Relevant Literature

Adhikari, Halden, 2022. Opportunities and limits of wastewater-based epidemiology for tracking global health and attainment of UN sustainable development goals. https://doi.org/10.1016/j.envint.2022.107217

Wastewater-based epidemiology (WBE) emerged as a powerful, actionable health management tool during the COVID-19 pandemic. Hypothesizing future uses, we explored its potential for real-time, tracking of progress in attaining United Nations Sustainable Development Goals (SDGs) globally as a non-expensive method using existing infrastructure. We inventoried (i) literature-documented sewerage infrastructure, (ii) demographics of populations served, and (iii) WBE markers informative of 9 SDGs. Among the 17 different sustainable development goals listed by the UN 2030 agenda, more than half of these may be monitored by using WBE monitoring at centralized treatment infrastructure as tabulated in this study. Driven mainly by COVID-19, WBE currently is practiced in at least 55 countries, reaching about 300 million people. Expansion of WBE to 109,000 + treatment plants inventoried in 129 countries would increase global coverage 9-fold to 34.7% or 2.7 billion, leaving out 5 billion people not served by centralized sewerage systems. Associations between population demographics and present-day infrastructure are explored, and geospatial regions particularly vulnerable to infectious disease outbreaks are identified. The results suggest that difference in the differential outcomes in well-being is an outcome of the sanitation infrastructure inequalities and lack of sanitation infrastructure creates doubly disadvantaged populations at risk of poor hygiene and cut off from the early-warning benefits of conventional WBE. This is the first study to explore the feasibility and potential barriers to the use of WBE for tracking the attainment of SDGs globally with at least 9 out of 17 SDGs.

Andrews et al., 2020. Environmental Surveillance as a Tool for Identifying High-risk Settings for Typhoid Transmission. https://doi.org/10.1093/cid/ciaa513

Enteric fever remains a major cause of morbidity in developing countries with poor sanitation conditions that enable fecal contamination of water distribution systems. Historical evidence has shown that contamination of water systems used for household consumption or agriculture are key transmission routes for Salmonella Typhi and Salmonella Paratyphi A. The World Health Organization now recommends that typhoid conjugate vaccines (TCV) be used in settings with high typhoid incidence; consequently, governments face a challenge regarding how to prioritize typhoid against other emerging diseases. A key issue is the lack of typhoid burden data in many low- and middle-income countries where TCV could be deployed. Here we present an argument for utilizing environmental sampling for the surveillance of enteric fever organisms to provide data on community-level typhoid risk. Such an approach could complement traditional blood culture-based surveillance or even replace it in settings where population-based clinical surveillance is not feasible. We review historical studies characterizing the transmission of enteric fever organisms through sewage and water, discuss recent advances in the molecular detection of typhoidal Salmonella in the environment, and outline challenges and knowledge gaps that need to be addressed to establish environmental sampling as a tool for generating actionable data that can inform public health responses to enteric fever.

Bivins et al., 2022. Passive sampling to scale wastewater surveillance of infectious disease: Lessons learned from COVID-19. http://dx.doi.org/10.1016/j.scitotenv.2022.155347

Much of what is known and theorized concerning passive sampling techniques has been developed considering chemical analytes. Yet, historically, biological analytes, such as Salmonella typhi, have been collected from wastewater via passive sampling with Moore swabs. In response to the COVID-19 pandemic, passive sampling is re-emerging as a promising technique to monitor SARS-CoV-2 RNA in wastewater. Method comparisons and disease surveillance using composite, grab, and passive sampling for SARS-CoV-2 RNA detection have found passive sampling with a variety of materials routinely produced qualitative results superior to grab samples and useful for sub-sewershed surveillance of COVID-19. Among individual studies, SARS-CoV-2 RNA concentrations derived from passive samplers demonstrated heterogeneous correlation with concentrations from paired composite samples ranging from weak (R2=0.27, 0.31) to moderate (R2=0.59) to strong (R2=0.76). Among passive sampler materials, electronegative membranes have shown great promise with linear uptake of SARS-CoV-2 RNA observed for exposure durations of 24 to 48 h and in several cases RNA positivity on par with composite samples. Continuing development of passive sampling methods for the surveillance of infectious diseases via diverse forms of fecal waste should focus on optimizing sampler materials for the efficient uptake and recovery of biological analytes, kit-free extraction, and resource-efficient testing methods capable of rapidly producing qualitative or quantitative data. With such refinements passive sampling could prove to be a fundamental tool for scaling wastewater surveillance of infectious disease, especially among the 1.8 billion persons living in low-resource settings served by non-traditional wastewater collection infrastructure.

Chigwechokha, Street, Holm. 2022. Advancing the Use of Fecal Sludge for Timelier and Better-Quality Epidemiological Data in Low- and Middle-Income Countries for Pandemic Prevention. https://doi.org/10.1021/acs.est.2c07788

Global Polio Eradication Initiative, 2022. Field Guidance for the Implementation of Environmental Surveillance for Poliovirus. https://polioeradication.org/wp-content/uploads/2022/11/Field-Guidance-for-the-Implementation-of-ES-20221118-ENG.pdf

Kilaru et al., 2021. Wastewater surveillance for infectious disease: a systematic review. https://doi.org/10.1101/2021.07.26.21261155

Wastewater surveillance of SARS-CoV-2 has shown to be a valuable source of information regarding SARS-CoV-2 transmission and COVID-19 cases. Though the method has been used for several decades to track other infectious diseases, there has not been a comprehensive review outlining all of the pathogens surveilled through wastewater. The aim of this study is to identify what infectious diseases have been previously studied via wastewater surveillance prior to the COVID-19 Pandemic and identify common characteristics between the studies, as well as identify current gaps in knowledge. Peer-reviewed articles published as of August 1, 2020 that examined wastewater for communicable and infectious human pathogens on 2 or more occasions were included in the study. Excluded from this list were all reviews and methods papers, single collection studies, and non-human pathogens. Infectious diseases and pathogens were identified in studies of wastewater surveillance, as well as themes of how wastewater surveillance and other measures of disease transmission were linked. This review did not include any numerical data from individual studies and thus no statistical analysis was done. 1005 articles were identified but only 100 were included in this review after applying the inclusion criteria. These studies came from 38 countries with concentration in certain countries including Italy, Israel, Brazil, Japan, and China. Twenty-five separate pathogen families were identified in the included studies, with the majority of studies examining pathogens from the family Picornaviridae, including polio and non-polio enteroviruses. Most studies of wastewater surveillance did not link what was found in the wastewater to other measures of disease transmission. Among those studies that did compare wastewater surveillance to other measures of disease transmission the value observed was dependent upon pathogen and varied by study. Wastewater surveillance has historically been used to assess water-borne and fecal-orally transmitted pathogens causing diarrheal disease. However, numerous other types of pathogens have been surveilled using wastewater and wastewater surveillance should be considered as a potential tool for many infectious diseases. Wastewater surveillance studies can be improved by incorporating other measures of disease transmission at the population-level including disease incidence and hospitalizations.

Kreier, 2021. The myriad ways sewage surveillance is helping fight COVID around the world. https://www.nature.com/articles/d41586-021-01234-1

Naughton et al., 2021. Show us the Data: Global COVID-19 Wastewater Monitoring Efforts, Equity, and Gaps. https://doi.org/10.1101/2021.03.14.21253564 

A year since the declaration of the global coronavirus disease 2019 (COVID-19) pandemic there were over 110 million cases and 2.5 million deaths. Learning from methods to track community spread of other viruses such as poliovirus, environmental virologists and those in the wastewater based epidemiology (WBE) field quickly adapted their existing methods to detect SARS-CoV-2 RNA in wastewater. Unlike COVID-19 case and mortality data, there was not a global dashboard to track wastewater monitoring of SARS-CoV-2 RNA worldwide. This study provides a one year review of the “COVIDPoops19” global dashboard of universities, sites, and countries monitoring SARS-CoV-2 RNA in wastewater. Methods to assemble the dashboard combined standard literature review, direct submissions, and daily, social media keyword searches. Over 200 universities, 1,000 sites, and 55 countries with 59 dashboards monitor wastewater for SARS-CoV-2 RNA. However, monitoring is primarily in high-income countries (65%) with less access to this valuable tool in low and middle income countries (35%). Data are not widely shared publicly or accessible to researchers to further inform public health actions, perform meta-analysis, better coordinate, and determine equitable distribution of monitoring sites. For WBE to be used to its full potential during COVID-19 and beyond, show us the data.

Nelson, 2022. What poo tells us: wastewater surveillance comes of age amid covid, monkeypox, and polio. https://doi.org/10.1371/journal.pgph.0001377

Pandey et al., 2021. SARS-CoV-2 in wastewater: Challenges for developing countries. https://doi.org/10.1016/j.ijheh.2020.113634

The COVID-19 pandemic that has engulfed the world, has affected the human lives in several aspects. The detection of SARS-CoV-2 in faeces and urine of the infected person, even after viral clearance in the respiratory tract, and its presence in untreated wastewater raises the possibility of fecal-oral transmission in future. The situation is likely to be more aggravated in developing and least developed countries struggling with the problem of ineffective waste disposal system, open defecation, poor sanitation, and limited access to clean drinking water. In this review, the available data on wastewater treatment, sanitation status and healthcare infrastructure from middle- and low-income countries is collected and correlated with the risk associated with the fecal-oral transmission of SARS-CoV-2. The review also highlights the limitation of COVID-19 surveillance through sewage monitoring in these countries owing to the absence of proper sewerage system. An inclusive approach of awareness, prevention, and mitigation from global to the local levels is required to overcome this challenging situation in developing countries.

Shrestha et al., 2021. Wastewater-Based Epidemiology for Cost-Effective Mass Surveillance of COVID-19 in Low- and Middle-Income Countries: Challenges and Opportunities. https://doi.org/10.3390/w13202897

Wastewater-based epidemiology (WBE) is an approach that can be used to estimate COVID-19 prevalence in the population by detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater. As the WBE approach uses pooled samples from the study population, it is an inexpensive and non-invasive mass surveillance method compared to individual testing. Thus, it offers a good complement in low- and middle-income countries (LMICs) facing high costs of testing or social stigmatization, and it has a huge potential to monitor SARS-CoV-2 and its variants to curb the global COVID-19 pandemic. The aim of this review is to systematize the current evidence about the application of the WBE approach in mass surveillance of COVID-19 infection in LMICs, as well as its future potential. Among other parameters, population size contributing the fecal input to wastewater is an important parameter for COVID-19 prevalence estimation. It is easier to back-calculate COVID-19 prevalence in the community with centralized wastewater systems, because there can be more accurate estimates about the size of contributing population in the catchment. However, centralized wastewater management systems are often of low quality (or even non-existent) in LMICs, which raises a major concern about the ability to implement the WBE approach. However, it is possible to mobilize the WBE approach, if large areas are divided into sub-areas, corresponding to the existing wastewater management systems. In addition, a strong coordination between stakeholders is required for estimating population size respective to wastewater management systems. Nevertheless, further international efforts should be leveraged to strengthen the sanitation infrastructures in LMICs, using the lessons gathered from the current COVID-19 pandemic to be prepared for future pandemics.

Tiwari et al., 2022. Wastewater surveillance of antibiotic-resistant bacterial pathogens: A systematic review. https://doi.org/10.3389/fmicb.2022.977106

Infectious diseases caused by antibiotic-resistant bacterial (ARB) pathogens are a serious threat to human and animal health. The active surveillance of ARB using an integrated one-health approach can help to reduce the emergence and spread of ARB, reduce the associated economic impact, and guide antimicrobial stewardship programs. Wastewater surveillance (WWS) of ARB provides composite samples for a total population, with easy access to the mixed community microbiome. This concept is emerging rapidly, but the clinical utility, sensitivity, and uniformity of WWS of ARB remain poorly understood especially in relation to clinical evidence in sewershed communities. Here, we systematically searched the literature to identify studies that have compared findings from WWS of ARB and antibiotic resistance genes (ARG) with clinical evidence in parallel, thereby evaluating how likely WWS of ARB and ARG can relate to the clinical cases in communities. Initially, 2,235 articles were obtained using the primary search keywords, and 1,219 articles remained after de-duplication. Among these, 35 articles fulfilled the search criteria, and an additional 13 relevant articles were included by searching references in the primary literature. Among the 48 included papers, 34 studies used a culture-based method, followed by 11 metagenomics, and three PCR-based methods. A total of 28 out of 48 included studies were conducted at the single sewershed level, eight studies involved several countries, seven studies were conducted at national or regional scales, and five at hospital levels. Our review revealed that the performance of WWS of ARB pathogens has been evaluated more frequently for Escherichia coli, Enterococcus spp., and other members of the family Enterobacteriaceae, but has not been uniformly tested for all ARB pathogens. Many wastewater-based ARB studies comparing the findings with clinical evidence were conducted to evaluate the public health risk but not to relate with clinical evidence and to evaluate the performance of WWS of ARB. Indeed, relating WWS of ARB with clinical evidence in a sewershed is not straightforward, as the source of ARB in wastewater cannot be only from symptomatic human individuals but can also be from asymptomatic carriers as well as from animal sources. Further, the varying fates of each bacterial species and ARG within the sewerage make the aim of connecting WWS of ARB with clinical evidence more complicated. Therefore, future studies evaluating the performance of many AMR pathogens and their genes for WWS one by one can make the process simpler and the interpretation of results easier.

World Health Organization, 2022.  Environmental surveillance for SARS-COV-2 to complement public health surveillance: Interim Guidance https://www.who.int/publications/i/item/WHO-HEP-ECH-WSH-2022.1

World Health Organization, 2022.  Wastewater surveillance of SARS-CoV-2: Questions and answers (Q&A) https://www.who.int/europe/publications/i/item/WHO-EURO-2022-5274-45038-64164

Ali at al., 2022. Community Wastewater-Based Surveillance Can Be a Cost-Effective Approach to Track COVID-19 Outbreak in Low-Resource Settings: Feasibility Assessment for Ethiopia Context. https://doi.org/10.3390/ijerph19148515

Wastewater surveillance systems have become an important component of COVID-19 outbreak monitoring in high-income settings. However, its use in most low-income settings has not been well-studied. This study assessed the feasibility and utility of wastewater surveillance system to monitor SARS-CoV-2 RNA in Addis Ababa, Ethiopia. The study was conducted at nine Membrane Bio-reactor (MBR) wastewater processing plants. The samples were collected in two separate time series. Wastewater samples and known leftover RT-PCR tested nasopharyngeal swabs were processed using two extraction protocols with different sample conditions. SARS-CoV-2 wastewater RT-PCR testing was conducted using RIDA GENE SARS-CoV-2 RUO protocol for wastewater SARS-CoV-2 RNA testing. Wastewater SARS-CoV-2 RNA RT-PCR protocol adaptation, optimization, and detection were conducted in an Addis Ababa, Ethiopia context. Samples collected during the first time series, when the national COVID-19 case load was low, were all negative. Conversely, samples collected during the second time series were all positive, coinciding with the highest daily reported new cases of COVID-19 in Ethiopia. The wastewater-based SARS-CoV-2 surveillance approach is feasible for Addis Ababa. The COVID-19 wastewater based epidemiological approach can potentially fill the evidence gap in distribution and dynamics of COVID-19 in Ethiopia and other low-income settings.

Archer et al., 2023. Occurrence of contaminants of emerging concern in the Eerste River, South Africa: Towards the optimisation of an urban water profiling approach for public- and ecological health risk characterisation. http://dx.doi.org/10.1016/j.scitotenv.2022.160254

The study evaluated the presence and fate of various contaminants of emerging concern (CECs) from a South African wastewater treatment works (WWTW) and surface waters located around an urban setting. A total of 45 CECs were quantified from nine sampling locations over an 11-month period. Daily loads (g/day) of the target analytes in the WWTW showed persistence of some CECs, along with population-normalised daily loads (mg/day/1000inh) of pharmaceuticals and drugs of abuse (DOA) that were estimated for the first time in the study area. Multiple chemical markers were recorded in river water located upstream of the WWTW discharge throughout the study period, suggesting a high degree of diffuse pollution from urban communities in the study area that are not connected to sewage networks or where sanitation services are limited. The potential of using defined surface water locations to perform community-wide substance use profiling for non-sewered communities was also explored. Environmental risk characterisation for the WWTW effluent and surface waters throughout the study period provided multiple risk quotients (RQ) for the target list of CECs spanning over various sentinel trophic levels. High risk profiles (RQ > 1.0) with a frequency of exceedance (FoE) larger than 75 % were recorded for several CECs in both WWTW effluent and surface water locations that suggest potential long-term ecological health risk impacts of pollution hotspot areas in the river catchment situated around the urban area. We present challenges in surface water quality within the study area that is relatable, or may even present more challenging, in other low- or middle-income country (LMICs) settings. The study also highlighted some challenges and limitations associated with the much-needed application of wastewaterbased epidemiology (WBE) intervention in non-sewered communities that can informon public health and communal substance use profiles of the entire urban setting.

Bust, et al., 2021. The SACCESS network for COVID-19 wastewater surveillance: a national collaboration for public health responsiveness. https://hdl.handle.net/10520/ejc-healthr-v2021-n1-a23

Capone et al., 2020. Analysis of Fecal Sludges Reveals Common Enteric Pathogens in Urban Maputo, Mozambique. https://doi.org/10.1021/acs.estlett.0c00610

Sewage surveillance is increasingly used in public health applications; metabolites, biomarkers, and pathogens are detectable in wastewater and can provide useful information about community health. Work on this topic has been limited to wastewaters in mainly high-income settings, however. In low-income countries, where the burden of enteric infection is high, nonsewered sanitation predominates. In order to assess the utility of fecal sludge surveillance as a tool to identify the most prevalent enteric pathogens circulating among at-risk children, we collected 95 matched child stool and fecal sludge samples from household clusters sharing latrines in urban Maputo, Mozambique. We analyzed samples for 20 common enteric pathogens via multiplex real-time quantitative PCR. Among the 95 stools matched to fecal sludges, we detected the six most prevalent bacterial pathogens (Enteroaggregative E. coli, Shigella/Enteroinvasive E. coli, Enterotoxigenic E. coli, Enteropathogenic E. coli, shiga-toxin producing E. coli, Salmonella), and all three protozoan pathogens (Giardia duodenalis, Cryptosporidium parvum, Entamoeba histolytica) in the same rank order in both matrices. We did not observe the same trend for viral pathogens or soil-transmitted helminths, however. Our results suggest that sampling fecal sludges from onsite sanitation offers potential for localized pathogen surveillance in low-income settings where enteric pathogen prevalence is high.

Capone et al., 2021. Impact of sampling depth on pathogen detection in pit latrines. https://doi.org/10.1371/journal.pntd.0009176

Wastewater based epidemiology (WBE) is increasingly used to provide decision makers with actionable data about community health. WBE efforts to date have primarily focused on sewer-transported wastewater in high-income countries, but at least 1.8 billion people in low- and middle-income countries (LMIC) use onsite sanitation systems such as pit latrines and septic tanks. Like wastewater, fecal sludges from such systems offer similar advantages in community pathogen monitoring and other epidemiological applications. To evaluate the distribution of enteric pathogens inside pit latrines–which could inform sampling methods for WBE in LMIC settings unserved by sewers–we collected fecal sludges from the surface, mid-point, and maximum-depth of 33 pit latrines in urban and peri-urban Malawi and analyzed the 99 samples for 20 common enteric pathogens via multiplex quantitative reverse transcription PCR. Using logistic regression adjusted for household population, latrine sharing, the presence of a concrete floor or slab, water source, and anal cleansing materials, we found no significant difference in the odds of detecting the 20 pathogens from the mid-point (adjusted odds ratio, aOR = 1.1; 95% confidence interval = 0.73, 1.6) and surface samples (aOR = 0.80, 95% CI = 0.54, 1.2) compared with those samples taken from the maximum depth. Our results suggest that, for the purposes of routine pathogen monitoring, pit latrine sampling depth does not strongly influence the odds of detecting enteric pathogens by molecular methods. A single sample from the pit latrines’ surface, or a composite of surface samples, may be preferred as the most recent material contributed to the pit and may be easiest to collect.

