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Corona Detective User Protocol V2.0 Resource Report Resource Website |
Rachel Aronoff, Guy Aidelberg | DOI:10.17504/protocols.io.bpwzmpf6 | Coronavirus Method Development Community, XPRIZE Rapid Covid Testing, Guy Aidelberg | Corona Detective is based upon a molecular amplification strategy inspired by the ‘GMO Detective’ method, in order to detect the virus causing Covid-19. Done not only without complicated equipment, but with a simple +/- fluorescent readout, the Corona Detective is very specific. Furthermore, controls to ensure sensitive detection, without false positives or negatives, are intrinsic to this solution. The final product, strips/plates of tubes with dry reagents, specific for Corona and a control gene (extraction control), can be shipped anywhere, without cold-chain dependence. Critically, monitoring tests could be run by ordinary people, by following this protocol. (Even kids have successfully participated in GMO detective workshops, also soldering their own fluor detectors.)This user guide will allow you to test samples with this system, provided as freeze-dried reaction components in 0.2ml tubes made by this protocol (other formats possible e.g. 8-tube strips, 96-well plates, 1000 reactions, etc.).Human or clinical samples should only be run in settings with access to appropriate biosafety facilities, of course.Acknowledging the JOGL Open Covid 19 Initiative and all the #proj nucleic-acid-amplification team for support. | Hackuarium, CRI (Center for research and interdisciplinarity) Paris | 2 | 2020 | Rachel Aronoff, Guy Aidelberg 2020. Corona Detective User Protocol V2.0. protocols.io https://dx.doi.org/10.17504/protocols.io.bpwzmpf6 | 2021-04-15 09:15:31 | |||
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nCoV-2019 sequencing protocol Resource Report Resource Website |
Josh Quick | DOI:10.17504/protocols.io.bbmuik6w | ARTIC, Coronavirus Method Development Community, COG-UK | ARTIC amplicon sequencing protocol for MinION for nCoV-2019 | University of Birmingham | https://doi.org/10.1016/j.remle.2020.05.007 | 1 | 2020 | Josh Quick 2020. nCoV-2019 sequencing protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bbmuik6w | 2021-04-15 09:15:30 | ||
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Breath Analysis System for Detecting Breath Pattern Signature of COVID-19 Resource Report Resource Website |
Salvatore D Morgera, Tiffany Miller, Arash Takshi, Stephen E Saddow, Matthew Palm | DOI:10.17504/protocols.io.bpcqmivw | Coronavirus Method Development Community, Front Line Technologies | The magnitude of how rapidly the COVID-19 virus could spread and infect others facilitated the need for a rapid COVID-19 test, accessible and affordable for both children and adults worldwide. As a result, an infected patient can quickly quarantine and isolate to slow the spread. Our research group has determined VOCs associated with COVID-19 and has built a prototype gas analysis system similar to a breathalyzer for detecting gasses of COVID-19. Some of the symptoms like headaches, coughing, and diarrhea result in an inflammatory response to create a unique variety of gasses like acetone, hydrogen, and carbon monoxide that can be detected when they are exhaled through a person’s breath. A sample of a person’s breath is first collected in a chamber when a patient breaths into the valve, the gas sensors then detect a voltage change when they contact a COVID-19 target gas. The concentration in parts-per-million is calculated based on the non-linear resistance ratio of the target gas and clean air. Log-based scale calculations and post-data processing calibrate the sensors to increase the accuracy and selectivity. Finally, the voltages and PPM of the target gas concentration data is stored in a computer database and sensor coding reveals the resulting breath pattern signature of COVID-19. At just under $15.00 United States Dollars (USD), test results are