ArticleJournal of clinical virology : the official publication of the Pan American Society for Clinical Virology2021
Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7.
Article in Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Multiplex RT-qPCR strategy for SARS-CoV-2 variants detection in developing countries without ngs: The Bolivian experience.Epidemiology and infection · 2025Article
- Disappearance of Imported Cases of Omicron Lineage BA.2.40 in West Kalimantan, Indonesia.Iranian journal of medical sciences · 2024Article
- New Postmortem Perspective on Emerging SARS-CoV-2 Variants of Concern, Germany.Emerging infectious diseases · 2023Article
- Sotrovimab in Hospitalized Patients with SARS-CoV-2 Omicron Variant Infection: a Propensity Score-Matched Retrospective Cohort Study.Microbiology spectrum · 2023Article
- Rapid Assessment of SARS-CoV-2 Variant-Associated Mutations in Wastewater Using Real-Time RT-PCR.Microbiology spectrum · 2023Article
- Double N501Y mutation hindering its detection by RT-PCR kit widely used at Clinical Microbiology laboratories.Enfermedades infecciosas y microbiologia clinica (English ed.) · 2023Article
- [Double N501Y mutation hindering its detection by RT-PCR kit widely used at Clinical Microbiology laboratories].Enfermedades infecciosas y microbiologia clinica · 2023Article
- Review
- Spike protein of SARS-CoV-2 variants: a brief review and practical implications.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2022Review
- SARS-CoV-2 Variants in Paraguay: Detection and Surveillance with an Economical and Scalable Molecular Protocol.Viruses · 2022Article
- Comparing susceptibility and contagiousness in concurrent outbreaks with a non-VOC and the VOC SARS-CoV-2 variant B.1.1.7 in daycare centers in Hamburg, Germany.International journal of hygiene and environmental health · 2022Article
- Evaluation and Validation of the Roche Elecsys SARS-CoV-2 Antigen Electro-Chemiluminescent Immunoassay in a Southeast Asian Region.Vaccines · 2022Article
- Article
- Performance evaluation of Novaplex SARS-CoV-2 variants assay kit series for SARS-CoV-2 detection using single nucleotide polymorphisms.Access microbiology · 2022Article
- SARS-CoV-2 Blood RNA Load Predicts Outcome in Critically Ill COVID-19 Patients.Open forum infectious diseases · 2021Article
- Surveillance of SARS-CoV-2 lineage B.1.1.7 in Slovakia using a novel, multiplexed RT-qPCR assay.Scientific reports · 2021Article
- Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection.Diagnostics (Basel, Switzerland) · 2021Article
- Fatal COVID-19 in a Child with Persistence of SARS-CoV-2 Despite Extensive Multidisciplinary Treatment: A Case Report.Children (Basel, Switzerland) · 2021Article
- Modifying a Diagnostic SARS-CoV-2 Spike PCR to Turn a Del69/70 Dropout into a Discriminatory On-Target Assay.The Journal of molecular diagnostics : JMD · 2021Article
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Abstract
backgroundNew SARS-CoV-2 variants with increased transmissibility, like B.1.1.7, first detected in England or B.1.351, first detected in South Africa, have caused considerable concern worldwide. In order to contain the spread of these lineages, it is of utmost importance to have rapid, sensitive and high-throughput detection methods at hand.
methodsA set of RT-qPCR assays was modified for a diagnostic SARS-CoV-2 multiplex assay including detection of the del-HV69/70 and N501Y mutations on the cobas6800 platform. Analytical sensitivity was assessed for both wild-type SARS-CoV-2 and B.1.1.7 lineage by serial dilution. For clinical performance, a total of 176 clinical samples were subjected to the test and results compared to a commercial manual typing-PCR assay and next generation sequencing as gold standard.
resultsThe multiplex assay was highly sensitive for detection of SARS-CoV-2 RNA in clinical samples, with an LoD of 6.16 cp/ml (CI: 4.00-8.31). LoDs were slightly higher for detection of the HV69/70 deletion (85.92, CI: 61-194.41) and the N501Y SNP (105.99 cp/ml, CI: 81.59 - 183.66). A total of 176 clinical samples were tested with the assay, including 50 samples containing SARS-CoV-2 of the B.1.1.7 lineage, one containing B.1.351 and 85 non-B.1.1.7/B.1.351 lineage, of which three also harbored a HV69/70 deletion. All were correctly identified by the multiplex assay.
conclusionWe describe here a highly sensitive, fully automated multiplex PCR assay for the simultaneous detection of the del-HV69/70 and N501Y mutations that can distinguish between B.1.1.7 and other lineages. The assay allows for high-throughput screening for currently relevant variants in clinical samples prior to sequencing.
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