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.

Abstract:

:The sensitivity of molecular diagnostics could be affected by nucleotide variants in pathogen genes, and the sites affected by such variants should be monitored. We report a single-nucleotide variant (SNV) in the nucleocapsid (N) gene of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), i.e., G29179T, which impairs the diagnostic sensitivity of the Xpert Xpress SARS-CoV-2 assay (Cepheid, Sunnyvale, CA, USA). We observed significant differences between the threshold cycle (Ct) values for envelope (E) and N genes and confirmed the SNV as the cause of the differences using Sanger sequencing. This SNV, G29179T, is the most prevalent in Korea and is associated with the B.1.497 virus lineage, which is dominant in Korea. Clinical laboratories should be aware of the various SNVs in the SARS-CoV-2 genome and consider their potential effects on the diagnosis of coronavirus disease 2019.

journal_name

Ann Lab Med

authors

Hong KH,In JW,Lee J,Kim SY,Lee KA,Kim S,An Y,Lee D,Sung H,Kim JS,Lee H

doi

10.3343/alm.2022.42.1.96

keywords:

["Coronavirus disease 2019 (COVID-19)","Diagnosis","Diagnostic sensitivity","Korea","Performance","Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)","Single nucleotide variant","Xpert Xpress SARS-CoV-2 assay"]

subject

Has Abstract

pub_date

2022-01-01 00:00:00

pages

96-99

issue

1

eissn

2234-3806

issn

2234-3814

pii

alm.2022.42.1.96

journal_volume

42

pub_type

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