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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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nCoV-2019 McGill Artic PCR Protocol, 5 ul RT and V3 only + LA1 at 63C Resource Report Resource Website |
Sarah Reiling, Josh Quick, Ioannis Ragoussis | DOI:10.17504/protocols.io.bjkrkkv6 | Coronavirus Method Development Community, McGill Genome Centre | V3 only primers can be found here:https://github.com/sarahreiling/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019_V3only.scheme.bed | McGill University, University of Birmingham, McGill University | 1 | 2020 | Sarah Reiling, Josh Quick, Ioannis Ragoussis 2020. nCoV-2019 McGill Artic PCR Protocol, 5 ul RT and V3 only + LA1 at 63C. protocols.io https://dx.doi.org/10.17504/protocols.io.bjkrkkv6 | 2021-04-15 09:15:38 | |||
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Coronavirus Lateral Flow Assay (LFA) sample preparation protocol v2 Resource Report Resource Website |
peijun he | DOI:10.17504/protocols.io.bqvnmw5e | Coronavirus Method Development Community, XPRIZE Rapid Covid Testing, Highfield Diagnostics | Coronavirus Lateral Flow Assay (LFA) sample preparation protocol | Highfield Diagnostics, UK | 2 | 2020 | peijun he 2020. Coronavirus Lateral Flow Assay (LFA) sample preparation protocol v2. protocols.io https://dx.doi.org/10.17504/protocols.io.bqvnmw5e | 2021-04-15 09:15:38 | |||
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RNA Extraction of SARS-CoV-2 from Wastewater Resource Report Resource Website |
Neha Mittal, Vbarua , Nick Stark, Cynthia Gibas, jschluet , Mariya Munir | Coronavirus Method Development Community, UNC Charlotte COVID WBE | UNC Charlotte Department of Bioinformatics and Genomics, UNC Charlotte Department of Civil and Environmental Engineering, UNC Charlotte Department of Bioinformatics and Genomics, UNC Charlotte Department of Bioinformatics and Genomics, UNC Charlotte Department of Bioinformatics and Genomics, UNC Charlotte Department of Civil and Environmental Engineering | 1 | 2021 | Neha Mittal, Vbarua , Nick Stark, Cynthia Gibas, jschluet , Mariya Munir 2021. RNA Extraction of SARS-CoV-2 from Wastewater. protocols.io https:// | 2021-04-15 09:15:14 | |||||
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Amplicon clean-up using SPRI beads for RAPID nanopore kit RBK004 Resource Report Resource Website |
Nikki Freed, Olin Silander | DOI:10.17504/protocols.io.bgsrjwd6 | Coronavirus Method Development Community | Massey University, Massey University | 3 | 2020 | Nikki Freed, Olin Silander 2020. Amplicon clean-up using SPRI beads for RAPID nanopore kit RBK004. protocols.io https://dx.doi.org/10.17504/protocols.io.bgsrjwd6 | 2021-04-15 09:15:14 | ||||
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Starting a MinION sequencing run using MinKNOW Resource Report Resource Website |
Muhammad Faisal, Olin Silander, Nikki Freed | DOI:10.17504/protocols.io.bfwqjpdw | Coronavirus Method Development Community | Massey University, Massey University, Massey University | 1 | 2020 | Muhammad Faisal, Olin Silander, Nikki Freed 2020. Starting a MinION sequencing run using MinKNOW. protocols.io https://dx.doi.org/10.17504/protocols.io.bfwqjpdw | 2021-04-15 09:15:14 | ||||
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Saliva Vapor Tests in a Home Environment for Point-of-care COVID-19 Tests Resource Report Resource Website |
Shadi Emam, nasrollahpourmotla.m , n.sun | DOI:10.17504/protocols.io.bkwrkxd6 | Coronavirus Method Development Community, XPRIZE Rapid Covid Testing | Northeastern University, Northeastern University, Northeastern University | 1 | 2020 | Shadi Emam, nasrollahpourmotla.m , n.sun 2020. Saliva Vapor Tests in a Home Environment for Point-of-care COVID-19 Tests. protocols.io https://dx.doi.org/10.17504/protocols.io.bkwrkxd6 | 2021-04-15 09:15:16 | ||||
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Preliminary Evaluation of RNA Extraction Methods Resource Report Resource Website |
Aniela Wozniak, Catalina Ibarra-Henriquez, Valentina Sebastian, Grace Armijo, Liliana Lamig, Carolina Miranda, Marcela Lagos, Sandra Solari, Ana María Guzmán, Teresa Quiroga, Susan Hitschfeld, Eleodoro Riveras, Marcela Ferres, Rodrigo A. Gutiérrez, Patricia García, Ariel Cerda | Coronavirus Method Development Community, Reclone.org (The Reagent Collaboration Network) | Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de chile, FONDAP Center for Genome Regulation. Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile, Laboratorio de Microbiología. Servicio de laboratorios Clínicos. Red de Salud UC-CHRISTUS, FONDAP Center for Genome Regulation. Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile, FONDAP Center for Genome Regulation. Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile, Laboratorio de Microbiología. Servicio de laboratorios Clínicos. Red de Salud UC-CHRISTUS, Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de chile, Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de chile, Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de chile, Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de chile, FONDAP Center for Genome Regulation. Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile, FONDAP Center for Genome Regulation. Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile, Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de chile, FONDAP Center for Genome Regulation. Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile, Departamento de Laboratorios Clínicos. Escuela de Medicina. Facultad de Medicina. Pontificia Universidad Católica de chile, FONDAP Center for Genome Regulation. Millennium Institute for Integrative Biology (iBio), Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile | https://doi.org/10.1101/2020.05.07.083048 | 1 | 2020 | Aniela Wozniak, Catalina Ibarra-Henriquez, Valentina Sebastian, Grace Armijo, Liliana Lamig, Carolina Miranda, Marcela Lagos, Sandra Solari, Ana María Guzmán, Teresa Quiroga, Susan Hitschfeld, Eleodoro Riveras, Marcela Ferres, Rodrigo A. Gutiérrez, Patricia García, Ariel Cerda 2020. Preliminary Evaluation of RNA Extraction Methods. protocols.io https:// | 2021-04-15 09:15:17 | ||||
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Opentrons COVID-19 testing (RT-qPCR path, Station C, 24+3+1 sample special) Resource Report Resource Website |
Max Marrone | DOI:10.17504/protocols.io.beqajdse | Coronavirus Method Development Community, Opentrons COVID-19 Testing | Opentrons Labworks | 2 | 2020 | Max Marrone 2020. Opentrons COVID-19 testing (RT-qPCR path, Station C, 24+3+1 sample special). protocols.io https://dx.doi.org/10.17504/protocols.io.beqajdse | 2021-04-15 09:15:46 | ||||
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Protocol for Extraction of Viral RNA with added DNase treatment Resource Report Resource Website |
Megan Folkerts, Ashlyn Pfeiffer, mnguyen , Danielle Vazquez, Amber Jones | DOI:10.17504/protocols.io.bnkhmct6 | Coronavirus Method Development Community | This protocol is modified from the MagMAX MVP II protocol from Thermo Fisher, and the MagMAX mirVana protocol from Thermo Fisher. Modifications were necessary to include a DNAse treatment step, which improves viral recovery in low-burden samples. | Translational Genomics Research Institute, Flagstaff AZ, Translational Genomics Research Institute, Flagstaff AZ, Translational Genomics Research Institute, Flagstaff AZ, Translational Genomics Research Institute, Flagstaff AZ, Translational Genomics Research Institute, Flagstaff AZ | 1 | 2020 | Megan Folkerts, Ashlyn Pfeiffer, mnguyen , Danielle Vazquez, Amber Jones 2020. Protocol for Extraction of Viral RNA with added DNase treatment. protocols.io https://dx.doi.org/10.17504/protocols.io.bnkhmct6 | 2021-04-15 09:15:19 | |||
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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR ORF1ab 2020 (Wuhan-ORF1ab; 2019-nCoV-related test) Resource Report Resource Website |
Judy Northill, Ian Mackay | DOI:10.17504/protocols.io.bchvit66 | protocols.io Ambassadors, Public Health Virology, Forensic and Scientific Services, Coronavirus Method Development Community | A real-time RT-PCR to specifically detect SARS-CoV-2 betacoronavirus also called nCoV-2019 or Wuhan seafood market pneumonia virus. Based on sequence MN908947 made available by Professor Yong-Zhen Zhang, Fudan University, Shanghai, China. The target region is within the ORF1ab sequence.NotesAssay is fully 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 | 3 | 2020 | Judy Northill, Ian Mackay 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR ORF1ab 2020 (Wuhan-ORF1ab; 2019-nCoV-related test). protocols.io https://dx.doi.org/10.17504/protocols.io.bchvit66 | 2021-04-15 09:15:19 | |||
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Culture of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; f.2019-nCoV) Resource Report Resource Website |
Alyssa Pyke, Ian Mackay, Frederick Moore, Andrew Van Den Hurk, Judy Northill, Mitchell Finger, Natalie Simpson, Neelima Nair, Peter Burtonclay, Peter Moore, Sarah Wheatley, Sean Moody, Sonja Hall-Mendelin, Elisabeth Gamez, Amanda De Jong, Ben Huang, Carmel Taylor, David Warrilow, Doris Genge, Glen Hewitson, Inga Sultana, Jamie McMahon, Jean Barcelon | DOI:10.17504/protocols.io.bcduis6w | protocols.io Ambassadors, Public Health Virology, Forensic and Scientific Services, Coronavirus Method Development Community | We briefly describe a method to inoculate a susceptible cell line with a human patient sample in order to culture the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease, COVID-19.Clinical samples including nasopharyngeal swabs and aspirates were inoculated onto confluent monolayers of African green monkey kidney Vero C1008, clone E6 cells (ATCC®-CRL-1586) grown in Opti-Mem reduced serum growth medium supplemented with 3% foetal bovine serum in polystyrene, flat-sided, screw-cap 3 mL cell culture tubes.This work was conducted in Queensland under PC3 laboratory conditions by experienced scientists. | Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services | 1 | 2020 | Alyssa Pyke, Ian Mackay, Frederick Moore, Andrew Van Den Hurk, Judy Northill, Mitchell Finger, Natalie Simpson, Neelima Nair, Peter Burtonclay, Peter Moore, Sarah Wheatley, Sean Moody, Sonja Hall-Mendelin, Elisabeth Gamez, Amanda De Jong, Ben Huang, Carmel Taylor, David Warrilow, Doris Genge, Glen Hewitson, Inga Sultana, Jamie McMahon, Jean Barcelon 2020. Culture of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; f.2019-nCoV). protocols.io https://dx.doi.org/10.17504/protocols.io.bcduis6w | 2021-04-15 09:15:24 | |||
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BSCI:414 Lab 8 Transform and Miniprep Plasmid Containing SARS-CoV-2 Spike Gene Resource Report Resource Website |
Harley King | Coronavirus Method Development Community, USG Fall 2020 BSCI:414, protocols.io for Educators | LuminUltra | 1 | 2020 | Harley King 2020. BSCI:414 Lab 8 Transform and Miniprep Plasmid Containing SARS-CoV-2 Spike Gene. protocols.io https:// | 2021-04-15 09:15:23 | |||||
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Antibody neutralization assay with SARS-CoV-2 and SARS-CoV pseudovirus Resource Report Resource Website |
Bei Wang, Wen-Hsin Sandy Lee, Cheng-I Wang | DOI:10.17504/protocols.io.biztkf6n | Coronavirus Method Development Community | Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore | 1 | 2020 | Bei Wang, Wen-Hsin Sandy Lee, Cheng-I Wang 2020. Antibody neutralization assay with SARS-CoV-2 and SARS-CoV pseudovirus. protocols.io https://dx.doi.org/10.17504/protocols.io.biztkf6n | 2021-04-15 09:15:24 | ||||
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Wastewater Concentration by Adsorption and Direct Extraction for SARS-CoV-2 RNA Detection and Quantification by RT-ddPCR Resource Report Resource Website |
Aaron Bivins, Warish Ahmed, Devin North, Kyle Bibby | Coronavirus Method Development Community, 2019-nCoV Wastewater Epidemiology | University of Notre Dame, CSIRO, University of Notre Dame, University of Notre Dame | https://www.sciencedirect.com/science/article/pii/S004896972033480X | 1 | 2020 | Aaron Bivins, Warish Ahmed, Devin North, Kyle Bibby 2020. Wastewater Concentration by Adsorption and Direct Extraction for SARS-CoV-2 RNA Detection and Quantification by RT-ddPCR. protocols.io https:// | 2021-04-15 09:15:48 | ||||
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Manual Silane magnetic bead-based high throughput protocol for SARS-CoV-2 RNA extraction Resource Report Resource Website |
Ainhoa Goñi-Salaverri, Jose A. Rodriguez, Nicholas Weber, Juan Pablo Unfried, Josepmaria Argemi, , David Lara Astiaso, | DOI:10.17504/protocols.io.bfmajk2e | Coronavirus Method Development Community | The COVID-19 pandemic has presented an unprecedent challenge to develop and validate testing tools for urgent disease diagnosis. Current testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) via molecular diagnostics is woefully inadequate due to myriad issues with cross-entity coordination, reagent availability, and labor- and time-intensive protocols. The bottleneck in the workflow from patient sampling to diagnosis is not in the identification of viral genetic material (RT-qPCR) but in the collection, processing, and purification of the viral genetic material (patient sampling and RNA extraction). The majority of tests performed in laboratories lacking sophisticated automation require individual sample processing that severely limits the possibilities of scale-up. Thus, throughput depends on the availability of trained operator person-hours. We have developed a protocol for SARS-CoV-2 RNA extraction based on silane ferrimagnetic beads that is easily scaled up to multiwell culture plates with the processing done using multichannel pipettes. This protocol significantly reduces the hands-on time per sample and increases throughput such that an individual operator can process 100-200 samples per hour. | Cima Universidad de Navarra, Pamplona, Spain, Cima Universidad de Navarra, Pamplona, Spain, Vivet Therapeutics SL, Pamplona, Spain, Cima Universidad de Navarra, Pamplona, Spain, Liver Unit. Internal Medicine Department. Clinica Universidad de Navarra, Pamplona, Spain, Division of Medicine - Gastroenterology and Hepatology Department, University of Pittsburgh, PA, USA, Cima Universidad de Navarra, Pamplona, Spain, Cambridge Stem Cell Institute, Cambridge, England | 2 | 2020 | Ainhoa Goñi-Salaverri, Jose A. Rodriguez, Nicholas Weber, Juan Pablo Unfried, Josepmaria Argemi, , David Lara Astiaso, 2020. Manual Silane magnetic bead-based high throughput protocol for SARS-CoV-2 RNA extraction. protocols.io https://dx.doi.org/10.17504/protocols.io.bfmajk2e | 2021-04-15 09:15:32 | |||
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One-Step RT-ddPCR for Detection of SARS-CoV-2, Bovine Coronavirus, and PMMoV RNA in RNA Derived from Wastewater or Primary Settled Solids v2 Resource Report Resource Website |
