SARS-CoV-2 N-gene mutation leading to Xpert Xpress SARS-CoV-2 assay instability

Article Medical Laboratory Technology

Prevalence of a Single-Nucleotide Variant of SARS-CoV-2 in Korea and Its Impact on the Diagnostic Sensitivity of the Xpert Xpress SARS-CoV-2 Assay

Ki Ho Hong et al.

Summary: The sensitivity of molecular diagnostics can be affected by nucleotide variants in pathogen genes, such as the G29179T variant in the nucleocapsid (N) gene of SARS-CoV-2, which impairs the diagnostic sensitivity of the Xpert Xpress SARS-CoV-2 assay. Clinical laboratories should be aware of these variants and their potential effects on the diagnosis of coronavirus disease 2019.

ANNALS OF LABORATORY MEDICINE (2022)

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Article Infectious Diseases

SARS-CoV-2 N gene mutations impact detection by clinical molecular diagnostics: reports in two cities in the United States

Mindy Leelawong et al.

Summary: Nasal and nasopharyngeal swab specimens tested by Cepheid Xpert Xpress SARS-CoV-2 were analyzed by whole-genome sequencing based on impaired detection of the N2 target. Each viral genome had at least one mutation in the N gene, which likely arose independently in the New York City and Pittsburgh study sites.

DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE (2021)

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Article Public, Environmental & Occupational Health

Emergence of SARS-CoV-2 B.1.1.7 Lineage — United States, December 29, 2020–January 12, 2021

Summer E. Galloway et al.

MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT (2021)

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Article Infectious Diseases

Understanding false positives and the detection of SARS-CoV-2 using the Cepheid Xpert Xpress SARS-CoV-2 and BD MAX SARS-CoV-2 assays

Dhammika H. Navarathna et al.

Summary: Several real-time RT-PCR assays have received Emergency Use Authorization from the FDA for detecting SARS-CoV-2. The BD MAX(TM) system and GeneXpert system are utilized for different qualitative tests, showing comparable sensitivity levels. Evaluation of patient samples revealed an approximately 3.5% false positive rate from the BD MAX(TM) system results.

DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE (2021)

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Article Microbiology

Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay

Sharon Miller et al.

Summary: Accurate and rapid diagnostic tests are crucial for early diagnosis and control strategies for the SARS-CoV-2 pandemic. This study identified two single-point mutations associated with N gene target detection failures and emphasizes the importance of continual monitoring and evaluation of diagnostic assay performance.

MICROBIOLOGY SPECTRUM (2021)

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Article Biochemistry & Molecular Biology

A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees

Jakob McBroome et al.

Summary: A database of SARS-CoV-2 phylogenetic trees inferred with public sequences is presented, updated daily to include new sequences and encoded in MAT format. The researchers also introduce matUtils software for querying and manipulating the MATs efficiently.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

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Article Infectious Diseases

Lack of N2-gene amplification on the Cepheid Xpert Xpress SARS-CoV-2 assay and potential novel causative mutations: A case series from Auckland, New Zealand

Shivani Fox-Lewis et al.

Summary: Three cases with viral strains showed impaired N2-gene detection on the SARS-CoV-2 assay, with two new SNPs identified. These SNPs are likely responsible for the impairment, further research is needed to clarify whether they abolish N2-gene detection individually or only in combination.

IDCASES (2021)

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Article Immunology

Multiplex Real-Time Reverse Transcription PCR for Influenza A Virus, Influenza B Virus, and Severe Acute Respiratory Syndrome Coronavirus 2

Bo Shu et al.

Summary: SARS-CoV-2 emerged in late 2019, causing symptoms similar to influenza viruses. The FDA granted emergency use authorization for a multiplex assay that can detect influenza A and B viruses, as well as SARS-CoV-2, increasing testing capacity and conserving resources.

EMERGING INFECTIOUS DISEASES (2021)

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Article Infectious Diseases