Applications Research areas
Infectious disease
Offering comprehensive, real-time insights into infectious disease samples — from pathogen identification and antimicrobial resistance (AMR) profiling to the assembly of high-quality genomes and variant identification — nanopore sequencing delivers immediate access to the critical genomic epidemiology data required for effective control of infectious disease outbreaks. Sequence in the lab or at sample source at a scale to suit your needs, with powerful portable and high-throughput nanopore sequencing devices.
Evidence-based public health decision-making in the COVID-19 pandemic
The combination of real-time whole genome sequencing with the data from the National Public Health response team has provided information that helped decide on the next steps in the decision-making Oude Munnink B.B. et al. Nature Medicine 26 (2020)
Oxford Nanopore sequencing
Traditional short-read technologies
Real-time data streaming
- Immediate access to actionable results, including pathogen identification, variant analysis, and antimicrobial resistance
- Stop sequencing when sufficient data generated — wash and reuse flow cell
- Comprehensive data analysis tools — including EPI2ME for real-time species identification and AMR profiling
Fixed run time with bulk data delivery
Increased time-to-result; less amenable to time-critical applications
Scalable — portable to high throughput
- Sequence anywhere with portable, low-cost MinION devices — starting at just $1,000, including sequencing reagents
- Scale up with modular GridION and PromethION — suitable for ultra-high-throughput sequencing of pathogen and complex metagenomic samples alongside other experiments, such as host genomics
Constrained to the lab
Considerable site infrastructure and set-up requirements combined with high platform costs can limit accessibility
Flexible and on-demand
- Scale your sequencing to your needs — run 1 to 1000s of samples on a single device
- Sequence what you want, when you want — no sample batching required
Limited flexibility
Sample batching may be required for optimal efficiency, potentially delaying results until sufficient samples are acquired
Unrestricted read length (>4 Mb achieved)
- Resolve complete genomes and plasmids
- Span and delineate challenging regions, including structural variants and repeat regions
- Assemble complete genomes from metagenomic samples
- Discriminate closely related species
Read length typically 50–300 bp
Short reads do not typically span entire regions of interest, including repeats and structural variants, or full-length RNA transcripts, resulting in fragmented assemblies and ambiguous transcript isoform identification
Streamlined, automatable workflows
- Sample prep in as little as 10 minutes, including multiplexing
- Whole genome, metagenomic, targeted, direct RNA, and cDNA sequencing approaches
- Eliminate amplification bias and detect base modifications alongside nucleotide sequence with amplification-free protocols
- Automate sample prep using the portable VolTRAX device
Laborious workflows
Lengthy sample preparation with requirement for amplification — removing base modifications (e.g. methylation) and increasing the potential for sequencing bias
Briefing paper
Using real-time molecular epidemiology to manage infectious disease outbreaks
From Ebola, Zika, and COVID-19, to antimicrobial resistant bacterial and fungal infections, discover how portable, real-time nanopore sequencing is being utilised by researchers worldwide to support rapid identification and control of infectious disease outbreaks. Find out how real-time genomic epidemiology is supporting the tracking of novel pathogen variants to inform infection control and public health policy.
Get more infectious disease content, including getting started guides, workflows, white papers, and videos, in our Resource centre.
Outbreak sequencing
Use of nanopore sequencing in outbreak situations
Infectious diseases are an increasing threat, for example in 2019 alone the WHO recorded over 100 outbreaks of 19 different infectious diseases, each posing a potential epidemic or pandemic risk. Portable and scalable, real-time nanopore sequencing has been used to support rapid identification and control of many infectious disease outbreaks across the world, including SARS-CoV-2, Ebola, Zika, antimicrobial-resistant bacteria, and many more.
‘Had this virus caused a severe outbreak or pandemic, our proactive surveillance efforts and vaccine derivation would have provided an approximate 8-week time advantage for vaccine manufacturing’
Rambo-Martin and Keller et al. mSphere e00822-19 (2020)
Case study
Local control of COVID-19 community and hospital outbreaks
As a new pandemic took hold across the UK, hospital admissions of patients with COVID-19 surged, including at the Cambridge University Hospitals. It was very important to understand where and how these infections were spreading to support the implementation of effective disease control measures. The recently established COVID-19 Genomics Consortium UK swung into action; a world-leading distributed network of hospitals, public health agencies, and academic partners, with a mission to provide rapid, high-throughput whole-genome sequencing of SARS-CoV-2 samples. The molecular epidemiology data generated was critical to implementing appropriate local and national public health policy.
‘Studying the virus’s genome helps to highlight cryptic or hidden transmission. That’s the real power of it — you can detect outbreaks and act while they’re happening’
Estée Török, University of Cambridge, UK
From species identification to metagenome assembly and variant calling, get detailed information in our application pages.
Get started
Scalable sequencing of infectious disease samples
Fully scalable, real-time nanopore sequencing devices are available to suit all infectious disease sequencing requirements — from in-field pathogen surveillance and characterisation to high-volume analysis of outbreak samples and host genetics.
Recommended for infectious disease sequencing
GridION
Running up to five independent MinION or Flongle Flow Cells with powerful, integrated compute, GridION provides the flexibility to run multiple experiments, on-demand — ideal for rapid and scalable analysis of pathogen samples and tracking novel variants.
PromethION 48
Combining up to 48 independently addressable, high-capacity flow cells with powerful, integrated compute, PromethION 48 delivers flexible, on-demand access to terabases of sequencing data.
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PromethION 24
Flexible, large-scale sequencing using up to 24 independent, high-capacity flow cells.
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MinION
Powerful, portable sequencing of pathogen samples from just $1,000, including sequencing reagents.
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MinION Mk1C
Fully integrated sequencing and analysis in a powerful handheld device — sequence at sample source.
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Flongle
Adapting MinION and GridION for the most cost-effective access to smaller, routine tests and analyses.
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