As wastewater monitoring expands beyond COVID-19, recent scientific advances are revealing its potential to detect emerging infectious diseases, track animal pathogens, monitor antimicrobial resistance and strengthen epidemic preparedness. Research published in 2026 suggests that wastewater could become an essential source of intelligence connecting human, animal and environmental health.
Wastewater is becoming a strategic tool for epidemic prevention
One of the most significant lessons of the COVID-19 pandemic was that wastewater contains valuable epidemiological information long before it is routinely collected through conventional disease reporting systems. Every day, infected individuals release viruses, bacteria and other biological material through faeces, urine and various bodily secretions. Some of these agents, or their genetic material, enter sewage networks, where they can be collected and analysed.
By measuring the concentrations of selected pathogens over time, wastewater-based epidemiology (WBE) provides an indirect assessment of infection dynamics within a population. Unlike conventional surveillance, which relies largely on healthcare consultations, diagnostic testing and disease notifications, wastewater monitoring can capture biological signals from symptomatic, asymptomatic and undiagnosed infections!
It can also provide information in areas where access to healthcare or laboratory testing is limited. The US Centers for Disease Control and Prevention (CDC) emphasise that wastewater monitoring offers a community-level perspective on infectious disease circulation and can complement clinical surveillance, particularly when testing practices change. The CDC's National Wastewater Surveillance System now monitors six major viral categories: SARS-CoV-2, influenza A, respiratory syncytial virus (RSV), measles, avian influenza A(H5) and mpox.
For public health authorities, the advantages extend beyond pathogen detection. Wastewater surveillance can help identify changes in epidemic intensity, monitor seasonal trends, support targeted investigations and evaluate the effects of preventive interventions. In certain epidemiological situations, changes in wastewater pathogen concentrations have preceded increases in clinically reported infections. However, the size and reliability of this early-warning advantage vary according to the disease, sampling frequency, laboratory methods and local surveillance practices.
The importance of these systems was further emphasised by the World Health Organization (WHO) in its June 2026 report, Wastewater and Environmental Surveillance: A Global Landscape Analysis.
This report examined existing surveillance programmes, operational models, governance arrangements and implementation challenges worldwide. It concluded that wastewater surveillance is most valuable when integrated into routine public health decision-making, supported by sustainable financing and adapted to national priorities.
A major development in 2026: wastewater surveillance moves into animal health
Although wastewater epidemiology has primarily been developed for human populations, its potential applications in veterinary medicine are increasingly attracting scientific attention.
Livestock production facilities, slaughterhouses and agricultural effluents contain biological material originating from large numbers of animals. These collective samples may reveal pathogens circulating within herds and production systems without requiring systematic individual sampling.
A review published in Viruses in March 2026 examined wastewater-based surveillance of emerging viral diseases in livestock. The authors concluded that livestock wastewater could provide a complementary early-warning system for emerging infections, while highlighting major limitations associated with standardisation, the diversity of agricultural effluents and the interpretation of environmental pathogen detection. The review also stressed the economic importance of improving surveillance, citing substantial losses associated with diseases such as highly pathogenic avian influenza and African swine fever.
The most convincing recent evidence comes from studies investigating environmental sampling at different stages of livestock production.
Slaughterhouse wastewater can reveal up to 80% of detected livestock viral diversity
A study published in One Health in June 2026 provides particularly important evidence for veterinary surveillance. Researchers collected 105 environmental samples over 11 months, including pig slurry, cattle manure, farm air and slaughterhouse wastewater. The samples were analysed using pathogen-specific PCR techniques and targeted viral metagenomics. Slaughterhouse wastewater revealed up to 80% of the total viral species diversity identified across the sampled matrices.
This result demonstrates the potential value of slaughterhouses as epidemiological sentinel sites, particularly because animals entering these facilities may originate from multiple farms and geographical areas.
The study identified several viruses of veterinary or zoonotic interest, including:
Rotavirus A, associated with enteric infections in multiple species.
Bovine coronavirus, involved in respiratory and enteric diseases in cattle.
Hepatitis E virus, which has important zoonotic implications.
Porcine bocaviruses, circoviruses and astroviruses.
Porcine bufavirus and other viruses whose pathogenic significance remains incompletely understood.