just a breath away, within seconds of taking the test and even before leaving the doctor’s office. Although, this system may also be modified to sniff out other pathogens of disease, spoiled meats, and ripened fruit, we are dedicated to build a gas sensor platform for low cost, noninvasive, and rapid detection of the breath pattern signature of COVID-19, in an attempt to slow the spread of the global health threat of infection and in turn to help save lives.Breath analysis systems serve as a noninvasive means for disease screening. Our objective is to utilize this prototype to obtain a database of H2, CO, NO, Acetone and Alcohol concentrations, whereby, COVID patient breath samples are compared to healthy individual breath samples using our breath analysis system prototype. This system is configured for measuring the aforementioned gas concentrations in ppm and recording the data to a text file in a computer database for subsequent analysis. The data obtained from this study is critical to the development of this system. | Department of Electrical Engineering, University of South Florida, Tampa, FL, United States of America, Department of Electrical Engineering, University of South Florida, Tampa, FL, United States of America, Inventions International Inc., Department of Electrical Engineering, University of South Florida, Tampa, FL, United States of America, Department of Electrical Engineering, University of South Florida, Tampa, FL, United States of America, Department of Medical Engineering, University of South Florida, Tampa, FL, United States of America, , Valhall K-9 International, LLC, Hull, GA, United States of America | 1 | 2020 | Salvatore D Morgera, Tiffany Miller, Arash Takshi, Stephen E Saddow, Matthew Palm 2020. Breath Analysis System for Detecting Breath Pattern Signature of COVID-19 . protocols.io https://dx.doi.org/10.17504/protocols.io.bpcqmivw | 2021-04-15 09:15:30 | |||
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Opentrons COVID-19 testing (Zymo, station B, 48 samples) Resource Report Resource Website |
Max Marrone | DOI:10.17504/protocols.io.bestjeen | Coronavirus Method Development Community, Opentrons COVID-19 Testing | Opentrons Labworks | 1 | 2020 | Max Marrone 2020. Opentrons COVID-19 testing (Zymo, station B, 48 samples). protocols.io https://dx.doi.org/10.17504/protocols.io.bestjeen | 2021-04-15 09:15:29 | ||||
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CDx autoXpress detection of COVID 19 Resource Report Resource Website |
Mickey Shah, Gary Niehaus | DOI:10.17504/protocols.io.bki4kugw | Coronavirus Method Development Community, XPRIZE Rapid Covid Testing | The Crystal Diagnostics AutoXpress provides rapid detection of COVID 19 at 10 - 100 CFU per ul of clinical sample (nasal swab, sputum, or saliva). The patented Liquid Crystal technology is combined with antibody-coated paramagnetic microspheres to selectively capture and detect COVID 19. | Crystal Diagnostics, Crystal Diagnostics | 1 | 2020 | Mickey Shah, Gary Niehaus 2020. CDx autoXpress detection of COVID 19. protocols.io https://dx.doi.org/10.17504/protocols.io.bki4kugw | 2021-04-15 09:15:35 | |||
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Study Vaccine (Part 5 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.bj5zkq76 | Coronavirus Method Development Community, PATH | This is Part 5 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. Study Vaccine (Part 5 of Phase 3 study of Vaccine Candidate for COVID-19). protocols.io https://dx.doi.org/10.17504/protocols.io.bj5zkq76 | 2021-04-15 09:15:40 | |||
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A Simple RNA Preparation Method for SARS-CoV-2 detection by RT-qPCR 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. A Simple RNA Preparation Method for SARS-CoV-2 detection by RT-qPCR. protocols.io https:// | 2021-04-15 09:15:47 | ||||
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Study Population (Part 4 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.bj5xkq7n | Coronavirus Method Development Community | This is Part 4 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. Study Population (Part 4 of Phase 3 study of Vaccine Candidate for COVID-19). protocols.io https://dx.doi.org/10.17504/protocols.io.bj5xkq7n | 2021-04-15 09:15:45 | |||
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ClearLab Flu+COVID19 Antigen Assay IFU Resource Report Resource Website |
petercb3 | DOI:10.17504/protocols.io.bj8fkrtn | Coronavirus Method Development Community | Indication: Qualitative detection of the nucleocapsid protein antigen from SARS-CoV-2 in nasopharyngeal aspirate specimens directly or after the aspirate have been added to viral transport media from individuals who are suspected of COVID-19 by their healthcare provider. Emergency use of this test is limited to authorized laboratories and other authorized testing locations. | Chris Baker MD (Aardvark Medical, Inc), Roger Kang (Princeton BioMediTech) | http://www.clearmynose.com | 1 | 2020 | petercb3 2020. ClearLab Flu+COVID19 Antigen Assay IFU. protocols.io https://dx.doi.org/10.17504/protocols.io.bj8fkrtn | 2021-04-15 09:15:48 | ||
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Background and Rationale (Part 1 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.bj5tkq6n | Coronavirus Method Development Community | This is a collection of protocols for: "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. Background and Rationale (Part 1 of Phase 3 study of Vaccine Candidate for COVID-19). protocols.io https://dx.doi.org/10.17504/protocols.io.bj5tkq6n | 2021-04-15 09:15:49 | |||
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SARS-CoV-2 McGill Nanopore sequencing protocol SuperScript IV_42C_ArticV3 Resource Report Resource Website |
Sarah Reiling, Shu-Huang Chen, Anne-Marie Roy, Josh Quick, Ioannis Ragoussis | DOI:10.17504/protocols.io.bjajkicn | Coronavirus Method Development Community, McGill Genome Centre | SARS-CoV-2 McGill Nanopore sequencing protocol SuperScript IV_42C_ArticV3 | McGill University, McGill University, McGill University, University of Birmingham, McGill University | 1 | 2020 | Sarah Reiling, Shu-Huang Chen, Anne-Marie Roy, Josh Quick, Ioannis Ragoussis 2020. SARS-CoV-2 McGill Nanopore sequencing protocol SuperScript IV_42C_ArticV3. protocols.io https://dx.doi.org/10.17504/protocols.io.bjajkicn | 2021-04-15 09:15:47 | |||
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Bivalent binding of a fully human IgG to the SARS-CoV-2 spike proteins reveals mechanisms of potent neutralization Resource Report Resource Website |
Bei Wang, Daniel Asarnow, Wen-Hsin Lee, Ching-Wen Huang, Bryan Faust, Patricia Miang Lon Ng, Eve Zi Xian Ngoh, Markus Bohn, David Bulkley, Andrés Pizzorno, Hwee Ching Tan, Chia-Yin Lee, Rabiatul Adawiyah Minhat, Olivier Terrier, Mun Kuen Soh, Frannie Jiuyi Teo, Yvonne Yee Chin Yeap, Yuanyu Hu, Shirley Gek Kheng Seah, Sebastian Maurer-Stroh, Laurent Renia, Brendon John Hanson, Manuel Rosa-Calatrava, Aashish Manglik, Yifan Cheng, Charles S. Craik, Cheng-I Wang | DOI:10.17504/protocols.io.bi35kgq6 | Coronavirus Method Development Community | In vitro antibody selection against pathogens from naïve combinatorial libraries can yield various classes of antigen-specific binders that are distinct from those evolved from natural infection. Also, rapid neutralizing antibody discovery can be made possible by a strategy that selects for those interfering with pathogen and host interaction. Here we report the discovery of antibodies that neutralize SARS-CoV-2, the virus responsible for the COVID-19 pandemic, from a highly diverse naïve human Fab library. Lead antibody 5A6 blocks the receptor binding domain (RBD) of the viral spike from binding to the host receptor angiotensin converting enzyme 2 (ACE2), neutralizes SARS-CoV-2 infection of Vero E6 cells, and reduces viral replication in reconstituted human nasal and bronchial epithelium models. 5A6 has a high occupancy on the viral surface and exerts its neutralization activity via a bivalent binding mode to the tip of two neighbouring RBDs at the ACE2 interaction interface, one in the “up” and the other in the “down” position, explaining its superior neutralization capacity. Furthermore, 5A6 is insensitive to several spike mutations identified in clinical isolates, including the D614G mutant that has become dominant worldwide. Our results suggest that 5A6 could be an effective prophylactic and therapeutic treatment of COVID-19. | Singapore Immunology Network, A*STAR, Singapore, Department of Biochemistry and Biophysics, University of California San Francisco (UCSF) School of Medicine, San Francisco, USA; QBI COVID-19 Research Group (QCRG), San Francisco, USA, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, Department of Biochemistry and Biophysics, University of California San Francisco (UCSF) School of Medicine, San Francisco, USA; QBI COVID-19 Research Group (QCRG), San Francisco, USA, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, QBI COVID-19 Research Group (QCRG), San Francisco, USA; Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, USA, Department of Biochemistry and Biophysics, University of California San Francisco (UCSF) School of Medicine, San Francisco, USA; QBI COVID-19 Research Group (QCRG), San Francisco, USA, Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, Lyon, France, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, Lyon, France, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, Biological Defence Program, DSO National Laboratories, Singapore, Bioinformatics Institute, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Biological Defence Program, DSO National Laboratories, Singapore, Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, Lyon, France; VirNext, Faculté de Médecine RTH Laennec, Université de Lyon, Lyon, France, QBI COVID-19 Research Group (QCRG), San Francisco, USA; Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, USA; Department of Anesthesia and Perioperative Care, University of California San Francisco (UCSF), San Francisco, USA, Department of Biochemistry and Biophysics, University of California San Francisco (UCSF) School of Medicine, San Francisco, USA; QBI COVID-19 Research Group (QCRG), San Francisco, USA; Howard Hughes Medical Institute, University of California San Francisco (UCSF), San Francisco, USA, QBI COVID-19 Research Group (QCRG), San Francisco, USA; Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, USA, Singapore Immunology Network, A*STAR, Singapore | https://www.biorxiv.org/content/10.1101/2020.07.14.203414v1?rss=1 | 1 | 2020 | Bei Wang, Daniel Asarnow, Wen-Hsin Lee, Ching-Wen Huang, Bryan Faust, Patricia Miang Lon Ng, Eve Zi Xian Ngoh, Markus Bohn, David Bulkley, Andrés Pizzorno, Hwee Ching Tan, Chia-Yin Lee, Rabiatul Adawiyah Minhat, Olivier Terrier, Mun Kuen Soh, Frannie Jiuyi Teo, Yvonne Yee Chin Yeap, Yuanyu Hu, Shirley Gek Kheng Seah, Sebastian Maurer-Stroh, Laurent Renia, Brendon John Hanson, Manuel Rosa-Calatrava, Aashish Manglik, Yifan Cheng, Charles S. Craik, Cheng-I Wang 2020. Bivalent binding of a fully human IgG to the SARS-CoV-2 spike proteins reveals mechanisms of potent neutralization. protocols.io https://dx.doi.org/10.17504/protocols.io.bi35kgq6 | 2021-04-15 09:15:56 | ||
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nCoV-2019 sequencing protocol (RAPID barcoding, 1200bp amplicon) Resource Report Resource Website |
