PHWR Public Health Weekly Report

The surveillance of various pathogens using wastewater is drawing attention as a useful tool for monitoring infectious diseases and antimicrobial resistance. In wastewater surveillance, samples are collected and analyzed to detect the emergence of pathogens circulating in the community. This also plays an important role in preventing the spread of infectious diseases by detecting their occurrence and mutations of pathogens before clinical cases appear, as pathogens can be shed before the onset of clinical symptoms [1].

Thus, wastewater surveillance can be an important objective indicator of virus circulation within a community. It can complement public health surveillance based on the screening of patients with suspected symptoms. It can be particularly useful in cases of asymptomatic infection and in situations in which the testing capacity and willingness to test are reduced [2]. Because both symptomatic and asymptomatic individuals shed pathogens into sewage, wastewater samples pooled from the entire population provide better insight into the genetic diversity of pathogens circulating in the community than insight obtained solely from testing and sequencing clinical samples [3,4].

The diverse mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus might have negatively impacted several aspects of public health, including increasing transmissibility as well as immune evasion and reducing the efficacy of vaccines and therapeutics [5]. For instance, the Delta and Omicron variants have spread rapidly worldwide due to their higher transmissibility and ability to evade existing immune responses [5]. Consequently, the emergence of these variants has jeopardized the speed and effectiveness of public health responses and highlighted the limitations of existing surveillance systems. Existing pathogen mutation surveillance has been conducted mainly through individual testing and genetic sequence analyses using clinical specimens. However, understanding the infection trends of the entire community only with clinical data from current sentinel surveillance institutions is difficult; thus, this approach cannot sufficiently play a role as an early warning system.

Pathogen surveillance using wastewater can complement these limitations and detect the genetic material of pathogens present in wastewater at the community level. Bioinformatics analysis technologies, such as the polymerase chain reaction and next-generation sequencing (NGS), are being utilized to monitor SARS-CoV-2 variants in wastewater [6]. The use of these technologies has significantly improved the sensitivity and specificity of wastewater surveillance, playing an important role in the early detection of pathogen outbreak trends and variants. Wastewater-based surveillance has become an important tool for pandemic responses and preparedness, with the potential to further improve the effectiveness of infectious disease management with the integration of clinical surveillance data [7,8].

In this study, we examined how wastewater-based pathogen surveillance could be applied to monitoring pathogen mutations through cases from various countries around the world. By doing so, we aimed to maximize the advantages of wastewater-based infectious disease surveillance, such as being able to detect infectious diseases outbreaks early in order to establish public health response strategies.

Wastewater-based infectious disease surveillance has shown promise as an early warning system for outbreaks of pathogens, such as SARS-CoV-2, in several countries. Case studies conducted in various countries have shown that wastewater-based infectious disease surveillance is more effective than traditional clinical surveillance in detecting the occurrence and mutation of infectious diseases early and preventing the spread of infectious diseases within the community [9].

1. United States of America

Public health laboratories across the United States are conducting wastewater surveillance by working with wastewater treatment facilities to develop surveillance sample collection plans. They are able to predict infectious disease outbreak trends by comparing wastewater surveillance data with clinical case data from a particular site and the surrounding communities [9]. In response to the coronavirus disease 2019 (COVID-19) pandemic, the Centers for Disease Control and Prevention (CDC) launched the National Wastewater Surveillance System (NWSS) in September 2020 to monitor SARS-CoV-2 in wastewater. The NWSS aims to build a robust and sustainable surveillance system through independent and regional wastewater surveillance. Through this system, the US Department of Health and Human Services and public health laboratories are developing the capacity needed to conduct wastewater surveillance, building on epidemiological resources, data analysis tools, and laboratory support. Data analyzed in this way can enable early detection of new infectious disease outbreaks and aid in local decision-making, such as selecting locations for mobile testing and vaccination sites [10].

The NWSS currently operates more than 1,200 surveillance sites nationwide. As of July 2022, wastewater surveillance systems have been deployed in 46 states and five major urban communities, collecting samples from wastewater systems serving more than 130 million people across the United States. The CDC continues to provide technical guidance, data analysis, and visualization methods to jurisdictions with wastewater surveillance systems [11]. Omicron (B.1.1.529) was detected in local wastewater in late November 2021 (before the Omicron variant was identified as a clinical case in the area in January 2022). This was a case of the preliminary detection of SARS-CoV-2 RNA in a wastewater system in Burlington, Vermont. Rapid sewage testing allowed local health authorities to respond by deploying personnel and resources to areas with high virus detection rates and disseminating information to specific audiences, focusing on vulnerable populations [11,12]. Additionally, the CDC initiated a traveler-based SARS-CoV-2 genomic surveillance program to detect novel SARS-CoV-2 variants at three US airports in September 2021 and expanded the program to eight international airports in the nation in the first half of 2024 [13]. The aim of this program is to proactively detect variant SARS-CoV-2 strains by collecting samples from arriving travelers (who play a vital role in the monitoring of the emergence of infectious diseases). Travelers are highly mobile and can become infected while traveling, possibly spreading diseases from one place to another in a short period. If mutations are found in human samples, this situation is likely to be after widespread infection has already occurred within the community [13]. The aforementioned case demonstrates that traveler-based wastewater surveillance at airports can play a critical role in the early detection of emerging infectious diseases and variants. Due to their high mobility and susceptibility to infection, travelers can be a major conduit for the rapid spread of variant viruses or new infectious diseases. Therefore, airport sewage surveillance is an important tool for detecting mutations in the early stages and responding preemptively before an infectious disease spreads widely throughout the community. In conclusion, sewage surveillance systems at major international airports can play an effective role in preventing the spread of infectious diseases by proactively managing public health risks in conjunction with sewage surveillance in the community.

