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Vega-Magaña N, Sánchez-Sánchez R, Hernández-Bello J, Venancio-Landeros AA, Peña-Rodríguez M, Vega-Zepeda RA, Galindo-Ornelas B, Díaz-Sánchez M, García-Chagollán M, Macedo-Ojeda G, García-González OP, Muñoz-Valle JF. RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. Front Cell Infect Microbiol 2021; 11:672562. [PMID: 34123874 PMCID: PMC8195289 DOI: 10.3389/fcimb.2021.672562] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/04/2021] [Indexed: 12/19/2022] Open
Abstract
Background Several variants of the SARS-CoV-2 have been documented globally during the current COVID-19 pandemic. The N501Y, 69-70del, K417N, and E484K SARS-CoV-2 mutations have been documented among the most relevant due to their potential pathogenic biological effects. This study aimed to design, validate, and propose a fast real-time RT-qPCR assay to detect SARS-CoV-2 mutations with possible clinical and epidemiological relevance in the Mexican population. Methods Targeting spike (S) gene mutations of SARS-CoV-2 (N501Y, 69-70del, K417N, and E484K), specific primers, and probes for three specific quantitative reverse transcription PCR (RT-qPCR) assays were designed, and validated using Sanger sequencing. These assays were applied in clinical samples of 1060 COVID-19 patients from Jalisco Mexico. Results In silico analyzes showed high specificity of the three assays. Amplicons of samples were confirmed through sequencing. The screening of samples of COVID-19 patients allowed the identification of the E484K mutation in nine individuals and the identification of P.2 Brazilian variant in Mexico. Conclusion This work provides low-cost RT-qPCR assays for rapid screening and molecular surveillance of mutations with potential clinical impact. This strategy allowed the detection of E484K mutation and P.2 variant for the first time in samples from the Mexican population.
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Affiliation(s)
- Natali Vega-Magaña
- Institute for Research in Biomedical Sciences (IICB), University Center for Health Sciences, University of Guadalajara, Guadalajara, Mexico
- Laboratory for the Diagnosis of Emerging and Reemerging Diseases (LaDEER), University Center for Health Sciences, University of Guadalajara, Guadalajara, Mexico
| | | | - Jorge Hernández-Bello
- Institute for Research in Biomedical Sciences (IICB), University Center for Health Sciences, University of Guadalajara, Guadalajara, Mexico
| | | | - Marcela Peña-Rodríguez
- Laboratory for the Diagnosis of Emerging and Reemerging Diseases (LaDEER), University Center for Health Sciences, University of Guadalajara, Guadalajara, Mexico
| | | | | | | | - Mariel García-Chagollán
- Institute for Research in Biomedical Sciences (IICB), University Center for Health Sciences, University of Guadalajara, Guadalajara, Mexico
- Laboratory for the Diagnosis of Emerging and Reemerging Diseases (LaDEER), University Center for Health Sciences, University of Guadalajara, Guadalajara, Mexico
| | - Gabriela Macedo-Ojeda
- Institute for Research in Biomedical Sciences (IICB), University Center for Health Sciences, University of Guadalajara, Guadalajara, Mexico
| | | | - José Francisco Muñoz-Valle
- Institute for Research in Biomedical Sciences (IICB), University Center for Health Sciences, University of Guadalajara, Guadalajara, Mexico
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Vega-Magaña N, Sánchez-Sánchez R, Hernández-Bello J, Venancio-Landeros AA, Peña-Rodríguez M, Vega-Zepeda RA, Galindo-Ornelas B, Díaz-Sánchez M, García-Chagollán M, Macedo-Ojeda G, García-González OP, Muñoz-Valle JF. RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. Front Cell Infect Microbiol 2021. [PMID: 34123874 DOI: 10.3389/fcimb.2021.672562/bibtex] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND Several variants of the SARS-CoV-2 have been documented globally during the current COVID-19 pandemic. The N501Y, 69-70del, K417N, and E484K SARS-CoV-2 mutations have been documented among the most relevant due to their potential pathogenic biological effects. This study aimed to design, validate, and propose a fast real-time RT-qPCR assay to detect SARS-CoV-2 mutations with possible clinical and epidemiological relevance in the Mexican population. METHODS Targeting spike (S) gene mutations of SARS-CoV-2 (N501Y, 69-70del, K417N, and E484K), specific primers, and probes for three specific quantitative reverse transcription PCR (RT-qPCR) assays were designed, and validated using Sanger sequencing. These assays were applied in clinical samples of 1060 COVID-19 patients from Jalisco Mexico. RESULTS In silico analyzes showed high specificity of the three assays. Amplicons of samples were confirmed through sequencing. The screening of samples of COVID-19 patients allowed the identification of the E484K mutation in nine individuals and the identification of P.2 Brazilian variant in Mexico. CONCLUSION This work provides low-cost RT-qPCR assays for rapid screening and molecular surveillance of mutations with potential clinical impact. This strategy allowed the detection of E484K mutation and P.2 variant for the first time in samples from the Mexican population.
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Affiliation(s)
- Natali Vega-Magaña
- Institute for Research in Biomedical Sciences (IICB), University Center for Health Sciences, University of Guadalajara, Guadalajara, Mexico
- Laboratory for the Diagnosis of Emerging and Reemerging Diseases (LaDEER), University Center for Health Sciences, University of Guadalajara, Guadalajara, Mexico
| | | | - Jorge Hernández-Bello
- Institute for Research in Biomedical Sciences (IICB), University Center for Health Sciences, University of Guadalajara, Guadalajara, Mexico
| | | | - Marcela Peña-Rodríguez
- Laboratory for the Diagnosis of Emerging and Reemerging Diseases (LaDEER), University Center for Health Sciences, University of Guadalajara, Guadalajara, Mexico
| | | | | | | | - Mariel García-Chagollán
- Institute for Research in Biomedical Sciences (IICB), University Center for Health Sciences, University of Guadalajara, Guadalajara, Mexico
- Laboratory for the Diagnosis of Emerging and Reemerging Diseases (LaDEER), University Center for Health Sciences, University of Guadalajara, Guadalajara, Mexico
| | - Gabriela Macedo-Ojeda
- Institute for Research in Biomedical Sciences (IICB), University Center for Health Sciences, University of Guadalajara, Guadalajara, Mexico
| | | | - José Francisco Muñoz-Valle
- Institute for Research in Biomedical Sciences (IICB), University Center for Health Sciences, University of Guadalajara, Guadalajara, Mexico
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