Dzinamarira et al., 2022. Epidemiological surveillance of enteric viral diseases using wastewater in Africa – A rapid review. https://doi.org/10.1016/j.jiph.2022.05.010

Viral enteric pathogens remain an important cause of diarrhoeal outbreaks among children in sub-Saharan Africa (SSA). Consequently, diarrhoeal illness remains a significant cause of morbidity and mortality in the under-fives in SSA. These outbreaks associated with viral pathogens tend to be seasonal and early warning systems for impending outbreaks could be very crucial for triggering preventive public health response and building public health resilience to deal with increased demand for medical services. Wastewater surveillance for pathogens is an important epidemiological component that could inform early warning systems. The objective of this rapid review was to evaluate the use of wastewater for epidemiology surveillance of enteric viral pathogens. Nine studies met the inclusion criteria. Eight viral pathogens were reviewed and analysed from 6 countries that performed wastewater analysis. Six studies explored the epidemiologic significance of viral pathogens in wastewater. The findings of this review revealed that monitoring of wastewater can provide an additional tool to determine the epidemiology of viral pathogens circulating in the community thereby providing early warning of potential outbreaks using wastewater-based epidemiology methods. Five of the included studies revealed the occurrence of viral pathogens in raw sewage and treated wastewater as an indication of inefficient elimination of viruses leading to potential release into water sources which presents a public health risk, increasing the risk of inducing gastroenteritis in the population. Six studies revealed the need for public health authorities to realise the potential benefit of environmental surveillance (ES) as an additional tool to determine the epidemiology of viral pathogens circulating in each community. Despite the significant public health challenge associated with enteric viral pathogens in sub-Saharan Africa, there remains remarkable underinvestment in potentially epidemiologically beneficial research, including wastewater-based epidemiology for these infections.

Dzinamarira et al., 2022. Utilization of SARS-CoV-2 Wastewater Surveillance in Africa—A Rapid Review. https://doi.org/10.1016/j.jiph.2022.05.010

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.

International Association of National Public Health Institutes, 2022. Wastewater Surveillance Programs for COVID-19 and Other Pathogens Led by African National Public Health Institutes. https://ianphi.org/news/2022/wastewater-surveillance-webinar.html

Johnson et al., 2022. Tracking the circulating SARS‑CoV‑2 variant of concern in South Africa using wastewater‑based epidemiology. https://doi.org/10.1038/s41598-022-05110-4

This study uses wastewater-based epidemiology (WBE) to rapidly and, through targeted surveillance, track the geographical distribution of SARS-CoV-2 variants of concern (Alpha, Beta and Delta) within 24 wastewater treatment plants (WWTPs) in the Western Cape of South Africa. Information obtained was used to identify the circulating variant of concern (VOC) within a population and retrospectively trace when the predominant variant was introduced. Genotyping analysis of SARS-CoV-2 showed that 50% of wastewater samples harbored signature mutations linked to the Beta variant before the third wave, with the Delta variant absent within the population. Over time, the prevalence of the beta variant decreased steadily. The onset of the third wave resulted in the Delta variant becoming the predominant variant, with a 100% prevalence supporting the theory that the Delta variant was driving the third wave. In silico molecular docking analysis showed that the signature mutations of the Delta variant increased binding to host proteins, suggesting a possible molecular mechanism that increased viral infectivity of the Delta variant.

Kasprzyk-Hordern et al., 2022. Wastewater-based epidemiology in hazard forecasting and early-warning systems for global health risks. https://doi.org/10.1016/j.envint.2022.107143

With the advent of the SARS-CoV-2 pandemic, Wastewater-Based Epidemiology (WBE) has been applied to track community infection in cities worldwide and has proven succesful as an early warning system for identification of hotspots and changing prevalence of infections (both symptomatic and asymptomatic) at a city or sub-city level. Wastewater is only one of environmental compartments that requires consideration. In this manuscript, we have critically evaluated the knowledge-base and preparedness for building early warning systems in a rapidly urbanising world, with particular attention to Africa, which experiences rapid population growth and urbanisation. We have proposed a Digital Urban Environment Fingerprinting Platform (DUEF) – a new approach in hazard forecasting and early-warning systems for global health risks and an extension to the existing concept of smart cities. The urban environment (especially wastewater) contains a complex mixture of substances including toxic chemicals, infectious biological agents and human excretion products. DUEF assumes that these specific endo- and exogenous residues, anonymously pooled by communities’ wastewater, are indicative of community-wide exposure and the resulting effects. DUEF postulates that the measurement of the substances continuously and anonymously pooled by the receiving environment (sewage, surface water, soils and air), can provide near real-time dynamic information about the quantity and type of physical, biological or chemical stressors to which the surveyed systems are exposed, and can create a risk profile on the potential effects of these exposures. Successful development and utilisation of a DUEF globally requires a tiered approach including: Stage I: network building, capacity building, stakeholder engagement as well as a conceptual model, followed by Stage II: DUEF development, Stage III: implementation, and Stage IV: management and utilization. We have identified four key pillars required for the establishment of a DUEF framework: (1) Environmental fingerprints, (2) Socioeconomic fingerprints, (3) Statistics and modelling and (4) Information systems. This manuscript critically evaluates the current knowledge base within each pillar and provides recommendations for further developments with an aim of laying grounds for successful development of global DUEF platforms.

Mahlangeni et al., 2023. Using Wastewater Surveillance to Compare COVID-19 Outbreaks during the Easter Holidays over a 2-Year Period in Cape Town, South Africa https://www.mdpi.com/1999-4915/15/1/162

Wastewater surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown to be an important approach to determine early outbreaks of infections. Wastewater-based epidemiology (WBE) is regarded as a complementary tool for monitoring SARS-CoV-2 trends in communities. In this study, the changes in the SARS-CoV-2 RNA levels in wastewater during Easter holidays in 2021 and 2022 in the City of Cape Town were monitored over nine weeks. Our findings showed a statistically significant difference in the SARS-CoV-2 RNA viral load between the study weeks over the Easter period in 2021 and 2022, except for study week 1 and 4. During the Easter week, 52% of the wastewater treatment plants moved from the lower (low viral RNA) category in 2021 to the higher (medium to very high viral RNA) categories in 2022. As a result, the median SARS-CoV-2 viral loads where higher during the Easter week in 2022 than Easter week in 2021 (p = 0.0052). Mixed-effects model showed an association between the SARS-CoV-2 RNA viral loads and Easter week over the Easter period in 2021 only (p < 0.01). The study highlights the potential of WBE to track outbreaks during the holiday period.

Mtetwa at al., 2021. Wastewater-Based Surveillance of Antibiotic Resistance Genes Associated with Tuberculosis Treatment Regimen in KwaZulu Natal, South Africa. https://doi.org/10.3390/antibiotics10111362

Essential components of public health include strengthening the surveillance of infectious diseases and developing early detection and prevention policies. This is particularly important for drug-resistant tuberculosis (DR-TB), which can be explored by using wastewater-based surveillance. This study aimed to use molecular techniques to determine the occurrence and concentration of antibiotic-resistance genes (ARGs) associated with tuberculosis (TB) resistance in untreated and treated wastewater. Raw/untreated and treated (post-chlorination) wastewater samples were taken from three wastewater treatment plants (WWTPs) in South Africa. The ARGs were selected to target drugs used for first- and second-line TB treatment. Both conventional polymerase chain reaction (PCR) and the more advanced droplet digital PCR (ddPCR) were evaluated as surveillance strategies to determine the distribution and concentration of the selected ARGs. The most abundant ARG in the untreated wastewater was the rrs gene, associated with resistance to the aminoglycosides, specifically streptomycin, with median concentration ranges of 4.69–5.19 log copies/mL. In contrast, pncA gene, associated with resistance to the TB drug pyrazinamide, was the least detected (1.59 to 2.27 log copies/mL). Resistance genes associated with bedaquiline was detected, which is a significant finding because this is a new drug introduced in South Africa for the treatment of multi-drug resistant TB. This study, therefore, establishes the potential of molecular surveillance of wastewater for monitoring antibiotic resistance to TB treatment in communities.

Ngwira et al., 2022. Cost of wastewater-based environmental surveillance for SARS-CoV-2: Evidence from pilot sites in Blantyre, Malawi and Kathmandu, Nepal. https://doi.org/10.1371/journal.pgph.0001377

Environmental surveillance of rivers and wastewater for SARS-CoV-2 detection has been explored as an innovative way to surveil the pandemic. This study estimated the economic costs of conducting wastewater-based environmental surveillance for SARS-CoV-2 to inform decision making if countries consider continuing these efforts. We estimated the cost of two SARS-CoV-2 environmental surveillance pilot studies conducted in Blantyre, Malawi, and Kathmandu, Nepal. The cost estimation accounted for the consumables, equipment, and human resource time costs used for environmental surveillance from sample selection until pathogen detection and overhead costs for the projects. Costs are reported in 2021 US $ and reported as costs per month, per sample and person per year. The estimated costs for environmental surveillance range from $6,175 to $8,272 per month (Blantyre site) and $16,756 to $30,050 (Kathmandu site). The number of samples processed per month ranged from 84 to 336 at the Blantyre site and 96 to 250 at the Kathmandu site. Consumables costs are variable costs influenced by the number of samples processed and are a large share of the monthly costs for ES (ranging from 39% to 72%). The relatively higher costs per month for the Kathmandu site were attributable to the higher allocation of dedicated human resources and equipment to environmental surveillance for SARS-CoV-2 compared to the Blantyre site where these resources were shared with other activities. The average cost per sample ranged from $25 to $74 (Blantyre) and $120 to $175 (Kathmandu). There were associated economies of scale for human resources and equipment costs with increased sample processing and sharing of resources with other activities. The cost per person in the catchment area per year ranged from $0.07 to $0.10 in Blantyre and $0.07 to $0.13 in Kathmandu. Environmental surveillance may be a low-cost early warning signal for SARS-CoV-2 that can complement other SARS-CoV2 monitoring efforts.

Pillay et al., 2021. Monitoring changes in COVID-19 infection using wastewater-based epidemiology: A South African perspective. https://doi.org/10.1016/j.scitotenv.2021.147273

Monitoring of COVID-19 infections within communities via wastewater-based epidemiology could provide a cost-effective alternative to clinical testing. This approach, however, still requires improvement for its efficient application. In this paper, we present the use of wastewater-based epidemiology inmonitoring COVID-19 infection dynamics in the KwaZulu-Natal province of South Africa, focusing on four wastewater treatment plants for 14 weeks. The SARS-CoV-2 viral load in influent wastewater was determined using droplet digital PCR, and the number of people infected was estimated using published models as well as using a modified model to improve efficiency. On average, viral loads ranged between 0 and 2.73 × 105 copies/100 ml, 0–1.52 × 105 copies/100 ml, 3 × 104–7.32 × 105 copies/100 ml and 1.55 × 104–4.12 × 105 copies/100 ml in the four wastewater treatment plants studied. The peak in viral load corresponded to the reported COVID-19 infections within the districts where these catchments are located. In addition,we also observed that easing of lockdown restrictions by authorities corresponded with an increase in viral load in the untreated wastewater. Estimation of infection numbers based on the viral load showed that a higher number of people could potentially be infected, compared to the number of cases reported based on clinical testing. The findings reported in this paper contribute to the field of wastewater-based epidemiology for COVID-19 surveillance, whilst highlighting some of the challenges associated with this approach, especially in developing countries.

Pillay et al., 2022. Environmental surveillance for non sewered communities: a tool for disease mitigation in developing countries. https://www.wrc.org.za/wp-content/uploads/mdocs/Science%20briefs_NSS%20Surveillance.pdf

Environmental surveillance and Wastewater-Based Epidemiology (WBE) has proven to a useful tool in fighting a pandemic. Recent application of techniques for SARS-CoV-2 detection in sewage has provided vital information on the emergence of disease, circulating variants of interest and variants of concern, and possibility of predicting hospital admissions. Developing countries do not have extensive sewer networks and therefore cannot use WBE for the same population scale. A South African study has successfully demonstrated the application of nonsewered surveillance across multiple sites and provinces in South Africa. To the authors’ knowledge, this has been the largest non sewered surveillance programme undertaken globally.

Pocock et al., 2020. Proof of concept study: Application of wastewater-based surveillance to monitor SARS-CoV-2 prevalence in South African communities. https://erwat.co.za/wrc-proof-of-concept-study-wastewater-basedepidemiology-for-surveillance-of-the-spread-of-covid-19-insouth-african-communities/

Pocock et al., 2021. The efficacy of passive samplers for water quality based COVID-19 epidemiology surveillance. https://www.watershare.eu/wp-content/uploads/Science-Brief_-10_COVID19-surveillance-for-Non-Sewered.pdf

-Wastewater-based surveillance of communities for SARS-CoV-2 viral prevalence by sampling from wastewater treatment works is a powerful complementary epidemiological tool. However, in South Africa almost 40% of the population is not connected to a waterborne sewerage system.
-Sampling and surveillance of greywater and faecal waste within our non-sewered areas may give an early warning of the presence of COVID-19 infections in these communities, where there is both the risk of rapid spread and low likelihood of conventional testing.
-Passive sampling of environmental sites has shown promise, and may overcome issues of low yield when viral load is low and during high dilution periods, particularly in rivers downstream of unsewered settlements.
-Passive samplers have the advantage of allowing for easier and cheaper transport of samples compared to grab samples that require the costly transport of large volumes of water maintenance of the cold chain out of rural areas. Sample processing is also much quicker compared to concentration of water samples.
-Inclusion of trend monitoring of SARS-CoV-2 prevalence in unsewered communities together with established wastewater-based epidemiology (WBE) data collection from WWTW sampling can greatly expand the knowledge base and serve to highlight the needs of vulnerable communities in South Africa. These passive samplers can now also potentially be used for wastewater-based epidemiology for a broader scope of pathogens than only SARS-CoV-2.
-The success of passive samplers from this initiative has demonstrated the future B41potential and opportunity to enable more widespread environmental water quality monitoring due to its low cost and ease of application in the collection of samples.

Richardson, 2021. How waste water is helping South Africa fight COVID-19. https://www.nature.com/articles/d41586-021-01399-9

Street et al., 2020. Wastewater surveillance for Covid-19: An African perspective. https://doi.org/10.1016/j.scitotenv.2020.140719

The COVID-19 pandemic has once again highlighted the importance of access to sufficient quantities of safe water and sanitation in public health. In the current COVID-19 pandemic, an early warning wastewater system has been proposed as a platformfor SARS-CoV-2 surveillance, and a potentially important public health strategy to combat the disease. This short communication on wastewater surveillance in sub-Saharan Africa highlights challenges, opportunities and alternatives taken into account the local context.

South Africa National Institute for Communicable Diseases, 2023. Dashboard: SARS-CoV-2 wastewater levels in South Africa. https://wastewater.nicd.ac.za/

Tegally et al., 2022. The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance https://doi.org/10.1126/science.abq5358

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern—particularly Alpha, Beta, Delta, and Omicron—on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

Tlhagale et al., 2022. Establishment of local wastewater-based surveillance programmes in response to the spread and infection of COVID-19 – case studies from South Africa, the Netherlands, Turkey and England. https://doi.org/10.2166/wh.2022.185

The COVID-19 pandemic has resulted in over 340 million infection cases (as of 21 January 2022) and more than 5.57 million deaths globally. In reaction, science, technology and innovation communities across the globe have organised themselves to contribute to national responses to COVID-19 disease. A significant contribution has been from the establishment of wastewater-based epidemiological (WBE) surveillance interventions and programmes for monitoring the spread of COVID-19 in at least 55 countries. Here, we examine and share experiences and lessons learnt in establishing such surveillance programmes. We use case studies to highlight testing methods and logistics considerations associated in scaling the implementing of such programmes in South Africa, the Netherlands, Turkey and England. The four countries were selected to represent different regions of the world and the perspective based on the considerable progress made in establishing and implementing their national WBE programmes. The selected countries also represent different climatic zones, economies, and development stages, which influence the implementation of national programmes of this nature and magnitude. In addition, the four countries’ programmes offer good experiences and lessons learnt since they are systematic, and cover extensive areas, disseminate knowledge locally and internationally and partnered with authorities (government). The programmes also strengthened working relations and partnerships between and among local and global organisations. This paper shares these experiences and lessons to encourage others in the water and public health sectors on the benefits and value of WBE in tackling SARS-CoV-2 and related future circumstances.

World Health Organization, 2022. How wastewater surveillance is helping the COVID-19 fight. https://www.afro.who.int/news/how-wastewater-surveillance-helping-covid-19-fight

Fongaro et al., 2021. SARS‑CoV‑2 in Human Sewage and River Water from a Remote and Vulnerable Area as a Surveillance Tool in Brazil. https://doi.org/10.1007/s12560-021-09487-9

In the present study, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was monitored in environmental samples from rural and vulnerable areas (a presidio, worker accommodation units, and river waters upstream and downstream of a rural community) from Minas Gerais State region, Southern Brazil, in August 2020. The sampling was performed prior to official declaration of the coronavirus disease (COVID-19) cases in those sites. SARS-CoV-2 RNA was detected in the presidio and workers accommodation units (3.0 × 104 virus genome copies (GC)/mL and 4.3 × 104 GC/mL of sewage, respectively). While SARS-CoV-2 was not detected in the river water upstream of the rural community, SARS-CoV-2 RNA was detected in downstream river waters (1.1 × 102 SARS-CoV-2 GC/mL). The results obtained in this study highlight the utility of SARS-CoV-2 monitoring in wastewater and human sewage as a non-invasive early warning tool to support health surveillance in vulnerable and remote areas, particularly in development countries.

Guerrero-Latorre et al., 2020. SARS-CoV-2 in river water: Implications in low sanitation countries. https://doi.org/10.1016/j.scitotenv.2020.140832

Since the beginning of COVID-19 pandemic studies on viral shedding have reported that this virus is excreted in feces in most patients. High viral loads are found at the sewage pipeline or at the entrance of wastewater treatment plants fromcitieswhere the number of COVID-19 cases are significant. In Quito (Ecuador) as inmany other cities worldwide, wastewater is directly discharged into natural waters. The aim of this study was to evaluate SARS-CoV-2 presence in urban streams from a low sanitation context. Three river locations along the urban rivers of Quito were sampled on the 5th of June during a peak of COVID-19 cases. River samples were evaluated for water quality parameters and afterwards, concentrated for viral analysis using skimmed milk flocculation method. The viral concentrates were quantified for SARS-CoV-2 (N1 and N2 target regions) and Human Adenovirus as a human viral indicator. The results showed that SARS-CoV-2 was detected for both target regions in all samples analyzed in a range of 2,91E+05 to 3,19E+06 GC/L for N1 and from2,07E+05 to 2,22E+06 GC/L for N2. The high values detected in natural waters from a low sanitation region have several implications in health and ecology that should be further assessed.

Sosa-Hernández et al., 2022. Extensive Wastewater-Based Epidemiology as a Resourceful Tool for SARS-CoV-2 Surveillance in a Low-to-Middle-Income Country through a Successful Collaborative Quest: WBE, Mobility, and Clinical Tests. https://doi.org/10.3390/w14121842

The COVID-19 pandemic has challenged healthcare systems worldwide. Efforts in low-to middle- income countries (LMICs) cannot keep stride with infection rates, especially during peaks. A strong international collaboration between Arizona State University (ASU), Tec de Monterrey (TEC), and Servicios de Agua y Drenaje de Monterrey (Local Water Utilities) is acting to integrate wastewater-based epidemiology (WBE) of SARS-CoV-2 in the region as a complementary approach to aid the healthcare system. Wastewater was collected from four sewer catchments in the Monterrey Metropolitan area in Mexico (pop. 4,643,232) from mid-April 2020 to February 2021 (44 weeks, n = 644). Raw wastewater was filtered and filter-concentrated, the RNA was extracted using columns, and the Charité/Berlin protocol was used for the RT-qPCR. The viral loads obtained between the first (June 2020) and second waves (February 2021) of the pandemic were similar; in contrast, the clinical cases were fewer during the first wave, indicating poor coverage. During the second wave of the pandemic, the SARS-CoV-2 quantification in wastewater increased 14 days earlier than the COVID-19 clinical cases reported. This is the first long-term WBE study in Mexico and demonstrates its value in pandemic management.

US Centers for Disease Control and Prevention, 2022. Wastewater Surveillance in Low-Resource Waste Systems. https://www.cdc.gov/nwss/low-resource/index.html

US Centers for Disease Control and Prevention, 2022. How Wastewater Surveillance Works. https://www.cdc.gov/nwss/how-wws-works/index.html

Haque et al., 2022. Wastewater surveillance of SARS-CoV-2 in Bangladesh: Opportunities and challenges. https://doi.org/10.1016/j.coesh.2022.100334

The ongoing pandemic of the coronavirus disease 2019 (COVID-19) is a public health crisis of global concern. The progression of the COVID-19 pandemic has been monitored in the first place by testing symptomatic individuals for SARS-CoV-2 virus in the respiratory samples. Concurrently, wastewater carries feces, urine, and sputum that potentially contains SARS-CoV-2 intact virus or partially damaged viral genetic materials excreted by infected individuals. This brings significant opportunities for understanding the infection dynamics by environmental surveillance. It has advantages for the country, especially in densely populated areas where individual clinical testing is difficult. However, there are several challenges including: 1) establishing a sampling plan and schedule that is representative of the various catchment populations 2) development and validation of standardized protocols for the laboratory analysis 3) understanding hydraulic flows and virus transport in complex wastewater drainage systems and 4) collaborative efforts from government agencies, NGOs, public health units and academia.

Murni et al., 2022. The feasibility of SARS-CoV-2 surveillance using wastewater and environmental sampling in Indonesia. https://doi.org/10.1371/journal.pone.0274793

Background: Wastewater-based epidemiology (WBE) surveillance as an early warning system (EWS) for monitoring community transmission of SARS-CoV-2 in low- and middle-income country (LMIC) settings, where diagnostic testing capacity is limited, needs further exploration. We explored the feasibility to conduct a WBE surveillance in Indonesia, one of the global epicenters of the COVID-19 pandemic in the middle of 2021, with the fourth largest population in the world where sewer and non-sewered sewage systems are implemented. The feasibility and resource capacity to collect samples on a weekly or fortnightly basis with grab and/or passive sampling methods, as well as to conduct qualitative and quantitative identification of SARS-CoV-2 ribonucleic acid (RNA) using real-time RT-PCR (RT-qPCR) testing of environmental samples were explored.
Materials and methods: We initiated a routine surveillance of wastewater and environmental sampling at three predetermined districts in Special Region of Yogyakarta Province. Water samples were collected from central and community wastewater treatment plants (WWTPs), including manholes flowing to the central WWTP, and additional soil samples were collected for the near source tracking (NST) locations (i.e., public spaces where people congregate).
Results: We began collecting samples in the Delta wave of the COVID-19 pandemic in Indonesia in July 2021. From a 10-week period, 54% (296/544) of wastewater and environmental samples were positive for SARS-CoV-2 RNA. The sample positivity rate decreased in proportion with the reported incidence of COVID-19 clinical cases in the community. The highest positivity rate of 77% in week 1, was obtained for samples collected in July 2021 and decreased to 25% in week 10 by the end of September 2021.
Conclusion: A WBE surveillance system for SARS-CoV-2 in Indonesia is feasible to monitor the community burden of infections. Future studies testing the potential of WBE and EWS for signaling early outbreaks of SARS-CoV-2 transmissions in this setting are required.

Ngwira et al., 2022. Cost of wastewater-based environmental surveillance for SARS-CoV-2: Evidence from pilot sites in Blantyre, Malawi and Kathmandu, Nepal. https://doi.org/10.1371/journal.pgph.0001377

Environmental surveillance of rivers and wastewater for SARS-CoV-2 detection has been explored as an innovative way to surveil the pandemic. This study estimated the economic costs of conducting wastewater-based environmental surveillance for SARS-CoV-2 to inform decision making if countries consider continuing these efforts. We estimated the cost of two SARS-CoV-2 environmental surveillance pilot studies conducted in Blantyre, Malawi, and Kathmandu, Nepal. The cost estimation accounted for the consumables, equipment, and human resource time costs used for environmental surveillance from sample selection until pathogen detection and overhead costs for the projects. Costs are reported in 2021 US $ and reported as costs per month, per sample and person per year. The estimated costs for environmental surveillance range from $6,175 to $8,272 per month (Blantyre site) and $16,756 to $30,050 (Kathmandu site). The number of samples processed per month ranged from 84 to 336 at the Blantyre site and 96 to 250 at the Kathmandu site. Consumables costs are variable costs influenced by the number of samples processed and are a large share of the monthly costs for ES (ranging from 39% to 72%). The relatively higher costs per month for the Kathmandu site were attributable to the higher allocation of dedicated human resources and equipment to environmental surveillance for SARS-CoV-2 compared to the Blantyre site where these resources were shared with other activities. The average cost per sample ranged from $25 to $74 (Blantyre) and $120 to $175 (Kathmandu). There were associated economies of scale for human resources and equipment costs with increased sample processing and sharing of resources with other activities. The cost per person in the catchment area per year ranged from $0.07 to $0.10 in Blantyre and $0.07 to $0.13 in Kathmandu. Environmental surveillance may be a low-cost early warning signal for SARS-CoV-2 that can complement other SARS-CoV2 monitoring efforts.

Tlhagale et al., 2022. Establishment of local wastewater-based surveillance programmes in response to the spread and infection of COVID-19 – case studies from South Africa, the Netherlands, Turkey and England. https://doi.org/10.2166/wh.2022.185

The COVID-19 pandemic has resulted in over 340 million infection cases (as of 21 January 2022) and more than 5.57 million deaths globally. In reaction, science, technology and innovation communities across the globe have organised themselves to contribute to national responses to COVID-19 disease. A significant contribution has been from the establishment of wastewater-based epidemiological (WBE) surveillance interventions and programmes for monitoring the spread of COVID-19 in at least 55 countries. Here, we examine and share experiences and lessons learnt in establishing such surveillance programmes. We use case studies to highlight testing methods and logistics considerations associated in scaling the implementing of such programmes in South Africa, the Netherlands, Turkey and England. The four countries were selected to represent different regions of the world and the perspective based on the considerable progress made in establishing and implementing their national WBE programmes. The selected countries also represent different climatic zones, economies, and development stages, which influence the implementation of national programmes of this nature and magnitude. In addition, the four countries’ programmes offer good experiences and lessons learnt since they are systematic, and cover extensive areas, disseminate knowledge locally and internationally and partnered with authorities (government). The programmes also strengthened working relations and partnerships between and among local and global organisations. This paper shares these experiences and lessons to encourage others in the water and public health sectors on the benefits and value of WBE in tackling SARS-CoV-2 and related future circumstances.

Zohra et al., 2021. Wastewater based environmental surveillance of toxigenic Vibrio cholerae in Pakistan. https://doi.org/10.1371/journal.pone.0257414

Background: Pakistan has been experiencing intervals of sporadic cases and localized outbreaks in the last two decades. No proper study has been carried out in order to find out the environmental burden of toxigenic V. cholerae as well as how temporal and environmental factors associated in driving cholera across the country.
Methods: We tested waste water samples from designated national environment surveillance sites in Pakistan with RT-PCR assay. Multistage sampling technique were utilized for samples collection and for effective sample processing Bag-Mediated Filtration system, were employed. Results were analysed by district and month wise to understand the geographic distribution and identify the seasonal pattern of V. cholera detection in Pakistan.
Results: Between May 2019, and February 2020, we obtained and screened 160 samples in 12 districts across Pakistan. Out of 16 sentinel environmental surveillance sites, 15 sites showed positive results against cholera toxigenic gene with mostly lower CT value (mean, 34±2) and have significant difference (p < 0.05). The highest number of positive samples were collected from Sindh in month of November, then in June it is circulating in different districts of Pakistan including four Provinces respectively. Conclusion: V. cholera detection do not follow a clear seasonal pattern. However, the poor sanitation problems or temperature and rainfall may potentially influence the frequency and duration of cholera across the country. Occurrence of toxigenic V. cholerae in the environment samples showed that cholera is endemic, which is an alarming for a potential future cholera outbreaks in the country.

Tlhagale et al., 2022. Establishment of local wastewater-based surveillance programmes in response to the spread and infection of COVID-19 – case studies from South Africa, the Netherlands, Turkey and England. https://doi.org/10.2166/wh.2022.185

The COVID-19 pandemic has resulted in over 340 million infection cases (as of 21 January 2022) and more than 5.57 million deaths globally. In reaction, science, technology and innovation communities across the globe have organised themselves to contribute to national responses to COVID-19 disease. A significant contribution has been from the establishment of wastewater-based epidemiological (WBE) surveillance interventions and programmes for monitoring the spread of COVID-19 in at least 55 countries. Here, we examine and share experiences and lessons learnt in establishing such surveillance programmes. We use case studies to highlight testing methods and logistics considerations associated in scaling the implementing of such programmes in South Africa, the Netherlands, Turkey and England. The four countries were selected to represent different regions of the world and the perspective based on the considerable progress made in establishing and implementing their national WBE programmes. The selected countries also represent different climatic zones, economies, and development stages, which influence the implementation of national programmes of this nature and magnitude. In addition, the four countries’ programmes offer good experiences and lessons learnt since they are systematic, and cover extensive areas, disseminate knowledge locally and internationally and partnered with authorities (government). The programmes also strengthened working relations and partnerships between and among local and global organisations. This paper shares these experiences and lessons to encourage others in the water and public health sectors on the benefits and value of WBE in tackling SARS-CoV-2 and related future circumstances.

Andrews et al., 2020. Environmental Surveillance as a Tool for Identifying High-risk Settings for Typhoid Transmission. https://doi.org/10.1093/cid/ciaa513

Enteric fever remains a major cause of morbidity in developing countries with poor sanitation conditions that enable fecal contamination of water distribution systems. Historical evidence has shown that contamination of water systems used for household consumption or agriculture are key transmission routes for Salmonella Typhi and Salmonella Paratyphi A. The World Health Organization now recommends that typhoid conjugate vaccines (TCV) be used in settings with high typhoid incidence; consequently, governments face a challenge regarding how to prioritize typhoid against other emerging diseases. A key issue is the lack of typhoid burden data in many low- and middle-income countries where TCV could be deployed. Here we present an argument for utilizing environmental sampling for the surveillance of enteric fever organisms to provide data on community-level typhoid risk. Such an approach could complement traditional blood culture-based surveillance or even replace it in settings where population-based clinical surveillance is not feasible. We review historical studies characterizing the transmission of enteric fever organisms through sewage and water, discuss recent advances in the molecular detection of typhoidal Salmonella in the environment, and outline challenges and knowledge gaps that need to be addressed to establish environmental sampling as a tool for generating actionable data that can inform public health responses to enteric fever.

Bust, et al., 2021. The SACCESS network for COVID-19 wastewater surveillance: a national collaboration for public health responsiveness. https://hdl.handle.net/10520/ejc-healthr-v2021-n1-a23

Dzinamarira et al., 2022. Epidemiological surveillance of enteric viral diseases using wastewater in Africa – A rapid review. https://doi.org/10.1016/j.jiph.2022.05.010

Viral enteric pathogens remain an important cause of diarrhoeal outbreaks among children in sub-Saharan Africa (SSA). Consequently, diarrhoeal illness remains a significant cause of morbidity and mortality in the under-fives in SSA. These outbreaks associated with viral pathogens tend to be seasonal and early warning systems for impending outbreaks could be very crucial for triggering preventive public health response and building public health resilience to deal with increased demand for medical services. Wastewater surveillance for pathogens is an important epidemiological component that could inform early warning systems. The objective of this rapid review was to evaluate the use of wastewater for epidemiology surveillance of enteric viral pathogens. Nine studies met the inclusion criteria. Eight viral pathogens were reviewed and analysed from 6 countries that performed wastewater analysis. Six studies explored the epidemiologic significance of viral pathogens in wastewater. The findings of this review revealed that monitoring of wastewater can provide an additional tool to determine the epidemiology of viral pathogens circulating in the community thereby providing early warning of potential outbreaks using wastewater-based epidemiology methods. Five of the included studies revealed the occurrence of viral pathogens in raw sewage and treated wastewater as an indication of inefficient elimination of viruses leading to potential release into water sources which presents a public health risk, increasing the risk of inducing gastroenteritis in the population. Six studies revealed the need for public health authorities to realise the potential benefit of environmental surveillance (ES) as an additional tool to determine the epidemiology of viral pathogens circulating in each community. Despite the significant public health challenge associated with enteric viral pathogens in sub-Saharan Africa, there remains remarkable underinvestment in potentially epidemiologically beneficial research, including wastewater-based epidemiology for these infections.

Fongaro et al., 2021. SARS‑CoV‑2 in Human Sewage and River Water from a Remote and Vulnerable Area as a Surveillance Tool in Brazil. https://doi.org/10.1007/s12560-021-09487-9

In the present study, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was monitored in environmental samples from rural and vulnerable areas (a presidio, worker accommodation units, and river waters upstream and downstream of a rural community) from Minas Gerais State region, Southern Brazil, in August 2020. The sampling was performed prior to official declaration of the coronavirus disease (COVID-19) cases in those sites. SARS-CoV-2 RNA was detected in the presidio and workers accommodation units (3.0 × 104 virus genome copies (GC)/mL and 4.3 × 104 GC/mL of sewage, respectively). While SARS-CoV-2 was not detected in the river water upstream of the rural community, SARS-CoV-2 RNA was detected in downstream river waters (1.1 × 102 SARS-CoV-2 GC/mL). The results obtained in this study highlight the utility of SARS-CoV-2 monitoring in wastewater and human sewage as a non-invasive early warning tool to support health surveillance in vulnerable and remote areas, particularly in development countries.

Global Polio Eradication Initiative, 2022. Field Guidance for the Implementation of Environmental Surveillance for Poliovirus. https://polioeradication.org/wp-content/uploads/2022/11/Field-Guidance-for-the-Implementation-of-ES-20221118-ENG.pdf

Guerrero-Latorre et al., 2020. SARS-CoV-2 in river water: Implications in low sanitation countries. https://doi.org/10.1016/j.scitotenv.2020.140832 

Since the beginning of COVID-19 pandemic studies on viral shedding have reported that this virus is excreted in feces in most patients. High viral loads are found at the sewage pipeline or at the entrance of wastewater treatment plants fromcitieswhere the number of COVID-19 cases are significant. In Quito (Ecuador) as inmany other cities worldwide, wastewater is directly discharged into natural waters. The aim of this study was to evaluate SARS-CoV-2 presence in urban streams from a low sanitation context. Three river locations along the urban rivers of Quito were sampled on the 5th of June during a peak of COVID-19 cases. River samples were evaluated for water quality parameters and afterwards, concentrated for viral analysis using skimmed milk flocculation method. The viral concentrates were quantified for SARS-CoV-2 (N1 and N2 target regions) and Human Adenovirus as a human viral indicator. The results showed that SARS-CoV-2 was detected for both target regions in all samples analyzed in a range of 2,91E+05 to 3,19E+06 GC/L for N1 and from2,07E+05 to 2,22E+06 GC/L for N2. The high values detected in natural waters from a low sanitation region have several implications in health and ecology that should be further assessed.

Kasprzyk-Hordern et al., 2022. Wastewater-based epidemiology in hazard forecasting and early-warning systems for global health risks. https://doi.org/10.1016/j.envint.2022.107143

With the advent of the SARS-CoV-2 pandemic, Wastewater-Based Epidemiology (WBE) has been applied to track community infection in cities worldwide and has proven succesful as an early warning system for identification of hotspots and changing prevalence of infections (both symptomatic and asymptomatic) at a city or sub-city level. Wastewater is only one of environmental compartments that requires consideration. In this manuscript, we have critically evaluated the knowledge-base and preparedness for building early warning systems in a rapidly urbanising world, with particular attention to Africa, which experiences rapid population growth and urbanisation. We have proposed a Digital Urban Environment Fingerprinting Platform (DUEF) – a new approach in hazard forecasting and early-warning systems for global health risks and an extension to the existing concept of smart cities. The urban environment (especially wastewater) contains a complex mixture of substances including toxic chemicals, infectious biological agents and human excretion products. DUEF assumes that these specific endo- and exogenous residues, anonymously pooled by communities’ wastewater, are indicative of community-wide exposure and the resulting effects. DUEF postulates that the measurement of the substances continuously and anonymously pooled by the receiving environment (sewage, surface water, soils and air), can provide near real-time dynamic information about the quantity and type of physical, biological or chemical stressors to which the surveyed systems are exposed, and can create a risk profile on the potential effects of these exposures. Successful development and utilisation of a DUEF globally requires a tiered approach including: Stage I: network building, capacity building, stakeholder engagement as well as a conceptual model, followed by Stage II: DUEF development, Stage III: implementation, and Stage IV: management and utilization. We have identified four key pillars required for the establishment of a DUEF framework: (1) Environmental fingerprints, (2) Socioeconomic fingerprints, (3) Statistics and modelling and (4) Information systems. This manuscript critically evaluates the current knowledge base within each pillar and provides recommendations for further developments with an aim of laying grounds for successful development of global DUEF platforms.

Nelson, 2022. What poo tells us: wastewater surveillance comes of age amid covid, monkeypox, and polio. http://dx.doi.org/10.1136/bmj.o1869

Ngwira et al., 2022. Cost of wastewater-based environmental surveillance for SARS-CoV-2: Evidence from pilot sites in Blantyre, Malawi and Kathmandu, Nepal. https://doi.org/10.1371/journal.pgph.0001377

Environmental surveillance of rivers and wastewater for SARS-CoV-2 detection has been explored as an innovative way to surveil the pandemic. This study estimated the economic costs of conducting wastewater-based environmental surveillance for SARS-CoV-2 to inform decision making if countries consider continuing these efforts. We estimated the cost of two SARS-CoV-2 environmental surveillance pilot studies conducted in Blantyre, Malawi, and Kathmandu, Nepal. The cost estimation accounted for the consumables, equipment, and human resource time costs used for environmental surveillance from sample selection until pathogen detection and overhead costs for the projects. Costs are reported in 2021 US $ and reported as costs per month, per sample and person per year. The estimated costs for environmental surveillance range from $6,175 to $8,272 per month (Blantyre site) and $16,756 to $30,050 (Kathmandu site). The number of samples processed per month ranged from 84 to 336 at the Blantyre site and 96 to 250 at the Kathmandu site. Consumables costs are variable costs influenced by the number of samples processed and are a large share of the monthly costs for ES (ranging from 39% to 72%). The relatively higher costs per month for the Kathmandu site were attributable to the higher allocation of dedicated human resources and equipment to environmental surveillance for SARS-CoV-2 compared to the Blantyre site where these resources were shared with other activities. The average cost per sample ranged from $25 to $74 (Blantyre) and $120 to $175 (Kathmandu). There were associated economies of scale for human resources and equipment costs with increased sample processing and sharing of resources with other activities. The cost per person in the catchment area per year ranged from $0.07 to $0.10 in Blantyre and $0.07 to $0.13 in Kathmandu. Environmental surveillance may be a low-cost early warning signal for SARS-CoV-2 that can complement other SARS-CoV2 monitoring efforts.

Pillay et al., 2022. Environmental surveillance for non sewered communities: a tool for disease mitigation in developing countries. https://www.wrc.org.za/wp-content/uploads/mdocs/Science%20briefs_NSS%20Surveillance.pdf

Environmental surveillance and Wastewater-Based Epidemiology (WBE) has proven to a useful tool in fighting a pandemic. Recent application of techniques for SARS-CoV-2 detection in sewage has provided vital information on the emergence of disease, circulating variants of interest and variants of concern, and possibility of predicting hospital admissions. Developing countries do not have extensive sewer networks and therefore cannot use WBE for the same population scale. A South African study has successfully demonstrated the application of nonsewered surveillance across multiple sites and provinces in South Africa. To the authors’ knowledge, this has been the largest non sewered surveillance programme undertaken globally.

