News from the customer community
Timeline: community work
From mid May: the Community continues to publish critical analyses of the transmission and biology of SARS-CoV-2. You can continue to follow these at our twitter feed @nanopore, and we will provide more infrequent updates on the timeline below.
In London Calling 2020, experts in epidemiology came together from across the world to discuss the sequencing-based response to the COVID-19 outbreak in the Kenya, China, the UK and the US. Read more here.
Oxford Nanopore Technologies announces advanced development of LamPORE, for rapid, highly scalable, low-cost COVID-19 detection. LamPORE is designed to detect the presence of SARS-CoV-2, the virus that causes COVID-19, in a saliva, swab or environmental samples. It is the first assay developed by Oxford Nanopore with the intention of future diagnostic use.
In Australia, researchers at the Garvan Institute of Medical Research have been sequencing SARS-CoV-2 samples on Nanopore's high-throughput sequencer PromethION, achieving 100X coverage in just 20 minutes.
Get over over 100x coverage for your #SARS_CoV_2 samples with @nanopore in ~20min with this one neat trick! Flongle and MinION users will hate you. All bow before the PromethION supremacy!— James Ferguson (@Psy_Fer_) May 19, 2020
2.5kb amplicons, rapid barcoding kit.
Also, daaaaaamn RAMPART v1.2 is good pic.twitter.com/U5D7n26okx
In a study published in The Lancet, a team of researchers investigated a COVID-19 outbreak in Bavaria, Germany. Combing epidemiology informaton, genomic data generated from a MinION device was used to understand transmission events and parameters that are relevant for successful containment.
A group of scientists in Canada led by Dr. Martin Smith have been ramping up their efforts to sequence SARS-CoV-2 genomes on MinION Mk1C. So far, 28 whole genome sequences have been made available on GISAID, with more to come. Read more about how Mk 1C has being used in the field.
Scientists in Sheffield hit the incredible milestone of 1000 COVID-19 nanopore genomes in just over 8 weeks.
Today we hit the incredible milestone of 1000 #COVID19 @nanopore genomes. A little over 8 weeks ago we had done 2. @SheffieldBRC @FloreyInstitute @SheffieldHosp @SheffieldMBB @SheffieldAPS @shefcompsci @Thushan_deSilva pic.twitter.com/5APDHviYAx— Sheffield Bioinformatics Core (@SheffBioinfCore) May 14, 2020
To better understand the SARS-CoV-2 epidemic in Minas Gerais (MG), the second most populous state in southeast Brazil, a team of scientists sequenced 40 complete genomes using Nanopore's MinION device. Combing with the existing epidemiological data from 3 states, these findings highlight the need for real-time and continued genomic surveillance strategies to prepare against the epidemic spread of emerging viral pathogens. Read the pre-print here.
At UCL, 458 SARS-CoV-2 genomes have been submitted to COVID-19 Genomic Consortium UK using nanopore sequencing. Find out more from the pre-print here.
458 genomes #SARSCoV2 submitted to #COGUK using 2kb amplicons and @nanopore sequencing. Public release today through @CovidGenomicsUK— uclpgu (@uclpgu) May 4, 2020
Protocols now online at https://t.co/FAk7am4zLp https://t.co/EzA87Cjj37
Preprint https://t.co/ilbu5yZH45@uclgenomics @PaolaResende1
A team of researchers published a study describing the sequencing of 320 SARS-CoV-2 genomes from COVID-19 patients in metropolitan Houston, Texas, on Oxford Nanopore's GridION device. "This study represents analysis of the largest sample of SARS-CoV-2 genome sequences to date from patients in the southern United States, The data provide a critical resource for assessing virus evolution, the origin of new outbreaks, and the effect of host immune response".
Scientists led by ErasmusMC combined epidemiological data with whole genome sequencing (WGS) of SARS-CoV-2 in clinical samples from using nanopore sequencing, to perform an in-depth analysis of sources and modes of transmission of SARS -CoV-2 in healthcare worker and patients. Read the pre-print here.
For the past 6 weeks, scientists at Cambridge COVID-19 genomic lab have been sequencing SARS-CoV-2 genomes on GridION sequencer. So far, they have sequenced 1000 genomes for Covid-19 Genomics Consortium UK.
