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LooK SPOT Antigen Rapid Test System Resource Report Resource Website |
Diego Lai | DOI:10.17504/protocols.io.bp32mqqe | Coronavirus Method Development Community, XPRIZE Rapid Covid Testing | LooK SPOT COVID-19 antigen rapid test is a lateral flow immunoassay intended for the qualitative detection of nucleocapsid protein antigen from SARS-CoV-2 in nasal swabs from patients suspected of COVID-19 within the first seven (7) days of symptom onset. Testing is limited to laboratories certified under the Clinical Laboratory Improvement Amendments of 1988 (CLIA), 42 U.S.C. §263a, that meet the requirements to perform moderate complexity tests. This test is authorized for use at the Point of Care (POC), i.e., in a patient care settings operating under a CLIA Certificate of Waiver, Certificate of Compliance, or Certificate of Accreditation.].Results are for the identification of SARS-CoV-2 nucleocapsid protein antigen. The antigen is generally detectable in nasal samples during the acute phase of infection. Positive results indicate the presence of viral antigens, but the clinical correlation with patient history and other diagnostic information is necessary to determine infection status. Positive results do not rule out a bacterial infection or co-infection with other viruses. The agent detected may not be the definite cause of thedisease. Laboratories within the United States and its territories are required to report all positive results to the appropriate public health authorities.Negative results should be treated as presumptive, and do not rule out SARS-CoV-2 infection, and should not be used as the sole basis for treatment or patient management decisions, including infection control decisions. Negative results should be considered in the context of a patient's recent exposures, history, and the presence of clinical signs and symptoms consistent with COVID-19, and confirmed with a molecular assay, if necessary, for patient management. LooK SPOT COVID-19 Antigen Rapid Test can deliver a diagnosis of the SARS-CoV-2 virus detection between 5 to 8 minutes by using machine learning AI. LooK SPOT’s AI algorithm has high accuracy and can identify the fluorescence response when human eyes cannot identify the low positive cases. Healthcare responders in the COVID-19 test sites often need to make time-sensitive decisions to determine the test results during the time many patients are within their vicinity. But the tempo, volume, stress, fatigue, lighting, fear, and various other factors can overwhelm healthcare responders when making the visual interpretation of antigen test results. It is of paramount importance to reduce healthcare responders' cognitive load by providing accurate test results in an easy-to-read format. LooK SPOT COVID-19 Antigen Rapid Test is a COVID-19 rapid test solution designed with a tactical edge to fight COVID-19. The LooK SPOT COVID-19 Antigen Rapid Test is intended for use at the Point of Care (POC) settings by trained personnel specifically instructed and trained in vitro diagnostic procedures. It is only for use under the Food and Drug Administration's Emergency Use Authorization. | Laipac Technology Inc. | https://laipac.com/look-spot-point-of-care-covid-19-test-kit/ | 2 | 2020 | Diego Lai 2020. LooK SPOT Antigen Rapid Test System. protocols.io https://dx.doi.org/10.17504/protocols.io.bp32mqqe | 2021-04-15 09:16:56 | ||
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SARS-CoV-2 Genome Sequencing Using Long Pooled Amplicons on Illumina Platforms Resource Report Resource Website |
John-Sebastian Eden, Eby Sim | DOI:10.17504/protocols.io.befyjbpw | Coronavirus Method Development Community | This protocol describes methods to sequence SARS-CoV-2 with pooled amplicons (14 x 2.5kb) using Illumina Platforms. | Westmead Institute for Medical Research; University of Sydney, University of Sydney; Centre for Infectious Diseases and Microbiology - Public Health; NSW Health Pathology - ICPMR | 1 | 2020 | John-Sebastian Eden, Eby Sim 2020. SARS-CoV-2 Genome Sequencing Using Long Pooled Amplicons on Illumina Platforms. protocols.io https://dx.doi.org/10.17504/protocols.io.befyjbpw | 2021-04-15 09:16:28 | |||
