Wastewater surveillance proves a critical tool to monitor SARS-CoV-2 prevalence

As COVID-19 restrictions are lifted and clinical testing is generally limited to diagnostic purposes in healthcare facilities, the full extent of SARS-CoV-2 infection is largely unknown. This makes it extremely difficult to understand and predict the impact of COVID-19 on public health infrastructure going forward. An alternative strategy to monitor the trend of SARS-CoV-2 infections in the community is to utilize wastewater collected from municipal water treatment facilities. Like some other pathogens, the SARS-CoV-2 virus is shed in the feces of infected individuals and an evaluation of total virus in wastewater can serve as an alternative to community-wide PCR testing. In recent papers published in Epidemiology, Science of the Total Environment, and Applied and Environmental Microbiology, CITF-funded researchers Drs. Lily Pang and Bonita Lee from the University of Alberta and Dr. Chris Sikora from Alberta Health Services, as well as researchers at the Public Health Agency of Canada (PHAC) demonstrate an optimal wastewater testing strategy  and an alternative commercially available multiplex rapid test kit to understand the ongoing community spread of COVID-19 in real-time in major metropolitan areas and remote locations alike.

Coinciding with the emergence of the Omicron variant, Drs. Pang, Lee and Sikora validated and optimized a protocol specifically focused on wastewater surveillance of SARS-CoV-2 in Canada (1). Their team optimized treatment, storage and assay parameters for 24 hour composite samples of raw sewage collected from wastewater facilities for daily/weekly surveillance activities. They showed that viral RNA could be effectively extracted from these samples using a variety of commercially available kits. Overall, the researchers demonstrated the applicability and potential of using wastewater for surveillance of SARS-CoV-2 infections in Canada.

Following up on that assay optimization, the group went on to demonstrate the applicability of wastewater monitoring in the field by deploying this strategy to evaluate the population-level burden of SARS-CoV-2 in Alberta (2). Researchers collected wastewater from municipal water treatment plants across the province up to three times per week. RNA was extracted from these samples and SARS-CoV-2 nucleic acid sequences against the Omicron or Delta variant were amplified and quantified by RT-qPCR. The use of this assay strategy has allowed the emergence and prevalence of Omicron to be tracked across communities throughout Alberta. This data was comparable to the daily case burden of clinically diagnosed COVID-19 cases from Alberta Health Services. As anticipated, large cities such as Calgary and Edmonton exhibited a rapid emergence of Omicron compared to smaller and more remote municipalities.

More interestingly, Omicron represented nearly 100% of the SARS-CoV-2 burden in wastewater samples nearly two weeks prior to the clinically observed drastic increase of cases seen in Alberta during the 6^th wave. This report demonstrates that wastewater surveillance can offer an early and sentinel signal to evaluate the population-level burden of SARS-CoV-2 VOCs in large metropolitan areas and across remote communities.

Virus surveillance in remote areas

There are some critical concerns on the feasibility of wastewater surveillance in remote locations across Canada. These assays cannot be performed on-site and generally require transportation of collected samples away from treatment plants to laboratories with specialized staff and expensive equipment. Recently, researchers from the Public Health Agency of Canada  (PHAC) published an article demonstrating the utility of a sensitive and rapid wastewater testing platform to enable testing in remote communities of Canada (3). In this article, they evaluated a rapid testing system from Cepheid® (GeneXpert® system) which can provide results in 37 minutes and can detect multiple pathogens, including SARS-CoV-2, Influenza A/B, and respiratory syncytial virus in near-real-time.

This GeneXpert® SARS-CoV-2 assay demonstrated a high degree of agreement (up to 98%) with conventional laboratory-based tests. As an application of this platform, PHAC deployed one of these systems in the field at Yellowknife, in the Northwest Territories. Wastewater there was tested multiple times per week with the GeneXpert system. It successfully detected the emergence of SARS-CoV-2 infections associated with recent travellers to the Territory. During the course of this pilot study, these results were also coupled with a PHAC/National Microbiology Laboratory standard lab-based assay to determine the identity of the virus responsible for increased infection rates.

Collectively, these studies demonstrate the powerful applications and advantages of a sensitive wastewater rapid test for SARS-CoV-2 which can be deployed for surveillance in remote areas, obtain results quickly, and, thereby, help guide immediate public health responses.

Wastewater testing has proven instrumental in public health monitoring in the past: for surveillance of polio outbreaks, illicit drug use, and detection of antimicrobial resistance (3). The ability to detect SARS-CoV-2 in human stool samples and early detection of community transmission signals – often preceding clinical signals of an increase in cases by up to 1 week – makes wastewater surveillance a useful tool for public health monitoring of infectious diseases.