Pocock et al., 2020. Proof of concept study: Application of wastewater-based surveillance to monitor SARS-CoV-2 prevalence in South African communities. https://erwat.co.za/wrc-proof-of-concept-study-wastewater-basedepidemiology-for-surveillance-of-the-spread-of-covid-19-insouth-african-communities/

Pocock et al., 2021. The efficacy of passive samplers for water quality based COVID-19 epidemiology surveillance. https://www.watershare.eu/wp-content/uploads/Science-Brief_-10_COVID19-surveillance-for-Non-Sewered.pdf

- Wastewater-based surveillance of communities for SARS-CoV-2 viral prevalence by sampling from wastewater treatment works is a powerful complementary epidemiological tool. However, in South Africa almost 40% of the population is not connected to a waterborne sewerage system.
- Sampling and surveillance of greywater and faecal waste within our non-sewered areas may give an early warning of the presence of COVID-19 infections in these communities, where there is both the risk of rapid spread and low likelihood of conventional testing.
- Passive sampling of environmental sites has shown promise, and may overcome issues of low yield when viral load is low and during high dilution periods, particularly in rivers downstream of unsewered settlements.
- Passive samplers have the advantage of allowing for easier and cheaper transport of samples compared to grab samples that require the costly transport of large volumes of water maintenance of the cold chain out of rural areas. Sample processing is also much quicker compared to concentration of water samples.
- Inclusion of trend monitoring of SARS-CoV-2 prevalence in unsewered communities together with established wastewater-based epidemiology (WBE) data collection from WWTW sampling can greatly expand the knowledge base and serve to highlight the needs of vulnerable communities in South Africa. These passive samplers can now also potentially be used for wastewater-based epidemiology for a broader scope of pathogens than only SARS-CoV-2.
- The success of passive samplers from this initiative has demonstrated the future B41potential and opportunity to enable more widespread environmental water quality monitoring due to its low cost and ease of application in the collection of samples.

Richardson, 2021. How waste water is helping South Africa fight COVID-19. https://www.nature.com/articles/d41586-021-01399-9 

Shrestha et al., 2021. Wastewater-Based Epidemiology for Cost-Effective Mass Surveillance of COVID-19 in Low- and Middle-Income Countries: Challenges and Opportunities. https://doi.org/10.3390/w13202897

Zohra et al., 2021. Wastewater based environmental surveillance of toxigenic Vibrio cholerae in Pakistan. https://doi.org/10.1371/journal.pone.0257414

Background: Pakistan has been experiencing intervals of sporadic cases and localized outbreaks in the last two decades. No proper study has been carried out in order to find out the environmental burden of toxigenic V. cholerae as well as how temporal and environmental factors associated in driving cholera across the country.
Methods: We tested waste water samples from designated national environment surveillance sites in Pakistan with RT-PCR assay. Multistage sampling technique were utilized for samples collection and for effective sample processing Bag-Mediated Filtration system, were employed. Results were analysed by district and month wise to understand the geographic distribution and identify the seasonal pattern of V. cholera detection in Pakistan.
Results: Between May 2019, and February 2020, we obtained and screened 160 samples in 12 districts across Pakistan. Out of 16 sentinel environmental surveillance sites, 15 sites showed positive results against cholera toxigenic gene with mostly lower CT value (mean, 34±2) and have significant difference (p < 0.05). The highest number of positive samples were collected from Sindh in month of November, then in June it is circulating in different districts of Pakistan including four Provinces respectively.
Conclusion: V. cholera detection do not follow a clear seasonal pattern. However, the poor sanitation problems or temperature and rainfall may potentially influence the frequency and duration of cholera across the country. Occurrence of toxigenic V. cholerae in the environment samples showed that cholera is endemic, which is an alarming for a potential future cholera outbreaks in the country.

Wastewater-based epidemiology (WBE) is an approach that can be used to estimate COVID-19 prevalence in the population by detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater. As the WBE approach uses pooled samples from the study population, it is an inexpensive and non-invasive mass surveillance method compared to individual testing. Thus, it offers a good complement in low- and middle-income countries (LMICs) facing high costs of testing or social stigmatization, and it has a huge potential to monitor SARS-CoV-2 and its variants to curb the global COVID-19 pandemic. The aim of this review is to systematize the current evidence about the application of the WBE approach in mass surveillance of COVID-19 infection in LMICs, as well as its future potential. Among other parameters, population size contributing the fecal input to wastewater is an important parameter for COVID-19 prevalence estimation. It is easier to back-calculate COVID-19 prevalence in the community with centralized wastewater systems, because there can be more accurate estimates about the size of contributing population in the catchment. However, centralized wastewater management systems are often of low quality (or even non-existent) in LMICs, which raises a major concern about the ability to implement the WBE approach. However, it is possible to mobilize the WBE approach, if large areas are divided into sub-areas, corresponding to the existing wastewater management systems. In addition, a strong coordination between stakeholders is required for estimating population size respective to wastewater management systems. Nevertheless, further international efforts should be leveraged to strengthen the sanitation infrastructures in LMICs, using the lessons gathered from the current COVID-19 pandemic to be prepared for future pandemics.

Archer et al., 2023. Occurrence of contaminants of emerging concern in the Eerste River, South Africa: Towards the optimisation of an urban water profiling approach for public- and ecological health risk characterisation. http://dx.doi.org/10.1016/j.scitotenv.2022.160254

The study evaluated the presence and fate of various contaminants of emerging concern (CECs) from a South African wastewater treatment works (WWTW) and surface waters located around an urban setting. A total of 45 CECs were quantified from nine sampling locations over an 11-month period. Daily loads (g/day) of the target analytes in the WWTW showed persistence of some CECs, along with population-normalised daily loads (mg/day/1000inh) of pharmaceuticals and drugs of abuse (DOA) that were estimated for the first time in the study area. Multiple chemical markers were recorded in river water located upstream of the WWTW discharge throughout the study period, suggesting a high degree of diffuse pollution from urban communities in the study area that are not connected to sewage networks or where sanitation services are limited. The potential of using defined surface water locations to perform community-wide substance use profiling for non-sewered communities was also explored. Environmental risk characterisation for the WWTW effluent and surface waters throughout the study period provided multiple risk quotients (RQ) for the target list of CECs spanning over various sentinel trophic levels. High risk profiles (RQ > 1.0) with a frequency of exceedance (FoE) larger than 75 % were recorded for several CECs in both WWTW effluent and surface water locations that suggest potential long-term ecological health risk impacts of pollution hotspot areas in the river catchment situated around the urban area. We present challenges in surface water quality within the study area that is relatable, or may even present more challenging, in other low- or middle-income country (LMICs) settings. The study also highlighted some challenges and limitations associated with the much-needed application of wastewaterbased epidemiology (WBE) intervention in non-sewered communities that can informon public health and communal substance use profiles of the entire urban setting.

Capone et al., 2020. Analysis of Fecal Sludges Reveals Common Enteric Pathogens in Urban Maputo, Mozambique. https://doi.org/10.1021/acs.estlett.0c00610

Sewage surveillance is increasingly used in public health applications; metabolites, biomarkers, and pathogens are detectable in wastewater and can provide useful information about community health. Work on this topic has been limited to wastewaters in mainly high-income settings, however. In low-income countries, where the burden of enteric infection is high, nonsewered sanitation predominates. In order to assess the utility of fecal sludge surveillance as a tool to identify the most prevalent enteric pathogens circulating among at-risk children, we collected 95 matched child stool and fecal sludge samples from household clusters sharing latrines in urban Maputo, Mozambique. We analyzed samples for 20 common enteric pathogens via multiplex real-time quantitative PCR. Among the 95 stools matched to fecal sludges, we detected the six most prevalent bacterial pathogens (Enteroaggregative E. coli, Shigella/Enteroinvasive E. coli, Enterotoxigenic E. coli, Enteropathogenic E. coli, shiga-toxin producing E. coli, Salmonella), and all three protozoan pathogens (Giardia duodenalis, Cryptosporidium parvum, Entamoeba histolytica) in the same rank order in both matrices. We did not observe the same trend for viral pathogens or soil-transmitted helminths, however. Our results suggest that sampling fecal sludges from onsite sanitation offers potential for localized pathogen surveillance in low-income settings where enteric pathogen prevalence is high.

Capone et al., 2021. Impact of sampling depth on pathogen detection in pit latrines. https://doi.org/10.1371/journal.pntd.0009176

Wastewater based epidemiology (WBE) is increasingly used to provide decision makers with actionable data about community health. WBE efforts to date have primarily focused on sewer-transported wastewater in high-income countries, but at least 1.8 billion people in low- and middle-income countries (LMIC) use onsite sanitation systems such as pit latrines and septic tanks. Like wastewater, fecal sludges from such systems offer similar advantages in community pathogen monitoring and other epidemiological applications. To evaluate the distribution of enteric pathogens inside pit latrines–which could inform sampling methods for WBE in LMIC settings unserved by sewers–we collected fecal sludges from the surface, mid-point, and maximum-depth of 33 pit latrines in urban and peri-urban Malawi and analyzed the 99 samples for 20 common enteric pathogens via multiplex quantitative reverse transcription PCR. Using logistic regression adjusted for household population, latrine sharing, the presence of a concrete floor or slab, water source, and anal cleansing materials, we found no significant difference in the odds of detecting the 20 pathogens from the mid-point (adjusted odds ratio, aOR = 1.1; 95% confidence interval = 0.73, 1.6) and surface samples (aOR = 0.80, 95% CI = 0.54, 1.2) compared with those samples taken from the maximum depth. Our results suggest that, for the purposes of routine pathogen monitoring, pit latrine sampling depth does not strongly influence the odds of detecting enteric pathogens by molecular methods. A single sample from the pit latrines’ surface, or a composite of surface samples, may be preferred as the most recent material contributed to the pit and may be easiest to collect.

Chigwechokha, Street, Holm, 2022. Advancing the Use of Fecal Sludge for Timelier and Better-Quality Epidemiological Data in Low- and Middle-Income Countries for Pandemic Prevention. https://doi.org/10.1021/acs.est.2c07788

Shrestha et al., 2021. Wastewater-Based Epidemiology for Cost-Effective Mass Surveillance of COVID-19 in Low- and Middle-Income Countries: Challenges and Opportunities. https://doi.org/10.3390/w13202897

Wastewater-based epidemiology (WBE) is an approach that can be used to estimate COVID-19 prevalence in the population by detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater. As the WBE approach uses pooled samples from the study population, it is an inexpensive and non-invasive mass surveillance method compared to individual testing. Thus, it offers a good complement in low- and middle-income countries (LMICs) facing high costs of testing or social stigmatization, and it has a huge potential to monitor SARS-CoV-2 and its variants to curb the global COVID-19 pandemic. The aim of this review is to systematize the current evidence about the application of the WBE approach in mass surveillance of COVID-19 infection in LMICs, as well as its future potential. Among other parameters, population size contributing the fecal input to wastewater is an important parameter for COVID-19 prevalence estimation. It is easier to back-calculate COVID-19 prevalence in the community with centralized wastewater systems, because there can be more accurate estimates about the size of contributing population in the catchment. However, centralized wastewater management systems are often of low quality (or even non-existent) in LMICs, which raises a major concern about the ability to implement the WBE approach. However, it is possible to mobilize the WBE approach, if large areas are divided into sub-areas, corresponding to the existing wastewater management systems. In addition, a strong coordination between stakeholders is required for estimating population size respective to wastewater management systems. Nevertheless, further international efforts should be leveraged to strengthen the sanitation infrastructures in LMICs, using the lessons gathered from the current COVID-19 pandemic to be prepared for future pandemics.

Pillay et al., 2022. Environmental surveillance for non sewered communities: a tool for disease mitigation in developing countries. https://www.wrc.org.za/wp-content/uploads/mdocs/Science%20briefs_NSS%20Surveillance.pdf

Environmental surveillance and Wastewater-Based Epidemiology (WBE) has proven to a useful tool in fighting a pandemic. Recent application of techniques for SARS-CoV-2 detection in sewage has provided vital information on the emergence of disease, circulating variants of interest and variants of concern, and possibility of predicting hospital admissions. Developing countries do not have extensive sewer networks and therefore cannot use WBE for the same population scale. A South African study has successfully demonstrated the application of nonsewered surveillance across multiple sites and provinces in South Africa. To the authors’ knowledge, this has been the largest non sewered surveillance programme undertaken globally.

Pocock et al., 2020. Proof of concept study: Application of wastewater-based surveillance to monitor SARS-CoV-2 prevalence in South African communities. https://erwat.co.za/wrc-proof-of-concept-study-wastewater-basedepidemiology-for-surveillance-of-the-spread-of-covid-19-insouth-african-communities/

Pocock et al., 2021. The efficacy of passive samplers for water quality based COVID-19 epidemiology surveillance. https://www.watershare.eu/wp-content/uploads/Science-Brief_-10_COVID19-surveillance-for-Non-Sewered.pdf

- Wastewater-based surveillance of communities for SARS-CoV-2 viral prevalence by sampling from wastewater treatment works is a powerful complementary epidemiological tool. However, in South Africa almost 40% of the population is not connected to a waterborne sewerage system.
- Sampling and surveillance of greywater and faecal waste within our non-sewered areas may give an early warning of the presence of COVID-19 infections in these communities, where there is both the risk of rapid spread and low likelihood of conventional testing.
- Passive sampling of environmental sites has shown promise, and may overcome issues of low yield when viral load is low and during high dilution periods, particularly in rivers downstream of unsewered settlements.
- Passive samplers have the advantage of allowing for easier and cheaper transport of samples compared to grab samples that require the costly transport of large volumes of water maintenance of the cold chain out of rural areas. Sample processing is also much quicker compared to concentration of water samples.
- Inclusion of trend monitoring of SARS-CoV-2 prevalence in unsewered communities together with established wastewater-based epidemiology (WBE) data collection from WWTW sampling can greatly expand the knowledge base and serve to highlight the needs of vulnerable communities in South Africa. These passive samplers can now also potentially be used for wastewater-based epidemiology for a broader scope of pathogens than only SARS-CoV-2.
- The success of passive samplers from this initiative has demonstrated the future B41potential and opportunity to enable more widespread environmental water quality monitoring due to its low cost and ease of application in the collection of samples.

World Health Organization, 2022. How wastewater surveillance is helping the COVID-19 fight. https://www.afro.who.int/news/how-wastewater-surveillance-helping-covid-19-fight

Adhikari, Halden, 2022. Opportunities and limits of wastewater-based epidemiology for tracking global health and attainment of UN sustainable development goals. https://doi.org/10.1016/j.envint.2022.107217

Wastewater-based epidemiology (WBE) emerged as a powerful, actionable health management tool during the COVID-19 pandemic. Hypothesizing future uses, we explored its potential for real-time, tracking of progress in attaining United Nations Sustainable Development Goals (SDGs) globally as a non-expensive method using existing infrastructure. We inventoried (i) literature-documented sewerage infrastructure, (ii) demographics of populations served, and (iii) WBE markers informative of 9 SDGs. Among the 17 different sustainable development goals listed by the UN 2030 agenda, more than half of these may be monitored by using WBE monitoring at centralized treatment infrastructure as tabulated in this study. Driven mainly by COVID-19, WBE currently is practiced in at least 55 countries, reaching about 300 million people. Expansion of WBE to 109,000 + treatment plants inventoried in 129 countries would increase global coverage 9-fold to 34.7% or 2.7 billion, leaving out 5 billion people not served by centralized sewerage systems. Associations between population demographics and present-day infrastructure are explored, and geospatial regions particularly vulnerable to infectious disease outbreaks are identified. The results suggest that difference in the differential outcomes in well-being is an outcome of the sanitation infrastructure inequalities and lack of sanitation infrastructure creates doubly disadvantaged populations at risk of poor hygiene and cut off from the early-warning benefits of conventional WBE. This is the first study to explore the feasibility and potential barriers to the use of WBE for tracking the attainment of SDGs globally with at least 9 out of 17 SDGs.

Ali at al., 2022. Community Wastewater-Based Surveillance Can Be a Cost-Effective Approach to Track COVID-19 Outbreak in Low-Resource Settings: Feasibility Assessment for Ethiopia Context. https://doi.org/10.3390/ijerph19148515

Wastewater surveillance systems have become an important component of COVID-19 outbreak monitoring in high-income settings. However, its use in most low-income settings has not been well-studied. This study assessed the feasibility and utility of wastewater surveillance system to monitor SARS-CoV-2 RNA in Addis Ababa, Ethiopia. The study was conducted at nine Membrane Bio-reactor (MBR) wastewater processing plants. The samples were collected in two separate time series. Wastewater samples and known leftover RT-PCR tested nasopharyngeal swabs were processed using two extraction protocols with different sample conditions. SARS-CoV-2 wastewater RT-PCR testing was conducted using RIDA GENE SARS-CoV-2 RUO protocol for wastewater SARS-CoV-2 RNA testing. Wastewater SARS-CoV-2 RNA RT-PCR protocol adaptation, optimization, and detection were conducted in an Addis Ababa, Ethiopia context. Samples collected during the first time series, when the national COVID-19 case load was low, were all negative. Conversely, samples collected during the second time series were all positive, coinciding with the highest daily reported new cases of COVID-19 in Ethiopia. The wastewater-based SARS-CoV-2 surveillance approach is feasible for Addis Ababa. The COVID-19 wastewater based epidemiological approach can potentially fill the evidence gap in distribution and dynamics of COVID-19 in Ethiopia and other low-income settings.

Andrews et al., 2020. Environmental Surveillance as a Tool for Identifying High-risk Settings for Typhoid Transmission. https://doi.org/10.1093/cid/ciaa513

Enteric fever remains a major cause of morbidity in developing countries with poor sanitation conditions that enable fecal contamination of water distribution systems. Historical evidence has shown that contamination of water systems used for household consumption or agriculture are key transmission routes for Salmonella Typhi and Salmonella Paratyphi A. The World Health Organization now recommends that typhoid conjugate vaccines (TCV) be used in settings with high typhoid incidence; consequently, governments face a challenge regarding how to prioritize typhoid against other emerging diseases. A key issue is the lack of typhoid burden data in many low- and middle-income countries where TCV could be deployed. Here we present an argument for utilizing environmental sampling for the surveillance of enteric fever organisms to provide data on community-level typhoid risk. Such an approach could complement traditional blood culture-based surveillance or even replace it in settings where population-based clinical surveillance is not feasible. We review historical studies characterizing the transmission of enteric fever organisms through sewage and water, discuss recent advances in the molecular detection of typhoidal Salmonella in the environment, and outline challenges and knowledge gaps that need to be addressed to establish environmental sampling as a tool for generating actionable data that can inform public health responses to enteric fever.

Archer et al., 2023. Occurrence of contaminants of emerging concern in the Eerste River, South Africa: Towards the optimisation of an urban water profiling approach for public- and ecological health risk characterisation. http://dx.doi.org/10.1016/j.scitotenv.2022.160254

The study evaluated the presence and fate of various contaminants of emerging concern (CECs) from a South African wastewater treatment works (WWTW) and surface waters located around an urban setting. A total of 45 CECs were quantified from nine sampling locations over an 11-month period. Daily loads (g/day) of the target analytes in the WWTW showed persistence of some CECs, along with population-normalised daily loads (mg/day/1000inh) of pharmaceuticals and drugs of abuse (DOA) that were estimated for the first time in the study area. Multiple chemical markers were recorded in river water located upstream of the WWTW discharge throughout the study period, suggesting a high degree of diffuse pollution from urban communities in the study area that are not connected to sewage networks or where sanitation services are limited. The potential of using defined surface water locations to perform community-wide substance use profiling for non-sewered communities was also explored. Environmental risk characterisation for the WWTW effluent and surface waters throughout the study period provided multiple risk quotients (RQ) for the target list of CECs spanning over various sentinel trophic levels. High risk profiles (RQ > 1.0) with a frequency of exceedance (FoE) larger than 75 % were recorded for several CECs in both WWTW effluent and surface water locations that suggest potential long-term ecological health risk impacts of pollution hotspot areas in the river catchment situated around the urban area. We present challenges in surface water quality within the study area that is relatable, or may even present more challenging, in other low- or middle-income country (LMICs) settings. The study also highlighted some challenges and limitations associated with the much-needed application of wastewaterbased epidemiology (WBE) intervention in non-sewered communities that can informon public health and communal substance use profiles of the entire urban setting.

