Genomics in Infectious Diseases
Genomics is transforming our understanding of infectious diseases, pathogen evolution, disease transmission, host–pathogen interactions, and antibiotic resistance. In turn, public health professionals are changing the methods they use to research and monitor 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, culture-free method for infectious disease characterization and surveillance that may be used with viruses, bacteria, fungi, and parasites, and can replace the need for multiple tests.
NGS and the Fight Against COVID-19
Coronavirus Sequencing
Compare NGS methods and find solutions to detect and characterize SARS-CoV2, track transmission routes, identify co-infections, and study viral transmission pathways and evolution.
Host Risk & Response
Studies of host genetic differences and individual immune responses to infectious diseases such as SARS-CoV-2 can increase understanding of disease susceptibility and severity.
Host-Pathogen Interactions
NGS facilitates studies of host and pathogen gene expression and the influence of the microbiome.
Drug Discovery & Development
NGS allows drug developers to explore genomic variation, which can inform drug target identification, validation, and clinical development.
Respiratory Pathogen NGS Solutions
Powering Metagenomic Detection and Characterization of Respiratory Pathogens
The COVID-19 pandemic has underscored the need for new tools to detect and monitor emerging pathogens like SARS-CoV-2. Together with the Illumina Respiratory Virus Oligo Panel (RVOP), the customized Explify RVOP analysis app from IDbyDNA provides a sample-to-result metagenomics solution.
View WebinarDetect 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 MiniSeq System Application NoteRead Analytical Performance Application Note
View Respiratory Pathogen Panel
Rapidly Detect Respiratory Viruses on Illumina MiniSeq System
Detection of respiratory viruses including coronavirus in <24 hours using NGS with the MiniSeq benchtop sequencer.
Read Application NoteFind and Characterize Respiratory Viruses with Target Enrichment
A rapid target enrichment sequencing workflow for highly sensitive detection and characterization of respiratory viruses, including COVID-19 strains.
Read Application NoteView Respiratory Virus Oligo Panel
Track Emergence & Prevalence of Novel SARS-CoV-2 Strains
COVIDSeq detects the SARS-CoV-2 virus and provides critical information on the epidemiology of new variants.
COVIDSeq Test (RUO:: 3072 samples) COVIDSeq Assay (96 samples)Vaccinating an Entire City in Brazil
How the Butantan Institute helped vaccinate the city of Serrana—and what they learned thereafter.
Read ArticleMolecular Epidemiology
Examine genetic variants that influence disease transmission and prevention, and better understand the mechanisms that lead to infection and spread.
Learn More
Pathogen Identification with Metagenomics
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 infectious disease labs, improves results, and much more.
View VideoIDbyDNA Explify and NGS Identify UTI Pathogens
Accurate identification of uropathogens can help limit the development of UTIs and spread of antimicrobial resistance.
Access Tech NoteEmploying Metagenomics for Uropathogen Detection
Learn how NGS-based metagenomics enables culture-free, hypothesis-free detection and identification of uropathogens.
View WebinarShotgun Metagenomic Sequencing
Comprehensively sample all genes in all organisms present in a complex sample. Identify emerging pathogens or gain insight into microbial community biodiversity and function.
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 ArticleNext-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 ArticlePortable iSeq System Used to Characterize Ebola Outbreak
In combination with extensive epidemiological findings, the iSeq 100 System allowed local scientists to analyze transmission patterns and trace the outbreak's origin.
Read ArticleAccurate Surveillance of Healthcare-Acquired Infections
NGS-based bacterial genome sequencing paired with user-friendly bioMérieux software allows comprehensive isolate discrimination and characterization.
Read Application NoteFeatured 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.
MiniSeq Reagent Kits
Access cost-efficient sequencing, even for low numbers of samples.
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.
MiniSeq System
The MiniSeq System offers a simple, affordable solution. Advance your research with the power and reliability of proven Illumina NGS technology.
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.
NextSeq System and Reagents
The NextSeq System provides the flexible power you need for whole-exome, transcriptome, and targeted resequencing.
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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.
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.
Deep Sequencing of HIV
Learn about detection of drug resistance variants and tracking of viral haplotypes.
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.