Wastewater Surveillance with Sequencing

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.

Precision metagenomics for rapid identification and characterization of pathogens

Download this eBook to learn how precision metagenomics is providing innovative solutions to rapidly detect and characterize pathogens through the power of next-generation sequencing.

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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.

	RT-PCR	NGS
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

Amplicon

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.

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.

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 workflow solutions

Prepare Library

Illumina COVIDSeq Assay (96 samples)

Illumina Microbial Amplicon Prep

Sequence

iSeq 100

MiniSeq

MiSeq

NextSeq 550

Analyze Data

DRAGEN COVID Lineage App

Prepare Library

Illumina RNA Prep with Enrichment

Respiratory Virus Oligo Panel (RVOP)

Viral Surveillance Panel (VSP)

Respiratory Pathogen Infectious Disease/AMR Panel

Urinary Pathogen Infectious Disease/AMR Panel

Sequence

iSeq 100

MiniSeq

MiSeq

NextSeq 550

NextSeq 1000/2000

Analyze Data

DRAGEN RNA Pathogen Detection App

IDbyDNA Explify RVOP Platform

DRAGEN Microbial Enrichment App

Explify RPIP Analysis App on BaseSpace Sequence Hub

BaseSpace Explify UPIP Data Analysis

Prepare Library

Illumina Stranded Total RNA Library Prep with Ligation, Ribo-Zero Plus Microbiome Depletion Kit (96 samples)

Illumina DNA Prep

Sequence

NextSeq 550

NextSeq 1000/2000

NovaSeq 6000 System

Analyze Data

BaseSpace Microbiome Metatranscriptomics App

DRAGEN Metagenomics Pipeline

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.

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-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.

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Ribo-Zero Plus Microbiome rRNA Depletion Kit

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Wastewater Surveillance