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Authors: Sarah Reiling, Josh Quick, Ioannis Ragoussis
Group: Coronavirus Method Development Community, McGill Genome Centre
Summary: 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

Proper citation: 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 Copy   

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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 v2. protocols.io https://dx.doi.org/10.17504/protocols.io.bqvnmw5e Copy   

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Authors: Neha Mittal, Vbarua , Nick Stark, Cynthia Gibas, jschluet , Mariya Munir
Group: Coronavirus Method Development Community, UNC Charlotte COVID WBE

Proper citation: Neha Mittal, Vbarua , Nick Stark, Cynthia Gibas, jschluet , Mariya Munir 2021. RNA Extraction of SARS-CoV-2 from Wastewater. protocols.io https:// Copy   

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Authors: Nikki Freed, Olin Silander
Group: Coronavirus Method Development Community

Proper citation: 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 Copy   

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Authors: Muhammad Faisal, Olin Silander, Nikki Freed
Group: Coronavirus Method Development Community

Proper citation: 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 Copy   

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Authors: Shadi Emam, nasrollahpourmotla.m , n.sun
Group: Coronavirus Method Development Community, XPRIZE Rapid Covid Testing

Proper citation: 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 Copy   

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Authors: 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
Group: Coronavirus Method Development Community, Reclone.org (The Reagent Collaboration Network)

Proper citation: 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:// Copy   

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Authors: Max Marrone
Group: Coronavirus Method Development Community, Opentrons COVID-19 Testing

Proper citation: 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 Copy   

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Authors: Megan Folkerts, Ashlyn Pfeiffer, mnguyen , Danielle Vazquez, Amber Jones
Group: Coronavirus Method Development Community
Summary: 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.

Proper citation: 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 Copy   

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Authors: Judy Northill, Ian Mackay
Group: protocols.io Ambassadors, Public Health Virology, Forensic and Scientific Services, Coronavirus Method Development Community
Summary: 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)

Proper citation: 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 Copy   

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Authors: 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
Group: protocols.io Ambassadors, Public Health Virology, Forensic and Scientific Services, Coronavirus Method Development Community
Summary: 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.

Proper citation: 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 Copy   

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Authors: Harley King
Group: Coronavirus Method Development Community, USG Fall 2020 BSCI:414, protocols.io for Educators

Proper citation: Harley King 2020. BSCI:414 Lab 8 Transform and Miniprep Plasmid Containing SARS-CoV-2 Spike Gene. protocols.io https:// Copy   

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Authors: Bei Wang, Wen-Hsin Sandy Lee, Cheng-I Wang
Group: Coronavirus Method Development Community

Proper citation: 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 Copy   

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Authors: Aaron Bivins, Warish Ahmed, Devin North, Kyle Bibby
Group: Coronavirus Method Development Community, 2019-nCoV Wastewater Epidemiology

Proper citation: 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:// Copy   

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Authors: Ainhoa Goñi-Salaverri, Jose A. Rodriguez, Nicholas Weber, Juan Pablo Unfried, Josepmaria Argemi, , David Lara Astiaso,
Group: Coronavirus Method Development Community
Summary: 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.

Proper citation: 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 Copy   

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Authors: Stephanie Loeb, Katy Graham, David Catoe, Marlene Wolfe, Alexandria Boehm, Krista Wigginton
Group: Coronavirus Method Development Community, Wastewater-based epidemiology working group
Summary: 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.

Proper citation: 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 Copy   

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Authors: Hsiao-Chung Tsai
Group: Coronavirus Method Development Community, ProtectLife-AnTaimmu, XPRIZE Rapid Covid Testing

Proper citation: Hsiao-Chung Tsai 2020. ENNOLIFE SARS-CoV-2 Antigen Test Kit Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bke3ktgn Copy   

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Authors: Emil Aarre Sorensen, Søren M. Karst, Simon Knutsson
Group: AlbertsenLab, Coronavirus Method Development Community
Summary: 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

Proper citation: 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 Copy   

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Authors:
Group: Coronavirus Method Development Community, Narwhale for XPrize

Proper citation: 2020. GM Covid-19 saliva test (v2). protocols.io https:// Copy   

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Authors: Sarah Reiling, Anne-Marie Roy, Shu-Huang Chen, Josh Quick, Ioannis Ragoussis
Group: Coronavirus Method Development Community, McGill Genome Centre
Summary: Artic nCoV-2019 McGill modified Lunascript Reverse Transcriptase nanopore sequencing protocol.

Proper citation: 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 Copy   

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