Protocols   Select Another Resource Report Type

Authors: Teodor Emilov Mentov
Group: XPRIZE Rapid Covid Testing

Proper citation: Teodor Emilov Mentov 2020. Colorimetric RT-LAMP Research group SARS-COV-2 detection protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bk59ky96 Copy   

•   Source:

Authors: Koen Vandelannoote
Group: Coronavirus Method Development Community, XPRIZE Rapid Covid Testing, Koen Vandelannoote
Summary: Here, we describe a semi-automated workflow for paramagnetic bead-based extraction of SARS-CoV-2 RNA from human upper respiratory samples that uses low-cost repurposed Creality3D Ender-3 3D-printers and readily accessible reagents. The protocol described here is for the use of four instruments in parallel, each processing 24 samples, 96 samples per batch.

Proper citation: Koen Vandelannoote 2020. High-throughput SARS-CoV-2 RNA extraction from nasopharyngeal swabs using repurposed 3D printers.. protocols.io https://dx.doi.org/10.17504/protocols.io.bkynkxve Copy   

•   Source:

Authors: Noah Toppings
Group: XPRIZE Rapid Covid Testing

Proper citation: Noah Toppings 2020. RAPID RNA Extraction. protocols.io https://dx.doi.org/10.17504/protocols.io.bkp8kvrw Copy   

•   Source:

Authors: tclark , Ahmad Hashem, Jun Yong Ha, Charlie Mize
Group: XPRIZE Rapid Covid Testing

Proper citation: tclark , Ahmad Hashem, Jun Yong Ha, Charlie Mize 2020. Boston Biopharma CareStart™ Rapid Diagnostic Antigen Test. protocols.io https://dx.doi.org/10.17504/protocols.io.bkzxkx7n Copy   

•   Source:

Authors: dkt
Group: Coronavirus Method Development Community, XPRIZE Rapid Covid Testing

Proper citation: dkt 2020. u-Smell-it olfactory test  . protocols.io https://dx.doi.org/10.17504/protocols.io.bkxkkxkw Copy   

•   Source:

Authors: Don Cooper
Group: Coronavirus Method Development Community, XPRIZE Rapid Covid Testing

Proper citation: Don Cooper 2020. COVIDscanDX LAMP. protocols.io https://dx.doi.org/10.17504/protocols.io.bk4dkys6 Copy   

•   Source:

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 S4 Multiplex Covid-19 /MERS-CoV/ Influenza A/B Rapid Antigens Test Kit developed by Sensing Self Pte. Ltd. can quickly and qualitatively detect Novel Coronavirus / Influenza A/ Influenza B /MERS in human saliva/sputum/stool samples. It can be used as an aid for COVID-19 diagnosis. It provides an aid in the diagnosis of infection by the above viruses.Objective:According to the clinical trial plan, the S4 Multiplex Covid-19 /MERS-CoV/ Influenza A/B Rapid Antigen test kit or “test reagent”, is to test saliva/sputum/stool samples from healthy subjects and confirmed patients with infections caused by these viruses. Test results are compared with another commercial Covid-19 /MERS-CoV/ Influenza A/B nucleic acid detection kit, 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 S4 Multplex Covid-19 /MERS-CoV/ Influenza A/B Rapid Antigen test kit and the gold standard SARS-COV-2/MERS-CoV/ Influenza A/B nucleic acid detection kit in parallel, to calculate the clinical sensitivity, clinical specificity and total agreement rate of the test reagent.Results:For SARS-CoV-2, compared to the gold standard:In Saliva, the clinical sensitivity of test reagent reached 88.3%, the clinical specificity reached 100.0%In Sputum, the clinical sensitivity of test reagent reached 93.3%, the clinical specificity reached 100.0% In Stool, the clinical sensitivity of test reagent reached 93.3%, the clinical specificity reached 100.0%For MERS, compared to the gold standard:In Saliva, the clinical sensitivity of test reagent reached 86%, the clinical specificity reached 100.0%In Sputum, the clinical sensitivity of test reagent reached 90%, the clinical specificity reached 100.0% In Stool, the clinical sensitivity of test reagent reached 90%, the clinical specificity reached 100.0%For Influenza Virus A, compared to the gold standard:In Saliva, the clinical sensitivity of test reagent reached 85.7%, the clinical specificity reached 98.3%In Sputum, the clinical sensitivity of test reagent reached 91.4%, the clinical specificity reached 100.0% In Stool, the clinical sensitivity of test reagent reached 90%, the clinical specificity reached 100.0%For Influenza Virus B, compared to the gold standard:In Saliva, the clinical sensitivity of test reagent reached 82.9%, the clinical specificity reached 100.0%In Sputum, the clinical sensitivity of test reagent reached 87.1%, the clinical specificity reached 96.7% In Stool, the clinical sensitivity of test reagent reached 85.7%, the clinical specificity reached 98.3%Conclusions:The performance of test reagent has a high agreement rate with the gold standard, proving its good feasibility in diagnosing suspected Covid-19 /MERS-CoV/ Influenza A/B cases.

