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Rapid detection and tracking of Omicron variant of SARS-CoV-2 using CRISPR-Cas12a-based assay.
Liang, Yuanhao; Lin, Hongqing; Zou, Lirong; Deng, Xiaoling; Tang, Shixing.
  • Liang Y; Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
  • Lin H; Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
  • Zou L; Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, 511430, China.
  • Deng X; Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, 511430, China. Electronic address: dengxiaoling@cdcp.org.cn.
  • Tang S; Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China; Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China. Electronic address: tamgshixing@smu.edu.cn.
Biosens Bioelectron ; 205: 114098, 2022 Jun 01.
Article in English | MEDLINE | ID: covidwho-1693895
ABSTRACT

BACKGROUND:

The newly emerged SARS-CoV-2 variant of concern (VOC) Omicron is spreading quickly worldwide, which manifests an urgent need of simple and rapid assay to detect and diagnose Omicron infection and track its spread.

METHODS:

To design allele-specific CRISPR RNAs (crRNAs) targeting the signature mutations in the spike protein of Omicron variant, and to develop a CRISPR-Cas12a-based assay to specifically detect Omicron variant.

RESULTS:

Our system showed a low limit of detection of 2 copies per reaction for the plasmid DNA of Omicron variant, and could readily detect Omicron variant in 5 laboratory-confirmed clinical samples and distinguish them from 57 SARS-CoV-2 positive clinical samples (4 virus isolates and 53 oropharyngeal swab specimens) infected with wild-type (N = 8) and the variants of Alpha (N = 17), Beta (N = 17) and Delta (N = 15). The testing results could be measured by fluorescent detector or judged by naked eyes. In addition, no cross-reaction was observed when detecting 16 clinical samples infected with 9 common respiratory pathogens.

CONCLUSIONS:

The rapid assay could be easily set up in laboratories already conducting SARS-CoV-2 nucleic acid amplification tests and implemented routinely in resource-limited settings to monitor and track the spread of Omicron variant.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Biosensing Techniques / COVID-19 Type of study: Diagnostic study / Randomized controlled trials Topics: Variants Limits: Humans Language: English Journal: Biosens Bioelectron Journal subject: Biotechnology Year: 2022 Document Type: Article Affiliation country: J.bios.2022.114098

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Biosensing Techniques / COVID-19 Type of study: Diagnostic study / Randomized controlled trials Topics: Variants Limits: Humans Language: English Journal: Biosens Bioelectron Journal subject: Biotechnology Year: 2022 Document Type: Article Affiliation country: J.bios.2022.114098