Researchers have made advances in viral detection in wastewater with the development of a new quantitative RT-qPCR assay that is able to detect the Omicron variant of SARS-CoV-2. Tests like these enable wastewater surveillance to accurately trace variants in any given community or population, and support and inform the implementation of appropriate public health measures tailored according to the specific traits of the variant.
Researchers from the Singapore-MIT Alliance for Research and Technology (SMART), in collaboration with researchers from Nanyang Technological University (NTU), National University of Singapore (NUS), Massachusetts Institute of Technology (MIT), Singapore Centre for Environmental Life Sciences Engineering (SCELSE), and Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER) in Italy published the findings. In another paper, SMART researchers and collaborators also reviewed the future of wastewater surveillance, outlining challenges and opportunities and mapping its potential to prepare societies for future viral outbreaks.
Wastewater monitoring emerged amid the COVID-19 pandemic as an effective and non-invasive way to track a viral outbreak, and advances in the technology have enabled researchers to not only identify but also quantify the presence of particular variants of concern (VOCs) in wastewater samples. This capacity to count and assess particular variants is unique to SMART’s open-source assay, and allows researchers to accurately determine displacement trends in a community. Hence, this assay can reveal what proportion of SARS-CoV-2 virus circulating in a community belongs to a particular variant.
SMART researchers made the news in July last year for the first of these breakthroughs, having developed a quantitative assay for the Alpha variant of SARS-CoV-2 in wastewater, while also working on a similar assay for the Delta variant. Previously, conventional wastewater detection methods could only detect the presence of SARS-CoV-2 viral material in a sample, without identifying the variant of the virus.
Delta taken over by Omicron within 3 weeks in Italy study
SMART researchers have developed a similar quantitative assay for the Omicron variant, an allele-specific RT-qPCR assay, enabling the quantitative detection of Omicron in wastewater. This is described in their paper, “Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater”, published in Water Research.
In their research, SMART found that the increase in booster vaccine population coverage in Italy concurred with the complete displacement of the Delta variant by the Omicron variant in wastewater samples obtained from the Torbole Casaglia wastewater treatment plant, with a catchment size of 62,722 people. Taking less than 3 weeks, the rapid pace of this displacement can be attributed to Omicron’s infection advantage over the previously dominant Delta in vaccinated individuals, which may stem from Omicron’s more efficient evasion of vaccination-induced immunity.
“In a world where COVID-19 is endemic, the monitoring of VOCs through wastewater surveillance will be an effective tool for the tracking of variants circulating in the community and will play an increasingly important role in guiding public health response,” said co-author of the paper and Senior Postdoctoral Associate at SMART AMR, Federica Armas. “This work has demonstrated that wastewater surveillance can be used to quickly and quantitatively trace VOCs present in a community.”