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Protocol for capture and concentration of viruses from wastewater samples (up to 50 mL) using Magnetic Nanotrap® particles. Resource Report Resource Website |
Anurag Patnaik, Ben Lepene, Alex Barclay | Coronavirus Method Development Community, 2019-nCoV Wastewater Epidemiology, Nanotrap Applications | Ceres Nanosciences, inc., Ceres Nanosciences, inc., Ceres Nanosciences, inc. | 1 | 2020 | Anurag Patnaik, Ben Lepene, Alex Barclay 2020. Protocol for capture and concentration of viruses from wastewater samples (up to 50 mL) using Magnetic Nanotrap® particles.. protocols.io https:// | 2021-04-15 09:16:35 | |||||
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Extraction of RNA from Wastewater Primary Solids Using a Direct Extraction Method for Downstream SARS-CoV-2 RNA Quantification Resource Report Resource Website |
Stephanie Loeb, Katy Graham, Marlene Wolfe, Krista Wigginton, Alexandria Boehm | DOI:10.17504/protocols.io.bi6skhee | Coronavirus Method Development Community, Wastewater-based epidemiology working group | OverviewThis SOP describes pre-analytical procedures to be followed for the isolation and identification of SARS-CoV-2 RNA in primary settled solids samples from wastewater treatment plants. This protocal should be paired with our digital PCR protocal. The protocol follows the approximate workflow:Separate and aliquot sample (~4 hrs)Spike with BCoV (~1 hr)Extract RNA (~ 12 hours total, may be split into 2-3 steps/days)Inhibitor removal (~1 hr)Biosafety ConcernsConcentration and extraction procedures that utilize raw samples must adhere to strict Biosafety Level 2+ procedures. These procedures should be performed in a dedicated room. Downstream products may be handled using standard laboratory safety guidelines. This protocol was developed by Stephanie Loeb, Katy Graham, Marlene Wolfe, Krista Wigginton, and Alexandria Boehm at Stanford University and University of Michigan. | Stanford University, Stanford University, Stanford University, University of Michigan, Stanford University | 1 | 2020 | Stephanie Loeb, Katy Graham, Marlene Wolfe, Krista Wigginton, Alexandria Boehm 2020. Extraction of RNA from Wastewater Primary Solids Using a Direct Extraction Method for Downstream SARS-CoV-2 RNA Quantification. protocols.io https://dx.doi.org/10.17504/protocols.io.bi6skhee | 2021-04-15 09:16:32 | |||
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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RdRp nested RT-PCR Resource Report Resource Website |
Judy Northill, Ian Mackay | DOI:10.17504/protocols.io.bgz2jx8e | Public Health Virology, Forensic and Scientific Services, Coronavirus Method Development Community | A nested RT-PCR targeting the RdRp region of the sub-genus Sarbecovirus. The primers are modified from the pan-coronavirus RT-PCR published by Hu et al. 2017 to be more specific to SARS-CoV-2, though other coronaviruses may still be detected. Assay may be used in resource poor settings where real-time cyclers are not available.Sanger sequencing should be used to confirm SARS-CoV-2 where WGS is not available or where WGS fails due to poor quality sample. | Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services | 3 | 2020 | Judy Northill, Ian Mackay 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RdRp nested RT-PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.bgz2jx8e | 2021-04-15 09:16:57 | |||
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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR E gene 2020 Resource Report Resource Website |
