Impact of G29179T Mutation on Two Commercial PCR Assays for SARS-CoV-2 Detection

Nucleic acid amplification test is the gold standard for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection, but the impact of genetic mutations in the virus on diagnostic tests remains unclear.To examine the cycle threshold (Ct) values of N genes and their association with mutations using SARS-CoV-2 positive specimens diagnosed by the Xpert Xpress SARS-CoV-2 assay.We evaluated 196 patients with suspected SARS-CoV-2 infection between August 7, 2020, and June 2, 2021. The Ct values of the N2 and E genes in SARS-CoV-2 positive samples were investigated, and ΔCt (CtN2 − CtE) was calculated. Whole genome sequencing (WGS) was performed for samples collected between April and May 2021 to identify the cause of ΔCt. Samples were also tested using the AllplexTM SARS-CoV-2 assay for Ct value comparison.In total, 196 nasopharyngeal swab specimens were tested for SARS-CoV-2 using the Xpert Xpress SARS-CoV-2 assay, and 34 were positive for SARS-CoV-2. WGS was performed for 11 samples among which four samples with the G29179T mutation in the N gene had a higher ΔCt value in the Xpert Xpress SARS-CoV-2 assay than in the AllplexTM SARS-CoV-2 assay. All samples with G29179T mutation were alpha variants.The G29179T mutation in the N gene of SARS-CoV-2 affected the results of the Xpert Xpress SARS-CoV-2 assay. Previous studies have also shown the impact of N gene mutations on diagnostic tests. Since viral mutations are a constant, natural occurrence, caution should be exercised when interpreting test results for SARS-CoV-2 detection.