The researchers also identified differences between sample types. Pig slurry and cattle manure were especially informative for certain enteric viruses, including rotavirus A and hepatitis E virus. Air sampling provided complementary information for respiratory-associated viruses.
Seasonal patterns were observed, with higher detection of rotavirus A and bovine coronavirus during winter.
Targeted metagenomic sequencing also identified porcine reproductive and respiratory syndrome virus (PRRSV), porcine epidemic diarrhoea virus (PEDV) and transmissible gastroenteritis virus (TGEV) sporadically in slaughterhouse wastewater, although these findings should be distinguished from results obtained through pathogen-specific PCR.
Municipal wastewater also contains signals from animal and plant viruses
Another important development was reported in Water Research. Researchers investigated wastewater viromes from five Finnish wastewater treatment plant catchments, using monthly samples from two periods: 2020–2021 and 2024–2025.
The study revealed that nearly half of the detected viral accessions were associated with non-human hosts, although human-associated viruses still represented 83% of normalised viral sequencing reads. Importantly, viruses associated with rodents, livestock and birds exhibited geographical patterns consistent with the distribution of their potential host populations.
The researchers also detected four plant pathogens regulated by the European Union.
These findings suggest that urban wastewater can contain epidemiological information extending far beyond human infections. However, the origin of individual viral signals may be complex. Wastewater can receive material from animals, food production, agriculture, wildlife and commercial activities. A positive result does not necessarily indicate infection in a particular animal population.
Avian influenza H5N1: a clear example of the One Health dimension
Highly pathogenic avian influenza A(H5N1) illustrates the value, and the complexity, of wastewater surveillance when a pathogen circulates across several animal species.
The continuing involvement of wild birds, poultry and mammals, including dairy cattle, has strengthened the need for surveillance systems capable of combining veterinary, human and environmental information. In the United States, the CDC monitors influenza A(H5) genetic material in wastewater as part of its national surveillance activities. Environmental testing may identify A(H5) signals even when no corresponding human infections have been reported locally.
However, these signals require careful interpretation. According to the CDC, wastewater testing cannot determine whether influenza A(H5) originates from infected humans, animals or animal products. For example, milk from infected dairy cattle entering a sewage system can contribute to a positive wastewater result.
Furthermore, detection of influenza A(H5) does not automatically demonstrate the presence of the H5N1 subtype, since additional genetic characterisation is required. When a positive signal is detected, public health and agricultural authorities may undertake complementary investigations to determine its possible origin and assess whether intervention is justified.
The objective is not to replace direct animal testing but to identify unusual environmental signals that may justify more targeted investigations. This approach is particularly relevant for zoonotic pathogens whose epidemiology involves multiple hosts and environmental pathways.
Japanese encephalitis: a promising application in pig production
Japanese encephalitis virus (JEV) provides another example of the potential value of livestock wastewater surveillance. Pigs are important amplifying hosts in the transmission cycle of this mosquito-borne flavivirus, creating a direct connection between livestock infection, vector ecology and human health.
A study published in Applied and Environmental Microbiology in 2025 examined the detection of Japanese encephalitis virus in piggery effluent and other environmental samples. The researchers demonstrated the feasibility of detecting viral RNA in these matrices during relevant transmission periods, supporting their potential use as complementary epidemiological indicators.
This approach is of particular interest because it could connect livestock surveillance with mosquito monitoring and human risk assessment. For example, a persistent increase in environmental viral detection could prompt more intensive mosquito surveillance, targeted veterinary investigations and enhanced communication between animal health and public health authorities.
However, validated thresholds for triggering specific control measures have not yet been established for routine veterinary wastewater surveillance.
Beyond viruses: environmental monitoring of major livestock diseases
A comprehensive review published in Frontiers in Veterinary Science on September 29, 2026 examined environmental surveillance methods for 15 infectious diseases affecting domestic animals. These included seven viral diseases, four bacterial diseases and four parasitic diseases. The pathogens covered included those responsible for foot-and-mouth disease, African swine fever, avian influenza, Newcastle disease, peste des petits ruminants, lumpy skin disease, salmonellosis, bovine tuberculosis, paratuberculosis and leptospirosis. For parasitic diseases, the review considered coccidiosis, fasciolosis, babesiosis and theileriosis.