Judy Northill, Ian Mackay | DOI:10.17504/protocols.io.bcv9iw96 | Public Health Virology, Forensic and Scientific Services, Coronavirus Method Development Community | A real-time RT-PCR designed to amplify a portion of the envelope gene of sequences from the Betacoronavirus sub-genus Sarbecovirus.The probe and primers were published by Corman et al., and we have slightly modified the protocol, increasing the concentration of the reverse primer, using a different kit and different cycling conditions.This test has identified clinical positive cases of coronavirus disease 2019 (COVID-19). | Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services | 1 | 2020 | Judy Northill, Ian Mackay 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR E gene 2020. protocols.io https://dx.doi.org/10.17504/protocols.io.bcv9iw96 | 2021-04-15 09:16:40 | |||
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Pillowcase & rubber band DIY face mask Resource Report Resource Website |
Jernej Turnsek | DOI:10.17504/protocols.io.bemjjc4n | Coronavirus Method Development Community | Wearing a face mask helps stop the spread of the new coronavirus. This protocol describes a very simple way to make one at home using a cotton pillowcase, 2 rubber bands, and a minute of your time. | University of California, Berkeley | https://www.cdc.gov/coronavirus/2019-ncov/prevent-getting-sick/diy-cloth-face-coverings.html | 1 | 2020 | Jernej Turnsek 2020. Pillowcase & rubber band DIY face mask. protocols.io https://dx.doi.org/10.17504/protocols.io.bemjjc4n | 2021-04-15 09:16:40 | ||
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SUPER rapid kit Resource Report Resource Website |
Hyeon Jin Kim, Seong T. Hong | DOI:10.17504/protocols.io.bkqvkvw6 | Coronavirus Method Development Community, XPRIZE Rapid Covid Testing | We developed a supersensitive capillary reaction kit intended for the direct and qualitative detection of SARS-CoV-2 virus in saliva and nasal swabs. It enables sensitive and specific detection of the SARS-CoV-2 spike antigens in respiratory specimens more accurately than most PCR method within 5 minutes. Our rapid capillary kit will help not only fight but also end COVID-19 by providing the first sensitive self-diagnosis at home as well as POC clinical diagnosis at the health care facilities. | SNJ Pharma Inc, Jeonbuk National University | 1 | 2020 | Hyeon Jin Kim, Seong T. Hong 2020. SUPER rapid kit. protocols.io https://dx.doi.org/10.17504/protocols.io.bkqvkvw6 | 2021-04-15 09:16:45 | |||
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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR N gene 2020 (Wuhan-N; 2019-nCoV-related test) -NOT RECOMMENDED Resource Report Resource Website |
Judy Northill, Ian Mackay | DOI:10.17504/protocols.io.bchwit7e | protocols.io Ambassadors, Public Health Virology, Forensic and Scientific Services, Coronavirus Method Development Community | NOT RECOMMENDED FOR SCREENINGThe sensitivity of the assay has been found to be lower than expected and we no longer recommend it be used.We do recommend the ORF1ab assay (Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR ORF1ab 2020) or the E gene assay by Corman et al. (Protocol v2-1)A real-time RT-PCR to designed to detect SARS-CoV-2 and other related sarbecoviruses. Based on sequence MN908947 made available by Professor Yong-Zhen Zhang, Fudan University, Shanghai, China. The target region encodes the nucleocapsid (N).Not tested on wild-type virus (as of 25Jan2020), it is expected to be capable of detecting Wuhan virus, bat-like SARS and SARS virus (members of the subgenus Sarbecovirus).Limit of detection not yet determined.A single 1 mismatch at probe-binding site identified with the BetaCoV/USA/CA1/2020|EPI_ISL_406034 variant of SARS-CoV-2 (as of 29JAN2020).Probe is in the 3'-5' (reverse complement) direction.A real-time RT-PCR to designed to detect SARS-CoV-2 and other related sarbecoviruses. Based on sequence MN908947 made available by Professor Yong-Zhen Zhang, Fudan University, Shanghai, China. The target region encodes the nucleocapsid (N).Not tested on wild-type virus (as of 25Jan2020), it is expected to be capable of detecting Wuhan virus, bat-like SARS and SARS virus (members of the subgenus Sarbecovirus).Limit of detection not yet determined.A single 1 mismatch at probe-binding site identified with the BetaCoV/USA/CA1/2020|EPI_ISL_406034 variant of SARS-CoV-2 (as of 29JAN2020).Probe is in the 3'-5' (reverse complement) direction.Notes: Assay is optimised (as of 24Jan2020).This test has identified a clinical positive case of coronavirus disease (COVID-19) | Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services | 4 | 2020 | Judy Northill, Ian Mackay 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR N gene 2020 (Wuhan-N; 2019-nCoV-related test) -NOT RECOMMENDED. protocols.io https://dx.doi.org/10.17504/protocols.io.bchwit7e | 2021-04-15 09:16:46 | |||
