Wastewater, waste, and water-based epidemiology (WWW-BE): A novel hypothesis and decision-support tool to unravel COVID-19 in low-income settings?

Population infection estimation from wastewater surveillance for SARS-CoV-2 in Nagpur, India during the second pandemic wave

Wastewater-based epidemiology (WBE) has emerged as an effective environmental surveillance tool for predicting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease outbreaks in high-income countries (HICs) with centralized sewage infrastructure. However, few studies have applied WBE alongside epidemic disease modelling to estimate the prevalence of SARS-CoV-2 in low-resource settings. This study aimed to explore the feasibility of collecting untreated wastewater samples from rural and urban catchment areas of Nagpur district, to detect and quantify SARS-CoV-2 using real-time qPCR, to compare geographic differences in viral loads, and to integrate the wastewater data into a modified Susceptible-Exposed-Infectious-Confirmed Positives-Recovered (SEIPR) model. Of the 983 wastewater samples analyzed for SARS-CoV-2 RNA, we detected significantly higher sample positivity rates, 43.7% (95% confidence interval (CI) 40.1, 47.4) and 30.4% (95% CI 24.66, 36.66), and higher viral loads for the urban compared with rural samples, respectively. The Basic reproductive number, R0, positively correlated with population density and negatively correlated with humidity, a proxy for rainfall and dilution of waste in the sewers. The SEIPR model estimated the rate of unreported coronavirus disease 2019 (COVID-19) cases at the start of the wave as 13.97 [95% CI (10.17, 17.0)] times that of confirmed cases, representing a material difference in cases and healthcare resource burden. Wastewater surveillance might prove to be a more reliable way to prepare for surges in COVID-19 cases during future waves for authorities.

Assessment of sewer connectivity in the United States and its implications for equity in wastewater-based epidemiology

Wastewater-based epidemiology is a promising public health tool that can yield a more representative view of the population than case reporting. However, only about 80% of the U.S. population is connected to public sewers, and the characteristics of populations missed by wastewater-based epidemiology are unclear. To address this gap, we used publicly available datasets to assess sewer connectivity in the U.S. by location, demographic groups, and economic groups. Data from the U.S. Census' American Housing Survey revealed that sewer connectivity was lower than average when the head of household was American Indian and Alaskan Native, White, non-Hispanic, older, and for larger households and those with higher income, but smaller geographic scales revealed local variations from this national connectivity pattern. For example, data from the U.S. Environmental Protection Agency showed that sewer connectivity was positively correlated with income in Minnesota, Florida, and California. Data from the U.S. Census' American Community Survey and Environmental Protection Agency also revealed geographic areas with low sewer connectivity, such as Alaska, the Navajo Nation, Minnesota, Michigan, and Florida. However, with the exception of the U.S. Census data, there were inconsistencies across datasets. Using mathematical modeling to assess the impact of wastewater sampling inequities on inferences about epidemic trajectory at a local scale, we found that in some situations, even weak connections between communities may allow wastewater monitoring in one community to serve as a reliable proxy for an interacting community with no wastewater monitoring, when cases are widespread. A systematic, rigorous assessment of sewer connectivity will be important for ensuring an equitable and informed implementation of wastewater-based epidemiology as a public health monitoring system.

Human viral pathogens in the wastewater-source water-drinking water continuum: Evidence, health risks, and lessons for future outbreaks in low-income settings

Human viral pathogens, including SARS-CoV-2 continue to attract public and research attention due to their disruption of society, global health, and the economy. Several earlier reviews have investigated the occurrence and fate of SARS-CoV-2 in wastewater, and the potential to use such data in wastewater-based epidemiology. However, comprehensive reviews tracking SARS-CoV-2 and other viral pathogens in the wastewater-water-drinking water continuum and the associated risk assessment are still lacking. Therefore, to address this gap, the present paper makes the following contributions: (1) critically examines the early empirical results to highlight the occurrence and stability of SARS-CoV-2 in the wastewater-source water-drinking water continuum, (2) discusses the anthropogenic and hydro(geo)logical processes controlling the circulation of SARS-CoV-2 in the wastewater-source water-drinking water continuum, (3) discusses the risky behaviour, drivers and high-risk settings in the wastewater-source water-drinking water continuum, (4) uses the available empirical data on SARS-CoV-2 occurrence in the wastewater-source water-drinking water continuum to discuss human health risks from multiple exposure pathways, gendered aspects of SARS-CoV-2 transmission via shared on-site sanitation systems, and (5) develops and risk mitigation strategy based on the available empirical evidence and quantitative human risk assessment data. Finally, it presents a comprehensive research agenda on SARS-CoV-2/COVID-19 to guide the mitigation of future similar outbreaks in low-income settings.

Combating antibiotic resistance using wastewater surveillance: Significance, applications, challenges, and future directions

The global increase of antibiotic resistance (AR) and resistant infections call for effective surveillance methods for understanding and mitigating (re)-emerging public health risks. Wastewater surveillance (WS) of antibiotic resistance is an emerging, but currently under-utilized decision-support tool in public health systems. Recent years have witnessed an increase in evidence linking antibiotic resistance in wastewaters to that of the community. To date, very few comprehensive reviews exist on the application of WS to understand AR and resistant infections in population. Current and emerging AR detection methods, and their merits and limitations are discussed. Wastewater surveillance has several merits relative to individual testing, including; (1) low per capita testing cost, (2) high spatial coverage, (3) low requirement for diagnostic equipment, and (4) detection of health threats ahead of real outbreaks. The applications of WS as an early warning system and decision support tool to understand and mitigate AR are discussed. Wastewater surveillance could be a tool of choice in low-income settings lacking resources and diagnostic facilities for individual testing. To demonstrate the utility of WS, empirical evidence from field case studies is presented. However, constraints still exist, including; (1) lack of standardized protocols, (2) the clinical utility and sensitivity of WS-based data, (3) uncertainties in relating WS data to pathogenic and virulent bacteria, and (4) whether or not AR in stools and ultimately wastewater represent the complete human resistome. Finally, further prospects are presented, include knowledge gaps on; (1) development of low-cost biosensors for AR, (2) development of WS protocols (sampling, processing, interpretation), (3) further pilot scale studies to understand the opportunities and limits of WS, and (4) development of computer-based analytical tools to facilitate rapid data collection, visualization and interpretation. Therefore, the present paper discusses the principles, opportunities, and constraints of wastewater surveillance applications to understand AR and safeguard public health.

Environmental monitoring of SARS-CoV-2 in the metropolitan area of Porto Alegre, Rio Grande do Sul (RS), Brazil

Since starts the coronavirus disease 2019 (COVID-19) pandemic identified the presence of genomic fragments of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in various environmental matrices: domestic sewage, surface waters, and contaminated freshwater. Environmental monitoring of SARS-CoV-2 is a tool for evaluating trend curves over the months, compared to several clinical cases of the disease. The objective of this study was to monitor the SARS-CoV-2 in environmental samples collected in different sites in a metropolitan area of Porto Alegre, Southern Brazil. During 10 months from 2020 to 2021, 300 samples were collected weekly and biweekly from nine points located in 3 cities: one point from a wastewater treatment plant (WWTP) in São Leopoldo (fortnightly collection), two points in Dilúvio Stream in Porto Alegre (fortnightly collection), two points in Pampa and Luiz Rau Streams (weekly collection), and two points in public fountains (fortnightly collection) in Novo Hamburgo. After collection, samples were concentrated by ultracentrifugation, and viral nucleic acids were extracted using MagMax® Core Nucleic Acid Purifications kits and submitted to RT-qPCR, using E, N1, and N2 gene targets of SARS-CoV-2. Only 7% (3/41) samples from public fountains were positive, with a mean viral load (VL) of SARS-CoV-2 RNA of 5.02 × 101 gc/l (2.41~8.59 × 101 gc/l), while the streams had average VL of 7.43 × 105 gc/l (Pampa), 7.06 × 105 gc/l (Luiz Rau), 2.01 × 105 gc/l (Dilúvio), and 4.46 × 105 cg/l (WWTP). The results showed varying levels of viral presence in different sample types, with a demonstrated correlation between environmental viral load and clinical COVID-19 cases. These findings contribute to understanding virus persistence and transmission pathways in the environment. Continuous monitoring, especially in less developed regions, is crucial for early detection of vaccine resistance, new variants, and potential COVID-19 resurgence.

