Waste Not, Want Not: Tracking SARS-CoV-2 Variants In Wastewater

To better track SARS-CoV-2 variants, scientists have developed a quicker, cheaper method for detecting the virus in wastewater. Here’s how they did it.

AsianScientist (Jul. 23, 2021) – Adding yet another tool to the arsenal in the fight against COVID-19, an international team of researchers have successfully developed a new method for detecting SARS-CoV-2’s Alpha variant in wastewater. Their findings are published in Environmental Science and Technology Letters.

While vaccinations are steadily rolling out across the world, there remains a crucial snag in our collective plans to end the pandemic: the SARS-CoV-2 variants. Currently, some of the more prominent variants include the Alpha variant first identified in the UK as well as the Delta variant first found in India.

Armed with higher transmissibility, increased severity and even the ability to evade the immune system, these variants have made virus tracking methods even more essential.

For researchers tracking these variants, it turns out that the gutter is a goldmine of information—literally. After all, even asymptomatic individuals can shed fragments of SARS-CoV-2, making wastewater a useful resource for covertly monitoring community spread of COVID-19.

Indeed, in Singapore, several clusters have been identified and contained through proactive wastewater surveillance efforts. Despite this, several challenges in wastewater surveillance remain.

For instance, the process used—called next-generation sequencing—is time-consuming and expensive. They also lack the sensitivity required to detect the virus in dilute and mixed wastewater samples.

To address these challenges, researchers from the Singapore-MIT Alliance for Research and Technology (SMART), alongside collaborators from Biobot Analytics, Nanyang Technological University and the Massachusetts Institute of Technology developed a polymerase chain reaction (PCR)-based method that targets the Alpha variant’s specific spike protein mutations.

After testing their method across 19 communities in the US, the team found that their technique could reliably detect and quantify even low levels of the Alpha variant with minimal cross-reactivity. The method could even identify as little as one percent of the variant in mixed samples.

Impressively, due to the detection method’s open-source nature, other organizations and research institutions can tap on the technique for their own wastewater surveillance. This is in contrast to the commercially available products that use proprietary primers and probes.

As Delta gains steam across the world, the researchers are now developing modified techniques to detect and quantify to identify the variant.

“[Wastewater surveillance] is especially important in countries battling SARS-CoV-2 variants. It will help find out the true proportion and spread of the variants in the local communities,” concluded first author Dr. Lee Wei Lin, a research scientist at SMART.

“Our method is sensitive enough to detect variants in highly diluted SARS-CoV-2 concentrations…and produces reliable results even for samples which contain multiple SARS-CoV-2 lineages,” she added.

The article can be found at: Lee et al. (2021) Quantitative SARS-CoV-2 Alpha Variant B.1.1.7 Tracking in Wastewater by Allele-Specific RT-qPCR.


Source: Singapore-MIT Alliance for Research and Technology; Photo: Shutterstock.
Disclaimer: This article does not necessarily reflect the views of AsianScientist or its staff.

Asian Scientist Magazine is an award-winning science and technology magazine that highlights R&D news stories from Asia to a global audience. The magazine is published by Singapore-headquartered Wildtype Media Group.

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