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Presumptive positive with the Cepheid Xpert Xpress SARS-CoV-2 assay due to N mutations in the Delta variant.
Choi, Hosoon; Hwang, Munok; Lukey, Janell; Jinadatha, Chetan; Navarathna, Dhammika H.
  • Choi H; Department of Research, Central Texas Veterans Health Care System, Temple, TX, USA.
  • Hwang M; Department of Research, Central Texas Veterans Health Care System, Temple, TX, USA.
  • Lukey J; Department of Pathology and Laboratory Medicine Services, Central Texas Veterans Health Care System, Temple, TX, USA.
  • Jinadatha C; Department of Medicine, Central Texas Veterans Health Care System, Temple, TX, USA; Department of Medicine, College of Medicine, Texas A&M University, Bryan, TX, USA.
  • Navarathna DH; Department of Pathology and Laboratory Medicine Services, Central Texas Veterans Health Care System, Temple, TX, USA. Electronic address: dhammika.navarathna@va.gov.
Diagn Microbiol Infect Dis ; 103(3): 115699, 2022 Jul.
Article in English | MEDLINE | ID: covidwho-1800113
ABSTRACT
The Cepheid Xpert® Xpress SARS-CoV-2 assay is 1 of the several real-time reverse transcription polymerase chain reaction (RT-PCR) assays that received Emergency Use Authorization from the United States Food and Drug Administration (FDA) for detection of SARS-CoV-2. Here we report 4 SARS-CoV-2 samples that were reported as presumptive positives on the Cepheid platform while reported as positives on alternative RT-PCR platforms. Whole genome sequencing indicated that the samples were Delta variants and had point mutations in the N gene which potentially interfered with SARS-CoV-2 detection. Two types of point mutations were found in these samples in the US CDC 2019-nCoV Real time PCR N2 Probe region C29203T and C29200T. C29203T is a novel point mutation, and C29200T has not been previously reported in the Delta variants. This underlines the fact that mutations in the real-time RT-PCR assay target region could hinder accurate detection of SARS-CoV-2.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Diagnostic study Topics: Variants Limits: Humans Country/Region as subject: North America Language: English Journal: Diagn Microbiol Infect Dis Year: 2022 Document Type: Article Affiliation country: J.diagmicrobio.2022.115699

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Diagnostic study Topics: Variants Limits: Humans Country/Region as subject: North America Language: English Journal: Diagn Microbiol Infect Dis Year: 2022 Document Type: Article Affiliation country: J.diagmicrobio.2022.115699