Detection of SARS-CoV-2 in wastewater in Halifax, Nova Scotia, Canada, using four RT-qPCR assays

Wastewater-based surveillance methods have been implemented in several countries as a tool for monitoring SARS-CoV-2 at a community scale. A variety of methods have been used for concentrating, extracting, and detecting the virus, with no clear consensus on the most effective approach. In this note, we report preliminary findings from a study that is tracking SARS-CoV-2 in wastewater in Halifax, Nova Scotia, with a specific focus on the use of four reverse transcriptase quantitative PCR (RT-qPCR) assays for detecting the virus in wastewater. We were able to detect the virus in wastewater samples during the initial rise of cases in the Halifax region in early November 2020. Levels of the targeted SARS-CoV-2 gene fragments increased and fell in response to reported cases of COVID-19. The CDC N1 and E RT-qPCR assays demonstrated greater relative sensitivity than the CDC N2 and N3 assays for detection of SARS-CoV-2 in raw sewage samples.

Automated summary

Wastewater-based surveillance methods have been used in various countries to monitor the presence of SARS-CoV-2 in communities. A study in Halifax, Nova Scotia, found that the virus could be detected in wastewater samples, with different RT-qPCR assays showing varying sensitivity in detecting the virus. The CDC N1 and E RT-qPCR assays demonstrated higher sensitivity compared to the CDC N2 and N3 assays.