Genomic Surveillance of Infectious Diseases

Identify & Track Infectious Disease Threats

Genomic surveillance with NGS can track infectious disease transmission and identify novel strains of coronavirus and other emerging pathogens. With near complete sequence data of pathogen genomes, we can implement effective infectious disease surveillance strategies to prevent further transmission and infection.

Infectious disease surveillance with next-generation sequencing (NGS) can:

  • Track the transmission routes of infectious diseases globally
  • Determine how quickly pathogens such as coronaviruses are mutating as they spread
  • Identify novel and known mutations in pathogens like coronavirus, influenza A & B and more
  • Study infectious disease therapy resistance
  • Investigate vaccine evasion mechanisms

Genomic surveillance helps public health officials track the path of an epidemic, perform contact tracing, determine the rate of pathogen evolution, and understand if a pathogen is changing in ways that could impact diagnostic or therapeutic effectiveness.

Detect & Characterize Coronavirus Mutations

Detect & Characterize Coronavirus Mutations

As the coronavirus mutates, new variants evolve such as the Alpha (B.1.1.7, UK), Beta (B.1.351, S. Africa), Gamma (P1, Brazil), Delta (B.1.617.2, India) and Omicron (B.1.1.529, S. Africa) variants. Surveillance and monitoring are critical because mutations can result in greater transmissibility or infectiousness. These coronavirus mutations can potentially make vaccines less effective/protective or even evade test diagnosis.

NGS is a valuable technology for genomic surveillance of infectious diseases such as COVID-19. Not only can it track the prevalence of coronavirus mutant strains, NGS can also identify novel coronavirus mutations, unlike PCR technology. Using NGS, scientists can detect low-frequency minority variants and multiple polymorphisms as well as novel variants.

Genome-wide strain typing with NGS can help epidemiologists identify and characterize mutations quickly to prevent further spread. Strain-level tracing can support identification of outbreak clusters and transmission routes.

In contrast, PCR is designed to detect specific regions of the pathogen genome; it 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.

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.

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Infectious Disease Surveillance Webinars

NGS for SARS-CoV-2 Detection and Surveillance

NGS has broad applicability for responding to the SARS-CoV-2 pandemic, from initial detection and characterization to monitoring, surveillance, and diagnostic detection.

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Role of Genomics in Global COVID-19 Surveillance

Join change-makers, thought leaders, and industry shapers for a discussion about the role of genomics in infectious disease surveillance.

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Targeted Enrichment for Disease and AMR Detection

Earlier and more comprehensive detection of infectious pathogens and antimicrobial resistance (AMR) markers can help optimize patient management and treatment.

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Coronavirus Genomic Surveillance Workflows

Featured Products

NovaSeq Reagent Kits

Reagent kits for the NovaSeq 6000 System provide ready-to-use cartridge-based reagents for cluster generation and SBS.

NextSeq 550 System

The flexible NextSeq 550 System offers a seamless transition between high-throughput sequencing and array scanning.

NextSeq 2000

Groundbreaking benchtop sequencers allow you to explore new science across a variety of current and emerging applications, with higher efficiency and fewer restraints.

Podcast: Genomic Surveillance & Testing for SARS-CoV-2
Christopher Mason from Weill Cornell Medicine describes his multifaceted approach to the urgent need for COVID-19 testing and surveillance. He also discusses his recent Nature paper involving use of omics methods to study COVID-19 host responses and drug interactions.
Preventing the Next Pandemic

Preventing the Next Pandemic

Up to 75% of new or emerging infectious diseases are estimated to have zoonotic origins.1,2 We now know that zoonotic reservoirs are significant in the spread of pathogens. With NGS, it is possible to screen reservoir animals such as bats to predict and prevent viral pathogen outbreaks.

Infectious disease surveillance with NGS-based target enrichment or metagenomics can help us understand interspecies transmission, how zoonotic diseases emerge, spread and become resistant to common therapies, and enable us to better contain, treat and prevent disease outbreaks.

Targeted enrichment sequencing can be scaled up to monitor zoonotic pathogens, while genomic surveillance with metagenomics allows for unbiased, culture-free detection and identification of a broad number of pathogens. Metagenomics also helps us understand the relationship between our microbiome and pathogen interactions, which is important when designing measures to control infectious diseases.

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Target Enrichment

Metagenomic Sequencing

More Infectious Disease Surveillance Applications

Food Surveillance

Microbial whole-genome sequencing can access all the genetic variant information of a pathogen as it spreads from food to humans. The more variants we can describe, the higher the probability of finding the sources of infections and routes of transmission.

Viral Surveillance

Target enrichment uses hybridization to capture genomic regions of interest. This method can provide the high sensitivity needed to detect a virus and provide information about its epidemiology and evolution.

Respiratory Infection Surveillance

These panels offer targeted enrichment sequencing solutions for respiratory pathogen and respiratory virus detection and characterization, including COVID-19 and flu.

Surveillance of Zoonotic Reservoirs

Shotgun metagenomics enables sequencing of DNA from the complete microbial community in zoonotic samples, including both novel and known species. The sequencing reads can be used to understand the emergence, evolution, and transmission of AMR gene and/or species distributions.

Healthcare-Acquired Infection Surveillance

NGS-based bacterial genome sequencing paired with user-friendly bioMérieux software allows comprehensive isolate discrimination and characterization.

Frequently Purchased Together

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

Infectious Disease Surveillance News

Illumina and Helix Collaborate on National Surveillance Infrastructure
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Leaders in COVID Surveillance: Utah Public Health Laboratory
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Extending COVID Surveillance Capabilities Beyond Big Cities
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Australia Tracks COVID-19 Nationwide to Understand Transmission and Spread
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How Sequencing-Based Surveillance Helps Fight COVID-19
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Featured Genomic Surveillance Publications

Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants
Genomic surveillance at scale is required to detect newly emerging strains at an early timepoint
Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based NGS

Related Solutions

Coronavirus Sequencing

NGS can characterize SARS-CoV-2 and other respiratory pathogens, identify novel coronaviruses, and more. Compare NGS methods for common coronavirus studies.

Coronavirus Software

Software tools to detect and identify viral sequences, examine COVID-19 host responses, and contribute findings to shared databases.

COVID-19 Host Genetics & Immune Response Profiling

Methods to interrogate host genetic variation and profile the molecular mechanisms that drive immune responses.