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Authors: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores
Group: Coronavirus Method Development Community, PATH
Summary: This is Appendix A 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.

Proper citation: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores 2020. Schedule of Study Visits and Evaluations (Appendix A of Phase 3 study of Vaccine Candidate for COVID-19). protocols.io https://dx.doi.org/10.17504/protocols.io.bj6bkran Copy   

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Authors: Chantal Vogels, Doug E. Brackney, Chaney Kalinich, Isabel Ott, Nathan Grubaugh, Anne Wyllie
Group: Coronavirus Method Development Community, XPRIZE Rapid Covid Testing
Summary: SalivaDirect is an RNA-extraction free, dual-plexed RT-qPCR method for SARS-CoV-2 detection. It can be broadly implemented as it (1) does not require saliva collection tubes containing preservatives, (2) does not require specialized equipment for RNA extraction, and (3) is validated for use with products from multiple vendors. Thus, the simplicity and flexibility of SalivaDirect means that it is not as affected by supply chain bottlenecks as some other assays. Our method is RNA-extraction free which enables testing of low volume and minimally processed saliva in dual-plexed RT-qPCR for SARS-CoV-2 detection. Saliva will be treated with proteinase K followed by a heat inactivation step, and is then directly used as input in the dual-plexed RT-qPCR test. Our aim was not to design new primers and probes for RT-qPCR testing, but rather to use validated primer and probe sets (N1 and RP) developed by the US CDC. The human Ribonuclease P (RP) probe was modified with a different fluorophore so that the primer/probe set could be combined in a dualplex assay, reducing the number of tests to 1 assay with 2 sets.Version 2 includes: Optimized thermocycler conditionsLocally validated alternative options for Proteinase K, RT-qPCR master mix, and thermocyclersUse of 8-strip tubes for sample processing step, due to contamination issues in 96-well plates.Version 3 has been updated to remove steps for sample self-collection.Version 4 has updated Ct thresholds for the ABI 7500 Fast Dx.

Proper citation: Chantal Vogels, Doug E. Brackney, Chaney Kalinich, Isabel Ott, Nathan Grubaugh, Anne Wyllie 2020. SalivaDirect: RNA extraction-free SARS-CoV-2 diagnostics. protocols.io https://dx.doi.org/10.17504/protocols.io.bjswknfe Copy   

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Authors: Peter Szabo, Steven Wells, Peter A. Sims, Donna Farber
Group: Human Cell Atlas Method Development Community, Coronavirus Method Development Community
Summary: This protocol describes the isolation of lymphocytes and pan-mononuclear cells from airway samples.

Proper citation: Peter Szabo, Steven Wells, Peter A. Sims, Donna Farber 2020. COVID Airway Processing for scRNAseq. protocols.io https://dx.doi.org/10.17504/protocols.io.bjj8kkrw Copy   

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Authors: matt , Eugene Joseph, Arun Manoharan Arunprimediscoveriescom
Group: Coronavirus Method Development Community, XPRIZE Rapid Covid Testing, Prime Discoveries

Proper citation: matt , Eugene Joseph, Arun Manoharan Arunprimediscoveriescom 2020. COVID19 RTLAMP Assay. protocols.io https://dx.doi.org/10.17504/protocols.io.bkx6kxre Copy   

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Authors: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores
Group: Coronavirus Method Development Community
Summary: This is Part 2 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.

Proper citation: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores 2020. Hypotheses, Objectives, Endpoints, and Case Definitions (Part 2 of Phase 3 study of Vaccine Candidate for COVID-19). protocols.io https://dx.doi.org/10.17504/protocols.io.bj5vkq66 Copy   

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Authors: Leonardo Caserta
Group: Coronavirus Method Development Community, Diel Lab

Proper citation: Leonardo Caserta 2021. First-strand synthesis and touchdown PCR for SARS-CoV-2. protocols.io https://dx.doi.org/10.17504/protocols.io.br54m88w Copy   

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Authors: Sureshnee Pillay, Jennifer Giandhari, Houriiyah Tegally, Eduan Wilkinson, Benjamin Chimukangara, Richard Lessells, Yunus Moosa, Inbal Gazy, Maryam Fish, Lavanya Singh, Khulekani Sedwell Khanyile, Vagner Fonseca, Marta Giovanetti, Luiz Carols Alcantara, Tulio de Oliveira, Jennifer Giandhari
Group: Coronavirus Method Development Community, KRISP
Summary: This protocol describes the procedure for generating cDNA from SARS-CoV-2 viral nucleic acid extracts and subsequently producing amplicons tiling the viral genome sequencing. It uses the V3 nCov-2019 primers from the ARTIC network. This is followed by library construction using Nextera Flex, which we found to save 9h of hands on time as compared with original protocol that use TrueSeq for library contstruction. It also describes the pooling of samples and quantitation, prior to sequencing on the Illumina Miseq and NextSeq. It is adapted from the nCov-2019 sequencing protocol from Quick and colleagues, which can be found here:

