Rapid Detection of SARS-CoV-2 Variants by Molecular Clamping Technology Based RT-qPCR
Preprint
- 16 August 2022
- preprint
- Published by Research Square Platform LLC
Abstract
Given the challenges that fast-changing SARS-CoV-2 variants have caused in terms of rapid spread and reduced vaccine efficacy, a rapid and cost-effective assay that can detect new and emerging variants is greatly needed worldwide. We have successfully applied the xenonucleic acid-based molecular-clamping technology to develop a multiplex RT-qPCR assay for SARS-CoV-2 multivariant detection. The assay was tested on 649 nasopharyngeal swab samples that were collected from California and Ohio. The assay was able to correctly identify all 36 Delta variant samples as it accurately detected D614G, T478K and L452R mutations. In addition, the assay was able to correctly identify all 34 Omicron samples by detecting K417N, T478K, N501Y and D614G mutations. This technique reliably detects a variety of variants and has an analytical sensitivity of 100 copies/mL. In conclusion, this novel assay can serve as a rapid and cost-effective tool to facilitate large-scale detection of SARS-CoV-2 variants.Keywords
This publication has 33 references indexed in Scilit:
- The UCSC SARS-CoV-2 Genome BrowserNature Genetics, 2020
- Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 VirusCell, 2020
- An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVarPublished by Cold Spring Harbor Laboratory ,2018
- The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 updateNucleic Acids Research, 2018
- Towards XNA nanotechnology: new materials from synthetic genetic polymersTrends in Biotechnology, 2014
- Wrangling Galaxy’s reference dataBioinformatics, 2014
- Molecular Beacons of Xeno-Nucleic Acid for Detecting Nucleic AcidTheranostics, 2013
- High-Throughput SNP Genotyping by Allele-Specific PCR with Universal Energy-Transfer-Labeled PrimersGenome Research, 2001
- A formula for thermal stability (Tm) prediction of PNA/DNA duplexesNucleic Acids Research, 1998
- Detection of the Hereditary Hemochromatosis Gene Mutation by Real-Time Fluorescence Polymerase Chain Reaction and Peptide Nucleic Acid ClampingAnalytical Biochemistry, 1998