The authors highlighted the value of analysing water, manure, soil, air, dust, surfaces and other environmental matrices. For instance, pooled faecal samples and slurry can help detect Mycobacterium avium subsp. paratuberculosis, while environmental water and sediment sampling can provide information relevant to avian influenza surveillance.
The review also confirmed the value of wastewater-based epidemiology for selected veterinary applications, particularly Japanese encephalitis virus detection in piggery effluent and the monitoring of antimicrobial resistance genes. Crucially, these examples do not imply that wastewater surveillance is already validated for all 15 diseases. For several pathogens, the available evidence concerns other environmental matrices rather than sewage or livestock effluents.
Antimicrobial resistance: wastewater as an indicator of a global health threat
Antimicrobial resistance (AMR) is another important area where wastewater surveillance could strengthen One Health strategies. Urban wastewater, hospital effluents and agricultural waste streams can contain antimicrobial-resistant bacteria and genetic determinants associated with resistance. These environmental matrices may reflect the combined influence of human activities, healthcare, animal production and environmental processes. Using quantitative PCR, culture-based methods and metagenomic sequencing, laboratories can investigate the distribution and evolution of resistance genes.
Such monitoring is particularly valuable because antimicrobial resistance is not restricted to individual patients or animal populations. Resistant organisms and resistance genes can circulate through interconnected ecosystems. Environmental surveillance may help identify changes in resistance profiles, investigate potential reservoirs and support the assessment of interventions.
Nevertheless, identifying a resistance gene in wastewater does not establish its source or demonstrate transmission between humans and animals. The revised European Urban Wastewater Treatment Directive, Directive (EU) 2024/3019, establishes a stronger framework for wastewater-based public health monitoring, including antimicrobial resistance surveillance in large urban agglomerations.
The development of harmonised methods could progressively improve comparisons between countries and provide additional information on resistance trends.
Advances in genomic sequencing could transform epidemic surveillance
The development of next-generation sequencing technologies is expanding wastewater monitoring from detecting individual pathogens to characterising entire viral communities. Conventional PCR-based surveillance requires predefined genetic targets. Metagenomic sequencing, by contrast, can provide a much broader picture of the viral diversity present in environmental samples.
An important study published in Nature Water on September 3, 2026 demonstrated the potential of this approach. Researchers at KU Leuven, Belgium, analysed 127 weekly composite wastewater samples collected over 31 months from a wastewater treatment plant in Leuven. Using hybrid-capture metagenomic sequencing, they identified 339 viral species and 715 viral strains.
The results also provided evidence of early warning capabilities:
Rotavirus A concentrations in wastewater generally preceded clinical surveillance indicators by approximately one week.
A parvovirus B19 increase was detectable from April 2023, approximately one year before a national public health alert.
Genomic sequencing enabled investigators to distinguish viral strains and examine changing patterns of circulation.
These findings demonstrate that wastewater monitoring can provide epidemiological information extending beyond simple positive or negative results. It can reveal changes in genetic diversity, detect unusual viral circulation and support investigations into emerging strains. Nevertheless, the apparent lead time for parvovirus B19 should not be interpreted as evidence that all wastewater surveillance systems can anticipate epidemics by one year. It represents a retrospective finding from one surveillance setting.
France: wastewater monitoring extends beyond COVID-19
France provides another illustration of how wastewater surveillance is evolving towards broader infectious disease prevention. Its national SUM’EAU programme was established to monitor SARS-CoV-2 circulation independently of individual diagnostic testing. By 2024, the network had expanded to 54 wastewater treatment plants, improving the geographical coverage of viral circulation monitoring. The programme is designed to complement existing clinical surveillance systems, including general practice, hospitals and long-term care facilities.
A separate study published in Water Research in October 2026 demonstrated the potential of wastewater surveillance for monitoring norovirus epidemics in the Greater Paris region. Researchers analysed more than 3,000 composite wastewater samples collected between November 2021 and March 2025, alongside environmental water samples from the Seine and Marne rivers. The results revealed moderate to strong correlations between norovirus genogroup II concentrations in wastewater and reported gastroenteritis incidence, with correlation coefficients ranging from 0.53 to 0.90. The study also identified important seasonal patterns, with higher norovirus concentrations during winter.
