Genomic Surveillance

NGS genomic surveillance

NGS methods to identify and track infectious disease threats

Next-generation sequencing (NGS) has revolutionized genomic surveillance, enabling us to detect and track both known and novel infectious diseases caused by viruses, bacteria, fungi, and parasites. This technology allows us to study pathogens at a molecular level, providing insights into their behavior and evolution in populations around the world.

There are various NGS methods used for genomic surveillance of infectious diseases, each with its own advantages and challenges. The choice of method is dependent on the pathogen(s) of interest, sample type, and data requirements. Illumina offers advanced library preparation, sequencers, and data analysis tools for each method, making it a reliable choice for researchers in this field.

Pathogen surveillance approaches

Genomic surveillance of pathogens with NGS offers exceptional scalability, speed, and accuracy in detecting pathogens, providing the confidence needed to protect public health. Choosing the approach for pathogen detection varies based on the laboratory capabilities and testing requirements, which includes the analysis of a single genome, detection of multiple pathogens, or pathogen discovery.

Single genome

Single-genome sequencing is an optimal method for identifying known targets. Regardless of whether the pathogen originates from an isolated microbial colony on a culture plate or a primary sample, only a single, known genome is being analyzed.


For instances where certain pathogens are suspected to be present, or for surveillance of multiple known pathogens from a primary sample, hybrid capture enrichment solutions are ideal.

Pathogen discovery

This is a useful approach when needing an unbiased analysis of a primary sample. Shotgun DNA/RNA sequencing (metagenomic or metatranscriptomic) analysis of the genetic material present in complex microbial communities can reveal the species-level composition of the community without any prior knowledge.

Compare NGS pathogen surveillance methods

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Whole-genome sequencing of isolates

Sequence entire bacterial, viral, and other microbial whole-genomes for generating accurate reference genomes, microbial identification, and other comparative genomic studies. The power of NGS enables multiplexing to identify low-frequency variants and genome rearrangements.

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Amplicon sequencing

Detect and fully characterize a known virus. Whole genome sequencing via an amplicon approach is ideal for known viruses with small genomes. This method involves analyzing genomic regions of interest with ultra-deep sequencing of PCR amplicons.

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Hybrid capture screening

Detect and characterize coronaviruses, flu viruses, and other pathogenic organisms, as well as associated antimicrobial resistance alleles. These insights can help public health officials monitor outbreaks and optimize infection control strategies. This method captures genomic regions of interest via hybridization to target-specific probes.

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Shotgun metagenomics

Comprehensively sequence all organisms in a given sample and identify novel, or emerging pathogens such as Mpox virus. This NGS method can help accelerate outbreak investigations and support development of new laboratory tests.

Testing Needs Whole-Genome Sequencing of Isolates Amplicon Hybrid Capture Shotgun Metagenomics
Speed & Turnaround Time        
Scalable & Cost-Effective        
Culture Free        
Identify Novel Pathogens        
Track Transmission        
Detect Mutations        
Identify Co-Infections & Complex Disease        
Detect Antimicrobial Resistance        

Adequately meets laboratory testing needs

Partially meets laboratory testing needs

Genomic surveillance FAQs

NGS can provide unbiased detection of pathogens from a variety of sample types without prior knowledge of the organism.

A key challenge in infectious disease surveillance is that many of the microbes, including viruses, that cause respiratory, digestive, and other diseases in humans, have not been researched and characterized and thus are not known or detected by targeted approaches such as PCR. Development of PCR assays requires knowledge of the pathogen genome. NGS plays a critical role in discovering these unknown, novel pathogens; the resulting genome sequence can then be used to develop routine tests such as PCR to help clinicians manage patients.

NGS can be used to track the evolution of the pathogen genome to help public health officials monitor the spread of infection and determine the best isolation plan at a population level. Sequencing pathogens from different patients, animals, and environments over time can determine the rate of evolution, and address whether the pathogen is changing in ways that could impact pathogenicity as well as diagnostic or therapeutic effectiveness. PCR is designed to detect the presence of specific regions of the pathogen genome and will not identify new mutations across rapidly evolving pathogen genomes. Furthermore, PCR performance can suffer if mutations occur in the primer or probe binding regions.

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A shotgun metagenomics workflow enables sequencing of both novel and known species. During an outbreak involving an unknown pathogen, multiple molecular diagnostic tests are often utilized; this may lead to unnecessary costs and delays in identifying the pathogen. Shotgun metagenomics can be used as a single comprehensive screening assay for identifying and characterizing pathogens. This research workflow can help accelerate outbreak investigations and support development of new lab tests for large-scale screening efforts.

Once a pathogen is identified, a hybrid capture workflow can provide the high sensitivity needed to detect the pathogen and provide information about its epidemiology and evolution. This information can help researchers optimize infection control strategies, including monitoring when it's acceptable to de-escalate isolation mechanisms and resume normal activities, and aid in the development of diagnostics, vaccines, and therapeutics.

These complementary workflows using Illumina sequencing can be performed alongside traditional testing methods and integrated into a comprehensive outbreak response model.

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Shotgun Metagenomic Sequencing

Hybrid Capture Sequencing

Hybrid capture is a resequencing method that captures genomic regions of interest by hybridization to target-specific biotinylated probes. Enrichment through hybrid–capture methods allows for highly sensitive detection and therefore does not require high read depth. Additionally, the hybrid capture NGS workflow allows for near-complete sequence data of targets and is more tolerant to mutations in the pathogen’s genome.