Proper citation: Shripal Gandhi, Santo Purnama, Keyur Patel, Praveen Sukumara, Dr Rinu R Ravi 2020. SensingSelf S4 Multiplex Covid-19 /MERS-CoV/ Influenza A/B Rapid Antigens Test Kit (Saliva/Sputum/Stool). protocols.io https://dx.doi.org/10.17504/protocols.io.bkwckxaw Copy   

•   Source:

Authors: Randy True
Group: FloodLAMP, XPRIZE Rapid Covid Testing
Summary: The Inactivation Solution includes TCEP, EDTA, NaOH, and water. It should be made in a chemical fume hood, as the TCEP is caustic. It is very straightforward to make if starting with liquid-form TCEP. We have not made it with powder-form TCEP, which is about 30% cheaper at low volume retail prices from Sigma. We have yet to do long-term stability studies; however, we think it's fine stored at room temperature for at least a few weeks. If yellow Binding Solution does not go clear upon addition to an inactivated sample or PBS+Inactivation Soln, suspect that the Inactivation Solution may have degraded, and repeat with another aliquot or freshly-made Inactivation Solution.It has also been suggested by Albert Yu of Brandeis has recommended using a 1.4N NaOH concentration for saliva instead of 1.15N NaOH. NaOH should be scale up by 1.4/1.15 and water down for this.

Proper citation: Randy True 2020. FloodLAMP Inactivation Solution Prep v1.0. protocols.io https://dx.doi.org/10.17504/protocols.io.bk5qky5w Copy   

•   Source:

Authors: peijun he
Group: Coronavirus Method Development Community, XPRIZE Rapid Covid Testing, Highfield Diagnostics
Summary: Coronavirus Lateral Flow Assay (LFA) sample preparation protocol

Proper citation: peijun he 2020. Coronavirus Lateral Flow Assay (LFA) sample preparation protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bksfkwbn Copy   

•   Source:

Authors: philippe.bechtold
Group: XPRIZE Rapid Covid Testing

Proper citation: philippe.bechtold 2020. Thermal cycling of the PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.bk6jkzcn Copy   

•   Source:

Authors: goncalo.doria
Group: XPRIZE Rapid Covid Testing
Summary: Instruction of use for Doctor Vida pocket - COVID-19 assay

Proper citation: goncalo.doria 2020. Doctor Vida Pocket - COVID-19 assay - Instructions for Use. protocols.io https://dx.doi.org/10.17504/protocols.io.bkc8kszw Copy   

•   Source:

Authors: Charlie Mize, Raj Reddy, Purav Badani
Group: Canary, XPRIZE Rapid Covid Testing

Proper citation: Charlie Mize, Raj Reddy, Purav Badani 2020. Canary VOC testing protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bkm4ku8w Copy   

•   Source:

Authors: Prem Premsrirut, Ana Vasileva, Huiting Cheng
Group: Coronavirus Method Development Community, XPRIZE Rapid Covid Testing
Summary: OverviewAt the start of the Pandemic in the US, New York was hit with more cases of COVID-19 than any single country in the world. Although case numbers are finally at an all-time low, the question of how to safely reopen the economy, school and businesses still remains unclear. Today, SARS-CoV-2 detection via RT-PCR methods remains the gold standard to detect active infection and recommend isolation of individuals in order to prevent further spread. Unfortunately, the cost and bottlenecks created from repeated massive testing efforts have become unsustainable. As a way to address this issue, we have devised a strategy of pooling samples and testing entire populations together as one unit. This cuts the cost of testing dramatically and still enables the detection of a susceptible group that would need to undergo individual testing.To meet the COVID-19 testing demands, we created an organizational-based pooling strategy, whereby organizations can enroll in surveillance testing to monitor groups of people through pooled testing. By using organizational-based pooling, we avoid random pooling of samples. Instead, we pool groups of known contacts from a defined workplace, school or organization where people regularly interact. Therefore, a positive case would likely have an impact on the entire pooled population and the entire pooled population can be treated as an infected cohort until further individual testing, potentially, through a healthcare provider is recommended or offered.Method of Pooled TestingFor pooled surveillance testing to be effective and widely adopted, sample collection methods must also be simplified and non-invasive in order to achieve high compliance and enrollment into a surveillance program. The method of testing must also be highly sensitive to accurately detect one positive case in a large pool of negative samples. For these reasons, we developed a simple saliva collection method with a validated pooled saliva specimens using RT-PCR and an acceptable limit of detection, which will be the most sensitive diagnostic test to date. We established automated methods to pool up to 24 saliva specimens and if a positive case is detected, the pools can be further broken down to pools of 2 specimens. The remaining 2 individuals within a pool will be referred to or, potentially, offered further clinical diagnostic testing by a healthcare provider.