Nikki Freed, Olin Silander | DOI:10.17504/protocols.io.bfwnjpde | Coronavirus Method Development Community | To enable faster, easier sequencing of SARS-COV2 genomes with fewer steps than current methods, we use multiplexed 1200 base pair PCR amplicons with the Oxford Nanopore RAPID barcoding kit (RBK004). This is a modification of the ARTIC amplicon V3 sequencing protocol for MinION for nCoV-2019 developed by Josh Quick, which produces 400 base pair amplicons and uses the Oxford Nanopore Ligation barcoding kit (LSK-109). We have increased the size of the amplicons to 1200bp and use the RAPID barcode kit (RBK004), which enables requires less time and fewer reagents than the LSK-109 protocol. The amplicons produced in this protocol could also be used for Illumina sequencing. Primers were all designed using Primal Scheme: http://primal.zibraproject.org/, described here https://www.nature.com/articles/nprot.2017.066.Primer sequences are here: https://docs.google.com/spreadsheets/d/1M5I_C56ZC8_2Ycgm9EFieVlVNqxsP7dXAnGoBZy3nDo/edit?usp=sharingWe can ship a small amount of pooled primers to interested labs for further testing, email [email protected] or [email protected] | Massey University, Massey University | 1 | 2020 | Nikki Freed, Olin Silander 2020. nCoV-2019 sequencing protocol (RAPID barcoding, 1200bp amplicon). protocols.io https://dx.doi.org/10.17504/protocols.io.bfwnjpde | 2021-04-15 09:15:51 | |||
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Simple Way to Make Homemade Cloth Masks: Fabrics Treated with NaCl and Starch Solution Resource Report Resource Website |
M Mehedi Hasan Rocky, Mohammad Amzad Hossain Bhuyan, Shamim Akhtar | DOI:10.17504/protocols.io.be9djh26 | Coronavirus Method Development Community | This protocol describes a simple way to make a mask at home using the cotton or linen woven fabric available in wearable cloth or household napkin. Fabric is soaked in a solution containing the table salt (NaCl) and starch. Starch is used to increase the droplet absorption efficiency of fabric whereas salt is added for improving the virus deactivation system. These simple preparation and wearing techniques will help anyone to prepare a mask for safety during COVID-19 pandemic, especially for those people having masks of little avail or no avail. .justify:after { content: ""; display:inline-block; width: 100%; } | Port City International University , University of Oulu, University of Chittagong | 1 | 2020 | M Mehedi Hasan Rocky, Mohammad Amzad Hossain Bhuyan, Shamim Akhtar 2020. Simple Way to Make Homemade Cloth Masks: Fabrics Treated with NaCl and Starch Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.be9djh26 | 2021-04-15 09:16:01 | |||
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Viral Sequencing, from Gunk to Graph (One-Step four-primer PCR alternative) Resource Report Resource Website |
David Eccles | DOI:10.17504/protocols.io.bd5ni85e | Coronavirus Method Development Community | This is a fast "gunk to graph" protocol for analysing viral RNA from nasopharyngeal swabs. The approach involves swab lysis and inactivation at the point of sampling, uses a cellulose binding / wash protocol to reduce extraction cost, incorporates sample-specific barcodes during first-strand synthesis, nanopore rapid-attachment primers during PCR amplification, and nanopore sequencing with parallel RAMPART analysis for fast assembly and phylogenetics.Note: this is a one-step RT-PCR reaction protocol. For an alternative method that allows more multiplexing flexibility, see the protocol that this has been forked from:https://dx.doi.org/10.17504/protocols.io.bd3yi8pw | Malaghan Institute of Medical Research (NZ) | 1 | 2020 | David Eccles 2020. Viral Sequencing, from Gunk to Graph (One-Step four-primer PCR alternative). protocols.io https://dx.doi.org/10.17504/protocols.io.bd5ni85e | 2021-04-15 09:16:02 | |||
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Detection of Sars-Cov2 Using qPCR Resource Report Resource Website |
Joseph Patterson, Allyson Cole-Strauss, John Beck, Caryl Sortwell, Jack Lipton | DOI:10.17504/protocols.io.bfaujiew | Coronavirus Method Development Community | PCR based tests, such as quantitative PCR (qPCR) are the gold standard to test for the novel coronavirus (SARS-Cov2). Many labs regularly use qPCR for their own specific projects. The ability to process samples and detect SARS-Cov2 is not very different from the methods these labs are already intimately familiar with. This protocol outlines the methods that our group is using to detect SARS-Cov2 RNA in human samples. | Michigan State University, Michigan State University, Michigan State University, Michigan State University, Michigan State University | 1 | 2020 | Joseph Patterson, Allyson Cole-Strauss, John Beck, Caryl Sortwell, Jack Lipton 2020. Detection of Sars-Cov2 Using qPCR. protocols.io https://dx.doi.org/10.17504/protocols.io.bfaujiew | 2021-04-15 09:15:58 | |||
