Journal Article

Detecting lineage-defining mutations in SARS-CoV-2 using colorimetric RT-LAMP without probes or additional primers

Silveira-Lacerda, Elisângela de Paula, Souza Júnior, Marcio Neres de, de Oliveira, Kézia Gomes, Silva, Lívia do Carmo, Duarte, Gabriela Rodrigues Mendes, Estrela, Paulo Felipe Neves, de Curcio, Juliana Santana, dos Santos, Carlos Abelardo, Pauvolid-Corrêa, Alex, Mendes, Geovana de Melo, Resende, Paola Cristina, Siqueira, Marilda Mendonça

2022

Overview

Despite the advance of vaccination worldwide, epidemic waves caused by more transmissible and immune evasive genetic variants of SARS-CoV-2 have sustained the ongoing pandemic of COVID-19. Monitoring such variants is expensive, as it usually relies on whole-genome sequencing methods. Therefore, it is necessary to develop alternatives that could help identify samples from specific variants. Reverse transcription loop-mediated isothermal amplification is a method that has been increasingly used for nucleic acid amplification, as it is cheaper and easier to perform when compared to other molecular techniques. As a proof of concept that can help distinguish variants, we present an RT-LAMP assay capable of detecting samples carrying a group of mutations that can be related to specific SARS-CoV-2 lineages, here demonstrated for the Variant of Concern Gamma. We tested 60 SARS-CoV-2 RNA samples extracted from swab samples and the reaction showed a sensitivity of 93.33%, a specificity of 88.89% and a kappa value of 0.822 for samples with a Ct ≤ 22.93. The RT-LAMP assay demonstrated to be useful to distinguish VOC Gamma and may be of particular interest as a screening approach for variants in countries with poor sequencing coverage.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 631/337 / 631/61 / Colorimetry / COVID-19 / DNA probes / Gene amplification / Genetic diversity / Genetic variance / Genomes / Humanities and Social Sciences / multidisciplinary / Mutation / Nucleic acids / Pandemics / Reverse transcription / Science / Science (multidisciplinary) / Severe acute respiratory syndrome coronavirus 2 / Vaccination / Whole genome sequencing