Proper citation: Sureshnee Pillay, Jennifer Giandhari, Houriiyah Tegally, Eduan Wilkinson, Benjamin Chimukangara, Richard Lessells, Yunus Moosa, Inbal Gazy, Maryam Fish, Lavanya Singh, Khulekani Sedwell Khanyile, Vagner Fonseca, Marta Giovanetti, Luiz Carols Alcantara, Tulio de Oliveira, Jennifer Giandhari 2020. Illumina Nextera DNA Flex library construction and sequencing for SARS-CoV-2: Adapting COVID-19 ARTIC protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bhjgj4jw Copy   

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Authors: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores
Group: Coronavirus Method Development Community
Summary: This is part 6 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.Note: Study procedures are vaccine-specific and will depend upon vaccine administration days (Day 1 and Day 15 versus Day 1 and Day 29) and serology collection days. The below section assumes that vaccine administrations take place on Days 1 and 15 with procedures as indicated.

Proper citation: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores 2020. Study Procedures (Part 6 of Phase 3 study of Vaccine Candidate for COVID-19). protocols.io https://dx.doi.org/10.17504/protocols.io.bj5ckq2w Copy   

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Authors: Judy Northill, Ian Mackay
Group: Public Health Virology, Forensic and Scientific Services, Coronavirus Method Development Community
Summary: 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).Tested on wild-type SARS-CoV-2 virus , it is expected to be capable of detecting SARS-CoV-2, bat-like SARS and SARS virus (members of the subgenus Sarbecovirus).Limit of detection not yet determined.The performance of the assay has not been tested with low viral load samples or samples from patients who are clinically well.The sensitivity of this assay was improved with the use of the SensiFast™Probe Lo-ROX One-step kit. A single 1 mismatch at probe-binding site identified with the BetaCoV/USA/CA1/2020|EPI_ISL_406034 (GenBank MN994467.1) variant of SARS-CoV-2 (as of 23JUNE2020).Probe is in the 3'-5' (reverse complement) direction.Reverse primers were replaced in March 2020.We also recommend the ORF1ab assay (Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR ORF1ab 2020), US-CDC-N1 assay or the E gene assay by Corman et al. (Protocol v2-1)Notes: Assay is optimised.This test has identified clinical positive cases of coronavirus disease (COVID-19)Notes: Assay is optimised.This test has identified clinical positive cases of coronavirus disease (COVID-19)

Proper citation: Judy Northill, Ian Mackay 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR N gene 2020 . protocols.io https://dx.doi.org/10.17504/protocols.io.bhpwj5pe Copy   

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Authors: Josh Quick
Group: ARTIC, Coronavirus Method Development Community, COG-UK
Summary: ARTIC amplicon sequencing protocol for MinION for nCoV-2019

Proper citation: Josh Quick 2020. nCoV-2019 sequencing protocol (single sample). protocols.io https://dx.doi.org/10.17504/protocols.io.bdbfi2jn Copy   

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Authors: Eve Ngoh, Bei Wang, Cheng-I Wang
Group: Coronavirus Method Development Community

Proper citation: Eve Ngoh, Bei Wang, Cheng-I Wang 2020. anti-SARS-CoV-2 spike RBD antibody discovery from phage display library. protocols.io https://dx.doi.org/10.17504/protocols.io.bitykepw Copy   

