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Timeline: community work
The Community continues to publish critical analyses of the transmission and biology of SARS-CoV-2. You can also follow these at our twitter feed @nanopore
The public health labs in Alaska have teamed up with University labs run by Eric Bortz & Devin Drown to improve sequencing capacity, time to result & detection of new variants of #SARSCoV2 in Alaska. Read more.
Alaska has built as team of scientists to hunt for new, more-contagious variants of the coronavirus. The state is already doing more that other states to track variants, but it aims to do even better. Here's how. https://t.co/YEX17RQNa6— Alaska Public Media News (@AKpublicnews) February 11, 2021
During infection there are several variants in the race for dominance. With #ngs technology we identified a natural attenuated #SARS_CoV_2 variant. @nanopore #sequencing unfortunately no success of isolation -> we did in silico analysis https://t.co/xNrtaP1IbZ— Gabor Kemenesi (@GaborKemenesi) February 8, 2021
Very proud of my team @JackDorman10, @iliciub1, Nicole Perry working tirelessly on #SARSCoV2 genome sequencing for variant surveillance and community transmission - Indiana. @PurdueBiolSci @nanopore @NetworkArtic pic.twitter.com/hKoRlLmSqN— Giovanna Carpi (@giocarpi) February 6, 2021
Researchers at the Malawi Liverpool Wellcome Trust successfully sequence SARS-CoV-2, reducing their reliance on laboratories in South Africa.
...& proud of the sequencing work that has resulted from this WT COVID grant which will inform the Malawian Governments COVID response. Led by @catanscombe & @KGBscience @LivUni_IVES @MlwTrust @WTCGHR @benjamesmorton pic.twitter.com/q5tHJyNhUV— Jen Cornick (@micro_jen) January 31, 2021
Researchers in Malta describe the results of sequencing local SARS-CoV-2 genomes using the ARTIC protocol, assigning them to the B1 lineage.
Introducing CoVariants.org — a one-stop location to track SARS-CoV-2 mutations & variants that scientists are keeping an eye on.
🎉The new and improved https://t.co/wVE7ucgcg6 is here! 🎉— Dr Emma Hodcroft (@firefoxx66) January 28, 2021
We're hoping to make this a one-stop location to track not only the 'headline' variants, but many different #SARSCoV2 mutations & variants that scientists are keeping an eye on.
Let's take a tour of the site!
CADDE teams in Brazil share their sample preparation workflow for SARS-CoV-2 sequencing on GridION
Check out @drajaquegoes @_severomari @IngraClaro @flah_salles @candido_darlan preparing @nanopore libraries for real-time sequencing of SARS-CoV-2 @caddeProject🧬🦠— CADDE Project (@CaddeProject) January 22, 2021
And don't forget to read the @WHO guidelines on SARS-CoV-2 genomic sequencing:
▶️ https://t.co/4BlCepFp6H pic.twitter.com/S4e3AH20qz
Teams from the University of Amsterdam publish vaccine development research for a two-component spike nanoparticle vaccine, where rapid SARS-CoV-2 sequencing is used to assess the potential emergence of viral escape variants in vaccinated versus control subjects.
The database GISAID now includes more than 80,000 SARS-CoV-2 genomes for which nanopore sequencing has been used, from more than 70 countries.
Nuno Faria and the CADDE team publish a report on a new emerging SARS-CoV-2 lineage, P.1, in Manaus, an area with previously high COVID infections in Brazil.
Teams in Ecuador report finding the first case of the B117 lineage of SARS-CoV-2.
.@INSPI_ECUADOR después de confirmar la presencia de la nueva variante Británica de #SARSCoV2 en el país, continúa trabajando articuladamente con @Salud_Ec en la Secuenciación Genómica de muestras de personas que se encuentran en el cerco epidemiológico levantado por el MSP pic.twitter.com/Agn1wRdlWg— INSPI ECUADOR (@INSPI_ECUADOR) January 12, 2021
World Health Organisation report provides detailed recommendations on implementation of systems to use sequence data of SARS-CoV-2 for maximum impact on human health.
