Abstract
We evaluated the performance of SARS-CoV-2 TaqMan real-time reverse-transcription PCR (RT-qPCR) assays (ThermoFisher) for detecting 2 nonsynonymous spike protein mutations, E484K and N501Y. Assay accuracy was evaluated by whole genome sequencing (WGS). Residual nasopharyngeal SARS-CoV-2 positive samples (N = 510) from a diverse patient population in New York City submitted for routine SARS-CoV-2 testing during January-April 2020 were used. We detected 91 (18%) N501Y and 101 (20%) E484K variants. Four samples (0.8%) were positive for both variants. The assay had nearly perfect concordance with WGS in the validation subset, detecting B.1.1.7 and B.1.526 variants among others. Sensitivity and specificity ranged from 0.95 to 1.00. Positive and negative predictive values were 0.98-1.00. TaqMan genotyping successfully predicted the presence of B.1.1.7, but had significantly lower sensitivity, 62% (95% CI, 0.53, 0.71), for predicting B.1.526 sub-lineages lacking E484K. This approach is rapid and accurate for detecting SARS-CoV-2 variants and can be rapidly implemented in routine clinical setting.
Keywords: Coronavirus disease 19 (COVID-19); Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); TaqMan; Variants of concern.
【저자키워드】 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), variants of concern., Coronavirus disease 19 (COVID-19), TaqMan, 【초록키워드】 SARS-CoV-2, coronavirus, Sequencing, mutations, variant, SARS-CoV-2 variant, variants, New York City, Spike protein, sensitivity, specificity, RT-qPCR, Concordance, Accuracy, SARS-CoV-2 testing, B.1.1.7, nasopharyngeal, N501Y, E484K, B.1.526, coronavirus disease 19, WGS, genotyping, Negative predictive value, acute respiratory syndrome, 95% CI, clinical setting, positive, patient population, whole genome, significantly lower, positive sample, Real-time reverse-transcription PCR, nonsynonymous, Thermofisher, approach, residual, predicted, evaluated, were used, submitted, subset, ranged, 【제목키워드】 SARS-CoV-2 variant, polymorphism, Rapid, genotyping, single nucleotide, TaqMan assay,