ArticleClinical chemistry2022
Multiplex Fragment Analysis for Flexible Detection of All SARS-CoV-2 Variants of Concern.
Article in Clinical chemistry, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Longitudinal genomic surveillance of SARS-CoV-2 in a university microcosm reflects global evolutionary trends.Microbiology spectrum · 2026Article
- Integrating Genomic Data into Test-negative Designs for Estimating Lineage-specific COVID-19 Vaccine Effectiveness.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2026Article
- Validation of a dual-purpose conventional PCR strategy for SARS-CoV-2 detection and lineage screening in resource-limited laboratories.Molecular biology reports · 2025Article
- Metallic nanoplatforms for COVID-19 diagnostics: versatile applications in the pandemic and post-pandemic era.Journal of nanobiotechnology · 2023Review
- Efficient Tracing of the SARS-CoV-2 Omicron Variants in Santa Barbara County Using a Rapid Quantitative Reverse Transcription PCR Assay.Diagnostics (Basel, Switzerland) · 2022Article
- Review
- Accessible and Adaptable Multiplexed Real-Time PCR Approaches to Identify SARS-CoV-2 Variants of Concern.Microbiology spectrum · 2022Article
- Review
- SARS-CoV-2 Variants Identification: Overview of Molecular Existing Methods.Pathogens (Basel, Switzerland) · 2022Review
- Multiplex Fragment Analysis for Flexible Detection of All SARS-CoV-2 Variants of Concern.Clinical chemistry · 2022Article
- PCR-Based Screening Tests for SARS-CoV-2 Mutations: What Is the Best Way to Identify Variants?Clinical chemistry · 2022Article
- SARS-CoV-2 coinfections with variant genomic lineages identified by multiplex fragment analysis.Frontiers in genetics · 2022Article
- Insight into genomic organization of pathogenic coronaviruses, SARS-CoV-2: Implication for emergence of new variants, laboratory diagnosis and treatment options.Frontiers in molecular medicine · 2022Review
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Authors and funding
19 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to emerge, and effective tracking requires rapid return of results. Surveillance of variants is typically performed by whole genome sequencing (WGS), which can be financially prohibitive and requires specialized equipment and bioinformatic expertise. Genotyping approaches are rapid methods for monitoring SARS-CoV-2 variants but require continuous adaptation. Fragment analysis may represent an approach for improved SARS-CoV-2 variant detection.
methodsA multiplex fragment analysis approach (CoVarScan) was validated using PCR targeting variants by size and fluorescent color. Eight SARS-CoV-2 mutational hot spots in variants of concern (VOCs) were targeted. Three primer pairs (recurrently deleted region [RDR] 1, RDR2, and RDR3-4) flank RDRs in the S-gene. Three allele-specific primers target recurrent spike receptor binding domain mutants. Lastly, 2 primer pairs target recurrent deletions or insertions in ORF1A and ORF8. Fragments were resolved and analyzed by capillary electrophoresis (ABI 3730XL), and mutational signatures were compared to WGS results.
resultsWe validated CoVarScan using 3544 clinical respiratory specimens. The assay exhibited 96% sensitivity and 99% specificity compared to WGS. The limit of detection for the core targets (RDR1, RDR2, and ORF1A) was 5 copies/reaction. Variants were identified in 95% of samples with cycle threshold (CT) <30 and 75% of samples with a CT 34 to 35. Assay design was frozen April 2021, but all subsequent VOCs have been detected including Delta (n = 2820), Mu, (n = 6), Lambda (n = 6), and Omicron (n = 309). Genotyping results are available in as little as 4 h.
conclusionsMultiplex fragment analysis is adaptable and rapid and has similar accuracy to WGS to classify SARS-CoV-2 variants.
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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 Socratic graph.