV-2 Wastewater Quantification Kit, enables SARS-CoV-2 virus detection in wastewater (sewage).

PREvalence ddPCR SARS-CoV-2 Wastewater Quantification Kit

The new PREvalence ddPCR SARS-CoV-2 Wastewater Quantification Kit includes assay, controls, and supermix to detect SARS-CoV-2 virus in wastewater (sewage). The kit contains reagents sufficient for 200 reactions. An automated software tool is also available for analysis.

See ddPCR Kit Details

CDC Wastewater Surveillance Testing Guidance

The CDC has published guidance on wastewater surveillance testing methods and laboratory workflows to detect SARS-CoV-2 across the U.S.A. In the guidance, droplet digital PCR has been recommended as the detection method for RNA measurement of SARS-CoV-2 in wastewater.

A 1-step RT-ddPCR protocol is advantageous for wastewater because RT is performed in individual droplets, which can reduce RT inhibition compared to RT in bulk solution, as in a 2-step process and in RT-qPCR.


Learn More about CDC Wastewater Guidelines

Aaron Bivins, University of Notre Dame and Raul Gonzalez, Hampton Roads Sanitation District

COVID-19 Wastewater-Based Epidemiology Webinar

Methods and Insights for SARS-CoV-2 Community Surveillance

Aaron Bivins, University of Notre Dame
Raul Gonzalez, Hampton Roads Sanitation District

Raul Gonzalez and Aaron Bivins discuss their ongoing wastewater surveillance efforts aimed at tracking community spread of SARS-CoV-2. Bio-Rad’s ddPCR platform plays a crucial role in these efforts by offering ultrasensitive SARS-CoV-2 detection in complex wastewater samples.

Watch the Webinar to Learn More

Contact a Specialist

Questions on COVID-19 Surveillance?

Contact a Specialist

More COVID-19 Surveillance Solutions

COVID-19 surveillance is needed to better inform public health decisions. Obstacles to surveillance work include large sample numbers, supply shortages, and complex sample types. Bio-Rad offers a range of solutions for COVID-19 surveillance.

Learn More about Our COVID-19 Surveillance Solutions »


  1. Silverman JD et al. (2020). Using influenza surveillance networks to estimate state-specific prevalence of SARS-CoV-2 in the United States. Science Translational Medicine, 12(554), eabc1126
  2. Wei WE et al. (2020). Presymptomatic Transmission of SARS-CoV-2 - Singapore, January 23-March 16, 2020. MMWR. Morbidity and Mortality Weekly Report, 69(14), 411–415
  3. Garg S et al. (2020). Hospitalization Rates and Characteristics of Patients Hospitalized with Laboratory-Confirmed Coronavirus Disease 2019 - COVID-NET, 14 States, March 1-30, 2020. MMWR. Morbidity and Mortality Weekly Report, 69(15), 458–464
  4. Medema G et al. (2020). Presence of SARS-Coronavirus-2 RNA in Sewage and Correlation with Reported COVID-19 Prevalence in the Early Stage of the Epidemic in the Netherlands. Environmental Science & Technology Letters, acs.estlett.0c00357
  5. Hart OE & Halden RU. (2020). Computational analysis of SARS-CoV-2/COVID-19 surveillance by wastewater-based epidemiology locally and globally: Feasibility, economy, opportunities and challenges. Science of the Total Environment, 730, 138875