Bivins et al., 2022. Passive sampling to scale wastewater surveillance of infectious disease: Lessons learned from COVID-19. http://dx.doi.org/10.1016/j.scitotenv.2022.155347

Much of what is known and theorized concerning passive sampling techniques has been developed considering chemical analytes. Yet, historically, biological analytes, such as Salmonella typhi, have been collected from wastewater via passive sampling with Moore swabs. In response to the COVID-19 pandemic, passive sampling is re-emerging as a promising technique to monitor SARS-CoV-2 RNA in wastewater. Method comparisons and disease surveillance using composite, grab, and passive sampling for SARS-CoV-2 RNA detection have found passive sampling with a variety of materials routinely produced qualitative results superior to grab samples and useful for sub-sewershed surveillance of COVID-19. Among individual studies, SARS-CoV-2 RNA concentrations derived from passive samplers demonstrated heterogeneous correlation with concentrations from paired composite samples ranging from weak (R2=0.27, 0.31) to moderate (R2=0.59) to strong (R2=0.76). Among passive sampler materials, electronegative membranes have shown great promise with linear uptake of SARS-CoV-2 RNA observed for exposure durations of 24 to 48 h and in several cases RNA positivity on par with composite samples. Continuing development of passive sampling methods for the surveillance of infectious diseases via diverse forms of fecal waste should focus on optimizing sampler materials for the efficient uptake and recovery of biological analytes, kit-free extraction, and resource-efficient testing methods capable of rapidly producing qualitative or quantitative data. With such refinements passive sampling could prove to be a fundamental tool for scaling wastewater surveillance of infectious disease, especially among the 1.8 billion persons living in low-resource settings served by non-traditional wastewater collection infrastructure.

Bust, et al., 2021. The SACCESS network for COVID-19 wastewater surveillance: a national collaboration for public health responsiveness. https://hdl.handle.net/10520/ejc-healthr-v2021-n1-a23

Capone et al., 2020. Analysis of Fecal Sludges Reveals Common Enteric Pathogens in Urban Maputo, Mozambique. https://doi.org/10.1021/acs.estlett.0c00610

Sewage surveillance is increasingly used in public health applications; metabolites, biomarkers, and pathogens are detectable in wastewater and can provide useful information about community health. Work on this topic has been limited to wastewaters in mainly high-income settings, however. In low-income countries, where the burden of enteric infection is high, nonsewered sanitation predominates. In order to assess the utility of fecal sludge surveillance as a tool to identify the most prevalent enteric pathogens circulating among at-risk children, we collected 95 matched child stool and fecal sludge samples from household clusters sharing latrines in urban Maputo, Mozambique. We analyzed samples for 20 common enteric pathogens via multiplex real-time quantitative PCR. Among the 95 stools matched to fecal sludges, we detected the six most prevalent bacterial pathogens (Enteroaggregative E. coli, Shigella/Enteroinvasive E. coli, Enterotoxigenic E. coli, Enteropathogenic E. coli, shiga-toxin producing E. coli, Salmonella), and all three protozoan pathogens (Giardia duodenalis, Cryptosporidium parvum, Entamoeba histolytica) in the same rank order in both matrices. We did not observe the same trend for viral pathogens or soil-transmitted helminths, however. Our results suggest that sampling fecal sludges from onsite sanitation offers potential for localized pathogen surveillance in low-income settings where enteric pathogen prevalence is high.

Dzinamarira et al., 2022. Utilization of SARS-CoV-2 Wastewater Surveillance in Africa—A Rapid Review. https://doi.org/10.1016/j.jiph.2022.05.010

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.

Haque et al., 2022. Wastewater surveillance of SARS-CoV-2 in Bangladesh: Opportunities and challenges. https://doi.org/10.1016/j.coesh.2022.100334 

The ongoing pandemic of the coronavirus disease 2019 (COVID-19) is a public health crisis of global concern. The progression of the COVID-19 pandemic has been monitored in the first place by testing symptomatic individuals for SARS-CoV-2 virus in the respiratory samples. Concurrently, wastewater carries feces, urine, and sputum that potentially contains SARS-CoV-2 intact virus or partially damaged viral genetic materials excreted by infected individuals. This brings significant opportunities for understanding the infection dynamics by environmental surveillance. It has advantages for the country, especially in densely populated areas where individual clinical testing is difficult. However, there are several challenges including: 1) establishing a sampling plan and schedule that is representative of the various catchment populations 2) development and validation of standardized protocols for the laboratory analysis 3) understanding hydraulic flows and virus transport in complex wastewater drainage systems and 4) collaborative efforts from government agencies, NGOs, public health units and academia.

Global Polio Eradication Initiative, 2022. Field Guidance for the Implementation of Environmental Surveillance for Poliovirus. https://polioeradication.org/wp-content/uploads/2022/11/Field-Guidance-for-the-Implementation-of-ES-20221118-ENG.pdf

IANPHI, 2022. Wastewater Surveillance Programs for COVID-19 and Other Pathogens Led by African National Public Health Institutes. https://ianphi.org/news/2022/wastewater-surveillance-webinar.html

Johnson et al., 2022. Tracking the circulating SARS‑CoV‑2 variant of concern in South Africa using wastewater‑based epidemiology. https://doi.org/10.1038/s41598-022-05110-4

This study uses wastewater-based epidemiology (WBE) to rapidly and, through targeted surveillance, track the geographical distribution of SARS-CoV-2 variants of concern (Alpha, Beta and Delta) within 24 wastewater treatment plants (WWTPs) in the Western Cape of South Africa. Information obtained was used to identify the circulating variant of concern (VOC) within a population and retrospectively trace when the predominant variant was introduced. Genotyping analysis of SARS-CoV-2 showed that 50% of wastewater samples harbored signature mutations linked to the Beta variant before the third wave, with the Delta variant absent within the population. Over time, the prevalence of the beta variant decreased steadily. The onset of the third wave resulted in the Delta variant becoming the predominant variant, with a 100% prevalence supporting the theory that the Delta variant was driving the third wave. In silico molecular docking analysis showed that the signature mutations of the Delta variant increased binding to host proteins, suggesting a possible molecular mechanism that increased viral infectivity of the Delta variant.

Kasprzyk-Hordern et al., 2022. Wastewater-based epidemiology in hazard forecasting and early-warning systems for global health risks. https://doi.org/10.1016/j.envint.2022.107143

With the advent of the SARS-CoV-2 pandemic, Wastewater-Based Epidemiology (WBE) has been applied to track community infection in cities worldwide and has proven succesful as an early warning system for identification of hotspots and changing prevalence of infections (both symptomatic and asymptomatic) at a city or sub-city level. Wastewater is only one of environmental compartments that requires consideration. In this manuscript, we have critically evaluated the knowledge-base and preparedness for building early warning systems in a rapidly urbanising world, with particular attention to Africa, which experiences rapid population growth and urbanisation. We have proposed a Digital Urban Environment Fingerprinting Platform (DUEF) – a new approach in hazard forecasting and early-warning systems for global health risks and an extension to the existing concept of smart cities. The urban environment (especially wastewater) contains a complex mixture of substances including toxic chemicals, infectious biological agents and human excretion products. DUEF assumes that these specific endo- and exogenous residues, anonymously pooled by communities’ wastewater, are indicative of community-wide exposure and the resulting effects. DUEF postulates that the measurement of the substances continuously and anonymously pooled by the receiving environment (sewage, surface water, soils and air), can provide near real-time dynamic information about the quantity and type of physical, biological or chemical stressors to which the surveyed systems are exposed, and can create a risk profile on the potential effects of these exposures. Successful development and utilisation of a DUEF globally requires a tiered approach including: Stage I: network building, capacity building, stakeholder engagement as well as a conceptual model, followed by Stage II: DUEF development, Stage III: implementation, and Stage IV: management and utilization. We have identified four key pillars required for the establishment of a DUEF framework: (1) Environmental fingerprints, (2) Socioeconomic fingerprints, (3) Statistics and modelling and (4) Information systems. This manuscript critically evaluates the current knowledge base within each pillar and provides recommendations for further developments with an aim of laying grounds for successful development of global DUEF platforms.

Kilaru et al., 2021. Wastewater surveillance for infectious disease: a systematic review. https://doi.org/10.1101/2021.07.26.21261155

Wastewater surveillance of SARS-CoV-2 has shown to be a valuable source of information regarding SARS-CoV-2 transmission and COVID-19 cases. Though the method has been used for several decades to track other infectious diseases, there has not been a comprehensive review outlining all of the pathogens surveilled through wastewater. The aim of this study is to identify what infectious diseases have been previously studied via wastewater surveillance prior to the COVID-19 Pandemic and identify common characteristics between the studies, as well as identify current gaps in knowledge. Peer-reviewed articles published as of August 1, 2020 that examined wastewater for communicable and infectious human pathogens on 2 or more occasions were included in the study. Excluded from this list were all reviews and methods papers, single collection studies, and non-human pathogens. Infectious diseases and pathogens were identified in studies of wastewater surveillance, as well as themes of how wastewater surveillance and other measures of disease transmission were linked. This review did not include any numerical data from individual studies and thus no statistical analysis was done. 1005 articles were identified but only 100 were included in this review after applying the inclusion criteria. These studies came from 38 countries with concentration in certain countries including Italy, Israel, Brazil, Japan, and China. Twenty-five separate pathogen families were identified in the included studies, with the majority of studies examining pathogens from the family Picornaviridae, including polio and non-polio enteroviruses. Most studies of wastewater surveillance did not link what was found in the wastewater to other measures of disease transmission. Among those studies that did compare wastewater surveillance to other measures of disease transmission the value observed was dependent upon pathogen and varied by study. Wastewater surveillance has historically been used to assess water-borne and fecal-orally transmitted pathogens causing diarrheal disease. However, numerous other types of pathogens have been surveilled using wastewater and wastewater surveillance should be considered as a potential tool for many infectious diseases. Wastewater surveillance studies can be improved by incorporating other measures of disease transmission at the population-level including disease incidence and hospitalizations.

Kreier, 2021. The myriad ways sewage surveillance is helping fight COVID around the world. https://www.nature.com/articles/d41586-021-01234-1

Mahlangeni et al., 2023. Using Wastewater Surveillance to Compare COVID-19 Outbreaks during the Easter Holidays over a 2-Year Period in Cape Town, South Africa https://www.mdpi.com/1999-4915/15/1/162

Wastewater surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown to be an important approach to determine early outbreaks of infections. Wastewater-based epidemiology (WBE) is regarded as a complementary tool for monitoring SARS-CoV-2 trends in communities. In this study, the changes in the SARS-CoV-2 RNA levels in wastewater during Easter holidays in 2021 and 2022 in the City of Cape Town were monitored over nine weeks. Our findings showed a statistically significant difference in the SARS-CoV-2 RNA viral load between the study weeks over the Easter period in 2021 and 2022, except for study week 1 and 4. During the Easter week, 52% of the wastewater treatment plants moved from the lower (low viral RNA) category in 2021 to the higher (medium to very high viral RNA) categories in 2022. As a result, the median SARS-CoV-2 viral loads where higher during the Easter week in 2022 than Easter week in 2021 (p = 0.0052). Mixed-effects model showed an association between the SARS-CoV-2 RNA viral loads and Easter week over the Easter period in 2021 only (p < 0.01). The study highlights the potential of WBE to track outbreaks during the holiday period. Mtetwa at al., 2021. Wastewater-Based Surveillance of Antibiotic Resistance Genes Associated with Tuberculosis Treatment Regimen in KwaZulu Natal, South Africa. https://doi.org/10.3390/antibiotics10111362

Essential components of public health include strengthening the surveillance of infectious diseases and developing early detection and prevention policies. This is particularly important for drug-resistant tuberculosis (DR-TB), which can be explored by using wastewater-based surveillance. This study aimed to use molecular techniques to determine the occurrence and concentration of antibiotic-resistance genes (ARGs) associated with tuberculosis (TB) resistance in untreated and treated wastewater. Raw/untreated and treated (post-chlorination) wastewater samples were taken from three wastewater treatment plants (WWTPs) in South Africa. The ARGs were selected to target drugs used for first- and second-line TB treatment. Both conventional polymerase chain reaction (PCR) and the more advanced droplet digital PCR (ddPCR) were evaluated as surveillance strategies to determine the distribution and concentration of the selected ARGs. The most abundant ARG in the untreated wastewater was the rrs gene, associated with resistance to the aminoglycosides, specifically streptomycin, with median concentration ranges of 4.69–5.19 log copies/mL. In contrast, pncA gene, associated with resistance to the TB drug pyrazinamide, was the least detected (1.59 to 2.27 log copies/mL). Resistance genes associated with bedaquiline was detected, which is a significant finding because this is a new drug introduced in South Africa for the treatment of multi-drug resistant TB. This study, therefore, establishes the potential of molecular surveillance of wastewater for monitoring antibiotic resistance to TB treatment in communities.

Murni et al., 2022. The feasibility of SARS-CoV-2 surveillance using wastewater and environmental sampling in Indonesia. https://doi.org/10.1371/journal.pone.0274793

Background: Wastewater-based epidemiology (WBE) surveillance as an early warning system (EWS) for monitoring community transmission of SARS-CoV-2 in low- and middle-income country (LMIC) settings, where diagnostic testing capacity is limited, needs further exploration. We explored the feasibility to conduct a WBE surveillance in Indonesia, one of the global epicenters of the COVID-19 pandemic in the middle of 2021, with the fourth largest population in the world where sewer and non-sewered sewage systems are implemented. The feasibility and resource capacity to collect samples on a weekly or fortnightly basis with grab and/or passive sampling methods, as well as to conduct qualitative and quantitative identification of SARS-CoV-2 ribonucleic acid (RNA) using real-time RT-PCR (RT-qPCR) testing of environmental samples were explored.
Materials and methods: We initiated a routine surveillance of wastewater and environmental sampling at three predetermined districts in Special Region of Yogyakarta Province. Water samples were collected from central and community wastewater treatment plants (WWTPs), including manholes flowing to the central WWTP, and additional soil samples were collected for the near source tracking (NST) locations (i.e., public spaces where people congregate).
Results: We began collecting samples in the Delta wave of the COVID-19 pandemic in Indonesia in July 2021. From a 10-week period, 54% (296/544) of wastewater and environmental samples were positive for SARS-CoV-2 RNA. The sample positivity rate decreased in proportion with the reported incidence of COVID-19 clinical cases in the community. The highest positivity rate of 77% in week 1, was obtained for samples collected in July 2021 and decreased to 25% in week 10 by the end of September 2021.
Conclusion: A WBE surveillance system for SARS-CoV-2 in Indonesia is feasible to monitor the community burden of infections. Future studies testing the potential of WBE and EWS for signaling early outbreaks of SARS-CoV-2 transmissions in this setting are required.

Naughton et al., 2021. Show us the Data: Global COVID-19 Wastewater Monitoring Efforts, Equity, and Gaps. https://doi.org/10.1101/2021.03.14.21253564

A year since the declaration of the global coronavirus disease 2019 (COVID-19) pandemic there were over 110 million cases and 2.5 million deaths. Learning from methods to track community spread of other viruses such as poliovirus, environmental virologists and those in the wastewater based epidemiology (WBE) field quickly adapted their existing methods to detect SARS-CoV-2 RNA in wastewater. Unlike COVID-19 case and mortality data, there was not a global dashboard to track wastewater monitoring of SARS-CoV-2 RNA worldwide. This study provides a one year review of the “COVIDPoops19” global dashboard of universities, sites, and countries monitoring SARS-CoV-2 RNA in wastewater. Methods to assemble the dashboard combined standard literature review, direct submissions, and daily, social media keyword searches. Over 200 universities, 1,000 sites, and 55 countries with 59 dashboards monitor wastewater for SARS-CoV-2 RNA. However, monitoring is primarily in high-income countries (65%) with less access to this valuable tool in low and middle income countries (35%). Data are not widely shared publicly or accessible to researchers to further inform public health actions, perform meta-analysis, better coordinate, and determine equitable distribution of monitoring sites. For WBE to be used to its full potential during COVID-19 and beyond, show us the data.

Nelson, 2022. What poo tells us: wastewater surveillance comes of age amid covid, monkeypox, and polio. http://dx.doi.org/10.1136/bmj.o1869

Ngwira et al., 2022. Cost of wastewater-based environmental surveillance for SARS-CoV-2: Evidence from pilot sites in Blantyre, Malawi and Kathmandu, Nepal. https://doi.org/10.1371/journal.pgph.0001377

Environmental surveillance of rivers and wastewater for SARS-CoV-2 detection has been explored as an innovative way to surveil the pandemic. This study estimated the economic costs of conducting wastewater-based environmental surveillance for SARS-CoV-2 to inform decision making if countries consider continuing these efforts. We estimated the cost of two SARS-CoV-2 environmental surveillance pilot studies conducted in Blantyre, Malawi, and Kathmandu, Nepal. The cost estimation accounted for the consumables, equipment, and human resource time costs used for environmental surveillance from sample selection until pathogen detection and overhead costs for the projects. Costs are reported in 2021 US $ and reported as costs per month, per sample and person per year. The estimated costs for environmental surveillance range from $6,175 to $8,272 per month (Blantyre site) and $16,756 to $30,050 (Kathmandu site). The number of samples processed per month ranged from 84 to 336 at the Blantyre site and 96 to 250 at the Kathmandu site. Consumables costs are variable costs influenced by the number of samples processed and are a large share of the monthly costs for ES (ranging from 39% to 72%). The relatively higher costs per month for the Kathmandu site were attributable to the higher allocation of dedicated human resources and equipment to environmental surveillance for SARS-CoV-2 compared to the Blantyre site where these resources were shared with other activities. The average cost per sample ranged from $25 to $74 (Blantyre) and $120 to $175 (Kathmandu). There were associated economies of scale for human resources and equipment costs with increased sample processing and sharing of resources with other activities. The cost per person in the catchment area per year ranged from $0.07 to $0.10 in Blantyre and $0.07 to $0.13 in Kathmandu. Environmental surveillance may be a low-cost early warning signal for SARS-CoV-2 that can complement other SARS-CoV2 monitoring efforts.

Pandey et al., 2021. SARS-CoV-2 in wastewater: Challenges for developing countries. https://doi.org/10.1016/j.ijheh.2020.113634

The COVID-19 pandemic that has engulfed the world, has affected the human lives in several aspects. The detection of SARS-CoV-2 in faeces and urine of the infected person, even after viral clearance in the respiratory tract, and its presence in untreated wastewater raises the possibility of fecal-oral transmission in future. The situation is likely to be more aggravated in developing and least developed countries struggling with the problem of ineffective waste disposal system, open defecation, poor sanitation, and limited access to clean drinking water. In this review, the available data on wastewater treatment, sanitation status and healthcare infrastructure from middle- and low-income countries is collected and correlated with the risk associated with the fecal-oral transmission of SARS-CoV-2. The review also highlights the limitation of COVID-19 surveillance through sewage monitoring in these countries owing to the absence of proper sewerage system. An inclusive approach of awareness, prevention, and mitigation from global to the local levels is required to overcome this challenging situation in developing countries.

Pillay et al., 2021. Monitoring changes in COVID-19 infection using wastewater-based epidemiology: A South African perspective. https://doi.org/10.1016/j.scitotenv.2021.147273

Monitoring of COVID-19 infections within communities via wastewater-based epidemiology could provide a cost-effective alternative to clinical testing. This approach, however, still requires improvement for its efficient application. In this paper, we present the use of wastewater-based epidemiology inmonitoring COVID-19 infection dynamics in the KwaZulu-Natal province of South Africa, focusing on four wastewater treatment plants for 14 weeks. The SARS-CoV-2 viral load in influent wastewater was determined using droplet digital PCR, and the number of people infected was estimated using published models as well as using a modified model to improve efficiency. On average, viral loads ranged between 0 and 2.73 × 105 copies/100 ml, 0–1.52 × 105 copies/100 ml, 3 × 104–7.32 × 105 copies/100 ml and 1.55 × 104–4.12 × 105 copies/100 ml in the four wastewater treatment plants studied. The peak in viral load corresponded to the reported COVID-19 infections within the districts where these catchments are located. In addition,we also observed that easing of lockdown restrictions by authorities corresponded with an increase in viral load in the untreated wastewater. Estimation of infection numbers based on the viral load showed that a higher number of people could potentially be infected, compared to the number of cases reported based on clinical testing. The findings reported in this paper contribute to the field of wastewater-based epidemiology for COVID-19 surveillance, whilst highlighting some of the challenges associated with this approach, especially in developing countries.

