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SARS-CoV-2 N Gene G29195T Point Mutation May Affect Diagnostic Reverse Transcription-PCR Detection.
Ko, Karrie K K; Abdul Rahman, Nurdyana Binte; Tan, Shireen Yan Ling; Chan, Kenneth X L; Goh, Sui Sin; Sim, James Heng Chiak; Lim, Kun Lee; Tan, Wan Loo; Chan, Kian Sing; Oon, Lynette L E; Nagarajan, Niranjan; Suphavilai, Chayaporn.
  • Ko KKK; Department of Microbiology, Singapore General Hospitalgrid.163555.1, Singapore.
  • Abdul Rahman NB; Department of Molecular Pathology, Singapore General Hospitalgrid.163555.1, Singapore.
  • Tan SYL; Genome Institute of Singapore, Genome Institute of Singapore, A*STAR, Singapore.
  • Chan KXL; Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
  • Goh SS; Duke-NUS Medical School, National University of Singapore, Singapore.
  • Sim JHC; Department of Microbiology, Singapore General Hospitalgrid.163555.1, Singapore.
  • Lim KL; Duke-NUS Medical School, National University of Singapore, Singapore.
  • Tan WL; Department of Microbiology, Singapore General Hospitalgrid.163555.1, Singapore.
  • Chan KS; Duke-NUS Medical School, National University of Singapore, Singapore.
  • Oon LLE; Department of Molecular Pathology, Singapore General Hospitalgrid.163555.1, Singapore.
  • Nagarajan N; Department of Microbiology, Singapore General Hospitalgrid.163555.1, Singapore.
  • Suphavilai C; Department of Microbiology, Singapore General Hospitalgrid.163555.1, Singapore.
Microbiol Spectr ; 10(1): e0222321, 2022 02 23.
Article in English | MEDLINE | ID: covidwho-1622006
ABSTRACT
Rapid onsite whole-genome sequencing of two suspected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) N gene diagnostic escape samples revealed a previously unreported N gene point mutation at genome position 29195. Because the G29195T mutation occurs within a region probed by a commonly referenced U.S. CDC N gene reverse transcription (RT)-PCR assay, we hypothesize that the G29195T mutation rendered the N gene target of a proprietary commercial assay undetectable. The putative diagnostic escape G29195T mutation demonstrates the need for nearly real-time surveillance, as emergence of a novel SARS-CoV-2 variant with the potential to escape diagnostic tests continues to be a threat. IMPORTANCE Accurate diagnostic detection of SARS-CoV-2 currently depends on the large-scale deployment of RT-PCR assays. SARS-CoV-2 RT-PCR assays target predetermined regions in the viral genomes by complementary binding of primers and probes to nucleic acid sequences in the clinical samples. Potential diagnostic escapes, such as those of clinical samples harboring the G29195T mutation, may result in false-negative SARS-CoV-2 RT-PCR results. The rapid detection and sharing of potential diagnostic escapes are essential for diagnostic laboratories and manufacturers around the world, to optimize their assays as SARS-CoV-2 continues to evolve.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Point Mutation / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Prognostic study Topics: Variants Language: English Journal: Microbiol Spectr Year: 2022 Document Type: Article Affiliation country: Spectrum.02223-21

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Point Mutation / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Prognostic study Topics: Variants Language: English Journal: Microbiol Spectr Year: 2022 Document Type: Article Affiliation country: Spectrum.02223-21