Researchers in Mindanao in the Philippines are starting their SARS-CoV-2 sequencing journey after a collaboration with AccessibleGenomics.org
It has finally arrived here in PGC MINDANAO!🤩— Philippine Genome Center Mindanao (@pgcmindanao) January 6, 2021
The portable genetic sequencer from Oxford Nanopore Technologies for the FIRST EVER on-site SEQUENCING of SARS-CoV-2 in Mindanao! 🧬
In partnership with https://t.co/HhHChBL3Fp and through funding from Just One Giant Lab#SARSCOV2 pic.twitter.com/jKlLR4mQ8L
3rd January, 2021
Teams in the Caribbean countries of Trinidad & Tobago and Jamaica have been collaborating on local rapid sequencing of SARS-CoV-2, and recently confirmed the presence of the B117 lineage in Jamaica
Our project @IMPACT_UWI established local capacity for @nanopore sequencing to enhance Caribbean public health efforts against COVID-19. Less than 2 wks after generating our 1st sequences, we responded to the call from @CARPHA1 and confirmed B.1.1.7 in Jamaica. Well done team!— Christine Carrington (@CVFCarrington) January 3, 2021
Teams in Wyoming describe the establishment of 'near real time genomic epidemiology' with <24 hour turnaround from positive sample to sequence; this service will be used to understand the emergence of new lineages
First few SARS-CoV-2 whole genome sequencing runs off the @ClearLabsInc @nanopore platform these past few days. This now brings near-real-time sequencing (on epidemiology request) to Wyoming #covid19seq #covid. From testing positive to having WGS, 24 hours. #lookingforB117— Noah Hull, PhD, MPH (@NoahHull_PhD) January 2, 2021
31 December 2020
The CADDE project in Brazil reports the first identification of the B117 lineage of SARS-CoV-2, in two samples that tested positive less than 36 hours beforehand. One case has no history of travel outside Brazil; the authors recommend increasing genomic surveillance of the virus to understand the extent of community transmission of the lineage. Read the report here.
Teams at McGill University, L'Institut national de santé publique du Québec and Canadian Centre for Computational Genomics (C3G) confirm a suspected case of the B117 lineage in Quebec.
Using nanopore sequencing, our team, in collaboration with @mcgillgenome & @inspq were able to confirm the B.1.1.7 lineage for 1 suspected case in Quebec. We are continuing to work hard with public health authorities the tools they require to shape policy and help us stay safe. https://t.co/B0mF3GWHDm— C3G (@C3Genomics) December 29, 2020
Teams in Uganda release a report of the genomic characteristics of the country's COVID-19 infections.
New SARS-CoV-2 sequences from Uganda now in @GISAID Big effort from many including: @BugembeLule @MRC_Uganda @cphluganda @UVRIug. Support from @wellcometrust @The_MRC @nanopore and others. Short Report in @virological_org https://t.co/iCVxtaSBEQ pic.twitter.com/vZddPekrbg— Matthew Cotten (@mlcotten13) December 29, 2020
So proud of the @aauengineering team! Skipping holidays and rocking 3738 SARS-CoV-2 samples in 3 days! Finishing a 13-hour day with 22 @nanopore flowcells with 1958 samples! Providing @SSI_dk and the DK government with a real-time overview of B.1.1.7 in Denmark! pic.twitter.com/jIMbr8wDc6— Mads Albertsen (@MadsAlbertsen85) December 23, 2020
The COG-UK network posts a comprehensive article on the new B117 variant of SARS-CoV-2
The WSJ reports on the use of nanopore sequencing to rapidly understand a COVID-19 outbreak within the Baltimore Ravens.
Using 157 SARS-CoV-2 positive samples and synthetic RNA controls, researchers in Australia reported that, using nanopore sequencing, '…highly accurate consensus-level sequence determination was achieved, with single nucleotide variants (SNVs) detected at >99% sensitivity and >99% precision…'. Read more
Our article on the accuracy of @nanopore sequencing for SARS-CoV-2 genomics is out now (spoiler alert: it's very accurate). Great effort from @thiruni1 @jil_hammond @Psy_Fer_ @Row_Bull and many others :) https://t.co/eeZkKUr5u8— Genomic Technologies Group (@GenTechGp) December 9, 2020
A preprint from teams led by Guy's and St Thomas's Hospital, London, describes the use of nanopore metagenomic sequencing to rapidly characterise co-infections in ICU patients with COVID-19, including drug resistance of bacterial infections.
