ArticleDiagnostics (Basel, Switzerland)2021
Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection.
Article in Diagnostics (Basel, Switzerland), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 17 citations in OpenAlex.
- Severe mpox in an immunocompromised patient complicated by deep tissue infection: A case report.Heliyon · 2024Article
- Multiplexed RT-qPCR Coupled with Whole-Genome Sequencing to Monitor a SARS-CoV-2 Omicron Variant of Concern in a Hospital Laboratory Setting in Latvia.Diagnostics (Basel, Switzerland) · 2023Article
- Sotrovimab in Hospitalized Patients with SARS-CoV-2 Omicron Variant Infection: a Propensity Score-Matched Retrospective Cohort Study.Microbiology spectrum · 2023Article
- A performance comparison of heterostructure surface plasmon resonance biosensor for the diagnosis of novel coronavirus SARS-CoV-2.Optical and quantum electronics · 2023Article
- Variant-specific RT-qPCR for rapid screening of B.1.617 mutations in SARS-CoV-2.The Libyan journal of medicine · 2022Article
- Clinical efficacy and in vitro neutralization capacity of monoclonal antibodies for severe acute respiratory syndrome coronavirus 2 delta and omicron variants.Journal of medical virology · 2022Article
- The puzzling mutational landscape of the SARS-2-variant Omicron.Journal of medical virology · 2022Article
- Article
- Nucleic acid testing of SARS-CoV-2: A review of current methods, challenges, and prospects.Frontiers in microbiology · 2022Review
- Special Issue "Molecular Detection and Typing of Viruses".Diagnostics (Basel, Switzerland) · 2021Article
- Biosensors for Point Mutation Detection.Frontiers in bioengineering and biotechnology · 2021Article
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Authors and funding
11 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe recent emergence of distinct and highly successful SARS-CoV-2 lineages has substantial implications for individual patients and public health measures. While next-generation-sequencing is routinely performed for surveillance purposes, RT-qPCR can be used to rapidly rule-in or rule-out relevant variants, e.g., in outbreak scenarios. The objective of this study was to create an adaptable and comprehensive toolset for multiplexed Spike-gene SNP detection, which was applied to screen for SARS-CoV-2 B.1.617 lineage variants.
methodsWe created a broad set of single nucleotide polymorphism (SNP)-assays including del-Y144/145, E484K, E484Q, P681H, P681R, L452R, and V1176F based on a highly specific multi-LNA (locked nucleic acid)-probe design to maximize mismatch discrimination. As proof-of-concept, a multiplex-test was compiled and validated (SCOV2-617VOC-UCT) including SNP-detection for L452R, P681R, E484K, and E484Q to provide rapid screening capabilities for the novel B.1.617 lineages.
resultsFor the multiplex-test (SCOV2-617VOC-UCT), the analytic lower limit of detection was determined as 182 IU/mL for L452R, 144 IU/mL for P681R, and 79 IU/mL for E484Q. A total of 233 clinical samples were tested with the assay, including various on-target and off-target sequences. All SNPs (179/179 positive) were correctly identified as determined by SARS-CoV-2 whole genome sequencing.
conclusionThe recurrence of SNP locations and flexibility of methodology presented in this study allows for rapid adaptation to current and future variants. Furthermore, the ability to multiplex various SNP-assays into screening panels improves speed and efficiency for variant testing. We show 100% concordance with whole genome sequencing for a B.1.617.2 screening assay on the cobas6800 high-throughput system.
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