Proper citation: Prem Premsrirut, Ana Vasileva, Huiting Cheng 2020. Mirimus COVID-19 Pool Surveillance RT-PCR Testing. protocols.io https://dx.doi.org/10.17504/protocols.io.bkv3kw8n Copy   

•   Source:

Authors: Jon Arizti-Sanz, Catherine A. Freije, Chloe K. Boehm, Sameed M. Siddiqui, Allen M. Goodman, Tinna-Solveig F. Kosoko-Thoroddsen, A'Doriann Y. Bradley, Jeremy Johnson, Pardis C. Sabeti, Cameron Myhrvold
Group: XPRIZE Rapid Covid Testing
Summary: This protocol describes how to perform a SHINE in-tube fluorescent assay to detect SARS-CoV-2 RNA from a self-collected nasopharyngeal sample. This protocol is intended for point-of-care use. All enzymatic components are provided as a single-test freeze-dried pellet for shelf-stable storage, and all steps of the protocol are performed at ambient temperature. The protocol requires a transilluminator or another equivalent blue light emitting device. The protocol presented here is an improved version of the method presented in Arizti-Sanz J*, Freije CA*, et al. Integrated sample inactivation, amplification, and Cas13-based detection of SARS-CoV-2. bioRxiv (2020).

Proper citation: Jon Arizti-Sanz, Catherine A. Freije, Chloe K. Boehm, Sameed M. Siddiqui, Allen M. Goodman, Tinna-Solveig F. Kosoko-Thoroddsen, A'Doriann Y. Bradley, Jeremy Johnson, Pardis C. Sabeti, Cameron Myhrvold 2020. XPRIZE SHINE - In-tube Fluorescent SARS-CoV-2 Saliva Test. protocols.io https://dx.doi.org/10.17504/protocols.io.bk3rkym6 Copy   

•   Source:

Authors: Ivan Rueda, peter.marx
Group: XPRIZE Rapid Covid Testing, Biology Works LLC
Summary: This protocol is the laboratory-based equivalent of the LAMP assay used for detecting SARS-CoV-2. A similar protocol is performed automatically within the Biology Works LLC at-home device.

Proper citation: Ivan Rueda, peter.marx 2020. BW SARS-CoV-2 Laboratory Test. protocols.io https://dx.doi.org/10.17504/protocols.io.bkztkx6n Copy   

•   Source:

Authors: samz
Group: Coronavirus Method Development Community, XPRIZE Rapid Covid Testing

Proper citation: samz 2020. AMDx Lateral Flow Assay WIth a Cover Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bk54ky8w Copy   

•   Source:

Authors: yliu
Group: OnsiteGene 1, XPRIZE Rapid Covid Testing
Summary: This OnsiteGene protocol is designed for testing the nasal swab samples with a superfast nucleic acid extraction procedure and a superfast real-time PCR procedure. It uses the Star Array® Hi-SenseTM COVID-19 Molecular Testing Kit 1.0 in the one-step real-time RT-qPCR test assay to qualitatively detect RNA from SARS-CoV-2 virus in the human respiratory specimen. It combines the reverse transcription technology and real-time PCR method to provide accurate detection of the SARS-CoV-2 coronavirus. The Star Array® magnetic beads RNA extraction instrument and kit can automatically extract and purify the RNA for 32 samples in 6 minutes. It is ideal for samples that contain high amount of PCR inhibitors and can't be processed by the direct amplification. The triplex fluorescence design of the kit simultaneously detects the N1 and Orf1ab genes of the virus and the human RNase P gene as an internal control to ensure the sample quality. This protocol uses the Star Array® XDiveTM Superfast Real-Time PCR instrument to perform 40-cycle PCR in 8 minutes, and can test up to 16 samples or controls in each run. The total protpcol time from sample collection to data interpretation is less than 15 minutes.

Proper citation: yliu 2020. OnsiteGene 3 Protocol Nasal Extract. protocols.io https://dx.doi.org/10.17504/protocols.io.bkugkwtw Copy   

•   Source:

Authors: Don Cooper, Timothy Wandell, ben
Group: XPRIZE Rapid Covid Testing

Proper citation: Don Cooper, Timothy Wandell, ben 2020. NuFaction SARS-CoV2 Antigen Test Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bkv2kw8e Copy   

•   Source:

Authors: Ladislav Nevery
Group: Coronavirus Method Development Community, XPRIZE Rapid Covid Testing, Ladislav Nevery
Summary: By passing saliva sample thru 150nm filter to remove particles larger than avg 125nm sized covid 19 virus particles and concentrating resulting fluid to very small 1 mm2 area of 110nm filter. Pores in this small area should be clogged up fast raising filter air/fluid resistance. Due to high virus density 5.2 log10 ml saliva of infected person should clogg filter much faster than healthy person. Test is setup in such way that we let gravity pass 2l of fluid thru clogged filter and record rate of drops from its bottom as audio on mobile phone placed bellow glass cup. rate of drops thru clogged filter should be measurably slower than clean filter.

Proper citation: Ladislav Nevery 2020. covid 19 indirect detection thru rise of 100nm filter fluid resistance. protocols.io https://dx.doi.org/10.17504/protocols.io.bmazk2f6 Copy   

•   Source:

Authors: bill , covidtesting
Group: XPRIZE Rapid Covid Testing

Proper citation: bill , covidtesting 2020. V-CHEK Coronavirus (SARS-CoV-2) Antigen Detection Kit. protocols.io https://dx.doi.org/10.17504/protocols.io.bkwukxew Copy   

•   Source: