1. Impact of G29179T mutation on two commercial PCR assays for SARS-CoV-2 detection.
- Author
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Kami W, Kinjo T, Hashioka H, Arakaki W, Uechi K, Takahashi A, Oki H, Tanaka K, Motooka D, Nakamura S, Nakamatsu M, Maeda S, Yamamoto K, and Fujita J
- Subjects
- Humans, COVID-19 Testing, Clinical Laboratory Techniques methods, Nasopharynx, Sensitivity and Specificity, Polymerase Chain Reaction, Nucleic Acid Amplification Techniques, Mutation, SARS-CoV-2 genetics, COVID-19 diagnosis
- Abstract
Nucleic acid amplification test (NAAT) is the gold standard for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. However, genetic mutations in the virus can affect the result. 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 were examined in this study. In total, 196 nasopharyngeal swab specimens were tested for SARS-CoV-2 infection using the Xpert Xpress SARS-CoV-2, and 34 were positive. WGS was performed for four outlier samples with increased ΔCt identified by Scatterplot analysis as well as seven control samples without increased ΔCt in the Xpert Xpress SARS-CoV-2. The presence of the G29179T mutation was identified as a cause of increased ΔCt. PCR using the Allplex™ SARS-CoV-2 Assay did not show a similar increase in ΔCt. Previous reports focusing on N-gene mutations and their effects on SARS-CoV-2 testing including the Xpert Xpress SARS-CoV-2 were also summarized. While a single mutation that impacts one target of a multiplex NAAT is not a true detection failure, mutation compromising NAAT target region can cause confusion of the results and render the assay susceptible to diagnostic failure., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)
- Published
- 2023
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