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

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

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

Afiliación

Dos Santos CA; Laboratório de Genética Molecular e Citogenética, Departamento de Genética, Instituto de Ciências Biológicas I, Universidade Federal de Goiás, Goiânia, Goiás State, 74001-970, Brazil.
Silva LDC; Laboratório de Genética Molecular e Citogenética, Departamento de Genética, Instituto de Ciências Biológicas I, Universidade Federal de Goiás, Goiânia, Goiás State, 74001-970, Brazil.
Souza Júnior MN; Instituto de Química, Universidade Federal de Goiás, Goiânia, Brazil.
Mendes GM; Instituto de Química, Universidade Federal de Goiás, Goiânia, Brazil.
Estrela PFN; Instituto de Química, Universidade Federal de Goiás, Goiânia, Brazil.
de Oliveira KG; Instituto de Química, Universidade Federal de Goiás, Goiânia, Brazil.
de Curcio JS; Laboratório de Genética Molecular e Citogenética, Departamento de Genética, Instituto de Ciências Biológicas I, Universidade Federal de Goiás, Goiânia, Goiás State, 74001-970, Brazil.
Resende PC; Laboratory of Respiratory Viruses and Measles, Reference Laboratory for COVID-19 (WHO) of Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil.
Siqueira MM; Laboratory of Respiratory Viruses and Measles, Reference Laboratory for COVID-19 (WHO) of Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil.
Pauvolid-Corrêa A; Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
Duarte GRM; Instituto de Química, Universidade Federal de Goiás, Goiânia, Brazil.
Silveira-Lacerda EP; Laboratório de Genética Molecular e Citogenética, Departamento de Genética, Instituto de Ciências Biológicas I, Universidade Federal de Goiás, Goiânia, Goiás State, 74001-970, Brazil. elacerda@ufg.br.

Sci Rep ; 12(1): 11500, 2022 07 07.

Article en En | MEDLINE | ID: mdl-35798777

RESUMEN

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.

Asunto(s)

COVID-19; SARS-CoV-2; COVID-19/diagnóstico; COVID-19/epidemiología; Colorimetría/métodos; Cartilla de ADN; Humanos; Técnicas de Diagnóstico Molecular/métodos; Mutación; Técnicas de Amplificación de Ácido Nucleico/métodos; ARN Viral/genética; SARS-CoV-2/genética; Sensibilidad y Especificidad

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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: SARS-CoV-2 / COVID-19 Tipo de estudio: Diagnostic_studies / Prognostic_studies Límite: Humans Idioma: En Revista: Sci Rep Año: 2022 Tipo del documento: Article País de afiliación: Brasil Pais de publicación: Reino Unido

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