Subsewershed SARS-CoV-2 Wastewater Surveillance and COVID-19 Epidemiology Using Building-Specific Occupancy and Case Data

Small-scale wastewater-based epidemiology (WBE) for infectious diseases and antibiotic resistance: A scoping review

Wastewater analysis can serve as a source of public health information. In recent years, wastewater-based epidemiology (WBE) has emerged and proven useful for the detection of infectious diseases. However, insights from the wastewater treatment plant do not allow for the small-scale differentiation within the sewer system that is needed to analyze the target population under study in more detail. Small-scale WBE offers several advantages, but there has been no systematic overview of its application. The aim of this scoping review is to provide a comprehensive overview of the current state of knowledge on small-scale WBE for infectious diseases, including methodological considerations for its application. A systematic database search was conducted, considering only peer-reviewed articles. Data analyses included quantitative summary and qualitative narrative synthesis. Of 2130 articles, we included 278, most of which were published since 2020. The studies analyzed wastewater at the building level (n = 203), especially healthcare (n = 110) and educational facilities (n = 80), and at the neighborhood scale (n = 86). The main analytical parameters were viruses (n = 178), notably SARS-CoV-2 (n = 161), and antibiotic resistance (ABR) biomarkers (n = 99), often analyzed by polymerase chain reaction (PCR), with DNA sequencing techniques being less common. In terms of sampling techniques, active sampling dominated. The frequent lack of detailed information on the specification of selection criteria and the characterization of the small-scale sampling sites was identified as a concern. In conclusion, based on the large number of studies, we identified several methodological considerations and overarching strategic aspects for small-scale WBE. An enabling environment for small-scale WBE requires inter- and transdisciplinary knowledge sharing across countries. Promoting the adoption of small-scale WBE will benefit from a common international conceptualization of the approach, including standardized and internationally accepted terminology. In particular, the development of good WBE practices for different aspects of small-scale WBE is warranted. This includes the establishment of guidelines for a comprehensive characterization of the local sewer system and its sub-sewersheds, and transparent reporting to ensure comparability of small-scale WBE results.

Monitoring SARS-CoV-2 RNA in wastewater from a shared septic system and sub-sewershed sites to expand COVID-19 disease surveillance

Wastewater-based epidemiology has expanded as a tool for collecting COVID-19 surveillance data, but there is limited information on the feasibility of this form of surveillance within decentralized wastewater systems (e.g., septic systems). This study assessed SARS-CoV-2 RNA concentrations in wastewater samples from a septic system servicing a mobile home park (66 households) and from two pumping stations serving a similarly sized (71 households) and a larger (1,000 households) neighborhood within a nearby sewershed over 35 weeks in 2020. Also, raw wastewater from a hospital in the same sewershed was sampled. The mobile home park samples had the highest detection frequency (39/39 days) and mean concentration of SARS-CoV-2 RNA (2.7 × 107 gene copies/person/day for the N1) among the four sampling sites. N1 gene and N2 gene copies were highly correlated across mobile home park samples (Pearson's r = 0.93, p < 0.0001). In the larger neighborhood, new COVID-19 cases were reported every week during the sampling period; however, we detected SARS-CoV-2 RNA in 12% of the corresponding wastewater samples. The results of this study suggest that sampling from decentralized wastewater infrastructure can be used for continuous monitoring of SARS-CoV-2 infections.

Highly Multiplexed Reverse-Transcription Loop-Mediated Isothermal Amplification and Nanopore Sequencing (LAMPore) for Wastewater-Based Surveillance

Wastewater-based surveillance (WBS) has gained attention as a strategy to monitor and provide an early warning for disease outbreaks. Here, we applied an isothermal gene amplification technique, reverse-transcription loop-mediated isothermal amplification (RT-LAMP), coupled with nanopore sequencing (LAMPore) as a means to detect SARS-CoV-2. Specifically, we combined barcoding using both an RT-LAMP primer and the nanopore rapid barcoding kit to achieve highly multiplexed detection of SARS-CoV-2 in wastewater. RT-LAMP targeting the SARS-CoV-2 N region was conducted on 96 reactions including wastewater RNA extracts and positive and no-target controls. The resulting amplicons were pooled and subjected to nanopore sequencing, followed by demultiplexing based on barcodes that differentiate the source of each SARS-CoV-2 N amplicon derived from the 96 RT-LAMP products. The criteria developed and applied to establish whether SARS-CoV-2 was detected by the LAMPore assay indicated high consistency with polymerase chain reaction-based detection of the SARS-CoV-2 N gene, with a sensitivity of 89% and a specificity of 83%. We further profiled sequence variations on the SARS-CoV-2 N amplicons, revealing a number of mutations on a sample collected after viral variants had emerged. The results demonstrate the potential of the LAMPore assay to facilitate WBS for SARS-CoV-2 and the emergence of viral variants in wastewater.

