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As COVID-19 infection rates continue to rise, the need for fast, sensitive, reliable tests to monitor cases and reduce the spread of COVID-19 has also become increasingly important. Even as vaccines roll out across the globe, new COVID-19-related challenges continue to arise. In particular, scientists and public health officials have raised the alarm about novel variants of the SARS-CoV-2 coronavirus that have emerged in the UK (B.1.1.7), South Africa (B.1.351), Brazil (P.1), California (B.1.429) and New York (B.1.526). Each variant is characterized by a set of specific, known mutations in its genomic sequence, some of which can increase transmissibility, virulence, or the viruses’ ability to evade immune responses. To fully understand these changes and respond accordingly, researchers need to reliably identify where the variants are, when they appear, and how prevalent they become over time.
Wastewater Surveillance with Droplet Digital PCR
Since symptomatic and asymptomatic SARS-CoV-2 infected individuals shed viral RNA in sewer systems, analysis of SARS-CoV-2 in sewage networks provides information about COVID-19 infection within the community. Wastewater based epidemiology (WBE) for detecting SARS-CoV-2 has been carried out in a range of countries, and a good 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). Wastewater based epidemiology 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 needing to perform extensive sequencing.
Wastewater surveillance using Droplet Digital PCR (ddPCR) is a comprehensive, cost-effective, highly sensitive way to detect specific variants of the SARS-CoV-2 coronavirus in communities, allowing scientists and public health officials to monitor spread and take action. Droplet Digital PCR takes wastewater testing to the next level with the sensitivity and precision needed to reliably detect the presence of specific variants in wastewater samples, even at extremely low concentrations. Using ddPCR for WBE enables scientists to detect virus 6 days before clinical testing at a sensitivity of 1 infected individual in 10,000, which is extremely important because only 32% of infected individuals seek medical attention. When identifying SARS-CoV-2 variants, ddPCR can accurately discriminate and quantify multiple variants in a sample using a single-well test. Importantly, multiplexing using ddPCR is less prone to artifacts and has simpler data analysis compared to multiplexing using other technologies; therefore, ddPCR can give an accurate measure of the copy number of both wild-type and variant genomes.
of individuals infected
seek medical attention1
before clinical testing
infected individual in 10,0005
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 wastewater surveillance to identify municipality outbreaks before they occur.
Wastewater testing can also be employed by the transport industry to monitor SARS-CoV-2 transmission among aircraft and cruise liner passengers. Another study used ddPCR to analyze wastewater from large transport vessels with their own sanitation systems with implications for contact tracing of disembarking passengers if SARS-CoV-2 is detected in wastewater. SARS-CoV-2 RNA was detected in aircraft and cruise ship wastewater, concluding that wastewater testing has the potential to aid clinical testing and contact tracing for disembarking passengers (Ahmed et el. 2020).
As colleges and universities transition from remote learning to in-person education, administrators must face tough decisions on how to support a safe learning environment. Campus WBE is a crucial component of a comprehensive COVID-19 prevention plan. Academic laboratories are beginning to leverage wastewater testing to prevent campus COVID-19 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.
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
|Number of Color Channels||
Benefits of Droplet Digital PCR for SARS-CoV-2 Molecular Testing
Directly count DNA molecules and eliminate standard curves
End-point PCR uncouples quantification from amplification efficiency
Partitioning allows for enrichment of rare targets
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.
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.
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.
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.