Over 2,500 delegates joined leading scientists from around the world to hear the latest research presented at the Nanopore Community Meeting 2020 online. A number of talks covered the extensive use of nanopore technology for genomic epidemiology of COVID-19, including:Áine O'Toole: SARS-CoV-2 outbreak investigation: from sample to response in a day
Kahili Corazo's talk at the Nanopore Community Meeting outlines Project Accessible Genomics; watch for an overview of genomic epidemiology in a low resource setting in the Philippines
View all talks
Nanopore sequencing using the ARTIC protocol was performed on SARS-CoV-2 samples from 22 individuals enrolled in a clinical trial in India, investigating the potential benefits of convalescent plasma therapy (CPT). All individuals were shown to be infected with SARS-CoV-2 clade 20A. Results of the wider study revealed significant benefits of CPT in individuals under the age of 67 with acute respiratory distress syndrome (ARDS). Read more
Researchers in the US utilised metagenomic nanopore sequencing to study the microbiome and potential co-infections in 50 individuals with suspected COVID-19. Possible bacterial or viral co-infections were observed for 12.5% of SARS-CoV-2 positive sample. In addition, a decrease in microbial diversity was found among COVID-19 confirmed individuals. The researchers commented: ‘This work illustrates the utility of mNGS for the detection of SARS-CoV-2, for diagnosing co-infections without viral target enrichment or amplification, and for the analysis of the respiratory microbiome.’ Read more
A study from the Quadram Institute, UK notes that large scale sequencing of the virus can allow detailed epidemiology and enable local outbreak management, including insights from food samples. Read more
Paper describing our coronavirus sequencing work. More genomes sequenced @QIB than most countries in the world! Data used to understand outbreaks in factories and care homes in the region with help from @PHE_uk, Test and Trace and @NNUH. Huge team effort. https://t.co/nxy3K6NA5K— justin ogrady (@Justin_OGrady) October 1, 2020
New SARS-CoV-2 genome personal-best by the lab-team @aauengineering. Running 17 (!) @nanopore MinIONs in parallel (1000+ samples). The bioinformatic-team looks a little scared of the volume of data influx... Great work by @SSI_dk and DK hospitals to keep sample-flow up! pic.twitter.com/LAUnvv81la— Mads Albertsen (@MadsAlbertsen85) November 18, 2020
Research has shown that SARS-CoV-2 can infect a variety of animals (e.g. non-human primates, cats, ferrets, hamsters). Published in Science, this paper presents an in-depth analysis of 16 SARS-CoV-2 outbreaks in mink farms in the Netherlands. Results indicated that the virus was introduced from humans to mink and subsequently evolved. Sixty eight percent of tested mink farm residents and employees had evidence of SARS-CoV-2 infection. In addition, some individuals were infected with strains with an animal sequence signature, providing evidence of animal-to-human transmission. Read more
Following previous studies showing enhanced fitness of SARS-CoV-2 exibiting the D614G spike (S) protein variant, this new study provides similar findings for the N439K variant in the S protein receptor binding motif (RBM). Furthermore, the researchers observed that the N439K mutation resulted in immune escape from a panel of neutralizing monoclonal antibodies, ‘highlighting the need for ongoing molecular surveillance to guide development and usage of vaccines and therapeutics’. Nanopore sequencing supported the phylogenetic analysis, revealing the N439K variant to have arisen independently multiple times and twice forming significant lineages. Read more
We passed a sad milestone of sequencing 10.000 SARS-CoV-2 positive samples in DK and are currently sequencing 1000+ pr. week to track how the pandemic unfolds in DK. You can dive into the danish data here https://t.co/0gnHfXRoDH and soon on GISAID again @aauengineering @SSI_dk— Mads Albertsen (@MadsAlbertsen85) November 2, 2020
Nanopore sequencing used to support study confirming enhanced fitness of the SARS-CoV-2 D614G substitution in the spike (S) protein. This substitution, which occurred early in the COVID-19 pandemic, rapidly became the dominant variant. This pre-print reveals how the D614G variant confers enhanced binding to the human ACE2 receptor (facilitating virus internalisation), increased replication in respiratory cells, and increased transmissibility – providing an explanation for its global predominance. Read more
Researchers in The Gambia published data for the first SARS-CoV-2 cases in the country. Phylogenetic analysis revealed three strains of European origin (UK and Spain) and two strains of Asian origin (Japan). Both nanopore sequencing and traditional short-read sequencing technologies were used in combination with the ARTIC protocol, providing results in 20 hours and 3 days after sample receipt, respectively. According to the researchers, ‘The nanopore platform with its flexibility for number of samples per run, and the generation of data in real-time and at a reasonable cost makes it most suitable for outbreaks’. Furthermore, long nanopore sequencing reads ‘…can help with the understanding of the linkage between SNPs within individual virions’. Read more
Although single nucleotide polymorphisms and point mutations occur during the replication of coronaviruses, one of the biggest drivers in genetic change is recombination. In this study, researchers utilised long nanopore sequencing reads to identify deletions in a number of SARS-CoV-2 genomes from clinical research samples. The researchers argue that the facility of long reads to identify recombination events is an essential requirement for genomic epidemiology, supporting potential contract tracing, assessing the suitability of diagnostic assays, and providing confidence in vaccine efficacy. Read more
Washington post article outlines how the insights provided by genomic epidemiology, including through the application of nanopore sequencing, are informing public health and policy response to COVID-19.
