Comparative analysis of screening methods for point mutations, by using the detection of SARS-CoV-2 N501Y mutation as an example


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Abstract

Objective. To compare different methods for detection of point nucleotide mutations in the study of SARS-CoV-2 genetic diversity. Materials and methods. The study was conducted on a batch of samples from patients, which contained SARS-CoV-2 genetic material. The investigators used three methods (Sanger sequencing/fragment analysis, real-time PCR, and loop-mediated isothermal amplification) as the gold standard. Results. Genotyping-by-sequencing analysis was carried out to examine 372 samples from patients; 54, 7, and 25 samples were found to belong to the Alpha, Beta, and B.1.1.523 genetic variants, respectively. It was shown that both the real-time PCR method and loop-mediated isothermal amplification could be employed to detect SARS-CoV-2 N501Y mutation, by using various samples, including those for various (Alpha, Beta) genetic variants. Conclusion. The use of PCR-based screening methods makes it possible not only to reduce the economic and time costs of genotyping SARS-CoV-2 samples, but also to increase study coverage, by obtaining results for the samples unsuitable for sequencing.

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About the authors

Anna S. Cherkashina

Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being

Email: cherkashina@pcr.ms
Cand. Chem. Sci., Head, Research Group of Genetic Engineering and Biotechnology

Anna G. Golubeva

Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being

Email: golubeva@cmd.su
Laboratory Researcher

Elena D. Solovyeva

Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being

Email: solovyova@cmd.su
Junior Researcher

Anna V. Valdokhina

Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being

Email: valdokhina@cmd.su
Researcher

Victoria P. Bulanenko

Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being

Email: bulanenko@cmd.su
Researcher

Vadim V. Petrov

Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being

Email: petrov@pcr.ms
Head, Researcher Group for Development of New Molecular Biological Technologies

Kirill V. Krasovitov

Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being

Email: krasovitov@cmd.su
White-Collared Planner

Anna S. Esman

Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being

Email: esman@cmd.su
Researcher

Konsantin O. Mironov

Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being

Email: mironov@pcr.ru
Dr. Biol. Sci., Head, Research Group for Development of New Methods for Detection of Genetic Polymorphisms

Elena N. Rodionova

Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being

Email: rodionova@cmd.su
Head, Initial Production Laboratory

Olga Yu. Shipulina

Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being

Email: olga.shipulina@pcr.ms
Senior Researcher

Kamil F. Khafizov

Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being

Email: khafizov@cmd.su
Cand. Biol. Sci., Head, Research Group for Development of New Diagnostic Methods Based on Next-Generation Sequencing Technologies

Vasily G. Akimkin

Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being

Email: crie@crie.ru
MD, Academician of the Russian Academy of Sciences, Director

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