A Rapid Decision Framework for Wastewater and Environmental Surveillance (WES) during Rapidly Emerging and Evolving Outbreak Settings

Abstract

Wastewater and environmental surveillance (WES) has demonstrated substantial value during the COVID-19 pandemic, providing early warning signals and supporting population-level disease surveillance. However, its application to emerging infectious disease threats remains inconsistent, with no structured framework to guide whether, and how WES should be deployed in emerging and evolving outbreak settings. In practice, decisions to implement WES for novel or re-emerging pathogens are often taken under substantial uncertainty around biological feasibility, pathogen detection reliability, and public health utility. , This can result in delayed deployment of WES, inefficient use of resources, or implementation of systems that generate limited actionable information. In addition, opportunities for coordinated learning and knowledge sharing across countries remain limited. During emerging and evolving outbreak settings, researchers interested in WES are often required to develop approaches independently, with limited access to validated protocols, standardised workflows, or evidence on pathogen detectability. This fragmentation can further delay implementation and reduce the efficiency and comparability of surveillance efforts.

Recent diphtheria outbreaks and emerging disease threats in Australia (https://www.cdc.gov.au/newsroom/news-and-articles/diphtheria-outbreak-update), the Bundibugyo virus disease (BVD) outbreak in the Democratic Republic of the Congo and Uganda (https://www.who.int/emergencies/disease-outbreak-news/item/2026-DON605), the Hantavirus event originating from Latin America (https://www.who.int/emergencies/disease-outbreak-news/item/2026-DON599), the Nipah virus outbreak in South Asia (https://www.who.int/emergencies/disease-outbreak-news/item/2026-DON593), illustrate situations in which a rapid assessment of WES feasibility could support timely public health decision-making during emerging and evolving outbreak settings. We propose a rapid iterative framework to support evidence-informed decisions on the use of WES during emerging and evolving outbreak settings. The framework incorporates several assessment steps and predefined decision points, while allowing reassessment as new biological, analytical, epidemiological, and operational evidence becomes available. The framework is designed to rapidly assess whether WES is technically feasible, operationally appropriate, and likely to provide sufficient public health value to justify deployment in a specific outbreak (Figure ).

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Iterative framework for rapid assessment and implementation of wastewater and environmental surveillance (WES) for emerging and evolving outbreak settings. The framework incorporates sequential evaluation steps with key decision points to determine whether to proceed, adapt, or defer WES implementation based on feasibility, assay performance, and public health value.

The approach integrates genomic intelligence, molecular assay refinement/development and validation for pathogen detection, and targeted field validation and implementation into a sequential pathway. Although presented as a sequential framework, the process is intended to be iterative, allowing reassessment as new biological, analytical, and epidemiological evidence becomes available. At each stage, predefined decision points determine whether WES should proceed, be modified, deferred pending further research, or discontinued based on emerging evidence and identified knowledge gaps. This structured approach aims to ensure that resources are directed towards surveillance and research activities with the greatest potential to address immediate public health needs while also generating evidence to support longer-term decision-making under uncertainty.

The framework begins with defining the potential public health use case(s), including the outbreak context, target pathogen, surveillance setting, intended decision questions, and actionable interventions that WES could inform. This step is followed by an assessment of biological feasibility, pathogen shedding by infected individuals, environmental persistence (stability in sewer systems), and existing evidence for its presence and detection in wastewater. − If biological feasibility is supported, subsequent stages focus on evaluating existing assays using genomic data, including primer/probe sequence mismatches, assay inclusivity and specificity, and potential assay gaps. Where suitable assays are unavailable or gaps are identified, existing assays can be adapted or new assays developed, followed by wet-lab validation to assess analytical and method sensitivities and specificity/inclusivity, and precision/reproducibility.

Early field deployment is incorporated as a structured proof-of-concept phase, prioritising settings with known or suspected cases to provide initial evidence of pathogen detectability, matrix effect, PCR inhibition, extraction recovery, and the relationship between detection signals and known cases. This is complemented by iterative refinement and characterization of detected targets using sequencing, where appropriate to strengthen confidence in detection results and evaluate diagnostic performance, including positive and negative predictive value where suitable reference data are available. Integration into surveillance and response systems is recommended only when sufficient evidence of feasibility and value is established. The framework supports negative decisions. Where evidence is insufficient, assay performance is inadequate, or surveillance outputs are unlikely to influence public health action, the framework provides a transparent basis for deferring WES implementation until further research establishes value and feasibility. This is critical to ensuring that limited resources are directed towards interventions with demonstrable value. The proposed framework is not intended to replace clinical surveillance or established outbreak response systems. Rather it is intended to complement clinical surveillance, case investigation, infection prevention and control activities, and environmental health assessment during outbreak responses, including in settings where surveillance is conducted at different spatial scales or locations (e.g., community or environmental sites). To operationalise, test, and refine the framework in practice, the following steps are proposed:

• Apply the framework prospectively to selected pathogens to assess feasibility, timelines, and key decision points.

• Evaluate application of the framework across laboratory and field settings, including high-and -low prevalence contexts and target concentrations near detection limits.

• Assess operational feasibility and integration with public health decision-making, including timeliness, interpretability, and actionability.

• Evaluate reproducibility and scalability across laboratories, with emphasis on consistent QA/QC, reporting, and interpretation to support comparability across methods.

• Identify key constraints and translate findings into fit-for-purpose protocols, workflows, and preparedness tools.

As the global community continues to face emerging and re-emerging infectious disease threats including viral haemorrhagic fevers, zoonotic spillover events, and vaccine-preventable disease outbreaks, there is an urgent need for scalable and evidence-based approaches to deploy WES. Beyond informing current outbreak responses, the framework provides a mechanism for developing ready-to-adapt protocols, assay assessment workflows, and preparedness tools that can accelerate future WES deployment. WES is evolving, and continued research and development will be important to expand its applications, strengthen its evidence base, and build the capacity and networks needed for timely and scalable deployment. A clear decision framework can help ensure that WES is used strategically, rapidly, and appropriately, maximising its impact in supporting public health responses.

Biography

Dr. Warish Ahmed is a Principal Research Scientist with CSIRO Environment in Brisbane, Australia. His research focuses on microbial source tracking, wastewater surveillance, and the development and application of molecular methods to monitor human and animal pathogens in environmental waters. He has authored more than 200 peer-reviewed publications and is recognized as a Highly Cited Researcher in Environment and Ecology. His research has advanced understanding of the occurrence, fate, and transmission of pathogens in aquatic environments and has contributed to the development and implementation of wastewater surveillance programs for public health decision-making. He collaborates extensively with industry, water utilities, public health organizations, and academic institutions in Australia and internationally.

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Kate Medlicott is responsible for the views expressed in this publication, which do not necessarily represent the views, decisions, or policies of the institution with which she is affiliated.

The authors declare no competing financial interest.