Review and Meta‐Analysis: SARS‐CoV‐2 and Enveloped Virus Detection in Feces and Wastewater

Assessing infectivity of emerging enveloped viruses in wastewater and sewage sludge: Relevance and procedures

The emergence of SARS-CoV-2 has heightened the need to evaluate the detection of enveloped viruses in the environment, particularly in wastewater, within the context of wastewater-based epidemiology. The studies published over the past 80 years focused primarily on non-enveloped viruses due to their ability to survive longer in environmental matrices such as wastewater or sludge compared to enveloped viruses. However, different enveloped viruses survive in the environment for different lengths of time. Therefore, it is crucial to be prepared to assess the potential infectious risk that may arise from future emerging enveloped viruses. This will require appropriate tools, notably suitable viral concentration methods that do not compromise virus infectivity. This review has a dual purpose: first, to gather all the available literature on the survival of infectious enveloped viruses, specifically at different pH and temperature conditions, and in contact with detergents; second, to select suitable concentration methods for evaluating the infectivity of these viruses in wastewater and sludge. The methodology used in this data collection review followed the systematic approach outlined in the PRISMA (Preferred Reporting Items for Systematic Review and Meta-Analysis) guidelines. Concentration methods cited in the data gathered are more tailored towards detecting the enveloped viruses' genome. There is a lack of suitable methods for detecting infectious enveloped viruses in wastewater and sludge. Ultrafiltration, ultracentrifugation, and polyethylene glycol precipitation methods, under specific/defined conditions, appear to be relevant approaches. Further studies are necessary to validate reliable concentration methods for detecting infectious enveloped viruses. The choice of culture system is also crucial for detection sensitivity. The data also show that the survival of infectious enveloped viruses, though lower than that of non-enveloped ones, may enable environmental transmission. Experimental data on a wide range of enveloped viruses is required due to the variability in virus persistence in the environment.

A scoping review of global SARS-CoV-2 wastewater-based epidemiology in light of COVID-19 pandemic

Recently, wastewater-based epidemiology (WBE) research has experienced a strong impetus during the Coronavirus disease 2019 (COVID-19) pandemic. However, a few technical issues related to surveillance strategies, such as standardized procedures ranging from sampling to testing protocols, need to be resolved in preparation for future infectious disease outbreaks. This review highlights the study characteristics, potential use of WBE and overview of methods, as well as methods utilized to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) including its variant in wastewater. A literature search was performed electronically in PubMed and Scopus according to PRISMA guidelines for relevant peer-reviewed articles published between January 2020 and March 2022. The search identified 588 articles, out of which 221 fulfilled the necessary criteria and are discussed in this review. Most global WBE studies were conducted in North America (n = 75, 34 %), followed by Europe (n = 68, 30.8 %), and Asia (n = 43, 19.5 %). The review also showed that most of the application of WBE observed were to correlate SARS-CoV-2 ribonucleic acid (RNA) trends in sewage with epidemiological data (n = 90, 40.7 %). The techniques that were often used globally for sample collection, concentration, preferred matrix recovery control and various sample types were also discussed. Overall, this review provided a framework for researchers specializing in WBE to apply strategic approaches to their research questions in achieving better functional insights. In addition, areas that needed more in-depth analysis, data collection, and ideas for new initiatives were identified.

Simultaneous microbial capture and nucleic acid extraction from wastewater with minimal pre-processing and high recovery efficiency

The COVID-19 pandemic accelerated research towards developing low-cost assays for automated urban wastewater monitoring assay that can be integrated into an environmental surveillance system for early warning of frequent disease outbreaks and future pandemics. Microbial concentration is one of the most challenging steps in wastewater surveillance, due to the sample heterogeneity and low pathogen load. Keeping in mind the requirements of large-scale testing in densely populated low- or middle-income countries (LMICs), such assays would need to be low-cost and have rapid turnaround time with high recovery efficiency. In this study, two such methods are presented and evaluated against commercially available kits for pathogen detection in wastewater. The first method utilizes paper dipsticks while the second method comprises of a PTFE membrane filter (PMF) integrated with a peristaltic pump. Both methods were used to concentrate and isolate nucleic acids from different microbes such as SARS-CoV-2, pepper mild mottle virus (PMMoV), bacteriophage Phi6, and E. coli from wastewater samples with minimal or no sample pre-processing. While the paper dipstick method is suitable for sub-milliliter sample volume, the PMF method can be used with larger volumes of wastewater sample (40 mL) and can detect multiple microbes with recovery efficiency comparable to commercially available kits.

