SARS-CoV-2 / COVID-19 Wastewater Variant Surveillance

How Can We Track New SARS-CoV-2 Variants in Real-Time?

Wastewater surveillance using Droplet Digital PCR (ddPCR) technology 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.

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 strains 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). With small but impactful genetic advantages, they rapidly spread to other nations around the world.

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. It turns out, the most practical strategy may involve an unlikely source of information: raw sewage.

Why Look for SARS-CoV-2 Variants in Wastewater?

Theoretically, scientists could detect different strains of SARS-CoV-2 by sequencing viral genomes from every person who tests positive for COVID-19. But in reality, genomic sequencing of individual cases is costly and sporadic, with results published days, weeks, or even months after the tests occur. Furthermore, many infected people never get tested for COVID-19 because they are asymptomatic or lack easy access to testing services. Communities need a cheaper, more efficient way to identify SARS-CoV-2 variants in their midst.

The solution: wastewater surveillance — an established epidemiological strategy that has previously been used to track infectious diseases like polio, hepatitis A, and norovirus. Infected individuals shed the SARS-CoV-2 coronavirus in their feces even if they are asymptomatic, and 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 testing can help us map the prevalence and spread of variants in our communities," says Carolyn Reifsnyder, Director of Global Marketing for Bio-Rad’s Digital Biology Group. "This serves as an early warning system that can be implemented in tandem with molecular testing and surveillance efforts."

Carol Wilusz, Ph.D., a microbiologist at Colorado State University, leads a laboratory that has been conducting COVID-19 wastewater surveillance to look for outbreaks in communities throughout the state of Colorado. "I believe this is not only a viable approach but an essential one, because we can detect presence of the variants early and we can estimate their prevalence over time based on wastewater testing — provided that an accurate and reliable test for the mutation in question is available," she says. "For places where wastewater testing is already ongoing, the additional cost is minimal."

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ddPCR Analysis

ddPCR detects community-level SARS-CoV-2 infections in wastewater

What Makes ddPCR Technology the Best Tool for the Job?

Droplet Digital PCR (ddPCR) technology 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. Compared to common alternative technologies, it is less variable and has simpler data analysis. When identifying SARS-CoV-2 variants, ddPCR systems can accurately discriminate and quantify multiple variants in a sample using a single-well test.

Reifsnyder agrees, emphasizing that reproducible, quantitative results from wastewater are crucial not only for studying the epidemiology of variants, but also for surveillance. "Knowing the amount of virus and which variants are present is important because local authorities can take action based on this information," she says. For example, Reifsnyder explains, "If you’re testing wastewater from a dormitory, the resulting quantitative result might lead campus officials to require students to get a COVID test at the health center and self-quarantine."

Staying Ahead of New COVID-19 Variants

Both Wilusz and Reifsnyder point to flexibility as an additional benefit of ddPCR wastewater assays going forward. Should new variants arise in the future, it is extremely easy for scientists to modify existing tests to detect the new strains’ characteristic mutations in wastewater samples.

"Once you have sequences of a variant, it only takes about five minutes to design an assay on our website and order it," says Reifsnyder. For existing variants of concern, starting with B.1.1.7, B.1.351, P.1, B.1.429 and B.1.526, Bio-Rad has predesigned assays so researchers can access and implement them as quickly as possible. The Bio-Rad digital assay design engine is available online, so researchers can also create their own custom assays to detect any SARS-CoV-2 strain, even those that are not yet designated variants of concern. After the custom design is complete, assay production takes as little as two weeks.

Emerging variants present new challenges, but the scientific community is ready with expertise and cutting-edge technology that will continue to drive communal efforts to control the COVID-19 pandemic.

See How Bio-Rad is Equipping Scientists and Communities to Detect and Respond to COVID-19 Variants »