Oxford Nanopore releases a novel protocol for the rapid metagenomic characterisation of DNA and RNA viruses

This protocol describes a simple metagenomic workflow that can be used to identify DNA and RNA viruses. This method has been applied in human clinical samples to characterise the pathogen currently known as the monkeypox virus.

Oxford Nanopore has published a protocol1 for the metagenomic characterisation of DNA and RNA viruses. Standard approaches for identifying viruses, such as PCR, rely on looking for a specific pathogen, however metagenomic approaches sequence all genetic material in a sample, therefore providing the capability to identify potential pathogens in an unbiased or ‘hypothesis-free’ manner. The protocol has been developed by a team led by Guy’s and St Thomas’ with support from Oxford Nanopore.

The method can be used on routine nasopharyngeal swab and bronchoalveolar lavage samples and has been successfully used to sequence the pathogen currently known as the monkeypox virus from skin lesion swabs, demonstrating that multiple sample types can be analysed with this protocol. The method is accompanied by an analysis pipeline on EPI2ME labs2 to support teams leading the surveillance of this outbreak.

This protocol has also been described in a manuscript in SSRN3. The authors outline how the emergence of new viral infections with significant public health impact can be frequent, therefore comprehensive methodologies are needed for routine surveillance to detect rare, novel or emerging pathogens as early as possible. Viral metagenomic methods offer this capability and demonstrate the value of ‘hypothesis free’ analysis that can be rapidly developed in response to broad and emerging public health issues.

As stated in the manuscript, the lack of a targeted PCR assay at the start of a pathogen outbreak often leads to delays in case confirmation, as traditional offsite laboratories can take a few days, sometimes up to five, from first patient contact to result. This novel workflow uses nanopore sequencing and takes seven hours from sample receipt, with results for viral identification available on the same day. Also as noted in the manuscript, the results of this work highlight the future potential for sequencing technologies, such as Oxford Nanopore’s, to be introduced to assist with rapid pathogen characterisation and public health surveillance before targeted assays can be developed, validated and deployed at scale.

Justin O’Grady, Senior Director, Translational Applications, Oxford Nanopore Technologies, commented:

“Broad implementation of Oxford Nanopore devices for SARS-CoV-2 sequencing during the COVID-19 pandemic has dramatically increased infectious diseases sequencing capacity globally. Consequently, the first monkeypox virus genomes were sequenced using nanopore technology. This data was shared openly so that scientists could rapidly begin to understand this emerging outbreak.

"The protocol described by the team at Guy’s and St Thomas’ is important as it allows scientists to rapidly detect and identify unknown DNA and RNA viruses directly from human clinical samples. This enables the early characterisation of novel and emerging viral pathogens and comprehensive viral surveillance in a public health context.

"Oxford Nanopore is proud that our technology is having such a positive impact in the fight against viral outbreaks including SARS-CoV-2 and monkeypox virus, but also Ebola and Zika in recent years.”


  1. The protocol can accessed via the Nanopore Community here.

  1. EPI2ME labs analysis pipeline here.

  1. The full SSRN publication is available here.

To hear more about ‘The frontlines of pathogen genomic surveillance with rapid nanopore sequencing’ join this Oxford Nanopore webinar on Thursday 23rd June.