Great to see our work on rapid sequencing of SARS-CoV-2 to investigate healthcare-associated #COVID @CUH_NHS featured in the @washingtonpost today @Cambridge_Uni @Cambridge_COGUK @CovidGenomicsUK https://t.co/7siCByKPZz— estee (@EsteeTorok) October 13, 2020
Co-infection with SARS-CoV-2 and another respiratory virus is a global health concern. In this study, nanopore sequencing was used to analyse differential gene expression between mice infected with either SARS-CoV-2, influenza A virus, or both. In the case of co-infections, the mice exhibited downregulation of several genes specific to airway epithelial cells, likely indicating increased lung epithelial cell damage. Interestingly, co-infection also resulted in significantly lower levels of SARS-CoV-2 viral RNA at day 6, indicating that IAV interferes with the SARS-CoV-2 infection at this timepoint. Read more
The LamPORE assay is now CE marked for in vitro diagnostic use for the detection of the SARS-CoV-2 virus, using the GridION device. Read more
Researchers in Kenya utilised nanopore technology to generate 274 SARS-CoV-2 genomes from samples collected early in the Kenyan pandemic. Phylogenetic analysis identified 8 global lineages and at least 76 independent introductions into the country. The team concluded that border screening and early surveillance efforts, combined with contact tracing and quarantining of identified cases, successfully prevented the majority of potential introductions. Read more
Independent evaluation study demonstrates that LamPORE provides equivalent accuracy to current gold-standard SARS-CoV-2 tests, paving the way for regulatory approval of the assay. Read more
The genomic surveillance of S and N proteins during the SARS-CoV-2 pandemic can be useful for developing vaccines, therapeutics, and diagnostic tests. In this study, researchers analysed the genomes of 43 South American SARS-CoV-2 virus samples, revealing that genomes with conserved position D614 were almost completely replaced by genomes with the G614 substitution between March to April 2020. Read more
SARS-CoV-2 outbreaks associated with 16 mink farms in the Netherlands were investigated using nanopore sequencing. Results indicate that the virus was introduced to mink from humans and has since evolved. Subsequent transmission from mink to humans was identified, with 68% of tested farm workers and/or their contacts shown to be infected. 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 — further supporting ongoing population-scale sequencing. Read more
First SARS-CoV-2 genomes from Botswana being sequenced on MinION.
Nanopore sequencing supports study of 210 SARS-CoV-2 samples from the state of Telangana, India. The dominant sample clade was identified as 10B; however, mutational analysis revealed genomic variants unique to the Telangana samples. The authors suggest the data will support informed public health decisions and knowledge on host immune evasion, with implications in vaccine development. Read more
Kai-Wang To et al used MinION with ARTIC whole genome sequencing methodology to perform rapid whole genome sequencing of samples collected during two episodes of COVID-19 in a patient — the first resulting in hospitalisation and the second asymptomatic, identified through routine travel screening. The data suggest that the second episode was caused by re-infection as opposed to persistent viral shedding. Read more
Nanopore sequencing technology was used to support the generation of 649 SARS-CoV-2 genome sequences from New Zealand. Despite its remoteness, the viruses imported into New Zealand represented nearly all of the genomic diversity sequenced from the global virus population. The data also helped to quantify the effectiveness of public health interventions, which, for the largest cluster, were shown to reduce the reproductive number from 7 to 0.2 within the first week of lockdown. According to the authors ‘these results demonstrate the utility of genomic pathogen surveillance to inform public health and disease mitigation’. Read more
Oxford Nanopore share preprint describing the LamPORE method for rapid, accurate, and highly scalable molecular screening for SARS-CoV-2 infection. Read the paper
We’re delighted to share this preprint describing the LamPORE method. The @nanopore team and external collaborators have been pushing innovation to the max these last few months developing LamPORE — a new assay for detection of #SARSCoV2. https://t.co/hlWHT1M3kg [1/2] pic.twitter.com/CsWf99wEni— Oxford Nanopore (@nanopore) August 11, 2020
