Oxford Nanopore provides updated protocols for rapid, scalable and low-cost sequencing of SARS-CoV-2 genomes

Oxford Nanopore has released new protocols enabling the rapid, cost effective sequencing of SARS-CoV-2 — the virus that causes COVID-19. Research teams are able to access sequencing technology in days, without capital cost, for quick set-up of rapid turnaround SARS-CoV-2 sequencing.

From initial characterisation of the SARS-CoV-2 virus genome to the rapid identification of variants, researchers have been utilising nanopore sequencing to generate data essential to combating the spread of COVID-19.

Oxford Nanopore protocols

Oxford Nanopore offers a number of protocols for sequencing SARS-CoV-2, the most utilised being the ARTIC Classic and the Midnight protocols.

The ARTIC Classic protocol was the first SARS-CoV-2 nanopore sequencing protocol to be utilised, and is the most well established. Featuring a normalisation step, the method is ideal for the routine sequencing of smaller batches of samples spanning a wide range of Ct values, and is optimised for maximum coverage across all genomes sequenced. The protocol is best for those with some prior experience of nanopore sequencing.

The recently released Midnight protocol is optimised for high throughput requirements, for highly multiplexed SARS-CoV-2 genome sequencing. Making use of the Rapid Sequencing Kits, the approach has the fastest turnaround time, least hands-on time, and lowest cost-per-sample; it is also a good choice for those wishing to incorporate automation.

COVID-19 surveillance

Rapid sequencing and sharing of SARS-CoV-2 genomic data enables rapid identification of variants and effective tracking of their prevalence and distribution. It also provides scientists with information about how strains of the virus are related, helping to indicate routes of transmission and investigate clusters — all ultimately helping to inform strategies to control the spread.

George Githinji from KEMRI, Wellcome Trust has been able to establish nanopore sequencing for COVID-19 surveillance in Kenya:

"Our capacity to run sequencing of SARS-CoV-2 has gone on to inform some of the resulting control measures."

Katarina Braun, University of Wisconsin has been using nanopore sequencing throughout the pandemic. She said:

"Nanopore sequencing has been the workhorse for us generating data as we looked at how the virus was spreading differently through different parts of our state."

Thank you to Mads Albertsen (Aalborg University, Denmark), Ira Deveson (Garvan Institute, Australia), Áine O'Toole (University of Edinburgh, UK), Gage Moreno & Kat Braun (University of Wisconsin), Kirstyn Brunker (University of Glasgow, UK), Criselda Bautista (Research Institute for Tropical Medicine, Manila, Philippines), Susan Engelbrecht (Network for Genomic Surveillance, South Africa) and George Githinji (The Kenya Medical Research Institute Wellcome Trust) for sharing their experiences in this video.

Get started

If you’d like to get started with nanopore sequencing for SARS-CoV-2 sequencing, find more information on our COVID-19 pages.

For more on the role of genomic epidemiology for infectious disease surveillance, download our genomic epidemiology briefing paper.