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.

The pit latrine paradox in low-income settings: A sanitation technology of choice or a pollution hotspot?

Pit latrines are widely promoted to improve sanitation in low-income settings, but their pollution and health risks receive cursory attention. The present narrative review presents the pit latrine paradox; (1) the pit latrine is considered a sanitation technology of choice to safeguard human health, and (2) conversely, pit latrines are pollution and health risk hotspots. Evidence shows that the pit latrine is a 'catch-all' receptacle for household disposal of hazardous waste, including; (1) medical wastes (COVID-19 PPE, pharmaceuticals, placenta, used condoms), (2) pesticides and pesticide containers, (3) menstrual hygiene wastes (e.g., sanitary pads), and (4) electronic wastes (batteries). Pit latrines serve as hotspot reservoirs that receive, harbour, and then transmit the following into the environment; (1) conventional contaminants (nitrates, phosphates, pesticides), (2) emerging contaminants (pharmaceuticals and personal care products, antibiotic resistance), and (3) indicator organisms, and human bacterial and viral pathogens, and disease vectors (rodents, houseflies, bats). As greenhouse gas emission hotspots, pit latrines contribute 3.3 to 9.4 Tg/year of methane, but this could be an under-estimation. Contaminants in pit latrines may migrate into surface water, and groundwater systems serving as drinking water sources and pose human health risks. In turn, this culminates into the pit latrine-groundwater-human continuum or connectivity, mediated via water and contaminant migration. Human health risks of pit latrines, a critique of current evidence, and current and emerging mitigation measures are presented, including isolation distance, hydraulic liners/ barriers, ecological sanitation, and the concept of a circular bioeconomy. Finally, future research directions on the epidemiology and fate of contaminants in pit latrines are presented. The pit latrine paradox is not meant to downplay pit latrines' role or promote open defaecation. Rather, it seeks to stimulate discussion and research to refine the technology to enhance its functionality while mitigating pollution and health risks.

SARS-CoV-2 surveillance-based on municipal solid waste leachate in Brazil

Municipal solid waste leachate-based epidemiology is an alternative viral tracking tool that applies fresh truck leachate as an early warning of public health emergencies. This study aimed to investigate the potential of SARS-CoV-2 surveillance based on solid waste fresh truck leachate. Twenty truck leachate samples were ultracentrifugated, nucleic acid extracted, and real-time RT-qPCR SARS-CoV-2 N1/N2 applied. Viral isolation, variant of concern (N1/N2) inference, and whole genome sequencing were also performed. SARS-CoV-2 was detected on 40% (8/20) of samples, with a concentration from 2.89 to 6.96 RNA Log10 100 mL-1. The attempt to isolate SARS-CoV-2 and recover the whole genome was not successful; however, positive samples were characterized as possible pre-variant of concern (pre-VOC), VOC Alpha (B.1.1.7) and variant of interest Zeta (P.2). This approach revealed an alternative tool to infer SARS-CoV-2 in the environment and may help the management of local surveillance, health, and social policies.

Dependency of sanitation infrastructure on the discharge of faecal coliform and SARS-CoV-2 viral RNA in wastewater from COVID and non-COVID hospitals in Dhaka, Bangladesh

The detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) RNA in wastewater can be used as an indicator of the presence of SARS-CoV-2 infection in specific catchment areas. We conducted a hospital-based study to explore wastewater management in healthcare facilities and analyzed SARS-CoV-2 RNA in the hospital wastewater in Dhaka city during the Coronavirus disease (COVID-19) outbreak between September 2020-January 2021. We selected three COVID-hospitals, two non-COVID-hospitals, and one non-COVID-hospital with COVID wards, conducted spot-checks of the sanitation systems (i.e., toilets, drainage, and septic-tank), and collected 90 untreated wastewater effluent samples (68 from COVID and 22 from non-COVID hospitals). E. coli was detected using a membrane filtration technique and reported as colony forming unit (CFU). SARS-CoV-2 RNA was detected using the iTaq Universal Probes One-Step kit for RT-qPCR amplification of the SARS-CoV-2 ORF1ab and N gene targets and quantified for SARS-CoV-2 genome equivalent copies (GEC) per mL of sample. None of the six hospitals had a primary wastewater treatment facility; two COVID hospitals had functional septic tanks, and the rest of the hospitals had either broken onsite systems or no containment of wastewater. Overall, 100 % of wastewater samples were positive with a high concentration of E. coli (mean = 7.0 log10 CFU/100 mL). Overall, 67 % (60/90) samples were positive for SARS-CoV-2. The highest SARS-CoV-2 concentrations (median: 141 GEC/mL; range: 13-18,214) were detected in wastewater from COVID-hospitals, and in non-COVID-hospitals, the median SARS-CoV-2 concentration was 108 GEC/mL (range: 30-1829). Our results indicate that high concentrations of E. coli and SARS-CoV-2 were discharged through the hospital wastewater (both COVID and non-COVID) without treatment into the ambient water bodies. Although there is no evidence for transmission of SARS-CoV-2 via wastewater, this study highlights the significant risk posed by wastewater from health care facilities in Dhaka for the many other diseases that are spread via faecal oral route. Hospitals in low-income settings could function as sentinel sites to monitor outbreaks through wastewater-based epidemiological surveillance systems. Hospitals should aim to adopt the appropriate wastewater treatment technologies to reduce the discharge of pathogens into the environment and mitigate environmental exposures.

Molecular testing devices for on-site detection of E. coli in water samples

Escherichia coli (E. coli) cells are present in fecal materials that can be the main source for disease-causing agents in water. As a result, E. coli is recommended as a water quality indicator. We have developed an innovative platform to detect E. coli for monitoring water quality on-site by integrating paper-based sample preparation with nucleic acid isothermal amplification. The platform carries out bacterial lysis and DNA enrichment onto a paper pad through ball-based valves for fluid control, with no need of laboratory equipment, followed by loop-mediated isothermal amplification (LAMP) in a battery-operated coffee mug, and colorimetric detection. We have used the platform to detect E. coli in environmental water samples in about 1 h, with a limit of quantitation of 0.2 CFU/mL, and 3 copies per reaction. The platform was confirmed for detecting multiple E. coli strains, and for water samples of different salt concentrations. We validated the functions of the platform by analyzing recreational water samples collected near the Atlantic Ocean that contain different concentrations of salt and bacteria.

Expanding the Pathogen Panel in Wastewater Epidemiology to Influenza and Norovirus

Since the start of the 2019 pandemic, wastewater-based epidemiology (WBE) has proven to be a valuable tool for monitoring the prevalence of SARS-CoV-2. With methods and infrastructure being settled, it is time to expand the potential of this tool to a wider range of pathogens. We used over 500 archived RNA extracts from a WBE program for SARS-CoV-2 surveillance to monitor wastewater from 11 treatment plants for the presence of influenza and norovirus twice a week during the winter season of 2021/2022. Extracts were analyzed via digital PCR for influenza A, influenza B, norovirus GI, and norovirus GII. Resulting viral loads were normalized on the basis of NH4-N. Our results show a good applicability of ammonia-normalization to compare different wastewater treatment plants. Extracts originally prepared for SARS-CoV-2 surveillance contained sufficient genomic material to monitor influenza A, norovirus GI, and GII. Viral loads of influenza A and norovirus GII in wastewater correlated with numbers from infected inpatients. Further, SARS-CoV-2 related non-pharmaceutical interventions affected subsequent changes in viral loads of both pathogens. In conclusion, the expansion of existing WBE surveillance programs to include additional pathogens besides SARS-CoV-2 offers a valuable and cost-efficient possibility to gain public health information.

