Wastewater-based surveillance as a tool for public health action: SARS-CoV-2 and beyond

Abstract

Wastewater-based surveillance (WBS) has undergone dramatic advancement in the context of the coronavirus disease 2019 (COVID-19) pandemic. The power and potential of this platform technology were rapidly realized when it became evident that not only did WBS-measured SARS-CoV-2 RNA correlate strongly with COVID-19 clinical disease within monitored populations but also, in fact, it functioned as a leading indicator. Teams from across the globe rapidly innovated novel approaches by which wastewater could be collected from diverse sewersheds ranging from wastewater treatment plants (enabling community-level surveillance) to more granular locations including individual neighborhoods and high-risk buildings such as long-term care facilities (LTCF). Efficient processes enabled SARS-CoV-2 RNA extraction and concentration from the highly dilute wastewater matrix. Molecular and genomic tools to identify, quantify, and characterize SARS-CoV-2 and its various variants were adapted from clinical programs and applied to these mixed environmental systems. Novel data-sharing tools allowed this information to be mobilized and made immediately available to public health and government decision-makers and even the public, enabling evidence-informed decision-making based on local disease dynamics. WBS has since been recognized as a tool of transformative potential, providing near-real-time cost-effective, objective, comprehensive, and inclusive data on the changing prevalence of measured analytes across space and time in populations. However, as a consequence of rapid innovation from hundreds of teams simultaneously, tremendous heterogeneity currently exists in the SARS-CoV-2 WBS literature. This manuscript provides a state-of-the-art review of WBS as established with SARS-CoV-2 and details the current work underway expanding its scope to other infectious disease targets.

Keywords: COVID-19; antimicrobial resistance; polio; sewage; wastewater; wastewater-based epidemiology.

Fig 1

Wastewater-based surveillance workflow. (A) Wastewater can be collected at multiple points in the sewershed, providing objective data on the monitored population. Careful handling and expedient transport are required to ensure sample integrity. (B) Concentration and extraction of wastewater are required in order to increase the relative abundance of SARS-CoV-2 RNA (or for other infectious targets, DNA) and to remove and mitigate inhibitory substances. (C) A range of molecular assays including (RT) qPCR, ddPCR, and LAMP can be used to quantify SARS-CoV-2 RNA, and variant detection can be performed using allele-targeted assays or agnostic metagenomic assessments. (D) Wastewater-measured SARS-CoV-2 can be adjusted based on a number of extrinsic factors (i.e., flow rates) and intrinsic factors (i.e., normalization for fecal biomarkers) and then compared with clinical data to develop appropriate models of community infection.

Fig 2

Wastewater-based surveillance can be conducted using a “nested approach.” (A) A schematic representation of the wastewater-based surveillance program in the province of Alberta, Canada that enables monitoring of 83% of the population through 43 municipalities. (B & C) Key nodes within the sewershed can be separately assessed in large municipalities to provide granular data on the populations that comprise these sub-catchments as profound regional variation exists between neighborhoods in population makeup (i.e., differences in social, economic, and ethnodemographics). (D) Targeted facilities can serve a specific sentinel role for monitoring specifically at-risk populations (i.e., hospitals and long-term care) and how infections propagate.

Fig 3

Wastewater-measured analytes may be normalized against both population and biologically relevant factors to increase the validity and reliability of site-to-site comparisons. (A) Communities differ in their population size, demographics as well as the nature of water usage—and therefore the makeup of their wastewater output. Understanding dynamic concentrations of target analytes is therefore dependent on factors relating to wastewater flow, contributions, and population size. (B) Behavioral factors relating to toileting patterns likewise may influence the accurate interpretation of wastewater-measured analytes. If an analyte is shed in the feces, measuring the analyte relative to a fecally shed biological marker may improve its correlation with case occurrence in the defined population. This may matter more on a granular scale such as individual facilities (i.e., a hospital/long-term care facility vs a bar or public venue) where defecation is expected to occur among patients/residents but not patrons transiently visiting an establishment.

Fig 4

Molecular strategies to identify and quantify target analytes in wastewater. (A) RT-qPCR, (B) RT-dPCR, and (C) RT-LAMP.

Fig 5

Natural history of analyte. The performance of wastewater-based surveillance of infectious targets is influenced by the natural history of infections they cause and how the measured analyte enters the sewershed. (A) For an agent to be tracked by WBS, its nucleic acid must ultimately end up in the wastewater. Nucleic acid may come directly or indirectly from stool, urine, vomit, and that exfoliated from the skin during bathing/showering. (B) The wastewater-measured signal will provide different population-level information depending on the natural history of the pathogen targeted, incidence (i.e., acute infection with rapid resolution of analyte shedding such as COVID-19), overall prevalence (i.e., chronic colonization or disease associated with protracted analyte shedding), or a combination of both (i.e., chronic viral diseases with acute seroconversion illnesses, i.e., HIV).