tetano
Editor, Senior Moderator
Ann Lab Med
. 2022 Jan 1;42(1):96-99.
doi: 10.3343/alm.2022.42.1.96.
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[SUP] 1 [/SUP], Ji Won In[SUP] 2 [/SUP], Jaehyeon Lee[SUP] 3 [/SUP], So Yeon Kim[SUP] 4 [/SUP], Kyoung Ah Lee[SUP] 2 [/SUP], Seunghyun Kim[SUP] 2 [/SUP], Yeoungim An[SUP] 2 [/SUP], Donggeun Lee[SUP] 2 [/SUP], Heungsup Sung[SUP] 5 [/SUP], Jae-Seok Kim[SUP] 6 [/SUP], Hyukmin Lee[SUP] 1 [/SUP]
Affiliations
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.
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.
. 2022 Jan 1;42(1):96-99.
doi: 10.3343/alm.2022.42.1.96.
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[SUP] 1 [/SUP], Ji Won In[SUP] 2 [/SUP], Jaehyeon Lee[SUP] 3 [/SUP], So Yeon Kim[SUP] 4 [/SUP], Kyoung Ah Lee[SUP] 2 [/SUP], Seunghyun Kim[SUP] 2 [/SUP], Yeoungim An[SUP] 2 [/SUP], Donggeun Lee[SUP] 2 [/SUP], Heungsup Sung[SUP] 5 [/SUP], Jae-Seok Kim[SUP] 6 [/SUP], Hyukmin Lee[SUP] 1 [/SUP]
Affiliations
- PMID: 34374354
- DOI: 10.3343/alm.2022.42.1.96
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.
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.