ArticleJournal of medical virology2021
Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State.
Article in Journal of medical virology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 36 citations in OpenAlex.
- Comparison of analytical performance and economic value of two biosurveillance methods for tracking SARS-COV-2 variants of concern.Microbiology spectrum · 2024Article
- SARS-CoV-2 viral variants can rapidly be identified for clinical decision making and population surveillance using a high-throughput digital droplet PCR assay.Scientific reports · 2023Article
- Dynamics of SARS-CoV-2 VOC Neutralization and Novel mAb Reveal Protection against Omicron.Viruses · 2023Article
- Ready for new waves: optimizing SARS-CoV-2 variants monitoring in pooled samples with droplet digital PCR.Frontiers in public health · 2023Article
- Digital PCR Applications in the SARS-CoV-2/COVID-19 Era: a Roadmap for Future Outbreaks.Clinical microbiology reviews · 2022Review
- Rapid and accurate identification of SARS-CoV-2 Omicron variants using droplet digital PCR (RT-ddPCR).Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2022Article
- Multiplex Fragment Analysis for Flexible Detection of All SARS-CoV-2 Variants of Concern.Clinical chemistry · 2022Article
- A Method for Variant Agnostic Detection of SARS-CoV-2, Rapid Monitoring of Circulating Variants, and Early Detection of Emergent Variants Such as Omicron.Journal of clinical microbiology · 2022Article
- Identification of Omicron-Delta Coinfections Using PCR-Based Genotyping.Microbiology spectrum · 2022Article
- Evaluation of a Rapid and Accessible Reverse Transcription-Quantitative PCR Approach for SARS-CoV-2 Variant of Concern Identification.Journal of clinical microbiology · 2022Article
- The ins and outs of SARS-CoV-2 variants of concern (VOCs).Archives of virology · 2022Review
- Rapid and Accurate Identification of SARS-CoV-2 Variants Using Real Time PCR Assays.Frontiers in cellular and infection microbiology · 2022Article
- Article
- Highly Sensitive Detection Method for HV69-70del in SARS-CoV-2 Alpha and Omicron Variants Based on CRISPR/Cas13a.Frontiers in bioengineering and biotechnology · 2022Article
- Development of a panel of three multiplex allele-specific qRT-PCR assays for quick differentiation of recombinant variants and Omicron subvariants of SARS-CoV-2.Frontiers in cellular and infection microbiology · 2022Article
- CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern.Microbiology spectrum · 2021Article
- Diagnostic, Prognostic, and Therapeutic Value of Droplet Digital PCR (ddPCR) in COVID-19 Patients: A Systematic Review.Journal of clinical medicine · 2021Review
- Single-Amplicon Multiplex Real-Time Reverse Transcription-PCR with Tiled Probes To Detect SARS-CoV-2Journal of clinical microbiology · 2021Article
- Finding the Middle Ground with the Clinical Laboratory's Role in SARS-CoV-2 Genomic Surveillance.Journal of clinical microbiology · 2021Article
- Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State.Journal of medical virology · 2021Article
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Authors and funding
14 authors at 1 institution in 1 country.
Funding
Abstract
Real-time epidemiological tracking of variants of concern (VOCs) can help limit the spread of more contagious forms of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), such as those containing the N501Y mutation. Typically, genetic sequencing is required to be able to track VOCs in real-time. However, sequencing can take time and may not be accessible in all laboratories. Genotyping by RT-ddPCR offers an alternative to rapidly detect VOCs through discrimination of specific alleles such as N501Y, which is associated with increased transmissibility and virulence. Here we describe the first cases of the B.1.1.7 lineage of SARS-CoV-2 detected in Washington State by using a combination of reverse-transcription polymerase chain reaction (RT-PCR), RT-ddPCR, and next-generation sequencing. We initially screened 1035 samples positive for SARS-CoV-2 by our CDC-based laboratory-developed assay using ThermoFisher's multiplex RT-PCR COVID-19 assay over four weeks from late December 2020 to early January 2021. S gene target failures (SGTF) were subsequently assayed by RT-ddPCR to confirm four mutations within the S gene associated with the B.1.1.7 lineage: a deletion at amino acid (AA) 69-70 (ACATGT), deletion at AA 145, (TTA), N501Y mutation (TAT), and S982A mutation (GCA). All four targets were detected in two specimens; follow-up sequencing revealed a total of 9 mutations in the S gene and phylogenetic clustering within the B.1.1.7 lineage. Next, we continued screening samples for SGTF detecting 23 additional B.1.1.7 variants by RT-ddPCR and confirmed by sequencing. As VOCs become increasingly prevalent, molecular diagnostic tools like RT-ddPCR can be utilized to quickly, accurately, and sensitively distinguish more contagious lineages of SARS-CoV-2.
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