Wastewater based surveillance can be used to reduce clinical testing intensity on a university campus

Clinical testing has been a vital part of the response to and suppression of the COVID-19 pandemic; however, testing imposes significant burdens on a population. College students had to contend with clinical testing while simultaneously dealing with health risks and the academic pressures brought on by quarantines, changes to virtual platforms, and other disruptions to daily life. The objective of this study was to analyze whether wastewater surveillance can be used to decrease the intensity of clinical testing while maintaining reliable measurements of diseases incidence on campus. Twelve months of human health and wastewater surveillance data for eight residential buildings on a university campus were analyzed to establish how SARS-CoV-2 levels in the wastewater can be used to minimize clinical testing burden on students. Wastewater SARS-CoV-2 levels were used to create multiple scenarios, each with differing levels of testing intensity, which were compared to the actual testing volumes implemented by the university. We found that scenarios in which testing intensity fluctuations matched rise and falls in SARS-CoV-2 wastewater levels had stronger correlations between SARS-CoV-2 levels and recorded clinical positives. In addition to stronger correlations, most scenarios resulted in overall fewer weekly clinical tests performed. We suggest the use of wastewater surveillance to guide COVID-19 testing as it can significantly increase the efficacy of COVID-19 surveillance while reducing the burden placed on college students during a pandemic. Future efforts should be made to integrate wastewater surveillance into clinical testing strategies implemented on college campuses.

Influences of 23 different equations used to calculate gene copies of SARS-CoV-2 during wastewater-based epidemiology

Following the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2019, the use of wastewater-based surveillance (WBS) has increased dramatically along with associated infrastructure globally. However, due to the global nature of its application, and various workflow adaptations (e.g., sample collection, water concentration, RNA extraction kits), numerous methods for back-calculation of gene copies per volume (gc/L) of sewage have also emerged. Many studies have considered the comparability of processing methods (e.g., water concentration, RNA extraction); however, for equations used to calculate gene copies in a wastewater sample and subsequent influences on monitoring viral trends in a community and its association with epidemiological data, less is known. Due to limited information on how many formulas exist for the calculation of SARS-CoV-2 gene copies in wastewater, we initially attempted to quantify how many equations existed in the referred literature. We identified 23 unique equations, which were subsequently applied to an existing wastewater dataset. We observed a range of gene copies based on use of different equations, along with variability of AUC curve values, and results from correlation and regression analyses. Though a number of individual laboratories appear to have independently converged on a similar formula for back-calculation of viral load in wastewater, and share similar relationships with epidemiological data, differential influences of various equations were observed for variation in PCR volumes, RNA extraction volumes, or PCR assay parameters. Such observations highlight challenges when performing comparisons among WBS studies when numerous methodologies and back-calculation methods exist. To facilitate reproducibility among studies, the different gc/L equations were packaged as an R Shiny app, which provides end users the ability to investigate variability within their datasets and support comparisons among studies.

Making waves: The benefits and challenges of responsibly implementing wastewater-based surveillance for rural communities

The sampling and analysis of sewage for pathogens and other biomarkers offers a powerful tool for monitoring and understanding community health trends and potentially predicting disease outbreaks. Since the early months of the COVID-19 pandemic, the use of wastewater-based testing for public health surveillance has increased markedly. However, these efforts have focused on urban and peri‑urban areas. In most rural regions of the world, healthcare service access is more limited than in urban areas, and rural public health agencies typically have less disease outcome surveillance data than their urban counterparts. The potential public health benefits of wastewater-based surveillance for rural communities are therefore substantial - though so too are the methodological and ethical challenges. For many rural communities, population dynamics and insufficient, aging, and inadequately maintained wastewater collection and treatment infrastructure present obstacles to the reliable and responsible implementation of wastewater-based surveillance. Practitioner observations and research findings indicate that for many rural systems, typical implementation approaches for wastewater-based surveillance will not yield sufficiently reliable or actionable results. We discuss key challenges and potential strategies to address them. However, to support and expand the implementation of responsible, reliable, and ethical wastewater-based surveillance for rural communities, best practice guidelines and standards are needed.

Effectiveness of environmental surveillance of SARS-CoV-2 as an early-warning system: Update of a systematic review during the second year of the pandemic

The aim of this updated systematic review was to offer an overview of the effectiveness of environmental surveillance (ES) of SARS-CoV-2 as a potential early-warning system (EWS) for COVID-19 and new variants of concerns (VOCs) during the second year of the pandemic. An updated literature search was conducted to evaluate the added value of ES of SARS-CoV-2 for public health decisions. The search for studies published between June 2021 and July 2022 resulted in 1,588 publications, identifying 331 articles for full-text screening. A total of 151 publications met our inclusion criteria for the assessment of the effectiveness of ES as an EWS and early detection of SARS-CoV-2 variants. We identified a further 30 publications among the grey literature. ES confirms its usefulness as an EWS for detecting new waves of SARS-CoV-2 infection with an average lead time of 1-2 weeks for most of the publication. ES could function as an EWS for new VOCs in areas with no registered cases or limited clinical capacity. Challenges in data harmonization and variant detection require standardized approaches and innovations for improved public health decision-making. ES confirms its potential to support public health decision-making and resource allocation in future outbreaks.

