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.

The availability of a portable sequencing technology opens new doors to travel to outbreak locations, sequence, and analyze samples without needing to transport them

Warr A. et al. bioRxiv (2021)

Technology comparison

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

Direct detection of DNA/RNA methylation

  • 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)

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

Laborious workflows

Lengthy sample preparation with requirement for amplification — removing base modifications (e.g. methylation) and increasing the potential for sequencing bias

White paper

Delivering the future of genomic pathogen surveillance

From Ebola, Zika, and COVID-19, to antimicrobial resistant (AMR) 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. Read customer case studies on monkeypox virus, poliovirus, and AMR profiling, and find out how nanopore sequencing overcomes the limitations of traditional genomic pathogen surveillance techniques.

Get more infectious disease content, including getting started guides, workflows, white papers, and videos, in our Resource centre.

Case study

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

Rapid detection of monkeypox virus

Adela Alcolea-Medina and colleagues at the Centre for Clinical Infection & Diagnostics Research, UK, used nanopore technology to develop a metagenomic workflow that detects low-abundance RNA and DNA viruses in different sample types. The workflow required only seven hours from sample receipt to answer — offering a significant advantage over metagenomic detection using traditional short-read sequencing technologies, which typically take three to five days. Testing the workflow on four monkeypox virus (MPXV) research samples, the team were able to detect MPXV in all four samples within 30 minutes of sequencing. The method also demonstrated the potential to differentiate between viruses that present with similar symptoms, with varicella-zoster virus (VZV), which causes chickenpox, detected in one of their research samples.

Find more details on this study and other infectious disease case studies in the pathogen surveillance white paper.

Emergence of new viral infections with significant public health impact are frequent events, which re-enforces the need for comprehensive methodologies to detect rare, novel or emerging pathogens

Alcolea-Medina, A. et al. medRxiv (2022)

From species identification to metagenome assembly and variant calling, get detailed information in our application pages.

Case study

Using nanopore sequencing for in-field investigation of yellow fever virus outbreaks

Using a portable nanopore sequencing approach, Sarah Hill (Royal Veterinary College, UK) and her colleagues were able to investigate outbreaks of yellow fever virus (YFV) in Brazil. They sequenced 498 YFV genomes, and combined with epidemiological data from neotropical primates, humans, and mosquito vectors, were able to identify the environmental, demographic, and climatic factors that influence virus spread.

Case study

Influenza surveillance at the state level with nanopore sequencing

Influenza is a rapidly mutating virus that causes severe respiratory disease and is responsible for critical illness and death worldwide. At the NCM 2022, Sarah Scott (Minnesota Public Health Laboratory, USA) presented her work using nanopore technology to characterise the influenza virus found in specimens collected as part of a pathogen surveillance programme in Minnesota, USA.

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.

* Theoretical max output (TMO). Assumes system is run for 72 hours (or 16 hours for Flongle) at 420 bases / second. Actual output varies according to library type, run conditions, etc. TMO noted may not be available for all applications or all chemistries.

Recommended for infectious disease sequencing


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.


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