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RTPCR Amplification of SARS-CoV2 Whole Genome for Illumina NGS Resource Report Resource Website |
Monica Galiano, Shahjahan Miah, Angie Lackenby, Omolola Akinbami, Joanna Ellis, Maria Zambon | DOI:10.17504/protocols.io.bew8jfhw | Coronavirus Method Development Community | SUMMARYThis document describes the procedure for performing RTPCR amplification for next-generation sequencing (NGS) of whole genomes from SARS-CoV2 positive clinical samples. This methodology was employed at the Respiratory Virus Unit, Microbiology Services Colindale, Public Health England (RVU-PHE) to sequence the first SARS-CoV2 positive samples.Reverse transcription (RT) is performed using random hexamer primers. PCR amplification is done using sequence-specific primers which amplify two sets of 30-31 overlapping amplicons (size 1.0 to 1.8 kb), each set independently covering the entire length of the MERS-CoV genome. Once amplicons are obtained, rough equimolar mixtures, clean-up, DNA quantitation and final dilutions are performed to prepare samples for library preparation for Illumina MiSeq next-generation sequencing (NGS). Primers from set A do not overlap location of primers from set B, except for those binding at the end of the genome (see figure 1). Amplicon mixtures from each set are treated as separate samples throughout the procedure, including assembly. Merging (or comparison) of consensus sequences of both sets is performed at the end. IMPORTANT: Please note that every amplicon is obtained in a separate PCR reaction and, if using both primer sets, there is a total of ~61 PCR reactions; this protocol is NOT a multiplex approach. We recommend using a 96-well plate per sample.ADVANTAGES AND LIMITATIONSThe use of both primer sets allows for redundancy in whole genome (WG) coverage, which increases the chances of obtaining full genome sequences when samples have low viral load. Although we haven’t formally determined the sensitivity of this assay (or limit of amplification of WG), we have obtained full coverage with samples with CT values of up to 38 (CT value obtained at RVU-PHE with RdRp gene detection within the SARS-CoV2 detection protocol as described by Corman et al. [1]). Variation in storage or transport conditions of samples may affect the integrity of viral nucleic acids.Another advantage of this protocol is that, as primers from set A and B match different locations on the genome, direct comparison of the sequences obtained with each set allows for curation of primer-induced contamination of the sequences, although we deal with this with a specific step on the bioinformatic assembly pipeline (not described here).Alternatively, when samples have a relatively good CT (The main limitation of this protocol is its unsuitability for high throughput processing of large batches of samples, although current efforts are being made to adapt the primers to a multiplex approach. | WHO Influenza Collaborating Centre, The Francis Crick Institute, Respiratory Virus Unit, Microbiology Services Colindale, Public Health England, Respiratory Virus Unit, Microbiology Services Colindale, Public Health England, Respiratory Virus Unit, Microbiology Services Colindale, Public Health England, Respiratory Virus Unit, Microbiology Services Colindale, Public Health England, Respiratory Virus Unit, Microbiology Services Colindale, Public Health England | 1 | 2020 | Monica Galiano, Shahjahan Miah, Angie Lackenby, Omolola Akinbami, Joanna Ellis, Maria Zambon 2020. RTPCR Amplification of SARS-CoV2 Whole Genome for Illumina NGS . protocols.io https://dx.doi.org/10.17504/protocols.io.bew8jfhw | 2021-04-15 09:16:44 | |||
