Wastewater Surveillance

Scientists conducting wastewater surveillance to detect pathogens found in wastewater.

What is wastewater surveillance?

Wastewater surveillance is a method to detect, identify and characterize pathogens found in wastewater. This method provides data to help monitor outbreaks and other threats at the community level. By knowing where these threats are, communities can better allocate resources during a public health response. Genomic information from wastewater can be used to determine which pathogens are present in a community and identify what strains and how many variants may be in the community.

Scientist conducting a wastewater surveillance process.

How does wastewater surveillance work?

Wastewater surveillance is a vital tool for detecting and characterizing pathogens in sewage samples and treatment plants. When used with NGS-based technologies, wastewater surveillance can expand our understanding of many different pathogens, including RNA and DNA viruses, bacteria, and antimicrobial resistance (AMR) markers. This information is crucial for tracking the spread of many infectious diseases and developing effective responses.

Using samples from sewage, wastewater surveillance can help supplement existing surveillance methods and has several advantages, including:

  • Population-based infection tracking
  • Anonymous pooled testing
  • Geographic information about disease spread
  • Easy and rapid sampling that can be obtained as needed from treatment facilities to identify community-level trends

Using wastewater sequencing to detect COVID-19

SARS-CoV-2, the virus that causes COVID-19, is present in the stool of infected people and can be found in samples from wastewater treatment plants. Using wastewater sequencing to test these samples, health officials can track the spread of the virus and identify new variants, like the B.1.17 strain that became widespread. Thanks to wastewater surveillance, local health communities can take action to prevent the spread of disease and prepare for surges at hospitals up to two weeks before cases are reported.

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Wastewater surveillance methods

While wastewater surveillance has been used to detect pharmaceutical, chemical, and industrial waste, it is now more important than ever to monitor wastewater to detect antibiotic resistance markers, bacteria, and viruses that have a significant impact on local communities. To detect pathogens of high risk to public health, RT-PCR and next-generation sequencing are at the forefront of surveillance techniques. See the comparison below to learn more about each approach.

RT-PCR for wastewater surveillance
  • Only targets small regions of the genome
  • Lower cost
  • Low-throughput workflow
  • Unable to detect variants
  • Data is easier to interpret

Learn more about PCR vs NGS

NGS for wastewater surveillance
  • Targets and characterizes whole genomes
  • Higher cost
  • High-throughput capabilities
  • Can detect and identify variants
  • Data is more complex and comprehensive
Scientist preparing sample for sequencing.

Wastewater sequencing considerations

Wastewater samples usually contain multiple pathogens and microbes, as opposed to clinical samples which usually only contain a single pathogen. To analyze pathogens of interest, it is recommended to use amplicon- or enrichment-based NGS library preparation methods. Amplicon-based approaches use primers to specifically target regions of microbes and/or whole genomes of single viruses, while enrichment approaches use probe hybridization to capture genomes of interest. In addition, shotgun metagenomic sequencing provides a comprehensive method to analyze all genes and microbes within a sample.

Wastewater surveillance webinars

Scientist reviewing wastewater sample results from sequencer.
Illumina sequencing for wastewater-based epidemiology (WBE)

Part one of the Wastewater Surveillance Series features an introductory overview of surveillance as well as solutions to challenges for WBE.

Researcher collecting wastewater sample for testing.
Sewers: understanding the impact on samples

In this series, Dr. Dotti Ramey, PhD from the Washington State Department of Health, discusses how sewers can impact samples.

Aerial view of wastewater treatment plant.
National wastewater surveillance system

Part three of the Wastewater Surveillance Series covers why wastewater is useful for mutation and variant trend tracking, public health interpretation challenges, and opportunities for wastewater surveillance beyond SARS-CoV-2.

Microscopic view of SARS-CoV-2 virus.
Illumina options for SARS-CoV-2 / COVID-19 epidemiology

Part four of the Wastewater Surveillance Webinar Series showcases Illumina solutions for SARS-CoV-2 / COVID-19 epidemiology. Viewers will learn more about Illumina end-to-end workflows to capture the complete genome sequence of SARS-CoV-2.

Wastewater droplet on a slide.
Wastewater-based epidemiology and next-generation sequencing (NGS)

Part five of the Wastewater Surveillance Webinar Series covers challenges in sample preparation, data analysis, and use of the Respiratory Oligo Viral Panel V2 for virus detection beyond SARS-CoV-2.

Data interpretation on a computer screen.
Considerations for wastewater-based epidemiology NGS data analysis

Part six of the Wastewater Surveillance Webinar Series reviews important considerations when handling wastewater-based epidemiology sample types and challenges in interpreting data.

Image supporting the DRAGEN COVID lineage application.
Wastewater-based epidemiology NGS data demonstration

Part seven of the Wastewater Surveillance Webinar Series features a demonstration of nasal swab and wastewater samples to examine how the samples perform in the DRAGEN COVID Lineage Application for data analysis.

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Additional Resources

Wastewater-based epidemiology

Discover how surveillance of infectious disease through wastewater sequencing can detect SARS-CoV-2 variants and other respiratory viruses in the community in this app note.

Can wastewater surveillance protect public health?

Read the article to learn how Biobot Analytics is using wastewater data to predict COVID surges and other outbreaks.

Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission

Learn how wastewater surveillance is aiding in revealing early COVID transmission in this scientific publication.

Improving public health management through pathogen surveillance

TGen North uses respiratory panels and wastewater sequencing to identify what’s leading to illness.

Wastewater surveillance and AMR markers during COVID-19

This paper shows how wastewater surveillance can identify emerging antimicrobial resistance (AMR) threats to improve community-level data.

Poliovirus environmental surveillance

In this publication, scientists discuss how they established an environmental surveillance program to detect non-polio enteroviruses and poliovirus in Haiti.