Rapid Detection of SARS-CoV-2 RNA Using Reverse Transcription Recombinase Polymerase Amplification (RT-RPA) with Lateral Flow for N-Protein Gene and Variant-Specific Deletion-Insertion Mutation in S-Protein Gene

Rapid molecular testing for severe acute respiratory coronavirus 2 (SARS-CoV-2) variants may contribute to the development of public health measures, particularly in resource-limited areas. Reverse transcription recombinase polymerase amplification using a lateral flow assay (RT-RPA-LF) allows rapid...

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Bibliographic Details
Published in:Viruses 2023-05, Vol.15 (6), p.1254
Main Authors: Malaga, Jose L, Pajuelo, Monica J, Okamoto, Michiko, Tsinda, Emmanuel Kagning, Otani, Kanako, Tsukayama, Pablo, Mascaro, Lucero, Cuicapuza, Diego, Katsumi, Masamichi, Kawamura, Kazuhisa, Nishimura, Hidekazu, Sakagami, Akie, Ueki, Yo, Omiya, Suguru, Okamoto, Satoshi, Nakayama, Asami, Fujimaki, Shin-Ichi, Yu, Chuyao, Azam, Sikandar, Kodama, Eiichi, Dapat, Clyde, Oshitani, Hitoshi, Saito, Mayuko
Format: Article
Language:English
Subjects:
antigen detection
Coronaviruses
COVID-19
COVID-19 - diagnosis
COVID-19 - genetics
deletion–insertion mutation
Design
detection limit
Disease transmission
Enzymes
Gene deletion
Gene flow
genes
Genomes
Humans
Insertion
Molecular diagnostic techniques
Mutagenesis, Insertional
Mutation
Nucleic Acid Amplification Techniques - methods
nucleocapsid
Nucleocapsids
Nucleotidyltransferases - genetics
Proteins
Public health
rapid methods
Recombinase
recombinase polymerase amplification
recombinase polymerase amplification (RPA)
Recombinases - genetics
Reverse Transcription
RNA
RNA, Viral - genetics
SARS-CoV-2
SARS-CoV-2 - genetics
Sensitivity and Specificity
Severe acute respiratory syndrome coronavirus 2
Technical Note
variant of concern (VOC)
viral load
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Summary:Rapid molecular testing for severe acute respiratory coronavirus 2 (SARS-CoV-2) variants may contribute to the development of public health measures, particularly in resource-limited areas. Reverse transcription recombinase polymerase amplification using a lateral flow assay (RT-RPA-LF) allows rapid RNA detection without thermal cyclers. In this study, we developed two assays to detect SARS-CoV-2 nucleocapsid (N) gene and Omicron BA.1 spike (S) gene-specific deletion-insertion mutations (del211/ins214). Both tests had a detection limit of 10 copies/µL in vitro and the detection time was approximately 35 min from incubation to detection. The sensitivities of SARS-CoV-2 (N) RT-RPA-LF by viral load categories were 100% for clinical samples with high (>9015.7 copies/µL, cycle quantification (Cq): < 25) and moderate (385.5-9015.7 copies/µL, Cq: 25-29.9) viral load, 83.3% for low (16.5-385.5 copies/µL, Cq: 30-34.9), and 14.3% for very low (
ISSN:1999-4915
1999-4915
DOI:10.3390/v15061254