Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351

Erster, Oran; Mendelson, Ella; Levy, Virginia; Kabat, Areej; Mannasse, Batya; Asraf, Hadar; Azar, Roberto; Ali, Yaniv; Shirazi, Rachel; Bucris, Efrat; Bar-Ilan, Dana; Mandelboim, Michal; Sofer, Danit; Fleishon, Shai; Zuckerman, Neta S.

doi:10.1128/spectrum.00506-21

Cited by 24 publications

(28 citation statements)

References 18 publications

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“…We recently developed quantitative PCR (qPCR)-based molecular tests that target mutations that are strongly associated with variants Alpha and Beta, thereby enabling rapid classification of such samples with high confidence. We demonstrated that the selected target mutations successfully reflect the lineage of the examined sample, as confirmed by Sanger and whole-genome sequencing ( 17 ). In this report, we describe the development and utilization of two qPCR tests that target mutations that are, thus far, unique to variant B.1.617 (Delta lineage).…”

Section: Introductionmentioning

confidence: 74%

Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay

et al. 2022

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The new assays described herein enable rapid, straightforward, and cost-effective detection of severe acute respiratory syndrome coronavirus 2 (SC-2) with immediate classification of the examined sample as Alpha, Delta, non-Alpha, or non-Delta variant. This is highly important for two main reasons: (i) it provides the scientific and medical community with a novel diagnostic tool to rapidly detect and classify any SC-2 sample of interest as Alpha, Delta, or none and can be applied to both clinical and environmental samples, and (ii) it demonstrates how to respond to the emergence of new variants of concern by developing a variant-specific assay.

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Section: Introductionmentioning

confidence: 74%

Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay

et al. 2022

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“…Clinical samples were prepared as described previously (Erster et al 2021a). Briefly, nasopharyngeal swabs were collected from patients for diagnostic purpose.…”

Section: Methodsmentioning

confidence: 99%

“…The rapid pace in which SARS-COV-2 (SC-2) variants emerge and spread globally, poses a substantial challenge for efficient surveillance, rendering cell culturing and whole genome sequencing often insufficient for providing fast and reliable data. We previously demonstrated that rapid, affordable and high throughput differentiation between co-circulating SC-2 variants can be accomplished using multiplex quantitative PCR (qPCR), and that this approach can complement and, in some cases, outperform genomic sequencing and similar approaches, for SC-2 variant identification (Erster et al 2021a, Erster et al 2021b). More recently, we reported on the development of qPCR-based assays that specifically identify BA.1 samples and allow straightforward scaling-up for high throughput testing (Erster et al 2022).…”

Section: Introductionmentioning

confidence: 99%

NOVEL RT-qPCR ASSAYS ENABLE RAPID DETECTION AND DIFFERENTIATION BETWEEN SARS-COV-2 OMICRON (BA.1) AND BA.2 VARIANTS

Erster

Kabat

Asraf

et al. 2022

Preprint

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In this report, we describe the development and initial validation of novel SARS-COV-2 Omicron-specific reactions that enable the identification of Omicron (BA.1) and BA.2 variants. Mutations that are either shared by both BA.1 and BA.2, or are exclusive for BA.1 or for BA.2 were identified by bioinformatic analysis, and corresponding probe-based quantitative PCR reactions were developed to identify them. We show that multiplex combinations of these reactions provide a single-reaction identification of the sample as BA.1, BA.2, or as non-Omicron SARS-COV-2. All four reactions described herein have a sensitivity of less than ten copies per reaction, and are amendable for multiplexing. The results of this study suggest that the new assays may be useful for testing both clinical and environmental samples to differentiate between these two variants.

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“…With this technique, in April 2021, the presence of key mutations of 20I/501Y.V1 and 20 J/501Y.V3 in the new SARS-CoV-2 variant were detected [ 105 ]. Several types of multiplex RT-qPCR targeting single nucleotide polymorphisms [ 106 , 107 , 108 , 109 , 110 ], TaqMan SARS-CoV-2 mutation panel molecular assay [ 111 , 112 ], combinations of novel PCR assays and genome sequencing [ 113 ], or CRISPR-Cas12-based multiplex allele-specific assay [ 114 ], just to mention a few, were able to identify VOCs, and, moreover, these tests can adapt to emerging viruses’ lineages.…”

Section: New Variants Emergence Require Tests Upgrading?mentioning

confidence: 99%

Testing Antigens, Antibodies, and Immune Cells in COVID-19 as a Public Health Topic—Experience and Outlines

Neagu

Constantin

Surcel

2021

IJERPH

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The current COVID-19 pandemic has triggered an accelerated pace in all research domains, including reliable diagnostics methodology. Molecular diagnostics of the virus and its presence in biological samples relies on the RT-PCR method, the most used and validated worldwide. Nonconventional tests with improved parameters that are in the development stages will be presented, such as droplet digital PCR or CRISPR-based assays. These molecular tests were followed by rapid antigen testing along with the development of antibody tests, whether based on ELISA platform or on a chemiluminescent microparticle immunoassay. Less-conventional methods of testing antibodies (e.g., lateral flow immunoassay) are presented as well. Left somewhere in the backstage of COVID-19 research, immune cells and, furthermore, immune memory cells, are gaining the spotlight, more so in the vaccination context. Recently, methodologies using flow-cytometry evaluate circulating immune cells in infected/recovered patients. The appearance of new virus variants has triggered a surge for tests improvement. As the pandemic has entered an ongoing or postvaccination era, all methodologies that are used to monitor public health focus on diagnostic strategies and this review points out where gaps should be filled in both clinical and research settings.

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Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351

Cited by 24 publications

References 18 publications

Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay

Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay

NOVEL RT-qPCR ASSAYS ENABLE RAPID DETECTION AND DIFFERENTIATION BETWEEN SARS-COV-2 OMICRON (BA.1) AND BA.2 VARIANTS

Testing Antigens, Antibodies, and Immune Cells in COVID-19 as a Public Health Topic—Experience and Outlines

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