ArticleJournal of clinical microbiology2021
Multiplex SARS-CoV-2 Genotyping Reverse Transcriptase PCR for Population-Level Variant Screening and Epidemiologic Surveillance.
Article in Journal of clinical microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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Who cites it
71 citing papers in PubMed, 93 citations in OpenAlex.
- Evaluation of Acebilustat, a Selective Inhibitor of Leukotriene B4 Biosynthesis, for Treatment of Outpatients With Mild-Moderate Coronavirus Disease 2019: A Randomized, Double-Blind, Placebo-Controlled Phase 2 Trial.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2023Trial
- One confirmed and one potential human case of influenza A(H5N1) detected through an expanded subtyping protocol.ASM case reports · 2026Article
- Outcomes of immunocompromised and non-immunocompromised patients in the ICU diverge late in the pandemic.PloS one · 2026Article
- Comprehensive metabolomics combined with machine learning for the identification of SARS-CoV-2 and other viruses directly from upper respiratory samples.Journal of clinical microbiology · 2025Article
- Application of novel dark-quencher labeled probes in multiplex qRT-PCR assays for rapid detection of SARS-CoV-2 variants.Journal of thoracic disease · 2025Article
- Development of multiplex allele-specific RT-qPCR assays for differentiation of SARS-CoV-2 Omicron subvariants.Applied microbiology and biotechnology · 2024Article
- Deep Learning Enabled Universal Multiplexed Fluorescence Detection for Point-of-Care Applications.ACS sensors · 2024Article
- A response playbook for early detection and population surveillance of new SARS-CoV-2 variants in a regional public health laboratory.BMC public health · 2024Article
- An Open One-Step RT-qPCR for SARS-CoV-2 detection.PloS one · 2024Article
- Epidemiological Insights into the Omicron Outbreak via MeltArray-Assisted Real-Time Tracking of SARS-CoV-2 Variants.Viruses · 2023Article
- Multiplexed discrimination of SARS-CoV-2 variants via plasmonic-enhanced fluorescence in a portable and automated device.Nature biomedical engineering · 2023Article
- Lessons identified for a future pandemic.The Journal of antimicrobial chemotherapy · 2023Article
- SARS-CoV-2 genomics and impact on clinical care for COVID-19.The Journal of antimicrobial chemotherapy · 2023Article
- 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
- The molecular epidemiology of SARS-CoV-2 in the Pityusic Islands shows multiple introductions and fast replacements of variants in a touristic worldwide hot spot.Scientific reports · 2023Article
- Tracking SARS-CoV-2 Omicron lineages using real-time reverse transcriptase PCR assays and prospective comparison with genome sequencing.Scientific reports · 2023Article
- Efficient SARS-CoV-2 Surveillance during the Pandemic-Endemic Transition Using PCR-Based Genotyping Assays.Microbiology spectrum · 2023Article
- Development and application of an RT‒PCR assay for the identification of the delta and omicron variants of SARS-COV-2.Heliyon · 2023Article
- 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
- Advances in point-of-care genetic testing for personalized medicine applications.Biomicrofluidics · 2023Review
11 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with concerning phenotypic mutations is of public health interest. Genomic surveillance is an important tool for a pandemic response, but many laboratories do not have the resources to support population-level sequencing. We hypothesized that a nucleic acid amplification test (NAAT) to genotype mutations in the viral spike protein could facilitate high-throughput variant surveillance. We designed and analytically validated a one-step multiplex allele-specific reverse transcriptase PCR (RT-qPCR) to detect three nonsynonymous spike protein mutations (L452R, E484K, N501Y). Assay specificity was validated with next-generation whole-genome sequencing. We then screened a large cohort of SARS-CoV-2-positive specimens from our San Francisco Bay Area population. Between 1 December 2020 and 1 March 2021, we screened 4,049 unique infections by genotyping RT-qPCR, with an assay failure rate of 2.8%. We detected 1,567 L452R mutations (38.7%), 34 N501Y mutations (0.84%), 22 E484K mutations (0.54%), and 3 (0.07%) E484K plus N501Y mutations. The assay had perfect (100%) concordance with whole-genome sequencing of a validation subset of 229 specimens and detected B.1.1.7, B.1.351, B.1.427, B.1.429, B.1.526, and P.2 variants, among others. The assay revealed the rapid emergence of the L452R variant in our population, with a prevalence of 24.8% in December 2020 that increased to 62.5% in March 2021. We developed and clinically implemented a genotyping RT-qPCR to conduct high-throughput SARS-CoV-2 variant screening. This approach can be adapted for emerging mutations and immediately implemented in laboratories already performing NAAT worldwide using existing equipment, personnel, and extracted nucleic acid.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.