Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART)

PLoS One. 2022 Mar 21;17(3):e0265748. doi: 10.1371/journal.pone.0265748. eCollection 2022.

Abstract

The new coronavirus infection (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be fatal, and several variants of SARS-CoV-2 with mutations of the receptor-binding domain (RBD) have increased avidity for human cell receptors. A single missense mutation of U to G at nucleotide position 1355 (U1355G) in the spike (S) gene changes leucine to arginine (L452R) in the spike protein. This mutation has been observed in the India and California strains (B.1.617 and B.1.427/B.1.429, respectively). Control of COVID-19 requires rapid and reliable detection of SARS-CoV-2. Therefore, we established a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay plus a bioluminescent assay in real-time (BART) to detect SARS-CoV-2 and the L452R spike mutation. The specificity and sensitivity of the RT-LAMP-BART assay was evaluated using synthetic RNAs including target sequences and RNA-spiked clinical nasopharyngeal and saliva specimens as well as reference strains representing five viral and four bacterial pathogens. The novel RT-LAMP-BART assay to detect SARS-CoV-2 was highly specific compared to the conventional real-time RT-PCR. Within 25 min, the RT-LAMP-BART assay detected 80 copies of the target gene in a sample, whereas the conventional real-time RT-PCR method detected 5 copies per reaction within 130 min. Using RNA-spiked specimens, the sensitivity of the RT-LAMP-BART assay was slightly attenuated compared to purified RNA as a template. The results were identical to those of the conventional real-time RT-PCR method. Furthermore, using a peptide nucleic acid (PNA) probe, the RT-LAMP-BART method correctly identified the L452R spike mutation. This is the first report describes RT-LAMP-BART as a simple, inexpensive, rapid, and useful assay for detection of SARS-CoV-2, its variants of concern, and for screening of COVID-19.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Substitution*
  • Binding Sites
  • COVID-19 / diagnosis*
  • California
  • Early Diagnosis
  • Humans
  • India
  • Limit of Detection
  • Luminescent Measurements
  • Molecular Diagnostic Techniques
  • Mutation, Missense
  • Nucleic Acid Amplification Techniques
  • Peptide Nucleic Acids / genetics*
  • Real-Time Polymerase Chain Reaction
  • Reverse Transcription
  • SARS-CoV-2 / classification*
  • SARS-CoV-2 / genetics
  • SARS-CoV-2 / isolation & purification
  • Sensitivity and Specificity
  • Spike Glycoprotein, Coronavirus / chemistry
  • Spike Glycoprotein, Coronavirus / genetics*

Substances

  • Peptide Nucleic Acids
  • Spike Glycoprotein, Coronavirus
  • spike protein, SARS-CoV-2

Supplementary concepts

  • LAMP assay

Grants and funding

MS was supported by Miyata Research Grant (A), Meikai University School of Dentistry. TI was supported by Miyata Research Grant (E), Meikai University School of Dentistry. The URL of the funder website; https://www.meikai.ac.jp/english/ The funder provided support in the form of salaries for authors [MS, TN, HK, TH], but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. LT is an employee of Erba Molecular, and NP is an employee of 3M Company. The companiesprovided support in the form of salaries for authors [LT, NP], but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.There was no additional external funding received for this stud.