Novel Coronavirus (COVID-19) Overview
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, the virus that causes COVID-19, as well as approaches that characterise a broader range of pathogens in a sample. Oxford Nanopore has recently developed LamPORE, a rapid, low-cost and scalable assay for the detection of SARS-CoV-2.
A large number of scientists,from large centralised labs to smaller decentralised ones, are using nanopore sequencing to support rapid sharing of SARS-CoV-2 sequence 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 increased, laboratories have built capacity to sequence larger numbers of the genomes, typically progressing from using the MinION device to the GridION device for sequencing. Thousands of genomes sequenced using nanopore technology are now available in public databases.
Oxford Nanopore’s vision is to support wide efforts to identify, track, trace, and isolate cases. We recently developed a new assay, LamPORE, for SARS-CoV-2 detection. Alongside whole genome sequencing of the virus, this means that the range of Oxford Nanopore solutions for detection and analysis of SARS-CoV-2 can be performed in more and more locations.
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:
October / November / December:
National & regional lockdowns continue
Regulatory approval of LamPORE COVID-19
August / September:
Regional lockdowns & travel restrictions reimplemented
Enhanced protocols for population-scale sequencing
- UK government partner with Oxford Nanopore to roll out rapid, large-scale SARS-CoV-2 screening using LamPORE. Read more
- ARTIC network pre-print describes enhanced SARS-CoV-2 genome coverage, improved demultiplexing, 1-hour reduction in hands on time, and reagents costs of ~£10 ($13) per sample. Read pre-print
- LamPORE evaluation study shows 99.1% sensitivity, 99.6% specificity. Read more
June / July:
Global increase in new cases
Continued product innovation
- New native barcoding kit enables analysis of up to 96 samples per flow cell
- Up to ~4,500 SARS-CoV-2 samples can be sequenced using the ARTIC whole genome protocol with PromethION
- Detailed LamPORE update — including multi-virus assays — provided at London Calling 2020. Watch now
- G42 announce population-scale LamPORE SARS-CoV-2 testing workflow in UAE — capable of processing hundreds of thousands of samples daily
May:
Pandemic continues, some lockdowns eased
Continued scale-up, innovation for testing
- Further national sequencing networks emerge
- Scaled-up sequencing continues in force
- Oxford Nanopore in advanced development of LamPORE, a SARS-CoV-2 detection assay for use with nanopore sequencing
April:
China recovery, Worldwide pandemic
Scaling up, new research areas emerging
- Nanopore sequencing technology is now used by researchers in 40 countries around the world for SARS-CoV-2 sequencing in COVID-19 patient samples. We are supporting users in more than 50 countries to get started.
- Larger sets of genomes being uploaded to public databases
- Initial work on the smallest Flongle is emerging.
- Emerging project to research immune response in paediatric COVID-19 patients using long-read nanopore RNA sequencing
March:
Pandemic
Broad adoption, expanding uses include:
- MinION use expands to most affected countries including US, UK, France, New Zealand, Australia, Germany, Netherland, Spain, Korea
- UK commits to sequence all positive samples
Expanded research scopes/approaches:
- Metagenomic/multipathogen approaches from Wuhan University and Dgensee (targeted approach to characterising SARS-CoV-2 and other respiratory viruses) + 3 UK centres
- 2 x Direct-RNA analyses: sub-genome and transcriptomes of the coronavirus
- Discussions with multiple parties on developing larger-scale capacity or projects
- Immune profiling
- Projects starting to approach whole human genome in relation to individual response to disease
February:
Epidemic
Rapid China adoption, ROW 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
January:
Outbreak
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
*At the end of Jan, WHO declared COVID an international public health emergency
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. Their latest pre-print describes how enhanced
SARS-CoV-2 genome coverage has been achieved while significantly reducing both hands-on time and reagent
costs.
You can also find information on currently supported workflows in the nanopore community (login required).
Direct RNA sequencing
Researchers from Australia and Korea have performed direct RNA sequencing of the virus, providing insights into the transcriptome and base modifications of the virus.
Metagenomic 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.
Rapid detection of the SARS-CoV-2 virus: LamPORE
Oxford Nanopore has recently developed of LamPORE, a new assay for the rapid, scalable detection of the SARS-CoV-2 virus. LamPORE is CE marked for in vitro diagnostic use and LamPORE devices are currently being piloted in a number of NHS labs, to support expanded high-accuracy testing for the UK. Oxford Nanopore is intending to submit an Emergency Use Authorisation application to the US FDA for LamPORE Covid-19 in the coming weeks. Read more here
Nanopore Community: extensive epidemiology and publications
Internationally, the nanopore community has been working extensively to provide public datasets for epidemiology work, or to research the virus, the broader disease, and associated pathogens. For full information of scientific news from the nanopore community view this timeline.
Recommended resources
Follow the cases of COVID-19 at the JHU dashboard, genomic epidemiology of the SARS-CoV-2 virus at Nextstrain, and analysis at virological.org. General WHO information and advice can be found here.
Get started with nanopore sequencing or if you would like support specific to the current outbreak please get in touch.
The ARTIC network has issued protocols that enable rapid nanopore sequencing of the SARS-CoV-2 virus.