The SARS-CoV-2 S glycoprotein is a leading vaccine targeted. In this study, researchers identified a 24-nucleotide deletion in over half of SARS-CoV-2 spike (S) glycoprotein transcripts from cultured cells. These findings emphasise the importance of monitoring viral genome sequence during the growth of viral stocks. Read more
Science publication describes the use of nanopore technology in conjunction with the ARTIC whole genome sequencing methodology to analyse 427 Brazilian SARS-CoV-2 genomes. The results indicated over 100 international introductions of the pathogen. The virus was shown to be well-established prior to the implementation of travel bans and non-pharmaceutical interventions, suggesting more rigorous measures may be required to further control virus spread. Read more
A team of scientists from @UniofOxford, @FMUSPoficial and more has determined the transmission rates and out-of-country origins of predominant #SARSCoV2 strains in #Brazil. Current interventions remain insufficient to control transmission there, they say: https://t.co/AysIrtVc3R pic.twitter.com/W4LBJckXeS— Science Magazine (@ScienceMagazine) July 23, 2020
Using direct RNA sequencing on the MinION, researchers in Germany demonstrated consistent RNA modification patterns across three SARS-CoV-2 isolates. These results suggest that base modifications may represent a possible target for drug interventions. Read the pre-print.
Direct RNAseq of SARS-CoV-2 with @nanopore in human lung epithelial cells with 3 replicates. Consistent RNA modification patterns of SARS-CoV-2 that are conserved during progression of the current pandemic. Preprint: https://t.co/gRVEP2Gibv— Milad Miladi (@MiladMiladi_) July 21, 2020
In a publication in the Lancet, researchers in Cambridge, UK, implemented a rapid nanopore sequencing workflow to investigate suspected healthcare-associated COVID-19 cases. The assay, which delivered sample-to-sequence in under 12 hours, was applied to 1,000 samples collected from hospitals across the East of England. The results allowed identification of hospital-acquired transmission and substantial transmission in healthcare-associated community settings — supporting the implementation of enhanced infection control measures. Read more
Nanopore sequencing used for first report into genetic diversity of Moroccan SARS-CoV-2 isolates. Sixty-one mutations were observed in the samples compared with the reference sample. Phylogenetic analysis revealed multiple introductions with no specific strain currently dominating. Read more
MedRiv pre-print describes use of ARTIC nanopore sequencing protocol to identify a SNP in SARS-CoV-2 genome that negatively impacts qRT-PCR testing. Analysis of GISAID data reveals same mutation has arisen independently multiple times.
Researchers use nanopore technology in conjunction with the ARTIC whole genome sequencing methodology to analyse 427 Brazilian SARS-CoV-2 genomes. The results indicated over 100 international introductions of the pathogen. The virus was shown to be well-established prior to the implementation of travel bans and non-pharmaceutical interventions, suggesting more rigorous measures may be required to further control virus spread. Read more
Nanopore sequencing used to investigate genetic diversity of SARS-CoV-2 in Brazil. Phylogenetic analysis revealed the multiple introductions and the existence of a major SARS-CoV-2 B1.1 lineage associated with widespread community transmission. Read more
At 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.
G42 announce population-scale LamPORE SARS-CoV-2 testing workflow in UAE — capable of processing hundreds of thousands of samples daily.
Twenty Ugandan SARS-CoV-2 genomes generated using nanopore sequencing added to GISAID.
Researchers @MRC_Uganda @UVRIug, @MinofHealthUG & partners have generated the first SARS-CoV-2 full genomes using Nanopore sequencing.— MRC Uganda (@MRC_Uganda) June 5, 2020
Data from twenty viral genomes are now available in @GISAID https://t.co/g9SymNSKTs
#COVID19 @The_MRC @LSHTM @DFID_UK @mlcotten13 pic.twitter.com/ummzknAlvA
Over 100 Kenyan SARS-CoV-2 genomes are now available on GISAID. Results reveal that early cases came from multiple introductions to the country from Europe and Asia.
We show that early SARS-CoV-2 cases came frm multiple importations into the country from Europe and Asia. Our current WGS data provides evidence for multiple (~10) circulating 'dynamic' lineages in Kenya. https://t.co/QP6OglOizO #KomeshaCorona #COVID19KE— George Githinji (@george_l) June 2, 2020
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
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