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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

Authors
 Ki Ho Hong  ;  Ji Won In  ;  Jaehyeon Lee  ;  So Yeon Kim  ;  Kyoung Ah Lee  ;  Seunghyun Kim  ;  Yeoungim An  ;  Donggeun Lee  ;  Heungsup Sung  ;  Jae-Seok Kim  ;  Hyukmin Lee 
Citation
 ANNALS OF LABORATORY MEDICINE, Vol.42(1) : 96-99, 2022-01 
Journal Title
ANNALS OF LABORATORY MEDICINE
ISSN
 2234-3806 
Issue Date
2022-01
MeSH
COVID-19* ; Humans ; Molecular Diagnostic Techniques ; Nasopharynx ; Nucleotides ; Prevalence ; Republic of Korea ; SARS-CoV-2* ; Sensitivity and Specificity
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
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.
Files in This Item:
T999202211.pdf Download
DOI
10.3343/alm.2022.42.1.96
Appears in Collections:
1. College of Medicine (의과대학) > Dept. of Internal Medicine (내과학교실) > 1. Journal Papers
1. College of Medicine (의과대학) > Dept. of Laboratory Medicine (진단검사의학교실) > 1. Journal Papers
Yonsei Authors
Lee, Hyuk Min(이혁민) ORCID logo https://orcid.org/0000-0002-8523-4126
Jeong, Su Jin(정수진) ORCID logo https://orcid.org/0000-0003-4025-4542
Hong, Ki Ho(홍기호) ORCID logo https://orcid.org/0000-0002-5700-9036
URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/188120
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