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Authors: Lyle J. Arnold Ph.D., Stella M. Sung Ph.D.
Group: Coronavirus Method Development Community, XPRIZE Rapid Covid Testing
Summary: This protocol is for the Aegea Biotechnologies rapid PCR-based SARS-CoV-2 test. This assay uses patented "Switch-Blocker" technology as well as taqman probes to test for presence of SARS-CoV-2 and simultaneously orthogonally validate. A single amplification reaction is performed, and "Switch Blocker" is used on the forward strand and taqman is used on the reverse strand. The assay design has high sensitivity & specificity--single nucleotide level. Moreover, it is able to detect the SARS-CoV-2 L strain vs the SARS-CoV-2 S strain. The test can be adapted to point of care (Roche LIAT) as well as for different SARS-CoV-2 strains as the virus mutates. A next generation version of the assay could identify the presence of the SARS-CoV-2 L/S strains vs. influenza A/B. Finally, because of the sensitivity and specificity, the Aegea PCR-based SARS-CoV-2 test should be able to use saliva samples, and it is suitable for pooled testing. This protocol is designed for high throughput PCR (96 or 384 well plate formats).Keywords: PCR, COVID-19, coronavirus, SARS-CoV-2, high throughput, multiplex, Switch-Blocker, taqman, high sensitivity, high specificity, accurate, pooling, saliva, strain types, L-strain, S-strain, combination SARS-CoV-2 and influenza

Proper citation: Lyle J. Arnold Ph.D., Stella M. Sung Ph.D. 2020. Aegea Biotechnologies rapid PCR SARS-CoV-2 test (high sensitivity & specificity; able to detect different strain types). protocols.io https://dx.doi.org/10.17504/protocols.io.bk2dkya6 Copy   

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Authors: Nabil-Fareed Alikhan, Emma Griffiths, Ruth Timme, Duncan MacCannell
Group: Coronavirus Method Development Community, PHA4GE
Summary: Guidance on how to populate the extended PHA4GE metadata package for SARS-CoV-2 submissions, maximizing interoperability for covid-19 surveillance.

Proper citation: Nabil-Fareed Alikhan, Emma Griffiths, Ruth Timme, Duncan MacCannell 2020. SOP for populating EBI submission templates (ENA). protocols.io https://dx.doi.org/10.17504/protocols.io.bh5dj826 Copy   

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Authors: Katharine H. D. Crawford, Rachel Eguia, Adam S. Dingens, Andrea N. Loes, Jesse D. Bloom
Group: Coronavirus Method Development Community
Summary: 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.

Proper citation: Katharine H. D. Crawford, Rachel Eguia, Adam S. Dingens, Andrea N. Loes, Jesse D. Bloom 2021. Pseudotyping lentiviral particles with SARS-CoV-2 Spike protein for neutralization assays. protocols.io https://dx.doi.org/10.17504/protocols.io.br44m8yw Copy   

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Authors: Oscar Whitney, Basem Al-Shayeb, Alex Crits-Cristoph, Mira Chaplin, Vinson Fan, Hannah Greenwald, Adrian Hinkle, Rose Kantor, Lauren Kennedy, Anna Maurer, Robert Tjian, Kara L. Nelson, UC Berkeley Wastewater-based epidemiology consortium
Group: Coronavirus Method Development Community
Summary: This protocol describes the procedure of the "4S" (Sewage, Salt, Silica and SARS-CoV-2) method for SARS-CoV-2 RNA extraction from wastewater. Offering a highly efficient, modular and economical alternative to existing wastewater RNA purification methods, this procedure lowers the barrier to entry for SARS-CoV-2 wastewater-based epidemiology. This procedure is intended to be carried out in a BSL2+ laboratory space, with precautions when handling raw wastewater samples.

Proper citation: Oscar Whitney, Basem Al-Shayeb, Alex Crits-Cristoph, Mira Chaplin, Vinson Fan, Hannah Greenwald, Adrian Hinkle, Rose Kantor, Lauren Kennedy, Anna Maurer, Robert Tjian, Kara L. Nelson, UC Berkeley Wastewater-based epidemiology consortium 2020. V.3 - Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method. protocols.io https://dx.doi.org/10.17504/protocols.io.bngsmbwe Copy   

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Authors: Megan Folkerts, mnguyen , Danielle Vazquez, Amber Jones
Group: Coronavirus Method Development Community
Summary: A protocol for rapid, low-throughput (24 samples or fewer) sequencing of Sars-CoV-2-containing samples using Illumina's DNA prep, and the ARTIC protocol for tiled amplicon sequencing. Turnaround time for this protocol from raw sample to sequence data is ~35 hours, making it ideal for use when rapid elucidation of samples is necessary.

