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.

ONT sequencing offers unique advantages to short-read sequencing including lower equipment costs, reduced turnaround times from days to hours, real-time basecalling, enrichment of samples via adaptive sampling and high portability

Kimani, R. et al., bioRxiv (2023)

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 one to thousands 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 mpox 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

Rapid detection of mpox virus

Adela Alcolea-Medina and colleagues at the Centre for Clinical Infection & Diagnostics Research, UK, used nanopore technology to develop a seven-hour metagenomic workflow — from sample receipt to answer — that enables the detection of low-abundance RNA and DNA viruses in different sample types. Discover how the team used this to rapidly detect mpox virus, demonstrating the potential utility of this method to differentiate between viruses with similar symptoms with a short turnaround time.

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)

Case study

Molecular surveillance of malaria with nanopore sequencing to investigate anti-malarial resistance

With nanopore sequencing, the malaria-causing protist Plasmodium falciparum can be genetically sequenced from a blood sample without the need to grow the parasite in a laboratory, reducing turnaround times and increasing scalability of the workflow for surveillance of disease transmission and drug resistance. At London Calling 2023, William Hamilton from the Wellcome Sanger Institute, UK, shared how they utilised the portable MinION to work with rural community facilities across Ghana to perform nanopore sequencing of blood research samples for the analysis of anti-malaria drug resistance in P. falciparum.

We could implement this entirely end-to-end [workflow] in an endemic setting, in a portable way, in a way that was not super resource-intensive

William Hamilton, Wellcome Sanger Institute, UK

Discover more

Find out how nanopore sequencing enables real-time pathogen and antimicrobial resistance (AMR) identification from mixed microbial samples.

Focus on COVID-19

Sequencing SARS-CoV-2

There are two methods available for whole-genome nanopore sequencing of SARS-CoV-2: Midnight and ARTIC Classic. Both methods employ a PCR tiling approach in which the viral genome is amplified in overlapping sections, maximising coverage across the full genome.

Midnight is a simple, rapid method of sequencing SARS-CoV-2 genomes at low cost per sample. The approach is highly flexible, allowing the on-demand sequencing of small numbers of samples or scaling up to high-throughput sequencing needs. Hands-on time is also minimal, facilitating automation. In the Midnight protocol, the SARS-CoV-2 genome is amplified in ~1,200 bp overlapping segments, making it more resilient to drop-out caused by mutations in the viral genome.

Midnight sequencing primers are available separately in the Midnight Expansion Kit or as part of a complete, cost-effective COVID-19 pack, including Rapid Barcoding Kits and MinION/GridION Flow Cells. Oxford Nanopore continually monitors new SARS-CoV-2 mutations to ensure complete amplification of the genome.

ARTIC Classic was the first SARS-CoV-2 nanopore sequencing protocol to be utilised, and has been used by scientists around the world. In this method, the SARS-CoV-2 genome is amplified in ~400 bp fragments. This shorter length may help improve coverage for RNA samples that are likely to be degraded — for example, due to freeze-thaw cycles or storage at temperatures above -80°C.

The Midnight workflow for preparation of SARS-CoV-2 whole-genome sequencing. This method is similar to the ARTIC amplicon sequencing protocol for MinION for SARS-CoV-2 v3 (LoCost) by Josh Quick and the method used in Freed et al., 2020. Timings shown are for preparation of 24 samples.

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


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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