Pillay et al., 2022. Environmental surveillance for non sewered communities: a tool for disease mitigation in developing countries. https://www.wrc.org.za/wp-content/uploads/mdocs/Science%20briefs_NSS%20Surveillance.pdf

Environmental surveillance and Wastewater-Based Epidemiology (WBE) has proven to a useful tool in fighting a pandemic. Recent application of techniques for SARS-CoV-2 detection in sewage has provided vital information on the emergence of disease, circulating variants of interest and variants of concern, and possibility of predicting hospital admissions. Developing countries do not have extensive sewer networks and therefore cannot use WBE for the same population scale. A South African study has successfully demonstrated the application of nonsewered surveillance across multiple sites and provinces in South Africa. To the authors’ knowledge, this has been the largest non sewered surveillance programme undertaken globally.

Pocock et al., 2020. Proof of concept study: Application of wastewater-based surveillance to monitor SARS-CoV-2 prevalence in South African communities. https://erwat.co.za/wrc-proof-of-concept-study-wastewater-basedepidemiology-for-surveillance-of-the-spread-of-covid-19-insouth-african-communities/

Pocock et al., 2021. The efficacy of passive samplers for water quality based COVID-19 epidemiology surveillance. https://www.watershare.eu/wp-content/uploads/Science-Brief_-10_COVID19-surveillance-for-Non-Sewered.pdf

-Wastewater-based surveillance of communities for SARS-CoV-2 viral prevalence by sampling from wastewater treatment works is a powerful complementary epidemiological tool. However, in South Africa almost 40% of the population is not connected to a waterborne sewerage system.
-Sampling and surveillance of greywater and faecal waste within our non-sewered areas may give an early warning of the presence of COVID-19 infections in these communities, where there is both the risk of rapid spread and low likelihood of conventional testing.
-Passive sampling of environmental sites has shown promise, and may overcome issues of low yield when viral load is low and during high dilution periods, particularly in rivers downstream of unsewered settlements.
-Passive samplers have the advantage of allowing for easier and cheaper transport of samples compared to grab samples that require the costly transport of large volumes of water maintenance of the cold chain out of rural areas. Sample processing is also much quicker compared to concentration of water samples.
-Inclusion of trend monitoring of SARS-CoV-2 prevalence in unsewered communities together with established wastewater-based epidemiology (WBE) data collection from WWTW sampling can greatly expand the knowledge base and serve to highlight the needs of vulnerable communities in South Africa. These passive samplers can now also potentially be used for wastewater-based epidemiology for a broader scope of pathogens than only SARS-CoV-2.
-The success of passive samplers from this initiative has demonstrated the future B41potential and opportunity to enable more widespread environmental water quality monitoring due to its low cost and ease of application in the collection of samples.

Richardson, 2021. How waste water is helping South Africa fight COVID-19. https://www.nature.com/articles/d41586-021-01399-9

Shrestha et al., 2021. Wastewater-Based Epidemiology for Cost-Effective Mass Surveillance of COVID-19 in Low- and Middle-Income Countries: Challenges and Opportunities. https://doi.org/10.3390/w13202897

Wastewater-based epidemiology (WBE) is an approach that can be used to estimate COVID-19 prevalence in the population by detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater. As the WBE approach uses pooled samples from the study population, it is an inexpensive and non-invasive mass surveillance method compared to individual testing. Thus, it offers a good complement in low- and middle-income countries (LMICs) facing high costs of testing or social stigmatization, and it has a huge potential to monitor SARS-CoV-2 and its variants to curb the global COVID-19 pandemic. The aim of this review is to systematize the current evidence about the application of the WBE approach in mass surveillance of COVID-19 infection in LMICs, as well as its future potential. Among other parameters, population size contributing the fecal input to wastewater is an important parameter for COVID-19 prevalence estimation. It is easier to back-calculate COVID-19 prevalence in the community with centralized wastewater systems, because there can be more accurate estimates about the size of contributing population in the catchment. However, centralized wastewater management systems are often of low quality (or even non-existent) in LMICs, which raises a major concern about the ability to implement the WBE approach. However, it is possible to mobilize the WBE approach, if large areas are divided into sub-areas, corresponding to the existing wastewater management systems. In addition, a strong coordination between stakeholders is required for estimating population size respective to wastewater management systems. Nevertheless, further international efforts should be leveraged to strengthen the sanitation infrastructures in LMICs, using the lessons gathered from the current COVID-19 pandemic to be prepared for future pandemics.

Sosa-Hernández et al., 2022. Extensive Wastewater-Based Epidemiology as a Resourceful Tool for SARS-CoV-2 Surveillance in a Low-to-Middle-Income Country through a Successful Collaborative Quest: WBE, Mobility, and Clinical Tests. https://doi.org/10.3390/w14121842

The COVID-19 pandemic has challenged healthcare systems worldwide. Efforts in low-to middle- income countries (LMICs) cannot keep stride with infection rates, especially during peaks. A strong international collaboration between Arizona State University (ASU), Tec de Monterrey (TEC), and Servicios de Agua y Drenaje de Monterrey (Local Water Utilities) is acting to integrate wastewater-based epidemiology (WBE) of SARS-CoV-2 in the region as a complementary approach to aid the healthcare system. Wastewater was collected from four sewer catchments in the Monterrey Metropolitan area in Mexico (pop. 4,643,232) from mid-April 2020 to February 2021 (44 weeks, n = 644). Raw wastewater was filtered and filter-concentrated, the RNA was extracted using columns, and the Charité/Berlin protocol was used for the RT-qPCR. The viral loads obtained between the first (June 2020) and second waves (February 2021) of the pandemic were similar; in contrast, the clinical cases were fewer during the first wave, indicating poor coverage. During the second wave of the pandemic, the SARS-CoV-2 quantification in wastewater increased 14 days earlier than the COVID-19 clinical cases reported. This is the first long-term WBE study in Mexico and demonstrates its value in pandemic management.

South Africa NICD, 2023. Dashboard: SARS-CoV-2 wastewater levels in South Africa. https://wastewater.nicd.ac.za/

Street et al., 2020. Wastewater surveillance for Covid-19: An African perspective. https://doi.org/10.1016/j.scitotenv.2020.140719

The COVID-19 pandemic has once again highlighted the importance of access to sufficient quantities of safe water and sanitation in public health. In the current COVID-19 pandemic, an early warning wastewater system has been proposed as a platformfor SARS-CoV-2 surveillance, and a potentially important public health strategy to combat the disease. This short communication on wastewater surveillance in sub-Saharan Africa highlights challenges, opportunities and alternatives taken into account the local context.

Tegally et al., 2022. The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance. https://doi.org/10.1126/science.abq5358

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern—particularly Alpha, Beta, Delta, and Omicron—on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

Tiwari et al., 2022. Wastewater surveillance of antibiotic-resistant bacterial pathogens: A systematic review. https://doi.org/10.3389/fmicb.2022.977106

Infectious diseases caused by antibiotic-resistant bacterial (ARB) pathogens are a serious threat to human and animal health. The active surveillance of ARB using an integrated one-health approach can help to reduce the emergence and spread of ARB, reduce the associated economic impact, and guide antimicrobial stewardship programs. Wastewater surveillance (WWS) of ARB provides composite samples for a total population, with easy access to the mixed community microbiome. This concept is emerging rapidly, but the clinical utility, sensitivity, and uniformity of WWS of ARB remain poorly understood especially in relation to clinical evidence in sewershed communities. Here, we systematically searched the literature to identify studies that have compared findings from WWS of ARB and antibiotic resistance genes (ARG) with clinical evidence in parallel, thereby evaluating how likely WWS of ARB and ARG can relate to the clinical cases in communities. Initially, 2,235 articles were obtained using the primary search keywords, and 1,219 articles remained after de-duplication. Among these, 35 articles fulfilled the search criteria, and an additional 13 relevant articles were included by searching references in the primary literature. Among the 48 included papers, 34 studies used a culture-based method, followed by 11 metagenomics, and three PCR-based methods. A total of 28 out of 48 included studies were conducted at the single sewershed level, eight studies involved several countries, seven studies were conducted at national or regional scales, and five at hospital levels. Our review revealed that the performance of WWS of ARB pathogens has been evaluated more frequently for Escherichia coli, Enterococcus spp., and other members of the family Enterobacteriaceae, but has not been uniformly tested for all ARB pathogens. Many wastewater-based ARB studies comparing the findings with clinical evidence were conducted to evaluate the public health risk but not to relate with clinical evidence and to evaluate the performance of WWS of ARB. Indeed, relating WWS of ARB with clinical evidence in a sewershed is not straightforward, as the source of ARB in wastewater cannot be only from symptomatic human individuals but can also be from asymptomatic carriers as well as from animal sources. Further, the varying fates of each bacterial species and ARG within the sewerage make the aim of connecting WWS of ARB with clinical evidence more complicated. Therefore, future studies evaluating the performance of many AMR pathogens and their genes for WWS one by one can make the process simpler and the interpretation of results easier.

Tlhagale et al., 2022. Establishment of local wastewater-based surveillance programmes in response to the spread and infection of COVID-19 – case studies from South Africa, the Netherlands, Turkey and England. https://doi.org/10.2166/wh.2022.185

The COVID-19 pandemic has resulted in over 340 million infection cases (as of 21 January 2022) and more than 5.57 million deaths globally. In reaction, science, technology and innovation communities across the globe have organised themselves to contribute to national responses to COVID-19 disease. A significant contribution has been from the establishment of wastewater-based epidemiological (WBE) surveillance interventions and programmes for monitoring the spread of COVID-19 in at least 55 countries. Here, we examine and share experiences and lessons learnt in establishing such surveillance programmes. We use case studies to highlight testing methods and logistics considerations associated in scaling the implementing of such programmes in South Africa, the Netherlands, Turkey and England. The four countries were selected to represent different regions of the world and the perspective based on the considerable progress made in establishing and implementing their national WBE programmes. The selected countries also represent different climatic zones, economies, and development stages, which influence the implementation of national programmes of this nature and magnitude. In addition, the four countries’ programmes offer good experiences and lessons learnt since they are systematic, and cover extensive areas, disseminate knowledge locally and internationally and partnered with authorities (government). The programmes also strengthened working relations and partnerships between and among local and global organisations. This paper shares these experiences and lessons to encourage others in the water and public health sectors on the benefits and value of WBE in tackling SARS-CoV-2 and related future circumstances.

US Centers for Disease Control and Prevention, 2022. Wastewater Surveillance in Low-Resource Waste Systems. https://www.cdc.gov/nwss/low-resource/index.html

US Centers for Disease Control and Prevention, 2022. How Wastewater Surveillance Works. https://www.cdc.gov/nwss/how-wws-works/index.html

World Health Organization, 2022. Environmental surveillance for SARS-COV-2 to complement public health surveillance: Interim Guidance. https://www.who.int/publications/i/item/WHO-HEP-ECH-WSH-2022.1

World Health Organization, 2022. Wastewater surveillance of SARS-CoV-2: Questions and answers (Q&A). https://www.who.int/europe/publications/i/item/WHO-EURO-2022-5274-45038-64164

World Health Organization, 2022. How wastewater surveillance is helping the COVID-19 fight. https://www.afro.who.int/news/how-wastewater-surveillance-helping-covid-19-fight

Andrews et al., 2020. Environmental Surveillance as a Tool for Identifying High-risk Settings for Typhoid Transmission. https://doi.org/10.1093/cid/ciaa513

Enteric fever remains a major cause of morbidity in developing countries with poor sanitation conditions that enable fecal contamination of water distribution systems. Historical evidence has shown that contamination of water systems used for household consumption or agriculture are key transmission routes for Salmonella Typhi and Salmonella Paratyphi A. The World Health Organization now recommends that typhoid conjugate vaccines (TCV) be used in settings with high typhoid incidence; consequently, governments face a challenge regarding how to prioritize typhoid against other emerging diseases. A key issue is the lack of typhoid burden data in many low- and middle-income countries where TCV could be deployed. Here we present an argument for utilizing environmental sampling for the surveillance of enteric fever organisms to provide data on community-level typhoid risk. Such an approach could complement traditional blood culture-based surveillance or even replace it in settings where population-based clinical surveillance is not feasible. We review historical studies characterizing the transmission of enteric fever organisms through sewage and water, discuss recent advances in the molecular detection of typhoidal Salmonella in the environment, and outline challenges and knowledge gaps that need to be addressed to establish environmental sampling as a tool for generating actionable data that can inform public health responses to enteric fever.

Andrews & Yu, 2020. Tackling typhoid with environmental surveillance. https://www.coalitionagainsttyphoid.org/tackling-typhoid-with-environmental-surveillance/

Capone et al., 2020. Analysis of Fecal Sludges Reveals Common Enteric Pathogens in Urban Maputo, Mozambique. https://doi.org/10.1021/acs.estlett.0c00610

Sewage surveillance is increasingly used in public health applications; metabolites, biomarkers, and pathogens are detectable in wastewater and can provide useful information about community health. Work on this topic has been limited to wastewaters in mainly high-income settings, however. In low-income countries, where the burden of enteric infection is high, nonsewered sanitation predominates. In order to assess the utility of fecal sludge surveillance as a tool to identify the most prevalent enteric pathogens circulating among at-risk children, we collected 95 matched child stool and fecal sludge samples from household clusters sharing latrines in urban Maputo, Mozambique. We analyzed samples for 20 common enteric pathogens via multiplex real-time quantitative PCR. Among the 95 stools matched to fecal sludges, we detected the six most prevalent bacterial pathogens (Enteroaggregative E. coli, Shigella/Enteroinvasive E. coli, Enterotoxigenic E. coli, Enteropathogenic E. coli, shiga-toxin producing E. coli, Salmonella), and all three protozoan pathogens (Giardia duodenalis, Cryptosporidium parvum, Entamoeba histolytica) in the same rank order in both matrices. We did not observe the same trend for viral pathogens or soil-transmitted helminths, however. Our results suggest that sampling fecal sludges from onsite sanitation offers potential for localized pathogen surveillance in low-income settings where enteric pathogen prevalence is high.

Capone et al., 2021. Impact of sampling depth on pathogen detection in pit latrines. https://doi.org/10.1371/journal.pntd.0009176

Wastewater based epidemiology (WBE) is increasingly used to provide decision makers with actionable data about community health. WBE efforts to date have primarily focused on sewer-transported wastewater in high-income countries, but at least 1.8 billion people in low- and middle-income countries (LMIC) use onsite sanitation systems such as pit latrines and septic tanks. Like wastewater, fecal sludges from such systems offer similar advantages in community pathogen monitoring and other epidemiological applications. To evaluate the distribution of enteric pathogens inside pit latrines–which could inform sampling methods for WBE in LMIC settings unserved by sewers–we collected fecal sludges from the surface, mid-point, and maximum-depth of 33 pit latrines in urban and peri-urban Malawi and analyzed the 99 samples for 20 common enteric pathogens via multiplex quantitative reverse transcription PCR. Using logistic regression adjusted for household population, latrine sharing, the presence of a concrete floor or slab, water source, and anal cleansing materials, we found no significant difference in the odds of detecting the 20 pathogens from the mid-point (adjusted odds ratio, aOR = 1.1; 95% confidence interval = 0.73, 1.6) and surface samples (aOR = 0.80, 95% CI = 0.54, 1.2) compared with those samples taken from the maximum depth. Our results suggest that, for the purposes of routine pathogen monitoring, pit latrine sampling depth does not strongly influence the odds of detecting enteric pathogens by molecular methods. A single sample from the pit latrines’ surface, or a composite of surface samples, may be preferred as the most recent material contributed to the pit and may be easiest to collect.

Chigwechokha, Street, Holm, 2022. Advancing the Use of Fecal Sludge for Timelier and Better-Quality Epidemiological Data in Low- and Middle-Income Countries for Pandemic Prevention. https://doi.org/10.1021/acs.est.2c07788

Dzinamarira et al., 2022. Epidemiological surveillance of enteric viral diseases using wastewater in Africa – A rapid review. https://doi.org/10.1016/j.jiph.2022.05.010

Viral enteric pathogens remain an important cause of diarrhoeal outbreaks among children in sub-Saharan Africa (SSA). Consequently, diarrhoeal illness remains a significant cause of morbidity and mortality in the under-fives in SSA. These outbreaks associated with viral pathogens tend to be seasonal and early warning systems for impending outbreaks could be very crucial for triggering preventive public health response and building public health resilience to deal with increased demand for medical services. Wastewater surveillance for pathogens is an important epidemiological component that could inform early warning systems. The objective of this rapid review was to evaluate the use of wastewater for epidemiology surveillance of enteric viral pathogens. Nine studies met the inclusion criteria. Eight viral pathogens were reviewed and analysed from 6 countries that performed wastewater analysis. Six studies explored the epidemiologic significance of viral pathogens in wastewater. The findings of this review revealed that monitoring of wastewater can provide an additional tool to determine the epidemiology of viral pathogens circulating in the community thereby providing early warning of potential outbreaks using wastewater-based epidemiology methods. Five of the included studies revealed the occurrence of viral pathogens in raw sewage and treated wastewater as an indication of inefficient elimination of viruses leading to potential release into water sources which presents a public health risk, increasing the risk of inducing gastroenteritis in the population. Six studies revealed the need for public health authorities to realise the potential benefit of environmental surveillance (ES) as an additional tool to determine the epidemiology of viral pathogens circulating in each community. Despite the significant public health challenge associated with enteric viral pathogens in sub-Saharan Africa, there remains remarkable underinvestment in potentially epidemiologically beneficial research, including wastewater-based epidemiology for these infections.

Global Polio Eradication Initiative, 2022. Field Guidance for the Implementation of Environmental Surveillance for Poliovirus. https://polioeradication.org/wp-content/uploads/2022/11/Field-Guidance-for-the-Implementation-of-ES-20221118-ENG.pdf

Kilaru et al., 2021. Wastewater surveillance for infectious disease: a systematic review. https://doi.org/10.1101/2021.07.26.21261155

Wastewater surveillance of SARS-CoV-2 has shown to be a valuable source of information regarding SARS-CoV-2 transmission and COVID-19 cases. Though the method has been used for several decades to track other infectious diseases, there has not been a comprehensive review outlining all of the pathogens surveilled through wastewater. The aim of this study is to identify what infectious diseases have been previously studied via wastewater surveillance prior to the COVID-19 Pandemic and identify common characteristics between the studies, as well as identify current gaps in knowledge. Peer-reviewed articles published as of August 1, 2020 that examined wastewater for communicable and infectious human pathogens on 2 or more occasions were included in the study. Excluded from this list were all reviews and methods papers, single collection studies, and non-human pathogens. Infectious diseases and pathogens were identified in studies of wastewater surveillance, as well as themes of how wastewater surveillance and other measures of disease transmission were linked. This review did not include any numerical data from individual studies and thus no statistical analysis was done. 1005 articles were identified but only 100 were included in this review after applying the inclusion criteria. These studies came from 38 countries with concentration in certain countries including Italy, Israel, Brazil, Japan, and China. Twenty-five separate pathogen families were identified in the included studies, with the majority of studies examining pathogens from the family Picornaviridae, including polio and non-polio enteroviruses. Most studies of wastewater surveillance did not link what was found in the wastewater to other measures of disease transmission. Among those studies that did compare wastewater surveillance to other measures of disease transmission the value observed was dependent upon pathogen and varied by study. Wastewater surveillance has historically been used to assess water-borne and fecal-orally transmitted pathogens causing diarrheal disease. However, numerous other types of pathogens have been surveilled using wastewater and wastewater surveillance should be considered as a potential tool for many infectious diseases. Wastewater surveillance studies can be improved by incorporating other measures of disease transmission at the population-level including disease incidence and hospitalizations.