Biosafety protection and workflow of clinical microbiology laboratory under COVID-19: A review

This paper mainly discusses how to do a good job of daily biosafety protection measures in clinical microbiology laboratories during the epidemic of COVID-19, so as to ensure the safe development of routine clinical microbiology testing items. According to the microbiological and epidemiological characteristics of the novel coronavirus, this paper analyzed the potential risks of the laboratory from the perspective of personal protection before, during, and after testing. Combined with the actual work situation, the improved biosafety protection measures and optimized work flow are introduced to ensure the safety of medical staff and the smooth development of daily work. Danyang People's Hospital of Jiangsu Province, clinical microbiology laboratory of clinical laboratory in strict accordance with the relevant laws and regulations, technical specifications and the expert consensus, combined with their own conditions, the biosafety measures to perfect the working process was optimized, effectively prevent the laboratory exposure, and maintain strict working condition for a long time, continue to improve. We found that the biosafety protection measures of clinical microbiology laboratory have good prevention and control effect on preventing infection of medical staff, which will greatly reduce the risk of infection of medical staff, form good working habits, and provide reference for biosafety protection of microbiology laboratory during the epidemic of COVID-19.

Waste management, COVID-19 and occupational safety and health: Challenges, insights and evidence

Different fields of knowledge have faced challenges due to the COVID-19 pandemic. Essential public services serving the population's needs were maintained. Previous studies have addressed the possibility of health hazards from handling solid waste (SW) among trash collection service workers, without introducing any data proving or dismissing those risks. Occupational health is stated in at least 2 of the 17 Sustainable Development Goals. Pearson Coefficient (r) was employed to analyze the correlation between the number of cases of COVID-19 in SW collection workers in the city of São Paulo, considering the district city halls where the COVID-19 patients live and the SW collection workers' route, from March 2020 to March 2021. Employees who collected wastes with COVID-19: 2% collected healthcare SD, 4% worked at the waste transshipment stations, 10% household variable route collection, and 83% in defined routes collecting household wastes. Positive and moderate correlation was confirmed (r = 0.59) between the total number of COVID-19 cases and the trash collection routes, and the number of contaminated COVID-19 workers from their trash collection routes. Considering concessionary companies separately, the correlation found in the Southeastern grouping is 0.77 (positive and high correlation), and the correlation found in the Northwestern grouping is 0.18 (positive but insignificant correlation). The Northwestern grouping's concessionary had implemented more effective occupational health and safety management policies and disclosed them among their stakeholders. Results suggest concern related to occupational health and safety for SW collection workers and substantiating the vulnerability of this essential activity during the pandemic.

First case of SARS-CoV-2 RNA detection in municipal solid waste leachate from Brazil

This work presents the first case of SARS-CoV-2 RNA detection in leachate collected from a transfer station in the city of São Paulo, Brazil. After calibration of the viral detection method already used for wastewater samples with a pilot leachate sample and virus fragments in laboratory, twelve polyethylene glycol concentrated leachates samples were tested by RT-qPCR. The results confirmed the presence of N1 gene in 9 of the 12 analyzed samples between epidemiological weeks 33 and 38 of the year 2021 (08/15/2021 to 09/19/2021). The occurrence of the N2 gene was only observed in 5 of the 12 samples. The concentration values for N1 and N2 genes varied between 3.1 and 4.6 log10.GC·L-1, which are values close to those measured in sanitary wastewater. This method showed to be a promising procedure to verify the presence of viral RNA in municipal solid waste leachate, being especially useful where there is no treatment system and sanitation infrastructure, which makes the conventional wastewater surveillance unfeasible.

Utilization of SARS-CoV-2 Wastewater Surveillance in Africa-A Rapid Review

Wastewater-based epidemiology for SARS-CoV-2 RNA detection in wastewater is desirable for understanding COVID-19 in settings where financial resources and diagnostic facilities for mass individual testing are severely limited. We conducted a rapid review to map research evidence on the utilization of SARS-CoV-2 wastewater surveillance in Africa. We searched PubMed, Google Scholar, and the World Health Organization library databases for relevant reports, reviews, and primary observational studies. Eight studies met the inclusion criteria. Narrative synthesis of the findings from included primary studies revealed the testing methodologies utilized and that detected amount of SARS-CoV-2 viral RNA correlated with the number of new cases in the studied areas. The included reviews revealed the epidemiological significance and environmental risks of SARS-CoV-2 wastewater. Wastewater surveillance data at the community level can be leveraged for the rapid assessment of emerging threats and aid pandemic preparedness. Our rapid review revealed a glaring gap in the primary literature on SARS-CoV-2 wastewater surveillance on the continent, and accelerated and adequate investment into research is urgently needed to address this gap.