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

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.

Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection

“…Spike gene mutations such as N501Y, E484K/Q, L452R, and P681H/R have occurred independently in multiple VOCs and VOIs (variants of interest), enabling dynamic adaptation of existing assay designs to detect emerging SARS-CoV-2 variants [7]. RT-qPCR is the gold standard for detection of SARS-CoV-2 in clinical samples [8] and has also been used for SARS-CoV-2 spike gene mutation detection in previous studies, often focusing on the HV69/70 deletion and the N501Y SNP (single nucleotide polymorphism) using various methods such as specific primers, simple probes, and melt curve analyses [9][10][11][12][13][14][15]. Locked nucleic acid (LNA)-Probes represent a well described method for specifically detecting SNPs by RT-PCR [16][17][18].…”

SARS-CoV-2 wastewater surveillance in Germany: long-term PCR monitoring, suitability of primer/probe combinations and biomarker stability

“…Mutations are distributed across the genome and either have no effect on the phenotype (silent mutation) or can lead to altered infectivity and pathogenicity (Mercatelli and Giorgi, 2020). At the end of 2020 and the beginning of 2021, variants (B.1.1.7 [alpha], B.1.351 [beta] and P.1 [gamma]) with increased transmission and clinical importance appeared (Sandoval Torrientes et al, 2021). These SARS-CoV-2 variants were classified as variants of concern (VoC).…”

Evaluation of the clinical and analytical performance of the Seegene allplex™ SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI)

“…Laboratory developed tests often offers this flexibility. For example, laboratory developed tests for the detection of L484R, E484K and N501Y (alone or in multiplex) in nasopharyngeal swabs specimen were reported earlier this year, demonstrating excellent clinical performance, and provide an even more economical option in laboratories that have the expertise and infrastructure to validate and perform them 34 , 35 , 36 , 37 . Given surveillance of circulating VOC/VOI remains critical for adequate public health control measures and for investigation of vaccine effectiveness when WGS is unavailable or limited, the Seegene Allplex TM SARS-CoV-2 Variants I assay offers a suitable alternative.…”