Kreier, 2021. The myriad ways sewage surveillance is helping fight COVID around the world. https://www.nature.com/articles/d41586-021-01234-1

Nelson, 2022. What poo tells us: wastewater surveillance comes of age amid covid, monkeypox, and polio. http://dx.doi.org/10.1136/bmj.o1869

Zohra et al., 2021. Wastewater based environmental surveillance of toxigenic Vibrio cholerae in Pakistan. https://doi.org/10.1371/journal.pone.0257414

Background: Pakistan has been experiencing intervals of sporadic cases and localized outbreaks in the last two decades. No proper study has been carried out in order to find out the environmental burden of toxigenic V. cholerae as well as how temporal and environmental factors associated in driving cholera across the country.
Methods: We tested waste water samples from designated national environment surveillance sites in Pakistan with RT-PCR assay. Multistage sampling technique were utilized for samples collection and for effective sample processing Bag-Mediated Filtration system, were employed. Results were analysed by district and month wise to understand the geographic distribution and identify the seasonal pattern of V. cholera detection in Pakistan.
Results: Between May 2019, and February 2020, we obtained and screened 160 samples in 12 districts across Pakistan. Out of 16 sentinel environmental surveillance sites, 15 sites showed positive results against cholera toxigenic gene with mostly lower CT value (mean, 34±2) and have significant difference (p < 0.05). The highest number of positive samples were collected from Sindh in month of November, then in June it is circulating in different districts of Pakistan including four Provinces respectively. Conclusion: V. cholera detection do not follow a clear seasonal pattern. However, the poor sanitation problems or temperature and rainfall may potentially influence the frequency and duration of cholera across the country. Occurrence of toxigenic V. cholerae in the environment samples showed that cholera is endemic, which is an alarming for a potential future cholera outbreaks in the country.

Ali at al., 2022. Community Wastewater-Based Surveillance Can Be a Cost-Effective Approach to Track COVID-19 Outbreak in Low-Resource Settings: Feasibility Assessment for Ethiopia Context. https://doi.org/10.3390/ijerph19148515

Wastewater surveillance systems have become an important component of COVID-19 outbreak monitoring in high-income settings. However, its use in most low-income settings has not been well-studied. This study assessed the feasibility and utility of wastewater surveillance system to monitor SARS-CoV-2 RNA in Addis Ababa, Ethiopia. The study was conducted at nine Membrane Bio-reactor (MBR) wastewater processing plants. The samples were collected in two separate time series. Wastewater samples and known leftover RT-PCR tested nasopharyngeal swabs were processed using two extraction protocols with different sample conditions. SARS-CoV-2 wastewater RT-PCR testing was conducted using RIDA GENE SARS-CoV-2 RUO protocol for wastewater SARS-CoV-2 RNA testing. Wastewater SARS-CoV-2 RNA RT-PCR protocol adaptation, optimization, and detection were conducted in an Addis Ababa, Ethiopia context. Samples collected during the first time series, when the national COVID-19 case load was low, were all negative. Conversely, samples collected during the second time series were all positive, coinciding with the highest daily reported new cases of COVID-19 in Ethiopia. The wastewater-based SARS-CoV-2 surveillance approach is feasible for Addis Ababa. The COVID-19 wastewater based epidemiological approach can potentially fill the evidence gap in distribution and dynamics of COVID-19 in Ethiopia and other low-income settings.

Bivins et al., 2022. Passive sampling to scale wastewater surveillance of infectious disease: Lessons learned from COVID-19. http://dx.doi.org/10.1016/j.scitotenv.2022.155347

Much of what is known and theorized concerning passive sampling techniques has been developed considering chemical analytes. Yet, historically, biological analytes, such as Salmonella typhi, have been collected from wastewater via passive sampling with Moore swabs. In response to the COVID-19 pandemic, passive sampling is re-emerging as a promising technique to monitor SARS-CoV-2 RNA in wastewater. Method comparisons and disease surveillance using composite, grab, and passive sampling for SARS-CoV-2 RNA detection have found passive sampling with a variety of materials routinely produced qualitative results superior to grab samples and useful for sub-sewershed surveillance of COVID-19. Among individual studies, SARS-CoV-2 RNA concentrations derived from passive samplers demonstrated heterogeneous correlation with concentrations from paired composite samples ranging from weak (R2=0.27, 0.31) to moderate (R2=0.59) to strong (R2=0.76). Among passive sampler materials, electronegative membranes have shown great promise with linear uptake of SARS-CoV-2 RNA observed for exposure durations of 24 to 48 h and in several cases RNA positivity on par with composite samples. Continuing development of passive sampling methods for the surveillance of infectious diseases via diverse forms of fecal waste should focus on optimizing sampler materials for the efficient uptake and recovery of biological analytes, kit-free extraction, and resource-efficient testing methods capable of rapidly producing qualitative or quantitative data. With such refinements passive sampling could prove to be a fundamental tool for scaling wastewater surveillance of infectious disease, especially among the 1.8 billion persons living in low-resource settings served by non-traditional wastewater collection infrastructure.

Bust, et al., 2021. The SACCESS network for COVID-19 wastewater surveillance: a national collaboration for public health responsiveness. https://hdl.handle.net/10520/ejc-healthr-v2021-n1-a23

Dzinamarira et al., 2022. Utilization of SARS-CoV-2 Wastewater Surveillance in Africa—A Rapid Review. https://doi.org/10.1016/j.jiph.2022.05.010

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.

Fongaro et al., 2021. SARS‑CoV‑2 in Human Sewage and River Water from a Remote and Vulnerable Area as a Surveillance Tool in Brazil. https://doi.org/10.1007/s12560-021-09487-9

In the present study, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was monitored in environmental samples from rural and vulnerable areas (a presidio, worker accommodation units, and river waters upstream and downstream of a rural community) from Minas Gerais State region, Southern Brazil, in August 2020. The sampling was performed prior to official declaration of the coronavirus disease (COVID-19) cases in those sites. SARS-CoV-2 RNA was detected in the presidio and workers accommodation units (3.0 × 104 virus genome copies (GC)/mL and 4.3 × 104 GC/mL of sewage, respectively). While SARS-CoV-2 was not detected in the river water upstream of the rural community, SARS-CoV-2 RNA was detected in downstream river waters (1.1 × 102 SARS-CoV-2 GC/mL). The results obtained in this study highlight the utility of SARS-CoV-2 monitoring in wastewater and human sewage as a non-invasive early warning tool to support health surveillance in vulnerable and remote areas, particularly in development countries.

Guerrero-Latorre et al., 2020. SARS-CoV-2 in river water: Implications in low sanitation countries. https://doi.org/10.1016/j.scitotenv.2020.140832 

Since the beginning of COVID-19 pandemic studies on viral shedding have reported that this virus is excreted in feces in most patients. High viral loads are found at the sewage pipeline or at the entrance of wastewater treatment plants fromcitieswhere the number of COVID-19 cases are significant. In Quito (Ecuador) as inmany other cities worldwide, wastewater is directly discharged into natural waters. The aim of this study was to evaluate SARS-CoV-2 presence in urban streams from a low sanitation context. Three river locations along the urban rivers of Quito were sampled on the 5th of June during a peak of COVID-19 cases. River samples were evaluated for water quality parameters and afterwards, concentrated for viral analysis using skimmed milk flocculation method. The viral concentrates were quantified for SARS-CoV-2 (N1 and N2 target regions) and Human Adenovirus as a human viral indicator. The results showed that SARS-CoV-2 was detected for both target regions in all samples analyzed in a range of 2,91E+05 to 3,19E+06 GC/L for N1 and from2,07E+05 to 2,22E+06 GC/L for N2. The high values detected in natural waters from a low sanitation region have several implications in health and ecology that should be further assessed.

Haque et al., 2022. Wastewater surveillance of SARS-CoV-2 in Bangladesh: Opportunities and challenges. https://doi.org/10.1016/j.coesh.2022.100334 

The ongoing pandemic of the coronavirus disease 2019 (COVID-19) is a public health crisis of global concern. The progression of the COVID-19 pandemic has been monitored in the first place by testing symptomatic individuals for SARS-CoV-2 virus in the respiratory samples. Concurrently, wastewater carries feces, urine, and sputum that potentially contains SARS-CoV-2 intact virus or partially damaged viral genetic materials excreted by infected individuals. This brings significant opportunities for understanding the infection dynamics by environmental surveillance. It has advantages for the country, especially in densely populated areas where individual clinical testing is difficult. However, there are several challenges including: 1) establishing a sampling plan and schedule that is representative of the various catchment populations 2) development and validation of standardized protocols for the laboratory analysis 3) understanding hydraulic flows and virus transport in complex wastewater drainage systems and 4) collaborative efforts from government agencies, NGOs, public health units and academia.

International Association of Public Health Institutes, 2022. Wastewater Surveillance Programs for COVID-19 and Other Pathogens Led by African National Public Health Institutes. https://ianphi.org/news/2022/wastewater-surveillance-webinar.html

Johnson et al., 2022. Tracking the circulating SARS‑CoV‑2 variant of concern in South Africa using wastewater‑based epidemiology. https://doi.org/10.1038/s41598-022-05110-4

This study uses wastewater-based epidemiology (WBE) to rapidly and, through targeted surveillance, track the geographical distribution of SARS-CoV-2 variants of concern (Alpha, Beta and Delta) within 24 wastewater treatment plants (WWTPs) in the Western Cape of South Africa. Information obtained was used to identify the circulating variant of concern (VOC) within a population and retrospectively trace when the predominant variant was introduced. Genotyping analysis of SARS-CoV-2 showed that 50% of wastewater samples harbored signature mutations linked to the Beta variant before the third wave, with the Delta variant absent within the population. Over time, the prevalence of the beta variant decreased steadily. The onset of the third wave resulted in the Delta variant becoming the predominant variant, with a 100% prevalence supporting the theory that the Delta variant was driving the third wave. In silico molecular docking analysis showed that the signature mutations of the Delta variant increased binding to host proteins, suggesting a possible molecular mechanism that increased viral infectivity of the Delta variant.

Kasprzyk-Hordern et al., 2022. Wastewater-based epidemiology in hazard forecasting and early-warning systems for global health risks. https://doi.org/10.1016/j.envint.2022.107143

With the advent of the SARS-CoV-2 pandemic, Wastewater-Based Epidemiology (WBE) has been applied to track community infection in cities worldwide and has proven succesful as an early warning system for identification of hotspots and changing prevalence of infections (both symptomatic and asymptomatic) at a city or sub-city level. Wastewater is only one of environmental compartments that requires consideration. In this manuscript, we have critically evaluated the knowledge-base and preparedness for building early warning systems in a rapidly urbanising world, with particular attention to Africa, which experiences rapid population growth and urbanisation. We have proposed a Digital Urban Environment Fingerprinting Platform (DUEF) – a new approach in hazard forecasting and early-warning systems for global health risks and an extension to the existing concept of smart cities. The urban environment (especially wastewater) contains a complex mixture of substances including toxic chemicals, infectious biological agents and human excretion products. DUEF assumes that these specific endo- and exogenous residues, anonymously pooled by communities’ wastewater, are indicative of community-wide exposure and the resulting effects. DUEF postulates that the measurement of the substances continuously and anonymously pooled by the receiving environment (sewage, surface water, soils and air), can provide near real-time dynamic information about the quantity and type of physical, biological or chemical stressors to which the surveyed systems are exposed, and can create a risk profile on the potential effects of these exposures. Successful development and utilisation of a DUEF globally requires a tiered approach including: Stage I: network building, capacity building, stakeholder engagement as well as a conceptual model, followed by Stage II: DUEF development, Stage III: implementation, and Stage IV: management and utilization. We have identified four key pillars required for the establishment of a DUEF framework: (1) Environmental fingerprints, (2) Socioeconomic fingerprints, (3) Statistics and modelling and (4) Information systems. This manuscript critically evaluates the current knowledge base within each pillar and provides recommendations for further developments with an aim of laying grounds for successful development of global DUEF platforms.

Kilaru et al., 2021. Wastewater surveillance for infectious disease: a systematic review. https://doi.org/10.1101/2021.07.26.21261155

Wastewater surveillance of SARS-CoV-2 has shown to be a valuable source of information regarding SARS-CoV-2 transmission and COVID-19 cases. Though the method has been used for several decades to track other infectious diseases, there has not been a comprehensive review outlining all of the pathogens surveilled through wastewater. The aim of this study is to identify what infectious diseases have been previously studied via wastewater surveillance prior to the COVID-19 Pandemic and identify common characteristics between the studies, as well as identify current gaps in knowledge. Peer-reviewed articles published as of August 1, 2020 that examined wastewater for communicable and infectious human pathogens on 2 or more occasions were included in the study. Excluded from this list were all reviews and methods papers, single collection studies, and non-human pathogens. Infectious diseases and pathogens were identified in studies of wastewater surveillance, as well as themes of how wastewater surveillance and other measures of disease transmission were linked. This review did not include any numerical data from individual studies and thus no statistical analysis was done. 1005 articles were identified but only 100 were included in this review after applying the inclusion criteria. These studies came from 38 countries with concentration in certain countries including Italy, Israel, Brazil, Japan, and China. Twenty-five separate pathogen families were identified in the included studies, with the majority of studies examining pathogens from the family Picornaviridae, including polio and non-polio enteroviruses. Most studies of wastewater surveillance did not link what was found in the wastewater to other measures of disease transmission. Among those studies that did compare wastewater surveillance to other measures of disease transmission the value observed was dependent upon pathogen and varied by study. Wastewater surveillance has historically been used to assess water-borne and fecal-orally transmitted pathogens causing diarrheal disease. However, numerous other types of pathogens have been surveilled using wastewater and wastewater surveillance should be considered as a potential tool for many infectious diseases. Wastewater surveillance studies can be improved by incorporating other measures of disease transmission at the population-level including disease incidence and hospitalizations.

Kreier, 2021. The myriad ways sewage surveillance is helping fight COVID around the world. https://www.nature.com/articles/d41586-021-01234-1

Mahlangeni et al., 2023. Using Wastewater Surveillance to Compare COVID-19 Outbreaks during the Easter Holidays over a 2-Year Period in Cape Town, South Africa https://www.mdpi.com/1999-4915/15/1/162

Wastewater surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown to be an important approach to determine early outbreaks of infections. Wastewater-based epidemiology (WBE) is regarded as a complementary tool for monitoring SARS-CoV-2 trends in communities. In this study, the changes in the SARS-CoV-2 RNA levels in wastewater during Easter holidays in 2021 and 2022 in the City of Cape Town were monitored over nine weeks. Our findings showed a statistically significant difference in the SARS-CoV-2 RNA viral load between the study weeks over the Easter period in 2021 and 2022, except for study week 1 and 4. During the Easter week, 52% of the wastewater treatment plants moved from the lower (low viral RNA) category in 2021 to the higher (medium to very high viral RNA) categories in 2022. As a result, the median SARS-CoV-2 viral loads where higher during the Easter week in 2022 than Easter week in 2021 (p = 0.0052). Mixed-effects model showed an association between the SARS-CoV-2 RNA viral loads and Easter week over the Easter period in 2021 only (p < 0.01). The study highlights the potential of WBE to track outbreaks during the holiday period. Mtetwa at al., 2021. Wastewater-Based Surveillance of Antibiotic Resistance Genes Associated with Tuberculosis Treatment Regimen in KwaZulu Natal, South Africa. https://doi.org/10.3390/antibiotics10111362

Essential components of public health include strengthening the surveillance of infectious diseases and developing early detection and prevention policies. This is particularly important for drug-resistant tuberculosis (DR-TB), which can be explored by using wastewater-based surveillance. This study aimed to use molecular techniques to determine the occurrence and concentration of antibiotic-resistance genes (ARGs) associated with tuberculosis (TB) resistance in untreated and treated wastewater. Raw/untreated and treated (post-chlorination) wastewater samples were taken from three wastewater treatment plants (WWTPs) in South Africa. The ARGs were selected to target drugs used for first- and second-line TB treatment. Both conventional polymerase chain reaction (PCR) and the more advanced droplet digital PCR (ddPCR) were evaluated as surveillance strategies to determine the distribution and concentration of the selected ARGs. The most abundant ARG in the untreated wastewater was the rrs gene, associated with resistance to the aminoglycosides, specifically streptomycin, with median concentration ranges of 4.69–5.19 log copies/mL. In contrast, pncA gene, associated with resistance to the TB drug pyrazinamide, was the least detected (1.59 to 2.27 log copies/mL). Resistance genes associated with bedaquiline was detected, which is a significant finding because this is a new drug introduced in South Africa for the treatment of multi-drug resistant TB. This study, therefore, establishes the potential of molecular surveillance of wastewater for monitoring antibiotic resistance to TB treatment in communities.

Murni et al., 2022. The feasibility of SARS-CoV-2 surveillance using wastewater and environmental sampling in Indonesia. https://doi.org/10.1371/journal.pone.0274793

Background: Wastewater-based epidemiology (WBE) surveillance as an early warning system (EWS) for monitoring community transmission of SARS-CoV-2 in low- and middle-income country (LMIC) settings, where diagnostic testing capacity is limited, needs further exploration. We explored the feasibility to conduct a WBE surveillance in Indonesia, one of the global epicenters of the COVID-19 pandemic in the middle of 2021, with the fourth largest population in the world where sewer and non-sewered sewage systems are implemented. The feasibility and resource capacity to collect samples on a weekly or fortnightly basis with grab and/or passive sampling methods, as well as to conduct qualitative and quantitative identification of SARS-CoV-2 ribonucleic acid (RNA) using real-time RT-PCR (RT-qPCR) testing of environmental samples were explored.
Materials and methods: We initiated a routine surveillance of wastewater and environmental sampling at three predetermined districts in Special Region of Yogyakarta Province. Water samples were collected from central and community wastewater treatment plants (WWTPs), including manholes flowing to the central WWTP, and additional soil samples were collected for the near source tracking (NST) locations (i.e., public spaces where people congregate).
Results: We began collecting samples in the Delta wave of the COVID-19 pandemic in Indonesia in July 2021. From a 10-week period, 54% (296/544) of wastewater and environmental samples were positive for SARS-CoV-2 RNA. The sample positivity rate decreased in proportion with the reported incidence of COVID-19 clinical cases in the community. The highest positivity rate of 77% in week 1, was obtained for samples collected in July 2021 and decreased to 25% in week 10 by the end of September 2021.
Conclusion: A WBE surveillance system for SARS-CoV-2 in Indonesia is feasible to monitor the community burden of infections. Future studies testing the potential of WBE and EWS for signaling early outbreaks of SARS-CoV-2 transmissions in this setting are required.

Naughton et al., 2021. Show us the Data: Global COVID-19 Wastewater Monitoring Efforts, Equity, and Gaps. https://doi.org/10.1101/2021.03.14.21253564

A year since the declaration of the global coronavirus disease 2019 (COVID-19) pandemic there were over 110 million cases and 2.5 million deaths. Learning from methods to track community spread of other viruses such as poliovirus, environmental virologists and those in the wastewater based epidemiology (WBE) field quickly adapted their existing methods to detect SARS-CoV-2 RNA in wastewater. Unlike COVID-19 case and mortality data, there was not a global dashboard to track wastewater monitoring of SARS-CoV-2 RNA worldwide. This study provides a one year review of the “COVIDPoops19” global dashboard of universities, sites, and countries monitoring SARS-CoV-2 RNA in wastewater. Methods to assemble the dashboard combined standard literature review, direct submissions, and daily, social media keyword searches. Over 200 universities, 1,000 sites, and 55 countries with 59 dashboards monitor wastewater for SARS-CoV-2 RNA. However, monitoring is primarily in high-income countries (65%) with less access to this valuable tool in low and middle income countries (35%). Data are not widely shared publicly or accessible to researchers to further inform public health actions, perform meta-analysis, better coordinate, and determine equitable distribution of monitoring sites. For WBE to be used to its full potential during COVID-19 and beyond, show us the data.