We have been hard at work at @CamPathology for the past 6 weeks using the SARS-CoV-2 protocols developed by @NetworkArtic to sequence coronavirus genomes on the @nanopore GridION! As of last week we have sequenced 1000 genomes for @CovidGenomicsUK!— Cambridge COVID-19 Genomics Lab (@Cambridge_COGUK) May 1, 2020
First COVID-19 samples sequenced on a MinION Mk1CThis week, a team at Fuyang City CDC in China became the first to sequence COVID-19 samples using MinION Mk1C. They sequenced nine samples using MinION Mk1C and have been sequencing SARS-CoV-2 genomes using the ARTIC protocol on MinION since the outbreak began, helping to inform the public health response.
The MinION Mk1C combines the real-time, rapid, portable sequencing of MinION and Flongle with real-time, powerful GPU based computing and a high resolution screen, in one portable device. The device became available to early access users at the start of the year and following success from this group, more MinION Mk1C’s are now making their way into the field. Find out more about Mk1C here.
Spike protein of SASE-CoV-2 plays an important role both in viral infectivity and as an antibody target. Researches at the University of Sheffield, UK develped a spike mutation pipeline that has the potential to reveal the emergence of a more transmissible form of SARS-CoV-2. In this paper, long-read nanopore whole genome sequencing was used for the detection and sequencing of SARS-CoV-2 isolates from clinical samples
In this pre-print, a team of researchers in Düsseldorf, Germany carried out a genomic epidemiology investigation for "Heinsberg Outbreak" -- Germany's first large-scale SARS-CoV-2 outbreak from nearby city, Düsseldorf (70km away). Whole-genome sequencing of 55 SARS-CoV-2 isolates were sequenced using the ARTIC protocol and nanopore technology, informing public health containment and contact tracing efforts.
Scientists join forces to form the Irish Coronavirus Sequencing Consortium – they’ll use nanopore technology to track viral epidemiology.
A study led by ErasmusMC and CDC in the Netherlands published a pre-print , describing the first three weeks of the SARS-CoV-2 outbreak in the Netherlands，The timely generation of whole genome sequences using nanopore technology combined with epidemiological investigations facilitated early decision making in an attempt to control local transmission of SARS-CoV-2 in the Netherlands.
A new pre-print on bioRxiv described nsp14-ExoN as a key determinant for both high fidelity CoV replication and recombination. Long-read direct RNA sequencing on the Oxfod Nanopore Technologies MinION platform was used to sequence complete RNA molecules.
In a new paper published by Public Health–Seattle and King County (PHSKC) and the CDC at Atlanta on NEJM, researchers identified residents in a skilled nursing home with asymptomatic SARS-CoV-2 infection used combined methods including rRT-PCR and Nanopore MinION sequencing to conduct further investigation for the prevalence and transmission in the facility.
Using ARTIC procotol on MinION sequencer, scientists completed the first batch of 328 Danish COVID-19 genomes. Sequences are now available on GISAID.
The first SARS-CoV-2 sequence is completed in The Gambia using ARTIC protocol on Nanopore MinION device. Genome sequence is now available on GISAID.
As part of the UK COVID-19 consortium, researchers at UCL are running nanopore sequencing at full capacity, generating 192 SARS-CoV-2 genomes in 6 hours.
Running @nanopore sequencing at full capacity #COGUKLondon 🇬🇧 192 #SARSCoV2 genomes in 6 hours monitoring by #articRAMPART @uclpgu @uclgenomics #COVID19 #COGUK #gridION #MinION pic.twitter.com/2qpTYBPADu— Paola Resende (@PaolaResende1) April 20, 2020
The first complete SARS-CoV-2 sequence in Montreal using ARTIC protocol on Nanopore MinION device.
Premier génome de #SARS_COV_2 québécois!— The Smith Laboratory (@TheRealSmithLab) April 16, 2020
On teste le protocole de séquençage en temps réel @NetworkArtic sur un échantillon contrôle en parallèle avec @McGillGenome. 162,000 lectures d'ADN après 1h sur une puce @nanopore #MinION réutilisée, avec 95% du génome couvert >200x pic.twitter.com/HPEVh8hQgX
Nearly 600 SARS-CoV-2 sequences have been uploaded by UK COVID-19 Consortium onto GISAID, with many other users scaling up nanopore sequencing of the SARS-CoV-2 virus.