Importantly, the researchers found that compliance with conventional bacterial indicators, such as Escherichia coli, did not necessarily indicate the absence of viral health risks in recreational waters. This demonstrates how wastewater surveillance can contribute simultaneously to infectious disease monitoring and environmental risk assessment.
Europe Is building a permanent wastewater surveillance infrastructure
The European Union is increasingly treating wastewater surveillance as a long-term public health capability rather than a temporary response to COVID-19. The EU-Wastewater Integrated Surveillance for Public Health initiative, known as EU-WISH, brings together 62 participants to strengthen national surveillance capacities, improve methodological harmonisation and facilitate the exchange of scientific knowledge. In September 2026, the programme announced additional training resources through the European Centre for Disease Prevention and Control (ECDC) learning platform. These activities aim to improve the comparability of results and the operational use of wastewater data across European countries.
The revised Urban Wastewater Treatment Directive provides a regulatory framework for closer cooperation between wastewater operators and public health authorities. While the European surveillance infrastructure is primarily designed for human health, its development may eventually facilitate closer cooperation with veterinary surveillance systems. Such integration would be particularly relevant for zoonotic pathogens and antimicrobial resistance, where environmental circulation can connect human, animal and ecological compartments.
Scientific and operational challenges remain
Despite these advances, wastewater surveillance cannot yet be regarded as a universal early-warning system. One of its principal limitations is that detecting viral RNA or DNA does not necessarily demonstrate the presence of viable or infectious pathogens. Environmental samples may contain genetic fragments originating from pathogens that have already been inactivated.
Interpretation is also complicated by variable wastewater dilution, rainfall, industrial discharges, temperature, sample storage and the presence of substances that inhibit molecular analyses.
Livestock effluents introduce further complexity because animal density, manure management, housing systems and cleaning practices can strongly influence pathogen concentrations.
Another challenge concerns the relationship between the amount of genetic material detected and the actual number of infected individuals or animals.
Although wastewater concentrations can provide reliable information on trends for certain pathogens, translating those measurements into infection prevalence is often considerably more difficult.
Now, it need for standardised sampling procedures, field-validated analytical methods and clearly defined thresholds linking environmental signals to veterinary interventions.
Cost-effectiveness must also be considered. Sampling design, laboratory capacity, sequencing costs, data processing and epidemiological interpretation all influence the sustainability of surveillance programmes. In March 2026, researchers published a framework for evaluating the implementation, impact and cost-effectiveness of wastewater and environmental surveillance. Their work highlighted the importance of assessing whether environmental monitoring actually improves health decisions and outcomes.
Towards a global One Health early warning network
The most promising development is the possibility of connecting wastewater surveillance systems across human health, veterinary medicine and environmental monitoring. Municipal wastewater networks can provide information about pathogen circulation in communities. Slaughterhouses may offer surveillance opportunities across livestock supply chains, while farm effluents can provide collective signals from individual production systems. Environmental monitoring at wildlife–livestock interfaces could add another dimension, particularly for pathogens with complex transmission cycles.
Combining these sources with clinical diagnostics, veterinary laboratory results, genomic sequencing and epidemiological investigations could improve the detection and interpretation of emerging health threats. For diseases such as avian influenza, Japanese encephalitis and certain enteric zoonoses, these complementary approaches may provide information that would otherwise remain unavailable until clinical cases or production losses become apparent.
However, implementing such systems requires sustained cooperation between veterinary services, public health agencies, environmental authorities, laboratories, wastewater operators and agricultural stakeholders.
The WHO's June 2026 global analysis emphasises that the long-term success of wastewater surveillance depends not simply on technological capabilities but on governance, financing and the integration of environmental data into actionable public health decisions.
Wastewater surveillance will not replace clinical diagnostics or veterinary epidemiology. Its importance lies in adding a complementary source of intelligence that can help detect threats earlier, strengthen outbreak investigations and improve prevention. In an increasingly interconnected world, where pathogens move between humans, animals and shared environments, wastewater may become an important component of the global infrastructure for epidemic preparedness and One Health protection.
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