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Sample Informed Consent Form Template (Appendix C of Phase 3 study of Vaccine Candidate for COVID-19) Resource Report Resource Website |
Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores | DOI:10.17504/protocols.io.bj6dkra6 | Coronavirus Method Development Community, PATH | This is Appendix C of "Phase 3 randomized, double-blinded, placebo-controlled trial to evaluate the safety, immunogenicity, and efficacy of Vaccine Candidate against COVID-19 in adults > 18 years of age"This generic Phase 3 protocol was developed by the PATH team with support of the Bill and Melinda Gates Foundation. The aim of the collection is to share recommended best practices in designing and implementing a Phase 3 study of a COVID-19 vaccine candidate. As Phase 3 trials of different Vaccine Candidates proceed around the world, following the same protocols will ensure consistency and comparability of the Phase 3 trial results.Please note that this is an evolving document, to be versioned and updated, based on community feedback and new data. | Center for Vaccine Innovation and Access, PATH (Washington D.C. and Seattle, Washington), Center for Vaccine Innovation and Access, PATH (Washington D.C. and Seattle, Washington), Center for Vaccine Innovation and Access, PATH (Washington D.C. and Seattle, Washington), Center for Vaccine Innovation and Access, PATH (Washington D.C. and Seattle, Washington) | 1 | 2020 | Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores 2020. Sample Informed Consent Form Template (Appendix C of Phase 3 study of Vaccine Candidate for COVID-19). protocols.io https://dx.doi.org/10.17504/protocols.io.bj6dkra6 | 2021-04-15 09:17:02 | |||
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COVID-19 ARTIC v3 Illumina library construction and sequencing protocol - high throughput 384 format Resource Report Resource Website |
DNA Pipelines R&D, Benjamin Farr, Diana Rajan, Emma Betteridge, Lesley Shirley, Michael Quail, Naomi Park, Nicholas Redshaw, Iraad Bronner, Louise Aigrain, Scott Goodwin, Scott Thurston, Stefanie Lensing, Carol Scott, Nicholas Salmon, Charlotte Beaver, Rachel Nelson, Alex Alderton, Ian Johnston | DOI:10.17504/protocols.io.biefkbbn | Coronavirus Method Development Community, COG-UK | This SOP describes the procedure for generating cDNA from SARS-CoV-2 viral nucleic acid extracts and subsequently producing 400nt amplicons tiling the viral genome using V3 nCov-2019 primers (ARTIC). This is followed by library construction, equivolume pooling of samples and quantitation, prior to sequencing on the Illumina NovaSeq. It offers the benefit of higher density sample processing in 384 format, whilst matching the data quality achieved in 96 format described in the original protocol:https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bgxjjxknBoth the above protocols were adapted from the nCov-2019 sequencing protocol: https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w | Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute | 1 | 2020 | DNA Pipelines R&D, Benjamin Farr, Diana Rajan, Emma Betteridge, Lesley Shirley, Michael Quail, Naomi Park, Nicholas Redshaw, Iraad Bronner, Louise Aigrain, Scott Goodwin, Scott Thurston, Stefanie Lensing, Carol Scott, Nicholas Salmon, Charlotte Beaver, Rachel Nelson, Alex Alderton, Ian Johnston 2020. COVID-19 ARTIC v3 Illumina library construction and sequencing protocol - high throughput 384 format. protocols.io https://dx.doi.org/10.17504/protocols.io.biefkbbn | 2021-04-15 09:16:49 | |||
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3D Printing Of Personal Protective Equipment And Repurposing Of Common Household Air Filters Resource Report Resource Website |