~900 scientists from 50 countries worldwide joined two webinars to learn how to use nanopore sequencing in COVID-19. You can find more information about the webinars here.
In Virginia, scientists at the Department of General Services’ (DGS) Division of Consolidated Laboratory Services (DCLS) are among the first to use Oxford Nanopore's portable MinION sequencer to decode Virginian OCVID-19 samples that contain the SARS-CoV-2 virus, which will help health officials better understand and track the scope of the COVID-19 pandemic - how the virus is changing and how it is being transmitted. Read NBC news report here.
141 new Belgian SARS2-CoV strains were released by the team at KU Leuven today on GISAID, sequenced with nanopore technology using Artic protocol.
In this new study, Guangdong provincial CDC in China combined genetic and epidemiological data to investigate the genetic diversity, evolution, and epidemiology of SARS-CoV-2 in Guangdong Province. The team generated virus genome sequences from 53 COVID-19 patients in Guangdong by a combination of metagenomic sequencing and multiplex PCR amplification followed by nanopore sequencing on a MinION device. Guangdong is the most populated province in China and had the highest confirmed cases in China outside of Hubei Province.
Using Oxford Nanopore's GridION device, scientists at UCL have been running a sequencing pipeline for COVID-19, from extraction to Nanopore sequencing. This is part of the UK's major new alliance to map the spread of coronavirus.
A collaborative research team led by Guangdong Provincial CDC published a pre-print for the identification of a common deletion in the spike protein of SARS-CoV-2. In this paper, direct cDNA sequencing in Nanopore platform was used as part of the multiple sequencing methods for whole genome sequencing and the validation of variants.
Nanopore sequencing technology is now used by researchers in 30 countries around the world for SARS-CoV-2 sequencing in COVID-19 patient samples. We are supporting users in more than 40 countries to get started.
43 new SARS-CoV-2 genomes have been sequenced by the University of Liège, Belgium on nanopore MinION using ARTIC protocol. Sequences are now available on Nextstrain.
Scientists in Singapore sequence the first nanopore SARS-CoV-2 genome on MinION -- from RNA to SARS-CoV-2 sequence in 7 hours.
OK, it took us much longer than expected but finally running the first COVID-19 extract through @nanopore Minion.— Diag Bacteriology (@10minus6cosm) March 30, 2020
RNA to SARS-CoV-2 sequence in 7 hours.
Does it look OK @pathogenomenick? pic.twitter.com/vUtGootWEk
63 new Canadian SARS-CoV-2 genomes are now available on GISAID shared by BCCDC Public Health Laboratory. These genomes were sequenced by using ARTIC protocol on Nanopore platform.
In Saudi Arabia , scientists at King Fahad Medical City (KFMC) in the capital city of Riyadh have started sequencing samples from COVID-19 patients using MinION.
First complete genomes of SARS-CoV-2 from 10 patients with COVID-19 were sequenced at The Institut Pasteur de Montevideo in Uruguay. Read here for more details.
Researchers noted that: "Sequence the genomes in less than 24 hours allows obtaining information on epidemiological behavior almost in real time during the course of an epidemic. It will allow them to know (1) where the strains that entered Uruguay come from; (2) when they arrived and (3) if there are different variants of the coronavirus in the country among others. This will be useful to inform how to manage border closures and healthcare."
The first Colombian genome of SARS-CoV-2 is sequenced using the ARTIC protocol on MinION -- now available on GISAID.
Excited to share this pic @nfrancosierra sequenced on our @nanopore MinION the 1st genome of #SARSCoV2 #Colombia 🇨🇴🦠 inspired by protocols from @NetworkArtic and currently stored @GISAID https://t.co/51J4KjZD4b pic.twitter.com/ac2RQSl3HT— Paola PS 🦉 (@paolapstz) March 29, 2020
Scientist in Malaysia sequences the first COVID-19 genome on MinION.
A team of scientist led by Yale School of Public Health published a pre-print characterising Coast-to-coast spread of SARS-CoV-2 in the United States with the portable MinION platform. The team was able to generate the first SARS-CoV-2 genome approximately 14 hours after receiving the sample and performing near real-time sequencing and bioinformatics.