2. The Netherlands

The National Institute for Public Health and the Environment (Rijksinstituut voor Volksgezondheid en Milieu, RIVM) has been conducting wastewater research for approximately 30 years. In 1992, the RIVM detected poliovirus in sewage samples during a polio outbreak in an anti-vaccination region [14]. Additionally, from 2020 onward, wastewater surveillance has been conducted to monitor the spread of SARS-CoV-2, with all wastewater treatment plants in the Netherlands participating in this study [14].

The Netherlands has more than 300 sewage treatment plants, and the RIVM collects sewage samples from all of them on a weekly basis [14]. The samples are tested for the SARS-CoV-2 virus in the “Monitoring coronavirus variants using sewage” laboratory of the NWSS program of the RIVM [14]. Additionally, the RIVM has been testing four sewage samples per week from Schiphol Airport since February 17, 2020. As this airport is a major point of entry into the Netherlands, monitoring for the SARS-CoV-2 virus variants is vital [14]. During the height of the COVID-19 pandemic in the Netherlands, high levels of the virus were detected in sewage at Schiphol Airport, and the same mutant strains were detected as in other countries, which is consistent with trends across the Netherlands [14]. In particular, the Omicron variant was first detected in sewage at Schiphol Airport in November 2021 [14].

3. South Africa

SARS-CoV-2 variants in sewage samples collected from urban centers across South Africa were detected and analyzed. South Africa has a population exceeding 55 million people, most of whom live in urban areas located in five of the country’s nine provinces [1]. It has over 1,000 sewage treatment plants, and 84% of the population uses toilets connected to a public sewage system or septic tank [1]. In June 2020, the first wastewater COVID-19 testing was performed in South Africa, which led to the creation of the South African Collaborative COVID-19 Environmental Monitoring System to monitor trends in the SARS-CoV-2 virus in wastewater across the country [1]. Recent studies have demonstrated that viral genetic analyses in wastewater are feasible and that both wastewater and clinical surveillance can be used to determine the phylogenetic relationships of similar mutant strains. This strategy allowed us to discover new mutations and strains in wastewater before they were identified in clinical specimens [1].

4. India

In 2021, wastewater samples were collected from 11 treatment plants in the Jaipur district and monitored for early detection of the Delta variant (B.1.617.2) [15]. Sewage samples were collected weekly from February 19 to June 8, 2021, and an NGS analysis was performed. By achieving an average genetic coverage of 94.39%, characteristics of the mutations were analyzed with high reliability. In other words, approximately 94.39% of the entire genetic sequence was read accurately. The analysis found that the Delta variant was detected in sewage 2–3 weeks earlier than such findings appeared in clinical reports [15]. This early detection has been instrumental in enabling public health authorities to take preemptive measures [15].

5. Switzerland

The spread of SARS-CoV-2 variants during a major international event was monitored by analyzing wastewater from the canton of Grisons in Switzerland [16]. The complex geography and diverse population of Grisons undergo significant changes during peak seasons due to tourists and events. Major sporting events in Davos and St. Moritz in December 2021 resulted in large population influxes [16]. To monitor the prevalence and spread of SARS-CoV-2 variants in Grisons, 24-hour composite wastewater samples were collected from a treatment plant before and after the Fédération Internationale de Ski Alpine and Nordic World Cup events in November and December 2021 and the World Economic Forum (WEF) in May 2022 and January 2023 [16]. The prevalence of variants identified in sewage sequencing data showed that the Omicron variant BA.1 was spread in Davos and St. Moritz during an international sporting event held in December 2021 [16]. During the WEF in January 2023, the Omicron BA.2.75 variant was detected in Davos but not in St. Moritz, showing that large international events can influence the spread of new variants [16]. These results demonstrate that the spread of new variants in large-scale events can be detected using wastewater surveillance, providing important information for developing public health strategies [16].

Monitoring pathogen occurrence and variants using wastewater can provide valuable information for infectious disease surveillance. Sewage-based testing provides information such as trends in pathogen occurrence and the emergence of variants. Further, it is useful for monitoring the occurrence of new infectious diseases in the community. Additionally, analyzing mutations of various pathogens in wastewater using advanced molecular biology technologies, such as NGS, can aid in understanding the emergence and occurrence trends of variants. However, since sewage samples can affect data results depending on the collection location and frequency due to the nature of the sample, standardized protocols and quality control are required. Pathogen detection and genetic data analyses using wastewater have limitations in distinguishing between the emergence of pathogen variants and simple sequence analysis errors due to the complexity of the microbial community in wastewater and the presence of non-pathogenic genes. Therefore, developing and validating analytical tools that are suitable, efficient, and reliable for wastewater samples is crucial. In addition, continuous research should be conducted to improve the sensitivity, specificity, and speed of detecting mutations in wastewater samples by improving sequencing and data analysis technologies and utilizing bioinformatics analysis tools.

Sewage surveillance is an efficient and useful tool that can encompass community infectious disease surveillance and help predict the occurrence of new pathogens as well as the emergence of variants even in areas where clinical specimens are scarce. Therefore, pathogen surveillance using wastewater can be effective in monitoring and detecting the occurrence of new infectious diseases and mutations, thereby protecting various community resources from future infectious diseases.

Ethics Statement: Not applicable.

Funding Source: None.

Acknowledgments: None.

Conflict of Interest: The authors have no conflicts of interest to declare.

Author Contributions: Conceptualization: JHL, HJP, HJY. Data curation: JHL. Formal analysis: JHL, HJP, HJY. Writing – original draft: JHL, HJP, HJY. Writing – review & editing: HJY, YSC.