Wastewater Surveillance

wastewater treatment plant

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 not only determine which pathogens are present in a community, but also 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 process of detecting pathogens from sewage plants. Samples are collected before waste treatment and analyzed in laboratories to identify the type of pathogen and their levels in a community.1 Next-generation sequencing (NGS) can be used to analyze samples, which provides public health officials with a faster and more comprehensive way to track infections at scale. NGS can also provide information on the geographic spread of diseases, the effectiveness of community-level responses, and more.

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Precision metagenomics for rapid identification and characterization of pathogens

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PCR vs NGS-based wastewater surveillance

While wastewater surveillance has been used to detect pharmaceutical, chemical, and industrial waste, it is now more important than ever to monitor wastewater for 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 NGS are at the forefront of surveillance techniques.2,3 See the comparison below to learn more about each approach to wastewater sequencing.

Target Only targets small regions of the genome Targets and characterizes whole genomes
Cost Lower cost Higher cost
Throughput capability Low-throughput High-throughput
Variant detection Unable to detect variants Can detect and identify variants
Data Data is easier to interpret Data is more complex and comprehensive

Learn more about PCR vs NGS

What are some methods for wastewater surveillance?

Wastewater samples usually contain multiple pathogens and microbes,4 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.5

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Amplicon-based approaches use primers to specifically target regions of microbes and/or whole genomes of single viruses. Read how scientists are using amplicon-based methods for wastewater surveillance.

Early detection through wastewater surveillance

Read how wastewater genomic epidemiology can provide an unbiased representation of community-wide infection dynamics and surveillance to help guide public health action and policy decisions.

Identifying SARS-CoV-2 variants in wastewater

Scientists describe how targeted amplicon sequencing of wastewater samples is a powerful surveillance tool and may contribute to the early detection of emerging SARS-CoV-2 variants.

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Hybrid capture enrichment

Hybridization-based enrichment is a useful strategy for analyzing specific genetic variants in a given sample, delivering dependable results across a wide range of input types and quantities. Learn more about how researchers are using hybrid capture enrichment methods for wastewater surveillance.

Monitoring antimicrobial resistance

See how wastewater-based epidemiology can complement more traditional surveillance efforts by providing community-level data to identify current and emerging antimicrobial resistance threats.

Detecting region-specific SARS-CoV-2 variants

Investigators detail how epidemiological surveillance through wastewater sequencing can aid in tracking exact viral strains in an epidemic context.

icon early amr detection
Shotgun metagenomics

Shotgun metagenomic sequencing allows researchers to comprehensively sample all genes in all organisms present in a given complex sample. Shotgun metagenomics also provides a means to study unculturable microorganisms that are otherwise difficult or impossible to analyze. See papers below to understand how shotgun metagenomics is being used for wastewater surveillance.

Using wastewater RNA-Seq to detect emerging and endemic viruses

Scientists use RNA-Seq to simultaneously detect multiple infectious diseases, providing geographical and epidemiological data to help direct healthcare interventions in India.

Metagenomic and resistome analysis

Read how scientists used metagenomic shotgun sequencing and real-time PCR to characterize the composition of bacteria and phage diversity and the resistome of major treatment processes within a wastewater treatment plant.

Wastewater surveillance webinars

Scientist reviewing wastewater sample results from sequencer.
Introduction to 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 part two of 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 workflows

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.

Related Products

Viral Surveillance Panel

Obtain whole-genome sequencing (WGS) data that can characterize 66 viruses that are of high risk to public health, including SARS-CoV-2, Influenza, Mpox Virus, and Poliovirus.

Illumina COVIDSeq Test

A high-throughput, next-generation sequencing test to detect SARS-CoV-2 in patients suspected of COVID-19 and enables virus genome analysis in research use.

Respiratory Pathogen ID/AMR Enrichment Panel Kit

A next-generation sequencing (NGS)-based respiratory pathogen panel that delivers highly sensitive, comprehensive pathogen detection and antimicrobial resistance (AMR) insights.

Urinary Pathogen ID/AMR Enrichment Kit

A next-generation sequencing (NGS) panel that detects and quantifies over 170 common, less common, challenging-to-grow, and frequently missed uropathogens.

Respiratory Virus Oligo Panel

A highly sensitive NGS panel to detect and characterize common respiratory viruses, including COVID-19 strains, with comprehensive, rapid target enrichment sequencing.

Ribo-Zero Plus Microbiome rRNA Depletion Kit

A streamlined RNA-to-analysis solution for metatranscriptome sequencing of complex microbial samples, including stool.

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Additional Resources

Wastewater-based epidemiology

Discover the 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 wasterwater surveillance is aiding in revealing early COVID transmission in this scientific publication.

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.

Using wastewater surveillance to detect COVID-19

Learn how health officials can track the spread of the virus and identify new variants, like the B.1.17 strain that became widespread using wastewater sequencing to test samples.

  1. Wastewater Monitoring—How Does It Work? cdc.gov/nwss/pdf/Wastewater-COVID-infographic-h.pdf. Accessed December 7, 2023.
  2. Science & Tech Spotlight: Wastewater Surveillance. gao.gov/products/gao-22-105841. Accessed December 7, 2023.
  3. Diamond MB, Keshaviah A, Bento AI, et al. Wastewater surveillance of pathogens can inform public health responses. Nature Medicine 2022; 28(10):1992-1995.
  4. Levy JI, Andersen KG, Knight R, et al. Wastewater surveillance for public health. Science 2023 Jan 6;379(6627):26-27.
  5. Wensel CR, Pluznick JL, Salzberg SL, et al. Next-generation sequencing: insights to advance clinical investigations of the microbiome. J Clin Invest. 2022 Apr 1; 132(7): e154944.