Giana Schena, Emma Murray | DOI:10.17504/protocols.io.bd77i9rn | Coronavirus Method Development Community | During the height of the COVID-19 outbreak, personal protective equipment shortages are felt around the world, in spite of the fact that traditional face masks are not even sufficient to fully protect against the 0.125 micron SARS-CoV-2 virus. Medical personnel, more than any other sector, are being hit hardest by this shortage, given their close contact with infected persons. During this time of crisis and shortage, alternative and atypical solutions are necessary to ensure the protection of those who are on the front lines against this disease. One solution is the creation of reusable 3D-printed personal protective equipment (PPE) in conjunction with appropriate disposable filtration.3D-printed face masks are available on a variety of different open source 3D-printing online platforms. Unfortunately, the general public remains largely unaware of these potential solutions and can also be intimidated by the lack of information available regarding how to integrate scientifically appropriate filters. The intention of this white paper is to make available the information needed for simple construction of effective 3D-printed masks. We recommend a 3D printed face mask design made available by CREALITY, a leader in 3D-printing machines. By using CREALITY’s open source designs and easily obtainable air filters, cut to a desired size, we can increase our ability to protect medical workers against this disease. Additionally, CREALITY offers designs for a 3D-printed eye mask that can be used with plexiglass to protect eyes against airborne droplets. In practice, CREALITY’s 3D model object STL files can be uploaded into any available slicer software allowing for creation of specific commands for 3D printers. Within the slicer, face mask and eye mask models can be scaled to small, medium, or large to fit a variety of face sizes. We have also included strap adjustment clip models for use with facemasks and a face shield to extend the life of traditional facemasks.We also propose a plan to coordinate large-scale construction of crowd-sourced 3D printed masks with collection and delivery of said masks to at-risk businesses, in particular hospitals and care facilities. | Temple University, Temple University | 1 | 2020 | Giana Schena, Emma Murray 2020. 3D Printing Of Personal Protective Equipment And Repurposing Of Common Household Air Filters. protocols.io https://dx.doi.org/10.17504/protocols.io.bd77i9rn | 2021-04-15 09:16:56 | |||
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Coronavirus Lateral Flow Assay (LFA) operation protocol v2 Resource Report Resource Website |
peijun he | DOI:10.17504/protocols.io.bqvpmw5n | Coronavirus Method Development Community, XPRIZE Rapid Covid Testing, Highfield Diagnostics | Coronavirus Lateral Flow Assay (LFA) operation protocol | Highfield Diagnostics, UK | 2 | 2020 | peijun he 2020. Coronavirus Lateral Flow Assay (LFA) operation protocol v2. protocols.io https://dx.doi.org/10.17504/protocols.io.bqvpmw5n | 2021-04-15 09:16:57 | |||
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SOP for populating NCBI submission templates for SARS-CoV-2 (BioSample, SRA, and GenBank) Resource Report Resource Website |
Ruth Timme, Emma Griffiths, Duncan MacCannell, Stacia Wyman | DOI:10.17504/protocols.io.bf89jrz6 | GenomeTrakr, Coronavirus Method Development Community, PHA4GE | PURPOSE: Guidance on how to populate the three NCBI metadata submission templates for SARS-CoV-2 submissions, maximizing interoperability for COVID-19 surveillance. | US Food and Drug Administration, University of British Columbia, Centers for Disease Control and Prevention, Innovative Genomics Institute, UC Berkeley | 1 | 2020 | Ruth Timme, Emma Griffiths, Duncan MacCannell, Stacia Wyman 2020. SOP for populating NCBI submission templates for SARS-CoV-2 (BioSample, SRA, and GenBank). protocols.io https://dx.doi.org/10.17504/protocols.io.bf89jrz6 | 2021-04-15 09:16:55 | |||
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Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (AI-LAMP) for Rapid Detection of SARS-CoV-2 Resource Report Resource Website |
Don Cooper | DOI:10.17504/protocols.io.bmp2k5qe | Coronavirus Method Development Community | Neuroganics Diagnostics LLC | https://www.mdpi.com/1999-4915/12/9/972 | 1 | 2020 | Don Cooper 2020. Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (AI-LAMP) for Rapid Detection of SARS-CoV-2. protocols.io https://dx.doi.org/10.17504/protocols.io.bmp2k5qe | 2021-04-15 09:17:04 | |||
