Multicenter international assessment of a SARS-CoV-2 RT-LAMP test for point of care clinical application

PLoS One. 2022 May 11;17(5):e0268340. doi: 10.1371/journal.pone.0268340. eCollection 2022.

Abstract

Continued waves, new variants, and limited vaccine deployment mean that SARS-CoV-2 tests remain vital to constrain the coronavirus disease 2019 (COVID-19) pandemic. Affordable, point-of-care (PoC) tests allow rapid screening in non-medical settings. Reverse-transcription loop-mediated isothermal amplification (RT-LAMP) is an appealing approach. A crucial step is to optimize testing in low/medium resource settings. Here, we optimized RT-LAMP for SARS-CoV-2 and human β-actin, and tested clinical samples in multiple countries. "TTTT" linker primers did not improve performance, and while guanidine hydrochloride, betaine and/or Igepal-CA-630 enhanced detection of synthetic RNA, only the latter two improved direct assays on nasopharygeal samples. With extracted clinical RNA, a 20 min RT-LAMP assay was essentially as sensitive as RT-PCR. With raw Canadian nasopharygeal samples, sensitivity was 100% (95% CI: 67.6% - 100%) for those with RT-qPCR Ct values ≤ 25, and 80% (95% CI: 58.4% - 91.9%) for those with 25 < Ct ≤ 27.2. Highly infectious, high titer cases were also detected in Colombian and Ecuadorian labs. We further demonstrate the utility of replacing thermocyclers with a portable PoC device (FluoroPLUM). These combined PoC molecular and hardware tools may help to limit community transmission of SARS-CoV-2.

Publication types

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

MeSH terms

  • COVID-19* / diagnosis
  • Canada
  • Humans
  • Molecular Diagnostic Techniques
  • Nucleic Acid Amplification Techniques
  • Point-of-Care Systems
  • RNA, Viral / analysis
  • RNA, Viral / genetics
  • SARS-CoV-2* / genetics
  • Sensitivity and Specificity

Substances

  • RNA, Viral

Supplementary concepts

  • LAMP assay

Grants and funding

Funding: Canada’s International Development Research Centre (RB, CG and KP, grant number: 109547-001) through the COVID-19 May 2020 Rapid Research Funding Opportunity, the Krembil Foundation (RB, grant number: Not applicable), and the University of Toronto COVID-19 Action Initiative 2020 (KP, grant number: Not applicable). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.