Wastewater Surveillance of Viral Infections

Wastewater surveillance of viral infections harnesses the pooled biological output of communities to monitor the presence, prevalence and evolution of human pathogens. Building on decades of poliovirus tracking, the field has rapidly expanded to encompass respiratory, enteric and emerging viruses. By sampling influent or treatment-stage effluent across sewersheds, researchers quantify viral genomes, identify variant lineages and infer transmission dynamics without reliance on individual clinical testing. This approach offers near–real-time insights into asymptomatic carriage, early warning of outbreaks and evaluation of public health interventions. Advances in molecular techniques, including quantitative PCR and high-throughput sequencing, have improved sensitivity and breadth of detection, revealing hundreds of known and novel viral species in urban catchments. Wastewater surveillance supports resource allocation, informs non-pharmaceutical measures and complements conventional epidemiology. Despite challenges in method standardisation, viral recovery and data interpretation, the global deployment of wastewater-based epidemiology has demonstrated its value in pandemic preparedness and routine infectious-disease monitoring, underscoring its role as an integral component of modern public health infrastructure.

Research from Nature Portfolio

Recent studies have employed comprehensive sequencing of urban wastewater to characterise the collective human virome and track variant dynamics over time and space. By targeting thousands of viral species via probe capture and analysing longitudinal samples from multiple cities, researchers uncovered over 450 pathogenic viruses, mapped community structure and correlated viral abundances with clinical reports of SARS-CoV-2, influenza and monkeypox. In parallel, innovative protocols for virus concentration, improved primer design and software deconvolution have enabled high-resolution genomic surveillance of mixed wastewater samples. These methods resolved multiple SARS-CoV-2 lineages concurrently, detected emerging variants up to two weeks before clinical identification and uncovered cryptic transmission chains. Together, these breakthrough efforts establish a scalable framework for early detection of viral threats and refined estimation of community-level prevalence.

Wastewater Surveillance of Viral Infections publication trend

The graph below shows the total number of articles in wastewater surveillance of viral infections across all publications each year (not limited to Nature Index journals).

Technical terms

Wastewater-based epidemiology (WBE): The practice of analysing communal wastewater to infer population-level infection trends.

RT-qPCR: Reverse-transcription quantitative polymerase chain reaction for detecting and quantifying viral RNA.

Metagenomic sequencing: High-throughput, untargeted sequencing of all genetic material in a sample to profile viral communities.

Probe capture: A targeted enrichment method using oligonucleotide probes to isolate specific viral sequences before sequencing.

Variant deconvolution: Computational separation of mixed viral lineages within a single sequencing dataset.

Sewershed: The drainage area served by a wastewater collection system or treatment plant.

References

1. Wastewater sequencing reveals community and variant dynamics of the collective human virome. Nature Communications (2023).
2. SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases. mSystems (2020).
3. Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants. mBio (2021).
4. Correlation of SARS-CoV-2 RNA in wastewater with COVID-19 disease burden in sewersheds. The Science of The Total Environment (2021).
5. Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission. Nature (2022).