Landscape Coronavirus Disease 2019 test (COVID-19 test) in vitro -- A comparison of PCR vs Immunoassay vs Crispr-Based test

Bai, Huajun; Cai, Xiaolong; Zhang, Xiaoyan

doi:10.31219/osf.io/6eagn

Cited by 18 publications

(21 citation statements)

References 18 publications

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“…RT-qPCR tests are indeed useful at the early disease stage, when the virus can be detected in the respiratory tract. Immunological assays are more adapted for a later disease stage when IgM antibodies are detectable in the blood stream 3 to 6 days after the first onset of symptoms, while in parallel the viral load starts to decrease in the body and cannot be detected by RT-qPCR anymore [ 14 , 15 , 16 , 17 ]. Therefore, RT-qPCR was rapidly adopted as the primary diagnostic test to quickly detect SARS-CoV-2 and to take the necessary medical and quarantining measures in time.…”

Section: Introductionmentioning

confidence: 99%

Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection

Gand

Vanneste

Thomas

et al. 2020

IJMS

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The current COronaVIrus Disease 2019 (COVID-19) pandemic started in December 2019. COVID-19 cases are confirmed by the detection of SARS-CoV-2 RNA in biological samples by RT-qPCR. However, limited numbers of SARS-CoV-2 genomes were available when the first RT-qPCR methods were developed in January 2020 for initial in silico specificity evaluation and to verify whether the targeted loci are highly conserved. Now that more whole genome data have become available, we used the bioinformatics tool SCREENED and a total of 4755 publicly available SARS-CoV-2 genomes, downloaded at two different time points, to evaluate the specificity of 12 RT-qPCR tests (consisting of a total of 30 primers and probe sets) used for SARS-CoV-2 detection and the impact of the virus’ genetic evolution on four of them. The exclusivity of these methods was also assessed using the human reference genome and 2624 closely related other respiratory viral genomes. The specificity of the assays was generally good and stable over time. An exception is the first method developed by the China Center for Disease Control and prevention. NIID: National Institute for Infectious Diseases (CDC), which exhibits three primer mismatches present in 358 SARS-CoV-2 genomes sequenced mainly in Europe from February 2020 onwards. The best results were obtained for the assay of Chan et al. (2020) targeting the gene coding for the spiking protein (S). This demonstrates that our user-friendly strategy can be used for a first in silico specificity evaluation of future RT-qPCR tests, as well as verifying that the former methods are still capable of detecting circulating SARS-CoV-2 variants.

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Section: Introductionmentioning

confidence: 99%

Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection

Gand

Vanneste

Thomas

et al. 2020

IJMS

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“…CRISPR (clustered regularly interspaced short palindromic repeats) based RNA detection can achieve an attomolar (10 À 18 ) level within 30 min (Bai et al, 2020a). A low-cost and accurate CRISPR-Cas12 based lateral flow assay for detection of SARS-CoV-2 was reported (Broughton et al, 2020b).…”

Section: Rt-qpcr Dpcr Lamp and Crisprmentioning

confidence: 99%

Diagnostic methods and potential portable biosensors for coronavirus disease 2019

Cui

Zhou

2020

Biosensors and Bioelectronics

305

251

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Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre-including this research content-immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

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“…Results of CRISPR-based techniques can be identified using a plate reader, lateral flow visualization, or fluorescent colors. Although several off-target effects may exist, these systems have the potential to pave the way for the next generation of devices at POC level, even in under-resourced regions of the world [ 97 , 98 ].…”

Section: Covid-19 Detection At Poc Levelmentioning

confidence: 99%

Point of Care Diagnostics in the Age of COVID-19

et al. 2020

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The recent outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its associated serious respiratory disease, coronavirus disease 2019 (COVID-19), poses a major threat to global public health. Owing to the lack of vaccine and effective treatments, many countries have been overwhelmed with an exponential spread of the virus and surge in the number of confirmed COVID-19 cases. Current standard diagnostic methods are inadequate for widespread testing as they suffer from prolonged turn-around times (>12 h) and mostly rely on high-biosafety-level laboratories and well-trained technicians. Point-of-care (POC) tests have the potential to vastly improve healthcare in several ways, ranging from enabling earlier detection and easier monitoring of disease to reaching remote populations. In recent years, the field of POC diagnostics has improved markedly with the advent of micro- and nanotechnologies. Due to the COVID-19 pandemic, POC technologies have been rapidly innovated to address key limitations faced in existing standard diagnostic methods. This review summarizes and compares the latest available POC immunoassay, nucleic acid-based and clustered regularly interspaced short palindromic repeats- (CRISPR)-mediated tests for SARS-CoV-2 detection that we anticipate aiding healthcare facilities to control virus infection and prevent subsequent spread.

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Landscape Coronavirus Disease 2019 test (COVID-19 test) in vitro -- A comparison of PCR vs Immunoassay vs Crispr-Based test

Cited by 18 publications

References 18 publications

Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection

Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection

Diagnostic methods and potential portable biosensors for coronavirus disease 2019

Point of Care Diagnostics in the Age of COVID-19

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