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Pseudotyping lentiviral particles with SARS-CoV-2 Spike protein for neutralization assays Resource Report Resource Website |
Katharine H. D. Crawford, Rachel Eguia, Adam S. Dingens, Andrea N. Loes, Jesse D. Bloom | DOI:10.17504/protocols.io.bfghjjt6 | Coronavirus Method Development Community | SARS-CoV-2 enters cells using its Spike protein, which is also the main target of neutralizing antibodies. Therefore, assays to measure how antibodies and sera affect Spike-mediated viral infection are important for studying immunity. Because SARS-CoV-2 is a biosafety-level-3 virus, one way to simplify such assays is to pseudotype biosafety-level-2 viral particles with Spike. Such pseudotyping has now been described for single-cycle lentiviral, retroviral and VSV particles, but the reagents and protocols are not widely available. Here we detail how to effectively pseudotype lentiviral particles with SARS-CoV-2 Spike and infect 293T cells engineered to express the SARS-CoV-2 receptor, ACE2. We also make all the key experimental reagents available in the BEI Resources repository of ATCC and the NIH. Furthermore, we demonstrate how these pseudotyped lentiviral particles can be used to measure the neutralizing activity of human sera or plasma against SARS-CoV-2 in convenient luciferase-based assays, thereby providing a valuable complement to ELISA-based methods that measure antibody binding rather than neutralization. | Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center; Department of Genome Sciences and Medical Scientist Training Program, University of Washington; , Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center; Howard Hughes Medical Institute | https://www.mdpi.com/1999-4915/12/5/513 | 1 | 2020 | Katharine H. D. Crawford, Rachel Eguia, Adam S. Dingens, Andrea N. Loes, Jesse D. Bloom 2020. Pseudotyping lentiviral particles with SARS-CoV-2 Spike protein for neutralization assays. protocols.io https://dx.doi.org/10.17504/protocols.io.bfghjjt6 | 2021-04-15 09:16:07 | ||
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nCoV-2019 sequencing protocol for illumina Resource Report Resource Website |
Kentaro Itokawa, Tsuyoshi Sekizuka, Masanori Hashino, Rina Tanaka, Makoto Kuroda | DOI:10.17504/protocols.io.bnn7mdhn | Coronavirus Method Development Community | This protocol is folked from "ARTIC amplicon sequencing protocol for MinION for nCoV-2019" by Josh Quick to adapt it to illumina sequencers. In this Version V3, the reverse-transcription step was changed to use of NEB's LunaScript RT SuperMix Kit instead of Thermo Fisher's SuperScript IV Reverse Transcriptase as adapting to the recent update of ARTIC Network's protocol (LoCost). Tyson et al., Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore bioRxiv2020.09.04.283077;doi:https://doi.org/10.1101/2020.09.04.283077 Because the PCR products are fragmented before ligated with adapters, this protocol is compatible to many sequencing kits with various read lengths (75PE, 150PE, etc.) in Illumina machines. While the library preparation uses QiaSeq FX by Qiagen and is basically straight forward (as par kit instruction but modified to 1/4 scale), some tweaks for much of simplicity and speed were added.Change histories (V2): The amount of cDNA input to multiplex PCR is increased (now almost same amount to the ARTIC Network's original protocol) (Step 10). This change gives better results for samples with extremely low RNA copy. Amount of adapter solution input was corrected (Step 19).Change histories (V3): RT step has been changed to use of LunaScript (Tyson et al., 2020).Corrected typos and wrong descriptions about amount of reagents.Added a link to library quantification protocol.Other minor changes.Change histories (V3): RT step has been changed to use of LunaScript (Tyson et al., 2020).Corrected typos and wrong descriptions about amount of reagents.Added a link to library quantification protocol.Other minor changes. | National Institute of Infectious Diseases, Japan, National Institute of Infectious Diseases, Japan, National Institute of Infectious Diseases, Japan, National Institute of Infectious Diseases, Japan, National Institute of Infectious Diseases, Japan | 3 | 2020 | Kentaro Itokawa, Tsuyoshi Sekizuka, Masanori Hashino, Rina Tanaka, Makoto Kuroda 2020. nCoV-2019 sequencing protocol for illumina. protocols.io https://dx.doi.org/10.17504/protocols.io.bnn7mdhn | 2021-04-15 09:16:05 | |||
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SARS-CoV-2 RBD ELISA Resource Report Resource Website |
Anita Iyer | Coronavirus Method Development Community | Massachusetts General Hospital and Harvard Medical School | 1 | 2020 | Anita Iyer 2020. SARS-CoV-2 RBD ELISA. protocols.io https:// | 2021-04-15 09:16:05 | |||||
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3D Printed Nasopharyngeal Swabs with Wrapped Rayon Fibers Developed and validated by SCREEN (San Diego Covid19 Research Enterprise Network) Resource Report Resource Website |
Justin Ryan, Nicole Coufal, Sage Aronson, Kelsey Ladt, Catelyn Andersen, Mark Zeller, Stephen Rawlings, Denise Malicki, Gene Yeo | DOI:10.17504/protocols.io.bemxjc7n | Coronavirus Method Development Community | The global pandemic due to SARS-CoV2 virus, also known as COVID-19, has drastically increased the need for nasopharyngeal-swab-based testing resulting in shortages of commercially available nasopharyngeal (NP) swabs. One solution to overcome the national deficit of swabs is for medical device manufacturers and hospitals to generate NP swabs. Numerous entities are attempting to manufacture a direct from 3D printing NP swab but presented here is a validated two-part swab manufacturing protocol utilizing 3D printing and manual intervention (wrapping of nylon fibers). We recommend material extrusion or powder bed fusion technologies utilizing materials that can be sterilized using high level heat decontamination. Through the application of 3D printing and manual fabrication, we present an NP swab that can be created in a controlled environment. Coupled with CDC published viral transport media, the following swab can be used for COVID-19 testing or for testing for other respiratory viruses (eg, influenza, respiratory syncytial virus). The CDC viral transport medium has only four reagents which are readily available. .justify:after { content: ""; display:inline-block; width: 100%; } | Rady's Children Hospital; San Diego Covid Research Enterprise Network, University of California, San Diego; San Diego Covid Research Enterprise Network, Neurophotometrics; San Diego Covid Research Enterprise Network, Neurophotometrics; San Diego Covid Research Enterprise Network, Scripps Research Institute; San Diego Covid Research Enterprise Network, Scripps Research Institute; San Diego Covid Research Enterprise Network, University of California San Diego; San Diego Covid Research Enterprise Network, Rady Children's Hospital; San Diego Covid Research Enterprise Network, University of California, San Diego; San Diego Covid Research Enterprise Network | 1 | 2020 | Justin Ryan, Nicole Coufal, Sage Aronson, Kelsey Ladt, Catelyn Andersen, Mark Zeller, Stephen Rawlings, Denise Malicki, Gene Yeo 2020. 3D Printed Nasopharyngeal Swabs with Wrapped Rayon Fibers Developed and validated by SCREEN (San Diego Covid19 Research Enterprise Network). protocols.io https://dx.doi.org/10.17504/protocols.io.bemxjc7n | 2021-04-15 09:16:05 |
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