Open AccessIsothermal amplification using sequence-specific fluorescence detection of SARS coronavirus 2 and variants in nasal swabs
Author(s) -
Les Jones,
Hemant Naikare,
YungYi C. Mosley,
Ralph A. Tripp
Publication year - 2022
Publication title -
biotechniques/biotechniques
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.617
H-Index - 131
eISSN - 1940-9818
pISSN - 0736-6205
DOI - 10.2144/btn-2022-0037
Subject(s) - loop mediated isothermal amplification , reverse transcription loop mediated isothermal amplification , nucleic acid , microbiology and biotechnology , reverse transcriptase , oligonucleotide , recombinase polymerase amplification , reverse transcription polymerase chain reaction , biology , polymerase chain reaction , virology , coronavirus , chemistry , dna , covid-19 , gene , messenger rna , genetics , medicine , infectious disease (medical specialty) , pathology , disease
Coronavirus disease 2019 is a public health challenge requiring rapid testing for the detection of infections and transmission. Nucleic acid amplification tests targeting SARS coronavirus 2 (CoV2) are used to detect CoV2 in clinical samples. Real-time reverse transcription quantitative PCR is the standard nucleic acid amplification test for CoV2, although reverse transcription loop-mediated isothermal amplification is used in diagnostics. The authors demonstrate a sequence-specific reverse transcription loop-mediated isothermal amplification-based nucleic acid amplification assay that is finished within 30 min using minimally processed clinical nasal swab samples and describe a fluorescence-quenched reverse transcription loop-mediated isothermal amplification assay using labeled primers and a quencher oligonucleotide. This assay can achieve rapid (30 min) and sensitive (1000 plaque-forming units/ml) fluorescence detection of CoV2 (WA1/2020), B.1.1.7 (Alpha) and variants of concern Delta (B.1.617.2) and Omicron (B.1.1.529) in nasal samples.