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Updated: Jul 12, 2025
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Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
Published on: June 16, 2011
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Nucleocapsid single point-mutation associated with drop-out on RT-PCR assay for SARS-CoV-2 detection.
Fernanda de Mello Malta1, Deyvid Amgarten1, Alexandre Rodrigues Marra1
1Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil.
BMC Infectious Diseases
|October 23, 2023
Summary
A specific mutation in the SARS-CoV-2 nucleocapsid gene (C29197T) caused false-negative results in the Xpert® Xpress SARS-CoV-2 RT-PCR test. Genomic surveillance is crucial for updating diagnostic tests and vaccines.
Area of Science:
- Virology
- Genomics
- Molecular Diagnostics
Background:
- The SARS-CoV-2 pandemic presented significant challenges for clinical and molecular diagnostics due to the novel nature of the virus.
- Whole-genome sequencing has been vital for characterizing SARS-CoV-2 and for genomic surveillance to identify potential impacts on vaccines and diagnostics.
Purpose of the Study:
- To investigate the cause of SARS-CoV-2 detection failures in RT-PCR testing.
- To identify specific genetic variations in SARS-CoV-2 that may affect diagnostic assay performance.
Main Methods:
- Nucleic acid extraction from patient samples (NP and OP swabs).
- Random amplification of RNA followed by whole-genome sequencing.
- Bioinformatic analysis including quality control, human DNA removal, and genome assembly.
- Molecular diagnosis using the Xpert® Xpress SARS-CoV-2 RT-PCR assay.
Main Results:
- Twenty-seven SARS-CoV-2 positive samples exhibited a nucleocapsid (N) gene dropout in the Cepheid Xpert® Xpress assay.
- Sequencing of two of these samples revealed a common C29197T mutation in the N gene, likely responsible for the detection failure.
Conclusions:
- Genomic data is essential for maintaining the accuracy of molecular diagnostic tests.
- Continuous genomic surveillance is necessary to inform updates for both diagnostic assays and vaccines to address viral evolution.
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