Proper citation: Megan Folkerts, mnguyen , Danielle Vazquez, Amber Jones 2020. Rapid Tiled Amplicon Sequencing of Sars-CoV-2 using Illumina's DNA Prep. protocols.io https://dx.doi.org/10.17504/protocols.io.bnnbmdan Copy   

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Authors: Emma Betteridge, Naomi Park, Keith James, Jillian Durham, Josh Quick
Group: Coronavirus Method Development Community
Summary: This SOP describes the procedure for generating cDNA from SARS-CoV-2 viral nucleic acid extracts and subsequently producing 275nt amplicons. This is followed by library construction, equivolume pooling of samples and quantitation, prior to sequencing on the Illumina NovaSeq. A key benefit of the short amplicon method is that it can be utilised on any Illumina platform with a 300 cycle (or greater) kit.It is an adaptation of the 400nt COVID-19 ARTIC v3 amplicon protocol which can be found here: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

Proper citation: Emma Betteridge, Naomi Park, Keith James, Jillian Durham, Josh Quick 2020. COVID-19 ARTIC v3 Illumina library construction and sequencing protocol - short amplicons (275bp). protocols.io https://dx.doi.org/10.17504/protocols.io.bh4zj8x6 Copy   

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Authors: Björn Meyer
Group: Coronavirus Method Development Community
Summary: This protocol outlines the process of plaque assay for the viral titration of SARS-CoV-2.

Proper citation: Björn Meyer 2020. Viral Titration of SARS-COV-2 by Plaque Assay (Semi-Solid Agarose). protocols.io https://dx.doi.org/10.17504/protocols.io.be4zjgx6 Copy   

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Authors: Nicola O'Reilly, Svend Kjaer, Maria Greco
Group: Coronavirus Method Development Community, Crick COVID-19 Consortium
Summary: Purpose of examination / Clinical relevanceAt the end of 2019, several pneumonia cases were reported in Wuhan, China and the pathogen was confirmed as a new viral strain. World Health organization has named the newly identified coronavirus as 2019-nCoV, also known as COVID19. The disease developed into a dangerous pandemic, posing major challenges to the NHS. Although more research is necessary to better understand the virus, in response to the emergency, simple and rapid testing is essential to identify the virus in infected individuals. This will aid the implementation of efficient interventions to contain the spread, and distinguish healthcare workers who have been infected, and are required to self-isolate, from those showing similar symptoms but which are not 2019-nCoV associated. The latter category may continue to work, alleviating stress on hard-pressed healthcare resources. 2019-nCoV is an RNA virus, and the diagnostic tests detect viral RNA in swabs from patient airways using a reverse transcriptase PCR assay. Samples are submitted to HSL, an accredited reporting laboratory, and transferred to FCI for testing.Principles of ExaminationThis procedure involves the preparation of binding buffer for the RNA extraction protocol.

Proper citation: Nicola O'Reilly, Svend Kjaer, Maria Greco 2020. Preparation of Binding Buffer (BB). protocols.io https://dx.doi.org/10.17504/protocols.io.bfd2ji8e Copy   

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Authors: Shripal Gandhi, Santo Purnama, Keyur Patel, Praveen Sukumara, Dr Rinu R Ravi
Group: Coronavirus Method Development Community, SensingSelfMission, XPRIZE Rapid Covid Testing
Summary: Summary:The S1 COVID-19 Rapid Antigen test kit developed by Sensing Self Pte. Ltd. can quickly and qualitatively detect the spike glycoprotein of novel coronavirus (SARS-COV-2) in human saliva/sputum/stool samples. It can be used as an aid for COVID-19 diagnosis.Objective:According to the clinical trial plan, the S1 COVID-19 Rapid Antigen test kit or “test reagent”, is to test saliva/sputum/stool samples from healthy subjects and confirmed COVID-19 patients. Test results are compared with another commercial SARS-COV-2 nucleic acid detection kit with CFDA approval, which is defined as the “gold standard”. The sensitivity, specificity, and total agreement rate are used to evaluate the feasibility of the test reagent in clinical applications.Method:A collection of clinical samples were examined by the S1 COVID-19 Rapid Antigen test kit and the gold standard SARS-COV-2 nucleic acid detection kit in parallel, to calculate the clinical sensitivity, clinical specificity and total agreement rate of the test reagent.Results:Compared to the gold standard, the clinical sensitivity of test reagent reached 90.0%, the clinical specificity reached 100.0%, and the total coincidence rate reached 95.0%.Conclusions:The performance of test reagent has a high agreement rate with the gold standard, proving its good feasibility in diagnosing suspected COVID-19 cases.

Proper citation: Shripal Gandhi, Santo Purnama, Keyur Patel, Praveen Sukumara, Dr Rinu R Ravi 2020. SensingSelf S1 Rapid Antigen Test (Saliva/Sputum/Stool). protocols.io https://dx.doi.org/10.17504/protocols.io.bj6ykrfw Copy   

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