Establishment and evaluation of a quantitative TaqMan RT-PCR for the detection of SARS-CoV-2 Omicron variants
10.3760/cma.j.cn112309-20221031-00356
- VernacularTitle:SARS-CoV-2 Omicron变异株TaqMan探针法荧光定量RT-PCR的建立及应用
- Author:
Yanhong SUN
1
;
Wenlong LI
;
Yaoyao CHEN
;
Xiaoqing FU
;
Xiaonan ZHAO
;
Duo LI
Author Information
1. 云南省疾病预防控制中心急性传染病防制所，昆明 650022
- Keywords:
SARS-CoV-2;
Omicron variants;
RT-qPCR
- From:
Chinese Journal of Microbiology and Immunology
2023;43(5):375-380
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To develop a rapid, simple and cost-effective quantitative TaqMan RT-PCR (RT-qPCR) that could be used as an alternative to sequencing for the detection of Omicron variants and to evaluate its performance.Methods:Primers and TaqMan probes targeting the conserved domains of SARS-CoV-2 ORF1ab and the high-frequency mutation sites in the S gene of Omicron variants were designed. Then a RT-qPCR for the detection of Omicron variants was established. The consistency of the method was verified using samples identified by whole-genome sequencing. The specificity and sensitivity of the method were also evaluated.Results:The established RT-qPCR could distinguish Omicron variants from early epidemic A strains and Alpha and Delta variants of SARS-CoV-2, and the results were consistent with those of whole-genome sequencing with a coincidence rate of 100% (28/28). There was no cross-reactivity with other six respiratory viruses or coxsackievirus group A16. For RNA standards, this method showed good linearity in the range of 10 9-10 3 copies/μl with a correlation coefficient ( R2) greater than 0.99 and detection sensitivity of 10 3 copies/μl. Conclusions:The RT-qPCR designed in this study for Omicron variant detection had good sensitivity and specificity and could be easily performed in laboratories, which would greatly facilitate the monitoring of Omicron variants.