Nelson, 2022. What poo tells us: wastewater surveillance comes of age amid covid, monkeypox, and polio. http://dx.doi.org/10.1136/bmj.o1869

Ngwira et al., 2022. Cost of wastewater-based environmental surveillance for SARS-CoV-2: Evidence from pilot sites in Blantyre, Malawi and Kathmandu, Nepal. https://doi.org/10.1371/journal.pgph.0001377

Environmental surveillance of rivers and wastewater for SARS-CoV-2 detection has been explored as an innovative way to surveil the pandemic. This study estimated the economic costs of conducting wastewater-based environmental surveillance for SARS-CoV-2 to inform decision making if countries consider continuing these efforts. We estimated the cost of two SARS-CoV-2 environmental surveillance pilot studies conducted in Blantyre, Malawi, and Kathmandu, Nepal. The cost estimation accounted for the consumables, equipment, and human resource time costs used for environmental surveillance from sample selection until pathogen detection and overhead costs for the projects. Costs are reported in 2021 US $ and reported as costs per month, per sample and person per year. The estimated costs for environmental surveillance range from $6,175 to $8,272 per month (Blantyre site) and $16,756 to $30,050 (Kathmandu site). The number of samples processed per month ranged from 84 to 336 at the Blantyre site and 96 to 250 at the Kathmandu site. Consumables costs are variable costs influenced by the number of samples processed and are a large share of the monthly costs for ES (ranging from 39% to 72%). The relatively higher costs per month for the Kathmandu site were attributable to the higher allocation of dedicated human resources and equipment to environmental surveillance for SARS-CoV-2 compared to the Blantyre site where these resources were shared with other activities. The average cost per sample ranged from $25 to $74 (Blantyre) and $120 to $175 (Kathmandu). There were associated economies of scale for human resources and equipment costs with increased sample processing and sharing of resources with other activities. The cost per person in the catchment area per year ranged from $0.07 to $0.10 in Blantyre and $0.07 to $0.13 in Kathmandu. Environmental surveillance may be a low-cost early warning signal for SARS-CoV-2 that can complement other SARS-CoV2 monitoring efforts.

Pandey et al., 2021. SARS-CoV-2 in wastewater: Challenges for developing countries. https://doi.org/10.1016/j.ijheh.2020.113634

The COVID-19 pandemic that has engulfed the world, has affected the human lives in several aspects. The detection of SARS-CoV-2 in faeces and urine of the infected person, even after viral clearance in the respiratory tract, and its presence in untreated wastewater raises the possibility of fecal-oral transmission in future. The situation is likely to be more aggravated in developing and least developed countries struggling with the problem of ineffective waste disposal system, open defecation, poor sanitation, and limited access to clean drinking water. In this review, the available data on wastewater treatment, sanitation status and healthcare infrastructure from middle- and low-income countries is collected and correlated with the risk associated with the fecal-oral transmission of SARS-CoV-2. The review also highlights the limitation of COVID-19 surveillance through sewage monitoring in these countries owing to the absence of proper sewerage system. An inclusive approach of awareness, prevention, and mitigation from global to the local levels is required to overcome this challenging situation in developing countries.

Pillay et al., 2021. Monitoring changes in COVID-19 infection using wastewater-based epidemiology: A South African perspective. https://doi.org/10.1016/j.scitotenv.2021.147273

Monitoring of COVID-19 infections within communities via wastewater-based epidemiology could provide a cost-effective alternative to clinical testing. This approach, however, still requires improvement for its efficient application. In this paper, we present the use of wastewater-based epidemiology inmonitoring COVID-19 infection dynamics in the KwaZulu-Natal province of South Africa, focusing on four wastewater treatment plants for 14 weeks. The SARS-CoV-2 viral load in influent wastewater was determined using droplet digital PCR, and the number of people infected was estimated using published models as well as using a modified model to improve efficiency. On average, viral loads ranged between 0 and 2.73 × 105 copies/100 ml, 0–1.52 × 105 copies/100 ml, 3 × 104–7.32 × 105 copies/100 ml and 1.55 × 104–4.12 × 105 copies/100 ml in the four wastewater treatment plants studied. The peak in viral load corresponded to the reported COVID-19 infections within the districts where these catchments are located. In addition,we also observed that easing of lockdown restrictions by authorities corresponded with an increase in viral load in the untreated wastewater. Estimation of infection numbers based on the viral load showed that a higher number of people could potentially be infected, compared to the number of cases reported based on clinical testing. The findings reported in this paper contribute to the field of wastewater-based epidemiology for COVID-19 surveillance, whilst highlighting some of the challenges associated with this approach, especially in developing countries.

Pillay et al., 2022. Environmental surveillance for non sewered communities: a tool for disease mitigation in developing countries. https://www.wrc.org.za/wp-content/uploads/mdocs/Science%20briefs_NSS%20Surveillance.pdf

Environmental surveillance and Wastewater-Based Epidemiology (WBE) has proven to a useful tool in fighting a pandemic. Recent application of techniques for SARS-CoV-2 detection in sewage has provided vital information on the emergence of disease, circulating variants of interest and variants of concern, and possibility of predicting hospital admissions. Developing countries do not have extensive sewer networks and therefore cannot use WBE for the same population scale. A South African study has successfully demonstrated the application of nonsewered surveillance across multiple sites and provinces in South Africa. To the authors’ knowledge, this has been the largest non sewered surveillance programme undertaken globally.

Pocock et al., 2020. Proof of concept study: Application of wastewater-based surveillance to monitor SARS-CoV-2 prevalence in South African communities. https://erwat.co.za/wrc-proof-of-concept-study-wastewater-basedepidemiology-for-surveillance-of-the-spread-of-covid-19-insouth-african-communities/

Pocock et al., 2021. The efficacy of passive samplers for water quality based COVID-19 epidemiology surveillance. https://www.watershare.eu/wp-content/uploads/Science-Brief_-10_COVID19-surveillance-for-Non-Sewered.pdf

-Wastewater-based surveillance of communities for SARS-CoV-2 viral prevalence by sampling from wastewater treatment works is a powerful complementary epidemiological tool. However, in South Africa almost 40% of the population is not connected to a waterborne sewerage system.
-Sampling and surveillance of greywater and faecal waste within our non-sewered areas may give an early warning of the presence of COVID-19 infections in these communities, where there is both the risk of rapid spread and low likelihood of conventional testing.
-Passive sampling of environmental sites has shown promise, and may overcome issues of low yield when viral load is low and during high dilution periods, particularly in rivers downstream of unsewered settlements.
-Passive samplers have the advantage of allowing for easier and cheaper transport of samples compared to grab samples that require the costly transport of large volumes of water maintenance of the cold chain out of rural areas. Sample processing is also much quicker compared to concentration of water samples.
-Inclusion of trend monitoring of SARS-CoV-2 prevalence in unsewered communities together with established wastewater-based epidemiology (WBE) data collection from WWTW sampling can greatly expand the knowledge base and serve to highlight the needs of vulnerable communities in South Africa. These passive samplers can now also potentially be used for wastewater-based epidemiology for a broader scope of pathogens than only SARS-CoV-2.
-The success of passive samplers from this initiative has demonstrated the future B41potential and opportunity to enable more widespread environmental water quality monitoring due to its low cost and ease of application in the collection of samples.

Richardson, 2021. How waste water is helping South Africa fight COVID-19. https://www.nature.com/articles/d41586-021-01399-9

Shrestha et al., 2021. Wastewater-Based Epidemiology for Cost-Effective Mass Surveillance of COVID-19 in Low- and Middle-Income Countries: Challenges and Opportunities. https://doi.org/10.3390/w13202897

Wastewater-based epidemiology (WBE) is an approach that can be used to estimate COVID-19 prevalence in the population by detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater. As the WBE approach uses pooled samples from the study population, it is an inexpensive and non-invasive mass surveillance method compared to individual testing. Thus, it offers a good complement in low- and middle-income countries (LMICs) facing high costs of testing or social stigmatization, and it has a huge potential to monitor SARS-CoV-2 and its variants to curb the global COVID-19 pandemic. The aim of this review is to systematize the current evidence about the application of the WBE approach in mass surveillance of COVID-19 infection in LMICs, as well as its future potential. Among other parameters, population size contributing the fecal input to wastewater is an important parameter for COVID-19 prevalence estimation. It is easier to back-calculate COVID-19 prevalence in the community with centralized wastewater systems, because there can be more accurate estimates about the size of contributing population in the catchment. However, centralized wastewater management systems are often of low quality (or even non-existent) in LMICs, which raises a major concern about the ability to implement the WBE approach. However, it is possible to mobilize the WBE approach, if large areas are divided into sub-areas, corresponding to the existing wastewater management systems. In addition, a strong coordination between stakeholders is required for estimating population size respective to wastewater management systems. Nevertheless, further international efforts should be leveraged to strengthen the sanitation infrastructures in LMICs, using the lessons gathered from the current COVID-19 pandemic to be prepared for future pandemics.

Sosa-Hernández et al., 2022. Extensive Wastewater-Based Epidemiology as a Resourceful Tool for SARS-CoV-2 Surveillance in a Low-to-Middle-Income Country through a Successful Collaborative Quest: WBE, Mobility, and Clinical Tests. https://doi.org/10.3390/w14121842

The COVID-19 pandemic has challenged healthcare systems worldwide. Efforts in low-to middle- income countries (LMICs) cannot keep stride with infection rates, especially during peaks. A strong international collaboration between Arizona State University (ASU), Tec de Monterrey (TEC), and Servicios de Agua y Drenaje de Monterrey (Local Water Utilities) is acting to integrate wastewater-based epidemiology (WBE) of SARS-CoV-2 in the region as a complementary approach to aid the healthcare system. Wastewater was collected from four sewer catchments in the Monterrey Metropolitan area in Mexico (pop. 4,643,232) from mid-April 2020 to February 2021 (44 weeks, n = 644). Raw wastewater was filtered and filter-concentrated, the RNA was extracted using columns, and the Charité/Berlin protocol was used for the RT-qPCR. The viral loads obtained between the first (June 2020) and second waves (February 2021) of the pandemic were similar; in contrast, the clinical cases were fewer during the first wave, indicating poor coverage. During the second wave of the pandemic, the SARS-CoV-2 quantification in wastewater increased 14 days earlier than the COVID-19 clinical cases reported. This is the first long-term WBE study in Mexico and demonstrates its value in pandemic management.

South Africa National Institute for Communicable Diseases, 2023. Dashboard: SARS-CoV-2 wastewater levels in South Africa. https://wastewater.nicd.ac.za/

Street et al., 2020. Wastewater surveillance for Covid-19: An African perspective. https://doi.org/10.1016/j.scitotenv.2020.140719

The COVID-19 pandemic has once again highlighted the importance of access to sufficient quantities of safe water and sanitation in public health. In the current COVID-19 pandemic, an early warning wastewater system has been proposed as a platformfor SARS-CoV-2 surveillance, and a potentially important public health strategy to combat the disease. This short communication on wastewater surveillance in sub-Saharan Africa highlights challenges, opportunities and alternatives taken into account the local context.

Tegally et al., 2022. The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance. https://doi.org/10.1126/science.abq5358

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern—particularly Alpha, Beta, Delta, and Omicron—on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

Tlhagale et al., 2022. Establishment of local wastewater-based surveillance programmes in response to the spread and infection of COVID-19 – case studies from South Africa, the Netherlands, Turkey and England. https://doi.org/10.2166/wh.2022.185

The COVID-19 pandemic has resulted in over 340 million infection cases (as of 21 January 2022) and more than 5.57 million deaths globally. In reaction, science, technology and innovation communities across the globe have organised themselves to contribute to national responses to COVID-19 disease. A significant contribution has been from the establishment of wastewater-based epidemiological (WBE) surveillance interventions and programmes for monitoring the spread of COVID-19 in at least 55 countries. Here, we examine and share experiences and lessons learnt in establishing such surveillance programmes. We use case studies to highlight testing methods and logistics considerations associated in scaling the implementing of such programmes in South Africa, the Netherlands, Turkey and England. The four countries were selected to represent different regions of the world and the perspective based on the considerable progress made in establishing and implementing their national WBE programmes. The selected countries also represent different climatic zones, economies, and development stages, which influence the implementation of national programmes of this nature and magnitude. In addition, the four countries’ programmes offer good experiences and lessons learnt since they are systematic, and cover extensive areas, disseminate knowledge locally and internationally and partnered with authorities (government). The programmes also strengthened working relations and partnerships between and among local and global organisations. This paper shares these experiences and lessons to encourage others in the water and public health sectors on the benefits and value of WBE in tackling SARS-CoV-2 and related future circumstances.

US Centers for Disease Control and Prevention, 2022. Wastewater Surveillance in Low-Resource Waste Systems. https://www.cdc.gov/nwss/low-resource/index.html

US Centers for Disease Control and Prevention, 2022. How Wastewater Surveillance Works. https://www.cdc.gov/nwss/how-wws-works/index.html

World Health Organization, 2022. Environmental surveillance for SARS-COV-2 to complement public health surveillance: Interim Guidance. https://www.who.int/publications/i/item/WHO-HEP-ECH-WSH-2022.1

World Health Organization, 2022. Wastewater surveillance of SARS-CoV-2: Questions and answers (Q&A). https://www.who.int/europe/publications/i/item/WHO-EURO-2022-5274-45038-64164

World Health Organization, 2022. How wastewater surveillance is helping the COVID-19 fight. https://www.afro.who.int/news/how-wastewater-surveillance-helping-covid-19-fight

Andrews et al., 2020. Environmental Surveillance as a Tool for Identifying High-risk Settings for Typhoid Transmission. https://doi.org/10.1093/cid/ciaa513

Enteric fever remains a major cause of morbidity in developing countries with poor sanitation conditions that enable fecal contamination of water distribution systems. Historical evidence has shown that contamination of water systems used for household consumption or agriculture are key transmission routes for Salmonella Typhi and Salmonella Paratyphi A. The World Health Organization now recommends that typhoid conjugate vaccines (TCV) be used in settings with high typhoid incidence; consequently, governments face a challenge regarding how to prioritize typhoid against other emerging diseases. A key issue is the lack of typhoid burden data in many low- and middle-income countries where TCV could be deployed. Here we present an argument for utilizing environmental sampling for the surveillance of enteric fever organisms to provide data on community-level typhoid risk. Such an approach could complement traditional blood culture-based surveillance or even replace it in settings where population-based clinical surveillance is not feasible. We review historical studies characterizing the transmission of enteric fever organisms through sewage and water, discuss recent advances in the molecular detection of typhoidal Salmonella in the environment, and outline challenges and knowledge gaps that need to be addressed to establish environmental sampling as a tool for generating actionable data that can inform public health responses to enteric fever.

Mtetwa at al., 2021. Wastewater-Based Surveillance of Antibiotic Resistance Genes Associated with Tuberculosis Treatment Regimen in KwaZulu Natal, South Africa. https://doi.org/10.3390/antibiotics10111362

Essential components of public health include strengthening the surveillance of infectious diseases and developing early detection and prevention policies. This is particularly important for drug-resistant tuberculosis (DR-TB), which can be explored by using wastewater-based surveillance. This study aimed to use molecular techniques to determine the occurrence and concentration of antibiotic-resistance genes (ARGs) associated with tuberculosis (TB) resistance in untreated and treated wastewater. Raw/untreated and treated (post-chlorination) wastewater samples were taken from three wastewater treatment plants (WWTPs) in South Africa. The ARGs were selected to target drugs used for first- and second-line TB treatment. Both conventional polymerase chain reaction (PCR) and the more advanced droplet digital PCR (ddPCR) were evaluated as surveillance strategies to determine the distribution and concentration of the selected ARGs. The most abundant ARG in the untreated wastewater was the rrs gene, associated with resistance to the aminoglycosides, specifically streptomycin, with median concentration ranges of 4.69–5.19 log copies/mL. In contrast, pncA gene, associated with resistance to the TB drug pyrazinamide, was the least detected (1.59 to 2.27 log copies/mL). Resistance genes associated with bedaquiline was detected, which is a significant finding because this is a new drug introduced in South Africa for the treatment of multi-drug resistant TB. This study, therefore, establishes the potential of molecular surveillance of wastewater for monitoring antibiotic resistance to TB treatment in communities.

Tiwari et al., 2022. Wastewater surveillance of antibiotic-resistant bacterial pathogens: A systematic review https://doi.org/10.3389/fmicb.2022.977106

Infectious diseases caused by antibiotic-resistant bacterial (ARB) pathogens are a serious threat to human and animal health. The active surveillance of ARB using an integrated one-health approach can help to reduce the emergence and spread of ARB, reduce the associated economic impact, and guide antimicrobial stewardship programs. Wastewater surveillance (WWS) of ARB provides composite samples for a total population, with easy access to the mixed community microbiome. This concept is emerging rapidly, but the clinical utility, sensitivity, and uniformity of WWS of ARB remain poorly understood especially in relation to clinical evidence in sewershed communities. Here, we systematically searched the literature to identify studies that have compared findings from WWS of ARB and antibiotic resistance genes (ARG) with clinical evidence in parallel, thereby evaluating how likely WWS of ARB and ARG can relate to the clinical cases in communities. Initially, 2,235 articles were obtained using the primary search keywords, and 1,219 articles remained after de-duplication. Among these, 35 articles fulfilled the search criteria, and an additional 13 relevant articles were included by searching references in the primary literature. Among the 48 included papers, 34 studies used a culture-based method, followed by 11 metagenomics, and three PCR-based methods. A total of 28 out of 48 included studies were conducted at the single sewershed level, eight studies involved several countries, seven studies were conducted at national or regional scales, and five at hospital levels. Our review revealed that the performance of WWS of ARB pathogens has been evaluated more frequently for Escherichia coli, Enterococcus spp., and other members of the family Enterobacteriaceae, but has not been uniformly tested for all ARB pathogens. Many wastewater-based ARB studies comparing the findings with clinical evidence were conducted to evaluate the public health risk but not to relate with clinical evidence and to evaluate the performance of WWS of ARB. Indeed, relating WWS of ARB with clinical evidence in a sewershed is not straightforward, as the source of ARB in wastewater cannot be only from symptomatic human individuals but can also be from asymptomatic carriers as well as from animal sources. Further, the varying fates of each bacterial species and ARG within the sewerage make the aim of connecting WWS of ARB with clinical evidence more complicated. Therefore, future studies evaluating the performance of many AMR pathogens and their genes for WWS one by one can make the process simpler and the interpretation of results easier.

Archer et al., 2023. Occurrence of contaminants of emerging concern in the Eerste River, South Africa: Towards the optimisation of an urban water profiling approach for public- and ecological health risk characterisation. http://dx.doi.org/10.1016/j.scitotenv.2022.160254

The study evaluated the presence and fate of various contaminants of emerging concern (CECs) from a South African wastewater treatment works (WWTW) and surface waters located around an urban setting. A total of 45 CECs were quantified from nine sampling locations over an 11-month period. Daily loads (g/day) of the target analytes in the WWTW showed persistence of some CECs, along with population-normalised daily loads (mg/day/1000inh) of pharmaceuticals and drugs of abuse (DOA) that were estimated for the first time in the study area. Multiple chemical markers were recorded in river water located upstream of the WWTW discharge throughout the study period, suggesting a high degree of diffuse pollution from urban communities in the study area that are not connected to sewage networks or where sanitation services are limited. The potential of using defined surface water locations to perform community-wide substance use profiling for non-sewered communities was also explored. Environmental risk characterisation for the WWTW effluent and surface waters throughout the study period provided multiple risk quotients (RQ) for the target list of CECs spanning over various sentinel trophic levels. High risk profiles (RQ > 1.0) with a frequency of exceedance (FoE) larger than 75 % were recorded for several CECs in both WWTW effluent and surface water locations that suggest potential long-term ecological health risk impacts of pollution hotspot areas in the river catchment situated around the urban area. We present challenges in surface water quality within the study area that is relatable, or may even present more challenging, in other low- or middle-income country (LMICs) settings. The study also highlighted some challenges and limitations associated with the much-needed application of wastewaterbased epidemiology (WBE) intervention in non-sewered communities that can informon public health and communal substance use profiles of the entire urban setting.