Challenges detecting SARS-CoV-2 in Costa Rican domestic wastewater and river water

This study presents the development of a SARS-CoV-2 detection method for domestic wastewater and river water in Costa Rica, a middle-income country in Central America. Over a three-year period (November to December 2020, July to November 2021, and June to October 2022), 80 composite wastewater samples (43 influent and 37 effluent) were collected from a Wastewater Treatment Plant (SJ-WWTP) located in San José, Costa Rica. Additionally, 36 river water samples were collected from the Torres River near the SJ-WWTP discharge site. A total of three protocols for SARS-CoV-2 viral concentration and RNA detection and quantification were analyzed. Two protocols using adsorption-elution with PEG precipitation (Protocol A and B, differing in the RNA extraction kit; n = 82) were used on wastewater samples frozen prior to concentration, while wastewater (n = 34) collected in 2022 were immediately concentrated using PEG precipitation. The percent recovery of Bovine coronavirus (BCoV) was highest using the Zymo Environ Water RNA (ZEW) kit with PEG precipitation executed on the same day as collection (mean 6.06 % ± 1.37 %). It was lowest when samples were frozen and thawed, and viruses were concentrated using adsorption-elution and PEG concentration methods using the PureLink™ Viral RNA/DNA Mini (PLV) kit (protocol A; mean 0.48 % ± 0.23 %). Pepper mild mottle virus and Bovine coronavirus were used as process controls to understand the suitability and potential impact of viral recovery on the detection/quantification of SARS-CoV-2 RNA. Overall, SARS-CoV-2 RNA was detected in influent and effluent wastewater samples collected in 2022 but not in earlier years when the method was not optimized. The burden of SARS-CoV-2 at the SJ-WWTP decreased from week 36 to week 43 of 2022, coinciding with a decline in the national COVID-19 prevalence rate. Developing comprehensive nationwide surveillance programs for wastewater-based epidemiology in low-middle-income countries involves significant technical and logistical challenges.

Biosensors for waterborne virus detection: Challenges and strategies

Waterborne viruses that can be harmful to human health pose significant challenges globally, affecting health care systems and the economy. Identifying these waterborne pathogens is essential for preventing diseases and protecting public health. However, handling complex samples such as human and wastewater can be challenging due to their dynamic and complex composition and the ultralow concentration of target analytes. This review presents a comprehensive overview of the latest breakthroughs in waterborne virus biosensors. It begins by highlighting several promising strategies that enhance the sensing performance of optical and electrochemical biosensors in human samples. These strategies include optimizing bioreceptor selection, transduction elements, signal amplification, and integrated sensing systems. Furthermore, the insights gained from biosensing waterborne viruses in human samples are applied to improve biosensing in wastewater, with a particular focus on sampling and sample pretreatment due to the dispersion characteristics of waterborne viruses in wastewater. This review suggests that implementing a comprehensive system that integrates the entire waterborne virus detection process with high-accuracy analysis could enhance virus monitoring. These findings provide valuable insights for improving the effectiveness of waterborne virus detection, which could have significant implications for public health and environmental management.