Using direct RNA sequencing on an Oxford Nanopore MinION, a group of scientists from Bristol university, Public Health England and Liverpool univeritsy characterised the transcriptome and proteome of SARS-CoV-2 grown in Vero E6 cells in this pre-print.
Scientists in Garvan Institute in Austrslia run a single SARS-CoV-2 sample on Flongle for real time monitoring. The team was able to achieve over 100x coverage in ~10min of sequencing.
UK government announces £20m funding to a new UK research alliance for sequencing-based studies of COVID-19, enabling rapid, large-scale analysis of samples from patients testing positive for COVID-19. Oxford Nanopore is supporting researchers in the cities of Birmingham, London, Edinburgh, Glasgow, Nottingham, Sheffield, Liverpool, Cardiff, Exeter and Cambridge in this programme. Read this news report on ITV about the team at the MRC’s Centre for Virus Research in Glasgow and the work at Edinburgh .
60 new Dutch genomes are now available on GISAID and Nextstrain shared by the Dutch COVID response team at Erasmus MC. On the same day, the BC Centre for Disease Control uploaded 14 new SARS-CoV-2 sequences on GISAID, using nanopore sequencing for rapid tracking of the novel coronvirus.
A group of Korean scientists published a pre-print on bioRxiv, providing insights into the architecture of SARS-CoV-2 transcriptome using nanopore direct-RNA sequencing technology.
Minnesota's first three SARS-CoV-2 whole genome sequences are deposited to Genbank (MT188339 - MT188341) , using MinION sequencing with the ARTIC protocol.
In Western Germany, ten new genomes are posted that suggest separate introduction events and give more clarity to the Heinsberg outbreak.
An additional 48 new SARS-CoV-2 sequences from the Netherlands - making it a total of 73 from the country, have been updated on GISAID and Nextstrain. So far Dutch scientists have sequenced 7% of all known COVID-19 infections in the Netherlands. "This has shown multiple independent outbreaks, which contributed to the government decision to cancel all >100 people events".
First 2 SARS-CoV-2 genomes sequenced at The University of Sheffield, UK on nanopore platform using ARTIC protocol.
First SARS-CoV-2 genome sequence from Ireland using MinION and the ARTIC protocol.
Guangdong Provincial CDC uploads 35 SARS-CoV-2 sequences onto GISAID using the ARTIC protocol and nanopore sequencing on MinION. These data were used by scientists to understand the number, size, persistence and dynamics of transmission chains and supported public health responses in Guangdong, where transmission chains were reduced and eventually eliminated. Read the report on virological.org.
First Edinburgh SARS-CoV-2 genome using the ARTIC protocol on MinION, achieving 100x coverage at 15 mins of sequencing run time.
A team of scientists from Public Health England (PHE) in collaboration with Liverpool School of Tropical Medicine reported the molecular characteristic of respiratory microbiome in UK COVID-19 patients within 10hr. In this paper, amplicon and metagenomic MinION based sequencing was used to rapidly identify SARS-CoV-2 and assess the microbiome in nasopharyngeal swabs obtained from patients with COVID-19 by the ISARIC 4C consortium. Read the BBC article about it here.
Erasmus University Medical Center(Erasmus MC) updated 28 new SARS-CoV-2 sequences from the Netherlands on GISAID and Nextstrain. Dr.Reina Sikkema from Erasmus MC noted that, so far all dutch sequences were generated using nanopore sequencing technology.
Researchers at the Doherty Institute in Australia publish the first native RNA sequence of SARS-CoV-2, using nanopore direct RNA sequencing. the work shows insights into subgenomic mRNA production and base modification in the virus.
The New Zealand Herald published an article describing ''A Mars Bar-sized device is helping Kiwi scientists speedily unravel the genetic jigsaw of the virus driving the Covid-19 crisis - part of an urgent global effort that could help create a vaccine.''
In Wales, researchers sequence viral genomes from the first two COVID-19 patients. Sequencing, uploading to GISAID and analysis by Nextstrain is all completed in under 24 hours, indicating that "the two genomes from Wales each group the large European outbreak clade, but don't group together, suggesting separate introductions." Public Health Wales has provided funding to sequence the viral genomes from the first 100 patients in Wales.
