A Sensitive and Rapid Wastewater Test for SARS-COV-2 and Its Use for the Early Detection of a Cluster of Cases in a Remote Community

Abstract

Throughout the COVID-19 pandemic, wastewater surveillance has been used to monitor trends in SARS-CoV-2 prevalence in the community. A major challenge in establishing wastewater surveillance programs, especially in remote areas, is the need for a well-equipped laboratory for sample analysis. Currently, no options exist for rapid, sensitive, mobile, and easy-to-use wastewater tests for SARS-CoV-2. The performance of the GeneXpert System, which offers cartridge-based, rapid molecular clinical testing for SARS-CoV-2 in a portable platform, was evaluated using wastewater as the input. The GeneXpert demonstrated a SARS-CoV-2 limit of detection in wastewater below 32 copies/mL with a sample processing time of less than an hour. Using wastewater samples collected from multiple sites across Canada during February and March 2021, a high overall agreement (97.8%) was observed between the GeneXpert assay and laboratory-developed tests regarding the presence or absence of SARS-CoV-2. Additionally, with the use of centrifugal filters the detection threshold of the GeneXpert system was improved to <10 copies/mL in wastewater. Finally, to support on-site wastewater surveillance, GeneXpert testing was implemented in Yellowknife, a remote community in Northern Canada where its use successfully alerted public health authorities to undetected transmission of COVID-19. The identification of SARS-CoV-2 in wastewater triggered clinical testing of recent travelers and identification of new COVID-19 cases/clusters. Taken together, these results suggest the GeneXpert is a viable option for surveillance of SARS-CoV-2 in wastewater in locations that do not have access to established testing laboratories. Importance: Wastewater-based surveillance is a powerful tool that provides an unbiased measure of COVID-19 prevalence in a community. This work describes a sensitive wastewater rapid test for SARS-CoV-2 based on a widely distributed technology, the GeneXpert. The advantages of an easy-to-use wastewater test for SARS-CoV-2 are clear – it supports surveillance in remote communities, improves access to testing, and provides faster results allowing for an immediate public health response. The application of wastewater rapid testing in a remote community facilitated the detection of a COVID-19 cluster and triggered public health action, clearly demonstrating the utility of this technology. Wastewater surveillance will become increasingly important in the post-vaccination pandemic landscape as individuals with asymptomatic/mild infections continue transmitting SARS-CoV-2 but are unlikely to be tested.

Wastewater surveillance in smaller college communities may aid future public health initiatives

“…This is a significant problem because under-reporting may lead to a false sense of security among the public and hinder data-driven decisions by policymakers. Overall, this study indicates the need to continue regular surveillance and heed the warnings of viral genome concentrations in the wastewater as a representative indicator of community health as well as COVID-19 cases in the area [6,[30][31][32][33]. Smaller communities do not always have access to the same resources or information available in larger cities.…”

The Detection of SARS-CoV2 Antigen in Wastewater Using an Automated Chemiluminescence Enzyme Immunoassay

“…However, sensitivity is acceptable at concentrations over 32 copy/mL in wastewater. Without concentration, the findings should be considered qualitative [26].…”

Community-Based SARS-CoV-2 Testing Using Saliva or Nasopharyngeal Swabs to Compare the Performance of Weekly COVID-19 Screening to Wastewater SARS-CoV-2 Signals

“…Recently, a significant number of studies have been published that improve confidence in the ability of WBE to assess SARS-CoV-2 transmission in the community. − The topics addressed by these studies range from assessment and normalization of SARS-CoV-2 RNA in wastewater to a better understanding of the relationship between RNA load and COVID-19 clinical cases and hospitalization. The unique feature of our study is the evaluation of the relationship between wastewater RNA load and COVID-19 in an underserved community and the importance of elevating visibility of these communities to public health authorities.…”