Evaluation of low-cost SARS-CoV-2 RNA purification methods for viral quantification by RT-qPCR and next-generation sequencing analysis: Implications for wider wastewater-based epidemiology adoption

Based Epidemiology (WBE) consists of quantifying biomarkers in sewerage systems to derive real-time information on the health and/or lifestyle of the contributing population. WBE usefulness was vastly demonstrated in the context of the COVID-19 pandemic. Many methods for SARS-CoV-2 RNA determination in wastewater were devised, which vary in cost, infrastructure requirements and sensitivity. For most developing countries, implementing WBE for viral outbreaks, such as that of SARS-CoV-2, proved challenging due to budget, reagent availability and infrastructure constraints. In this study, we assessed low-cost methods for SARS-CoV-2 RNA quantification by RT-qPCR, and performed variant identification by NGS in wastewater samples. Results showed that the effect of adjusting pH to 4 and/or adding MgCl₂ (25 mM) was negligible when using the adsorption-elution method, as well as basal physicochemical parameters in the sample. In addition, results supported the standardized use of linear rather than plasmid DNA for a more accurate viral RT-qPCR estimation. The modified TRIzol-based purification method in this study yielded comparable RT-qPCR estimation to a column-based approach, but provided better NGS results, suggesting that column-based purification for viral analysis should be revised. Overall, this work provides evaluation of a robust, sensitive and cost-effective method for SARS-CoV-2 RNA analysis that could be implemented for other viruses, for a wider WEB adoption.

Wastewater-based prediction of COVID-19 cases using a highly sensitive SARS-CoV-2 RNA detection method combined with mathematical modeling

Wastewater-based epidemiology (WBE) has the potential to predict COVID-19 cases; however, reliable methods for tracking SARS-CoV-2 RNA concentrations (C_RNA) in wastewater are lacking. In the present study, we developed a highly sensitive method (EPISENS-M) employing adsorption-extraction, followed by one-step RT-Preamp and qPCR. The EPISENS-M allowed SARS-CoV-2 RNA detection from wastewater at 50 % detection rate when newly reported COVID-19 cases exceed 0.69/100,000 inhabitants in a sewer catchment. Using the EPISENS-M, a longitudinal WBE study was conducted between 28 May 2020 and 16 June 2022 in Sapporo City, Japan, revealing a strong correlation (Pearson's r = 0.94) between C_RNA and the newly COVID-19 cases reported by intensive clinical surveillance. Based on this dataset, a mathematical model was developed based on viral shedding dynamics to estimate the newly reported cases using C_RNA data and recent clinical data prior to sampling day. This developed model succeeded in predicting the cumulative number of newly reported cases after 5 days of sampling day within a factor of √2 and 2 with a precision of 36 % (16/44) and 64 % (28/44), respectively. By applying this model framework, another estimation mode was developed without the recent clinical data, which successfully predicted the number of COVID-19 cases for the succeeding 5 days within a factor of √2 and 2 with a precision of 39 % (17/44) and 66 % (29/44), respectively. These results demonstrated that the EPISENS-M method combined with the mathematical model can be a powerful tool for predicting COVID-19 cases, especially in the absence of intensive clinical surveillance.

Implementing wastewater surveillance for SARS-CoV-2 on a university campus: Lessons learned

Wastewater surveillance, also known as wastewater-based epidemiology (WBE), has been successfully used to detect SARS-CoV-2 and other viruses in sewage in many locations in the United States and globally. This includes implementation of the surveillance on college and university campuses. A two-phase study was conducted during the 2020-2021 academic year to test the feasibility of a WBE system on campus and to supplement the clinical COVID-19 testing performed for the student, staff, and faculty body. The primary objective during the Fall 2020 semester was to monitor a large portion of the on-campus population and to obtain an understanding of the spreading of the SARS-CoV-2 virus. The Spring 2021 objective was focused on selected residence halls and groups of residents on campus, as this was more efficient and relevant for an effective follow-up response. Logistical problems and planning oversights initially occurred but were corrected with improved communication and experience. Many lessons were learned, including effective mapping, site planning, communication, personnel organization, and equipment management, and obtained along the way, thereby paving an opportune guide for future planning efforts. PRACTITIONER POINTS: WBE was successful in the detection of many SARS-CoV-2 variants incl. Alpha, Beta, Gamma, Delta, Lambda, Mu, and Omicron. Careful planning and contingencies were essential for a successful implementation of a SARS-CoV-2 monitoring program. A surveillance program may be important for detection and monitoring of other public health relevant targets in wastewater incl. bacteria, viruses, fungi and viruses. Diverse lessons were learned incl. effective mapping, site planning, communication, personnel organization, and equipment management, thereby providing a guide for future planning efforts.