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COVID-19 ARTIC v3 Illumina library construction and sequencing protocol Resource Report Resource Website |
DNA Pipelines R&D, Benjamin Farr, Diana Rajan, Emma Betteridge, Lesley Shirley, Michael Quail, Naomi Park, Nicholas Redshaw, Iraad Bronner, Louise Aigrain, Scott Goodwin, Scott Thurston, Stefanie Lensing, James Bonfield, Keith James, Nicholas Salmon, Charlotte Beaver, Rachel Nelson, David K. Jackson, Alex Alderton, Ian Johnston | DOI:10.17504/protocols.io.bibtkann | Coronavirus Method Development Community, COG-UK | This SOP describes the procedure for generating cDNA from SARS-CoV-2 viral nucleic acid extracts and subsequently producing 400nt amplicons tiling the viral genome using V3 nCov-2019 primers (ARTIC). This is followed by library construction, equivolume pooling of samples and quantitation, prior to sequencing on the Illumina NovaSeq. It is adapted from the nCov-2019 sequencing protocol which can be found here: https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w | Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute | 5 | 2020 | DNA Pipelines R&D, Benjamin Farr, Diana Rajan, Emma Betteridge, Lesley Shirley, Michael Quail, Naomi Park, Nicholas Redshaw, Iraad Bronner, Louise Aigrain, Scott Goodwin, Scott Thurston, Stefanie Lensing, James Bonfield, Keith James, Nicholas Salmon, Charlotte Beaver, Rachel Nelson, David K. Jackson, Alex Alderton, Ian Johnston 2020. COVID-19 ARTIC v3 Illumina library construction and sequencing protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bibtkann | 2021-04-15 09:17:01 | |||
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NEBNext® ARTIC SARS-CoV-2 FS Library Prep Kit (Illumina®) E7658 Resource Report Resource Website |
New England Biolabs | DOI:10.17504/protocols.io.bsy5nfy6 | New England Biolabs (NEB), Coronavirus Method Development Community | This protocol details methods for the NEBNext® ARTIC SARS-CoV-2 FS Library Prep Kit (Illumina®), NEB #E7658S/L 24/96 reactions. | New England Biolabs | https://www.neb.com/-/media/nebus/files/manuals/manuale7658.pdf?rev=7253d569aa3040069cb09a9aa3724f2d&hash=53C7EDF0D2FDEDAE75308379A5EB2D89 | 2 | 2021 | New England Biolabs 2021. NEBNext® ARTIC SARS-CoV-2 FS Library Prep Kit (Illumina®) E7658. protocols.io https://dx.doi.org/10.17504/protocols.io.bsy5nfy6 | 2021-04-15 09:17:01 | ||
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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RdRp nested RT-PCR Resource Report Resource Website |
Judy Northill, Ian Mackay | DOI:10.17504/protocols.io.bdcpi2vn | Public Health Virology, Forensic and Scientific Services, Coronavirus Method Development Community | A nested RT-PCR targeting the RdRp region of the sub-genus Sarbecovirus. The primers are modified from the pan-coronavirus RT-PCR published by Hu et al. 2017 to be more specific to SARS-CoV-2.Assay may be used in resource poor settings where real-time cyclers are not available.Sanger sequencing can be used to confirm SARS-CoV-2 where WGS is not available or where WGS fails due to poor quality sample. | Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services | 2 | 2020 | Judy Northill, Ian Mackay 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RdRp nested RT-PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.bdcpi2vn | 2021-04-15 09:17:04 | |||
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TaqMan Genotyping Assay for Detection of B.1.1.7 SARS-CoV-2 Resource Report Resource Website |
isaac.bell , Mark Adams | Coronavirus Method Development Community, JGM CLIA Research and Development | The Jackson Laboratory for Genomic Medicine, The Jackson Laboratory for Genomic Medicine | 1 | 2021 | isaac.bell , Mark Adams 2021. TaqMan Genotyping Assay for Detection of B.1.1.7 SARS-CoV-2. protocols.io https:// | 2021-04-15 09:17:02 |
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