A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants

M Sandoval Torrientes; C Castelló Abietar; J Boga Riveiro; M E Álvarez-Argüelles; S Rojo-Alba; F Abreu Salinas; I Costales González; Z Pérez Martínez; G Martín Rodríguez; J Gómez de Oña; E Coto García; S Melón García

doi:10.1016/j.jviromet.2021.114143

A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants

J Virol Methods. 2021 Aug:294:114143. doi: 10.1016/j.jviromet.2021.114143. Epub 2021 Mar 24.

Affiliations

¹ Microbiology Department, Hospital Universitario Central de Asturias, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain. Electronic address: [email protected].
² Microbiology Department, Hospital Universitario Central de Asturias, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain. Electronic address: [email protected].
³ Microbiology Department, Hospital Universitario Central de Asturias, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain. Electronic address: [email protected].
⁴ Microbiology Department, Hospital Universitario Central de Asturias, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain. Electronic address: [email protected].
⁵ Microbiology Department, Hospital Universitario Central de Asturias, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain. Electronic address: [email protected].
⁶ Microbiology Department, Hospital Universitario Central de Asturias, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain. Electronic address: [email protected].
⁷ Microbiology Department, Hospital Universitario Central de Asturias, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain. Electronic address: [email protected].
⁸ Microbiology Department, Hospital Universitario Central de Asturias, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain. Electronic address: [email protected].
⁹ Microbiology Department, Hospital Universitario Central de Asturias, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain. Electronic address: [email protected].
¹⁰ Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain; Genetic Department, Hospital Universitario Central de Asturias, Oviedo, Spain. Electronic address: [email protected].
¹¹ Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain; Genetic Department, Hospital Universitario Central de Asturias, Oviedo, Spain. Electronic address: [email protected].
¹² Microbiology Department, Hospital Universitario Central de Asturias, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain. Electronic address: [email protected].

Abstract

The N501Y mutation in SARS-CoV-2 variants found in several strains from the UK, South Africa and Brazil has been linked to increased transmission. In order to discriminate N501Y variants quickly, a single nucleotide polymorphism (SNP) discrimination assay was designed and validated. It was then deployed prospectively in 757 nasopharyngeal swabs. Validation of the novel variant discrimination assay corroborated the results in all validation panel samples (n = 63) through sequencing. This novel variant discrimination assay was then deployed prospectively in 757 clinical nasopharyngeal swabs during the last week of January 2021. N501Y was found in 206 (27.4 %) of the samples: 94 (28.2 %) men and 112 (26.85 %) women (p = 0.73). The patients in whom it was identified had a mean age of 47.8 ± 25.8 (0-96) years, similar to that of patients without this variant: 51.7 ± 25.9 (0-104) years (p = 0.06). 501Y variant was confirmed in 34 samples by sequence method and 501 N wild type was confirmed in 67. This method is sensitive, specific, and simple to apply in any microbiology lab.

Keywords: Mutation; N501Y; New generation sequencing; SARS-CoV-2; Sequencing; Variant discrimination assay.

Publication types

Validation Study

MeSH terms

Adolescent
Adult
Aged
Aged, 80 and over
COVID-19 / diagnosis*
COVID-19 / virology
COVID-19 Nucleic Acid Testing / methods*
Child
Child, Preschool
Female
Humans
Infant
Infant, Newborn
Male
Middle Aged
Mutation*
Nasopharynx / virology
Polymorphism, Single Nucleotide*
Prospective Studies
SARS-CoV-2 / genetics*
SARS-CoV-2 / isolation & purification
Sensitivity and Specificity
Spike Glycoprotein, Coronavirus / genetics
Young Adult

Substances

Spike Glycoprotein, Coronavirus
spike protein, SARS-CoV-2