Alternatively, amplicon sequencing uses gene-specific primers to enrich known targets for ultradeep sequencing. Amplicon sequencing can produce near-complete sequence data of viruses or targeted regions of pathogen species with larger genomes (e.g., Mycobaterium tuberculosis). This method is less tolerant to mutations so it’s important to monitor the primer designs.

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Amplicon Sequencing

Hybrid Capture Sequencing

Amplicon sequencing is best utilized in situations when scientists know what they are looking for. This method does not require cultured isolates and can be used to detect specific, predefined genes associated with microbial identity, AMR mutations, or variants of concern.

For instances where certain pathogens are suspected to be present, or for surveillance of multiple known pathogens from a primary sample, hybrid capture enrichment solutions are ideal.

Visit our sequencing platforms page to explore our portfolio, or see the workflows on our coronavirus sequencing page for recommendations on which sequencer is optimal for a particular method. The choice of sequencer depends on which method(s) you use most frequently. 

Surveillance of infectious disease through wastewater sequencing

Learn how to use wastewater sequencing to monitor SARS-CoV-2 variants and other respiratory viruses in the community.

Read Application Note

Featured products

COVIDSeq Family
COVIDSeq Family

COVIDSeq Assay and COVIDSeq Test are amplicon-based next-generation sequencing (NGS) assays designed to help public health labs identify novel strains of SARS-CoV-2.

iSeq 100
iSeq 100

The iSeq 100 system leverages the speed and affordability of complementary metal-oxide-semiconductor (CMOS) technology and the accuracy of sequencing by synthesis (SBS) chemistry.

kit for Illumina Respiratory Virus Enrichment
Illumina Respiratory Virus Enrichment Kit

The Illumina Respiratory Virus Enrichment Kit allows researchers to obtain whole-genome next-generation sequencing (NGS) data for over 40 important respiratory viruses including SARS-CoV-2 and influenza A/B viruses.

Viral Surveillance Panel
Using the Viral Surveillance Panel with Illumina RNA Prep with Enrichment kit allows researchers to 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, allowing for proactive, broad pathogen surveillance.

Infectious disease surveillance applications

Coronavirus surveillance

NGS provides unbiased identification of new coronavirus strains. Illumina offers rapid detection of SARS-CoV-2 coronavirus mutations to meet the demands for efficient sequencing needs.

Tuberculosis surveillance

Learn about Integrative NGS-based solutions for tuberculosis detection, characterization, and analysis.

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.

Healthcare-associated infection surveillance

Powered by NGS, labs and clinics can perform genomic Healthcare-associated infections (HAI) related studies at unprecedented speed and scalability using massively parallel workflows.

Antimicrobial resistance

Learn more about how NGS is empowering antimicrobial resistance research in areas of early detection, outbreak responses, and clinical studies.

Frequently Purchased Together

Get help finding the right infectious disease surveillance solution for your needs.

Genomic surveillance customer stories

Fighting drug-resistant tuberculosis in South Africa

Shaheed Vally Omar, the scientific lead at South Africa’s Centre for Tuberculosis - National Institute for Communicable Diseases in Johannesburg, believes that next-generation sequencing can help his country detect and track MDR-TB.

Realizing the potential of pathogen genomics in Africa

Professor Tulio de Oliveira, founding director of CERI and professor at the Universities of Stellenbosch and KwaZulu-Natal, talks about using pathogen genomic surveillance as a public health tool and its future.

Inside a Mumbai lab using genomics for tuberculosis surveillance

Dr. Camilla Rodrigues is fighting tuberculosis at the P. D. Hinduja Hospital & Medical Research Centre, a private, nonprofit hospital in Mumbai, India. Read about her thoughts on the growing threat of drug-resistant tuberculosis and her vision to provide treatment for every patient.

Featured genomic surveillance publications

Mpox virus multiplexed PCR amplicon sequencing (PrimalSeq) V.2.

Read about an amplicon-based sequencing (PrimalSeq) approach for Mpox virus that improved the depth and breadth of genome coverage with low viral concentration specimens compared to metagenomic sequencing.

Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of Mpox virus

Read how scientists used genomic and phylogenomic data to gain insights into the evolutionary trajectory of the 2022 Mpox virus outbreak strain as well as potential mechanisms and targets of human adaptation.

Genome sequencing of sewage detects regionally prevalent SARS-CoV-2 variants

In this publication, scientists describe how they performed epidemiological surveillance through wastewater sequencing and the ability to track specific viral strains.

Genomic surveillance at scale is required to detect newly emerging strains at an early timepoint

See how Illumina scientists developed a model to assess the sampling required to detect emerging SARS-CoV-2 strains when they are less than 1% of all strains in a population.

Discovery of bat coronaviruses through surveillance and probe capture-based NGS

Learn more about a capture-based NGS approach using baits to target coronaviruses. Here, scientists show the feasibility of targeted, cost-effective, large-scale, genome-level surveillance of bat coronaviruses.

Illumina Microbial Amplicon Prep for viral surveillance

Download the application note to see how to get comprehensive coverage across diverse viral genomes for effective surveillance.