Stephanie Loeb, Katy Graham, David Catoe, Marlene Wolfe, Alexandria Boehm, Krista Wigginton | DOI:10.17504/protocols.io.br96m99e | Coronavirus Method Development Community, Wastewater-based epidemiology working group | This protocol is an updated version of the original protocols.io protocol for these procedures from this group, with changes in the cycling conditions for the BCoV/PMMoV assay and the concentration of the PMMoV probe.Goal: Quantify concentration of N1, N2, BCoV, and PMMoV in RNA extractions using RT-ddPCR. | Stanford University, Stanford University, Stanford University, Stanford University, Stanford University, University of Michigan | 1 | 2021 | Stephanie Loeb, Katy Graham, David Catoe, Marlene Wolfe, Alexandria Boehm, Krista Wigginton 2021. One-Step RT-ddPCR for Detection of SARS-CoV-2, Bovine Coronavirus, and PMMoV RNA in RNA Derived from Wastewater or Primary Settled Solids v2 . protocols.io https://dx.doi.org/10.17504/protocols.io.br96m99e | 2021-04-15 09:15:29 | |||
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ENNOLIFE SARS-CoV-2 Antigen Test Kit Protocol Resource Report Resource Website |
Hsiao-Chung Tsai | DOI:10.17504/protocols.io.bke3ktgn | Coronavirus Method Development Community, ProtectLife-AnTaimmu, XPRIZE Rapid Covid Testing | General manager, ProtectLife International Biomedical Inc. | 1 | 2020 | Hsiao-Chung Tsai 2020. ENNOLIFE SARS-CoV-2 Antigen Test Kit Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bke3ktgn | 2021-04-15 09:15:50 | ||||
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AAU-nCoV-2019_Tailed_Long_Amplicon_Sequncing Resource Report Resource Website |
Emil Aarre Sorensen, Søren M. Karst, Simon Knutsson | DOI:10.17504/protocols.io.bfc3jiyn | AlbertsenLab, Coronavirus Method Development Community | This protocol describes the preparation of long read amplicon libraries of nCoV-2019 for sequencing with the Oxford Nanopore MinION platform. The protocol is based on samples of rRNA extracts of the nCoV-2019 virus.Sequences for primers can be found under guidelines, currently using V3.1 from CJ020. The protocol is based on the ARTIC Networks nCoV-2019 sequencing protocol and modified to our lab at Aalborg Univeristy. https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w | Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Denmark, Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Denmark, Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Denmark | 2 | 2020 | Emil Aarre Sorensen, Søren M. Karst, Simon Knutsson 2020. AAU-nCoV-2019_Tailed_Long_Amplicon_Sequncing. protocols.io https://dx.doi.org/10.17504/protocols.io.bfc3jiyn | 2021-04-15 09:15:32 | |||
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GM Covid-19 saliva test (v2) Resource Report Resource Website |
Coronavirus Method Development Community, Narwhale for XPrize | GM Biosciences | 2 | 2020 | 2020. GM Covid-19 saliva test (v2). protocols.io https:// | 2021-04-15 09:15:42 | ||||||
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nCoV-2019 McGill Nanopore LibPrep Protocol, 5 ng NB Resource Report Resource Website |
Sarah Reiling, Anne-Marie Roy, Shu-Huang Chen, Josh Quick, Ioannis Ragoussis | DOI:10.17504/protocols.io.bjkvkkw6 | Coronavirus Method Development Community, McGill Genome Centre | Artic nCoV-2019 McGill modified Lunascript Reverse Transcriptase nanopore sequencing protocol. | McGill University, McGill University, McGill University, University of Birmingham, McGill University | 1 | 2020 | Sarah Reiling, Anne-Marie Roy, Shu-Huang Chen, Josh Quick, Ioannis Ragoussis 2020. nCoV-2019 McGill Nanopore LibPrep Protocol, 5 ng NB. protocols.io https://dx.doi.org/10.17504/protocols.io.bjkvkkw6 | 2021-04-15 09:15:40 |
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