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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.
Annals of Laboratory Medicine ( IF 4.9 ) Pub Date : 2021-8-11 , DOI: 10.3343/alm.2022.42.1.96
Ki Ho Hong 1 , Ji Won In 2 , Jaehyeon Lee 3 , So Yeon Kim 4 , Kyoung Ah Lee 2 , Seunghyun Kim 2 , Yeoungim An 2 , Donggeun Lee 2 , Heungsup Sung 5 , Jae-Seok Kim 6 , Hyukmin Lee 1
Affiliation  

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.

中文翻译:

SARS-CoV-2 单核苷酸变异体在韩国的流行情况及其对 Xpert Xpress SARS-CoV-2 检测诊断灵敏度的影响。

分子诊断的敏感性可能受到病原体基因中核苷酸变异的影响,应监测受此类变异影响的位点。我们报告了严重急性呼吸系统综合症冠状病毒 2 (SARS-CoV-2) 的核衣壳 (N) 基因中的单核苷酸变异 (SNV),即 G29179T,它削弱了 Xpert Xpress SARS-CoV-2 的诊断敏感性化验(Cepheid,森尼维尔,加利福尼亚州,美国)。我们观察到包络 ( E ) 和N的阈值循环 (Ct) 值之间存在显着差异基因并使用 Sanger 测序确认 SNV 是差异的原因。这种 SNV G29179T 在韩国最为流行,并且与在韩国占主导地位的 B.1.497 病毒谱系有关。临床实验室应了解 SARS-CoV-2 基因组中的各种 SNV,并考虑它们对 2019 年冠状病毒病诊断的潜在影响。
更新日期:2021-08-11
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