Analyzing community wastewater in sub-sewersheds for the small-scale detection of SARS-CoV-2 variants in a German metropolitan area

Wastewater surveillance of SARS-CoV-2 proved useful, including for identifying the local appearance of newly identified virus variants. Previous studies focused on wastewater treatment plants (WWTP) with sewersheds of several hundred thousand people or at single building level, representing only a small number of people. Both approaches may prove inadequate for small-scale intra-urban inferences for early detection of emerging or novel virus variants. Our study aims (i) to analyze SARS-CoV-2 single nucleotide variants (SNVs) in wastewater of sub-sewersheds and WWTP using whole genome sequencing in order to (ii) investigate the potential of small-scale detection of novel known SARS-CoV-2 variants of concern (VOC) within a metropolitan wastewater system. We selected three sub-sewershed sampling sites, based on estimated population- and built environment-related indicators, and the inlet of the receiving WWTP in the Ruhr region, Germany. Untreated wastewater was sampled weekly between October and December 2021, with a total of 22 samples collected. SARS-CoV-2 RNA was analyzed by RT-qPCR and whole genome sequencing. For all samples, genome sequences were obtained, while only 13 samples were positive for RT-qPCR. We identified multiple specific SARS-CoV-2 SNVs in the wastewater samples of the sub-sewersheds and the WWTP. Identified SNVs reflected the dominance of VOC Delta at the time of sampling. Interestingly, we could identify an Omicron-specific SNV in one sub-sewershed. A concurrent wastewater study sampling the same WWTP detected the VOC Omicron one week later. Our observations suggest that the small-scale approach may prove particularly useful for the detection and description of spatially confined emerging or existing virus variants circulating in populations. Future studies applying small-scale sampling strategies taking into account the specific features of the wastewater system will be useful to analyze temporal and spatial variance in more detail.

Wastewater-based epidemiology for comprehensive communitywide exposome surveillance: A gradient of metals exposure

Community wastewater surveillance is an established means to measure health threats. Exposure to toxic metals as one of the key environmental contaminants has been attracting public health attention as exposure can be related to contamination across air, water, and soil as well as associated with individual factors. This research uses Jefferson County, Kentucky, as an urban exposome case study to analyze sub-county metal concentrations in wastewater as a possible indicator of community toxicant exposure risk, and to test the feasibility of using wastewater to identify potential community areas of elevated metals exposure. Variability in wastewater metal concentrations were observed across the county; 19 of the 26 sites had one or more metal results greater than one standard deviation above the mean and were designated areas of concern. Additionally, thirteen of the nineteen sites were of increased concern with levels greater than two standard deviations above the mean. This foundational research found variability in several instances between smaller nested upstream contributing neighborhood sewersheds when measured in the associated downstream treatment plant. Wastewater provides an opportunity to look at integrated toxicology to complement other toxicology data, looking at where people live and what toxicants need to be focused on to protect the health of people in that area.

Building-Level Detection Threshold of SARS-CoV-2 in Wastewater

We established wastewater surveillance of SARS-CoV-2 in a small, residential, urban college as part of an integrated public health response during the COVID-19 pandemic. Students returned to campus in spring 2021. During the semester, students were required to perform nasal PCR tests twice weekly. At the same time, wastewater monitoring was established in 3 campus dormitory buildings. Two were dedicated dormitories with populations of 188 and 138 students; 1 was an isolation building where students were moved within 2 h of receiving positive test results. Analysis of wastewater from isolation indicated that the amount of viral shedding was highly variable and that viral concentration could not be used to estimate the number of cases at the building level. However, rapid movement of students to isolation enabled determination of predictive power, specificity, and sensitivity from instances in which generally one positive case at a time occurred in a building. Our assay yields effective results with an ~60% positive predictive power, ~90% negative predictive power, and ~90% specificity. Sensitivity, however, is low at ~40%. Detection is improved in the few instances of 2 simultaneous positive cases, with sensitivity of 1 case versus 2 cases increasing from ~20% to 100%. We also measured the appearance of a variant of concern on campus and noted a similarity in timeline with increased prevalence in surrounding New York City. Monitoring SARS-CoV-2 in the sewage outflow of individual buildings can be used with a realistic goal of containing outbreak clusters but not necessarily single cases. IMPORTANCE Diagnostic testing of sewage can detect levels of circulating viruses to help inform public health. Wastewater-based epidemiology has been particularly active during the COVID-19 pandemic to measure the prevalence of SARS-CoV-2. Understanding the technical limitations of diagnostic testing for individual buildings would help inform future surveillance programs. We report our diagnostic and clinical data monitoring of buildings on a college campus in New York City during the spring 2021 semester. Frequent nasal testing, mitigation measures, and public health protocols provided a context in which to study the effectiveness of wastewater-based epidemiology. Our efforts could not consistently detect individual positive COVID-19 cases, but sensitivity is significantly improved in detecting two simultaneous cases. We therefore contend that wastewater surveillance may be more practically suited for the mitigation of outbreak clusters.