Genomics in Infectious Diseases
Genomics is transforming modern infectious disease surveillance, expanding our understanding of pathogen evolution, host–pathogen interactions, and antibiotic resistance. In turn, public health professionals are changing the methods they use to research, monitor, and prevent epidemics and pandemics of high-profile infectious diseases such as influenza, tuberculosis, Ebola, and more recently, coronavirus.
Traditional methods of assessing infectious agents include antibody-based testing, real-time PCR, pulsed field gel electrophoresis, and multilocus sequence typing. These methods are typically useful only for a small and defined number of organisms, and data analysis can be subjective. In contrast, next-generation sequencing (NGS) provides a universal, hypothesis-free method for infectious disease surveillance that may be used with viruses, bacteria, fungi, or parasites, and can replace the need for multiple tests.
NGS and the Fight Against Coronavirus
COVID-19 Solutions
Next-generation sequencing is uniquely positioned in an infectious disease surveillance and outbreak model. Compare NGS methods and find solutions to detect and characterize SARS-CoV2, track transmission routes, study co-infection, and investigate viral evolution.
Learn More
Find and Characterize Respiratory Viruses with Illumina RNA Prep with Enrichment
A rapid target enrichment sequencing workflow for highly sensitive detection and characterization of respiratory viruses, including COVID-19 strains.
Read Application NoteRapid Detection of Respiratory Infections on Illumina MiniSeq System
Detection of respiratory viruses including coronavirus in <24 hours.
Read Application NoteDetect Respiratory Pathogens & Associated Resistance Genes
Rapid target enrichment workflow for broad detection of respiratory pathogens (including SARS-CoV-2 and flu viruses) and antimicrobial resistance genes.
Read Application NotePowering Metagenomic Detection of Respiratory Pathogens and Antimicrobial Resistance
This pandemic has underscored the need for new tools to detect, diagnose, and monitor emerging pathogens like SARS-CoV-2. Together with the Illumina respiratory virus oligo probe (RVOP) enrichment panel, this customized Explify RVOP application from IDbyDNA provides a sample-to-result solution for clinical metagenomics.
View Webinar
Powerful, Easy to Perform Analysis with the IDbyDNA Explify Platform
The Explify Platform is a fully supported NGS-based, clinical metagenomics technology suite for clinical laboratories. Watch this video for a virtual tour to better understand how the Explify Platform streamlines processes, supports labs, improves results, and much, much more.
Watch Video
COVID-19 Host Risk and Response
Understanding host genetic differences and individual responses to the SARS-CoV-2 virus increases understanding of disease susceptibiliity and severity. Read more about the methods for host risk & immune response studies.
Learn More
Featured Infectious Disease Articles
Illumina and IDbyDNA Partner to Deliver NGS Infectious Disease Solutions
The partnership aims to accelerate and improve testing for emerging public health threats like SARS-Cov-2.
Read More
Next-Generation Sequencing Helps Fight Infectious Diseases Globally
NGS technology enabled infectious disease experts to identify and characterize the genome of the novel coronavirus in China.
Read Review
How Sequencing-Based Surveillance Helps Fight COVID-19
Chief Medical Officer, Phil Febbo, MD, discusses how public officials follow the path of the epidemic and what that means for tracking the spread of coronavirus mutations.
Read MoreMicrobes and Metagenomics Research Review
This summary highlights recent peer-reviewed publications in which researchers used NGS to analyze viral populations, microbial pathogenesis, zoonotic reservoirs, the gut microbiome, and more.
Read Review
Benefits of NGS for Infectious Disease Surveillance
Genomic analysis with NGS provides high-resolution information to distinguish pathogen strains that differ by as little as one single-nucleotide polymorphism (SNP). It also allows identification of both novel and known infectious agents.
Illumina NGS technology delivers rapid results and high-quality data that public health professionals are utilizing to identify, track, and respond to infectious disease outbreaks.
Featured Infectious Disease Products
Illumina RNA Prep with Enrichment
Achieve rapid, targeted interrogation of an expansive number of target genes with exceptional capture efficiency and coverage uniformity.
View Product
iSeq System
The iSeq 100 System makes next-generation sequencing easier and more affordable than ever. Labs of all sizes can now easily sequence small genomes, interrogate gene sets, analyze gene expression, and more.
View Product
MiniSeq System
The MiniSeq System offers a simple, affordable solution. Advance your research with the power and reliability of proven Illumina NGS technology.
View Product
MiSeq System
With the MiSeq System you can access focused applications such as targeted resequencing, metagenomics, small genome sequencing, targeted gene expression profiling, and more.
View Product
NextSeq System and Reagents
The NextSeq System provides the flexible power you need for whole-exome, transcriptome, and targeted resequencing.
View ProductInterested in receiving newsletters, case studies, and information on microbial genomics? Enter your email address.
Additional Resources
Targeted Sequencing with the Pan-Viral Panel
This NGS workflow enables culture-free detection of viral targets without prior knowledge, even for mutagenic regions.
Virology NGS Solutions
Illumina NGS offers a comprehensive picture of viruses, host interactions, and phages specific to microbes.
Influenza Surveillance in China
Learn how researchers at the Jiangsu CDC use Illumina NGS for influenza surveillance.
Reconstructing Tuberculosis Outbreaks
NGS was used to reconstruct outbreaks of tuberculosis in British Columbia, Canada.
Deep Sequencing of HIV
Learn about detection of drug resistance variants and tracking of viral haplotypes.
Diagnosing Infectious Disease with NGS
Dr Peyro-Saint-Paul explains how the CE-IVD marked iDTECT™ Blood Test can be used to detect pathogens in blood samples.
IDbyDNA Explify and NGS Identify UTI Pathogens
Accurate identification of uropathogens limits the development of UTIs and spread of antimicrobial resistance.
References
- Lipkin WI (2013) The changing face of pathogen discovery and surveillance. Nat Rev Micobiol 11:133–141.
- Feero WG, Guttmacher AE. (2013) Microbial genomics and infectious diseases. N Engl J Med 365:347–357.
- Bao C-J, Cui L-B, Zhou M-H, Long L, Gao GF (2013) Live-animal markets and Influenza A (H7N9) virus infection. N Engl J Med 10.1056/NEJMc1306100.
- Lienau EK, Strain E, Wang C, Xheng J, Ottesen AR, et al. (2011) Identification of a Salmonellosis outbreak by means of a molecular sequencing. N Engl J Med 364:10.