Novel Coronavirus (COVID-19): information and updates
Wed 1st April 2020
Oxford Nanopore is working with public health laboratories around the world, and researchers in related areas, to support the current COVID-19 pandemic. This includes rapid sequencing of the novel coronavirus SARS-CoV-2, as well as approaches that characterise a broader range of pathogens in a sample.
A large number of scientists from large centralised labs - and also smaller decentralised ones - are now using nanopore sequencing to support rapid data sharing of genomic data. Rapid data sharing has been key to the public health response, and researchers all over the world have been fast to share the genomes they have sequenced on public databases such as GISAID, GenBank or elsewhere. As numbers of cases have increased, laboratories have been building capacity to sequence larger numbers of the genomes, typically progressing from using the MinION device to the GridION device for sequencing.
Sequencing the virus can support ‘genomic epidemiology’- characterising the virus and helping public health authorities to understand the identity of the virus, whether it is changing and how it is being transmitted - all in conjunction with other epidemiological data.
The scientific community has previously developed methods for the rapid, near-sample nanopore sequencing of pathogens in multiple outbreak situations including Zika, Ebola, Yellow Fever and Swine Flu and a range of other pathogens. This experience has supported the rapid deployment of nanopore sequencing for the current outbreak.
Nanopore workflows can provide a consensus viral genome in 7 hours. See the resources below for more information.
Several researchers are also using nanopore sequencing to characterise multiple pathogens that may be present in a sample.
The evolving use of nanopore sequencing in the COVID epidemic:
First analysis, open protocols to prepare for broad adoption
- First sequencing of original virus that emerged in Wuhan
- Human-to-human transmission confirmed, Wuhan
- Release of the ARTIC protocol enables labs anywhere to sequence the virus
- Oxford Nanopore sends 200 MinIONs to China
Sequencing used more broadly in China, rest of world starts surveillance
- ARTIC protocol enables multiple countries to start epidemiology: China, Belgium Canada, Brazil
- Da’rui, a leading Chinese diagnostics company, start exploring test methods
Broad adoption, expanding uses include:
- MinION usein COVID expands to most affected countries including US, UK, France, New Zealand, Australia, Germany, Netherland, Spain, Korea. At the end of March, around 30 countries are using nanopore sequencing for COVID, with another >40 countries preparing to do so.
- Beyond sequencing of the virus for epidemiology, scope of nanopore sequencing work broadens to include:
- Metagenomic/multipathogen approaches from Wuhan University (targeted approach to characterising SARS-CoV-2 and other respiratory viruses) + other international centres
- 2 x Direct-RNA analyses: sub-genome and transcriptomes of the coronavirus
How can we help?
At this time, Oxford Nanopore staff are working with the community to support the development and sharing of best practice and protocols for the sequencing of this virus. We are offering technical support to public health authorities and researchers, and working to understand the needs of these users so that we can continue to provide the most useful support to the community. If you are a public health laboratory/scientist in the microbiology community and wish to discuss how we can support you in the current outbreak please get in touch.
Nanopore sequencing of the SARS-CoV-2 virus
Oxford Nanopore's sequencing technology has been used to sequence the virus in 7 hours. Many researchers are using the portable MinION device, with higher throughput labs using the larger GridION, and initial work starting on the ultra-high throughput PromethION. Early work on the smallest Flongle is expected to emerge soon.
Researchers are using a variety of different workflow approaches. For example:
Whole genome sequencing
For completing a whole genome sequence the ARTIC network has issued protocols that enable rapid nanopore sequencing of the SARS-CoV-2 virus. You can also find information on currently supported workflows in the nanopore community (login required).
Direct RNA sequencing
Multiple groups are investigating approaches that characterise not only the SARS-CoV-2 virus, but other pathogens or microorganisms present in the sample. These aim to understand co-morbidity patterns of the disease, and also have the potential to be useful in broader surveillance of outbreaks in a population.
Timeline of developments
For full information of scientific news from the nanopore community view this timeline.
The ARTIC network has issued protocols that enable rapid nanopore sequencing of the SARS-CoV-2 virus.