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Updated: Sep 5, 2025
Author Spotlight: Advancing Pathogen Diagnostics with Standardized LAMP
Published on: September 8, 2023
Detecting lineage-defining mutations in SARS-CoV-2 using colorimetric RT-LAMP without probes or additional primers
Carlos Abelardo Dos Santos1, Lívia do Carmo Silva1, Marcio Neres de Souza Júnior2
1Laboratório de Genética Molecular e Citogenética, Departamento de Genética, Instituto de Ciências Biológicas I, Universidade Federal de Goiás, Goiânia, Goiás State, 74001-970, Brazil.
A new reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay can efficiently detect SARS-CoV-2 variants like Gamma. This cost-effective method offers a valuable screening tool for identifying specific COVID-19 variants, especially where sequencing is limited.
Area of Science:
- Molecular Biology
- Virology
- Epidemiology
Background:
- Ongoing COVID-19 pandemic driven by transmissible and immune-evasive SARS-CoV-2 variants.
- High cost and complexity of whole-genome sequencing for variant monitoring.
- Need for accessible and affordable molecular diagnostic alternatives.
Purpose of the Study:
- To develop and validate a cost-effective RT-LAMP assay for detecting specific SARS-CoV-2 genetic variants.
- To demonstrate the assay's capability in identifying mutations associated with particular lineages, exemplified by the Gamma variant.
- To assess the utility of RT-LAMP as a screening approach for variant identification.
Main Methods:
- Development of a Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) assay.
- Testing the assay on 60 SARS-CoV-2 RNA samples extracted from clinical swab samples.
- Evaluation of assay performance metrics including sensitivity, specificity, and kappa value for samples with Ct ≤ 22.93.
Main Results:
- The RT-LAMP assay demonstrated high performance in detecting SARS-CoV-2 variants.
- Achieved a sensitivity of 93.33% and a specificity of 88.89% for detecting the Gamma variant.
- A kappa value of 0.822 indicated substantial agreement in variant identification.
Conclusions:
- The developed RT-LAMP assay is effective for distinguishing the SARS-CoV-2 Gamma variant.
- This method presents a valuable and cost-efficient alternative to whole-genome sequencing for variant screening.
- The assay holds particular promise for variant surveillance in regions with limited sequencing infrastructure.
