Novel Coronavirus (nCoV-2019): information and updates
Wed 22nd January 2020
Oxford Nanopore is working with a number of public health laboratories, in China and elsewhere, to support the rapid sequencing of the novel coronavirus that was first seen in Wuhan, China.
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 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. Nanopore sequencing workflows can provide a consensus viral genome from sample within a day.
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 working to understand the needs of public health staff 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.
We will continue to provide updates on this page.
Updates from the Community of nanopore users:
22 Jan: The ARTIC project is developing an end-to-end system for processing samples from viral outbreaks, to generate real-time epidemiological information that is interpretable and actionable by public health bodies. The ARTIC network has released a set of materials to assist groups in sequencing the nCoV-2019 virus including a set of primers, laboratory protocols, bioinformatics tutorials and datasets.
Oxford Nanopore continues to work with community collaborators on protocol optimisation, and continues to support public health authorities using sequencing in their epidemiology work
24 Jan: New England Journal of Medicine publishes extensive reports on the virus and the outbreak, including "A Novel Coronavirus from Patients with Pneumonia in China, 2019". This manuscript describes the work conducted from 31st December 2019, when the "Chinese Center for Disease Control and Prevention (China CDC) dispatched a rapid response team to accompany Hubei provincial and Wuhan city health authorities and to conduct an epidemiologic and etiologic investigation. We report the results of this investigation, identifying the source of the pneumonia clusters, and describe a novel coronavirus detected in patients with pneumonia whose specimens were tested by the China CDC at an early stage of the outbreak. We also describe clinical features of the pneumonia in two of these patients." This paper describes the use of nanopore sequencing as part of the investigational methods.
24 Jan: The Lancet also publishes extensive nCoV materials. This includes a paper describing the analysis of a family cluster, sequencing using MinION, supplemented by Sanger sequencing, that indicates person-to-person transmission of the virus.
26 Jan: China CDC provides an update on viral mutation status, noting that '3rd generation' sequencing technology is enabling them to understand whether the virus is mutating (Mandarin language)
29 Jan: A paper in the Lancet from China CDC characterised full-length genomes of 2019-nCov patients using a combination of technologies including Nanopore sequencing, providing important information on possible virus origins and cell-binding receptors that is crucial for determine transmission capacity.
30 Jan: Prime Minister Li Keqiang visits China CDC to inspect the current scientific research on the new coronavirus for outbreak control, witnessing the use of "3rd generation" nanopore sequencing of the novel coronavirus".
31 Jan: Further nCoV genomes continue to be released via GISAID (approved login required). Genomes from Bavaria and Australia have used nanopore sequencing.
31 Jan: NEJM paper reports on the first nCoV case in the USA, describing the use of nanopore as part of the sequencing toolkit.
31 Jan: Following a week of support and liaison with scientists in China, 200 nanopore MinION devices start shipping to China to support coronavirus surveillance Read more
3 Feb: First Belgian nCoV sample arrives in the lab at KU Leuven, at 5pm. Using the ARTIC protocol, the team completes the sequence by 9am the next day.
5 Feb: Hanzhou CDC enters nanopore-only nCoV genome into GISAID, using ARTIC protocol.
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We continue to support public health authorities, please get in touch if you wish to discuss this with us.
Oxford Nanopore products are for Research Use Only. Where community members have issued nCoV protocols, at this time we recommend contacting those publishers for further information.