France’s CIBU/PGP completes a sequence of SARS-CoV-2 within 8 hours
As part of our 24/7 duty for #COVID19 diagnosis in France we obtained the full genome #SARSCoV2 from a #coronavirus case with @nanopore MinION within only 8 hours using the bioinformatics pipeline of @NetworkArtic ! Thanks to the CIBU team @InstitutPasteur pic.twitter.com/5KshvDVXyt— cibu-pgp (@cibu_pgp) March 6, 2020
Nextstrain notes that the Düsseldorf01 genome, sequenced with the ARTIC protocol by Center of Medical Microbiology, shows "6 unique point mutations ...it doesn’t group with any other known European sequences."
MIT Tech Review reviews the use of rapid viral sequencing in the outbreak, noting that "Because scientists are posting data so quickly, this is the first outbreak in which a germ’s evolution and spread have been tracked in so much detail, and almost in real time."
The first case in New Zealand commences sequencing using the ARTIC protocol.
The SARS-CoV2 virus from Scotland's first COVID-19 case is sequenced in under 24 hours using nanopore sequencing and the ARTIC protocol.
A joint team from Wuhan University, Wuhan University Peoples' Hospital and Wuhan Dgensee Clinical Laboratory Co.,Ltd, an emerging diagnostics company in China, report the testing of a rapid nanopore-based workflow for targeted sequencing of SARS-Cov2 and ten additional viruses.
US CDC describes sequencing the first US COVID-19 patient using nanopore sequencing. Read the paper
Darui Biotechnology, the leading diagnostics company in China, reports on the work they have been doing on rapid, accessible characterisation of SARS-Cov2 using nanopore sequencing and based on the ARTIC protocol. Data shows that the workflow is able to rapidly produce accurate test results (comparisons are shown with traditional sequencing approaches), resolving false negatives in qPCR caused by low viral load or mutations. Full viral sequence information and the presence of mutations in the genome are both shown reliably and rapidly. For more information view this post (Mandarin language).
British Columbia CDC release the genome of a Canadian SARSCoV2 genome, providing the first sequence of a genome where the patient has travelled from Iran, and thus providing the first phylogenetic view of the Iran outbreak. @Nexstrain notes: "This groups most closely with a Shandong virus, but it is still consistent with Wuhan - Iran - BC transmission." The genome was sequenced using the MinION and the ARTIC protocol.
In Brazil, the CADDE project 36 at the Instituto Adolfo Lutz, São Paulo, releases sequence data for the first South American case of COVID-19, from a patient who had travelled to Lombardia, Italy. Sequencing and data release were performed in record time using the ARTIC protocol and nanopore sequencing. Researchers report that “the virus estimated phylogeny consistently places the Brazil/SPBR1/2020 in a strongly supported cluster with the Germany/BavPat1/2020 strain”. Read the BBC article(Portuguese language).
Genome British Columbia, Canada, describes the importance of sequencing in genomic epidemiology of the virus, and announces a new project that incorporates nanopore sequencing: "Responding to Emerging Serious Pathogen Outbreaks using Next-gen Data: RESPOND"
Darui Biotechnology, the leading diagnostics company in China, is accelerating the development of an Oxford Nanopore-based rapid solution for the sequencing of the virus responsible for COVID-19 (novel coronavirus), which can then easily be used in any laboratory, public heath body and hospital.
Hanzhou CDC enters the first nanopore-only nCoV genome into GISAID, using ARTIC protocol.
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.
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
Further nCoV genomes continue to be released via GISAID (approved login required). Genomes from Bavaria and Australia have used nanopore sequencing.
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".
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.
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)
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.
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.
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.
When we started developing RAMPART the idea that you could analyse seq data in real time seemed rather aspirational. Today: a still-sequencing #SARSCoV2 @nanopore genome from Brazil already up on @nextstrain. Amazing to get to work with @jaquegj @CaddeProject @NetworkArtic et al pic.twitter.com/epekvUHoqF— james hadfield (@hamesjadfield) February 28, 2020
Oxford Nanopore continues to work with community collaborators on protocol optimisation, and continues to support public health authorities using sequencing in their epidemiology work. 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 protocols, at this time we recommend contacting those publishers for further information.