tetano
Editor, Senior Moderator
J Virol Methods
. 2022 Feb 16;114497.
doi: 10.1016/j.jviromet.2022.114497. Online ahead of print.
Rapid detection of SARS-CoV-2 variants using allele-specific PCR
Sanjita Brito-Mutunayagam[SUP] 1 [/SUP], Daniel Maloney[SUP] 2 [/SUP], Gina McAllister[SUP] 3 [/SUP], Rebecca Dewar[SUP] 4 [/SUP], Martin McHugh[SUP] 5 [/SUP], Kate Templeton[SUP] 6 [/SUP]
Affiliations
Abstract
Tracking severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants through whole genome sequencing (WGS) is vital for effective infection control and prevention (IPC) measures, but can be time-consuming and resource-heavy. We describe an in-house validation of an allele-specific polymerase chain reaction (ASP) variant assay to detect variants of concern (VOC). ASP sensitivity for detecting Delta, Alpha and Beta was 99.45%, 100%, and 66.67%, respectively, compared with WGS. Specificity was 100% in detecting all three VOC. ASP generated results 1.3 days faster compared with WGS. These findings suggest using variant assays such as ASP may enhance epidemiological surveillance and IPC measures.
Keywords: SARS-CoV-2; allele-specific PCR; variant assay; variants of concerns; whole genome sequencing.
. 2022 Feb 16;114497.
doi: 10.1016/j.jviromet.2022.114497. Online ahead of print.
Rapid detection of SARS-CoV-2 variants using allele-specific PCR
Sanjita Brito-Mutunayagam[SUP] 1 [/SUP], Daniel Maloney[SUP] 2 [/SUP], Gina McAllister[SUP] 3 [/SUP], Rebecca Dewar[SUP] 4 [/SUP], Martin McHugh[SUP] 5 [/SUP], Kate Templeton[SUP] 6 [/SUP]
Affiliations
- PMID: 35182711
- DOI: 10.1016/j.jviromet.2022.114497
Abstract
Tracking severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants through whole genome sequencing (WGS) is vital for effective infection control and prevention (IPC) measures, but can be time-consuming and resource-heavy. We describe an in-house validation of an allele-specific polymerase chain reaction (ASP) variant assay to detect variants of concern (VOC). ASP sensitivity for detecting Delta, Alpha and Beta was 99.45%, 100%, and 66.67%, respectively, compared with WGS. Specificity was 100% in detecting all three VOC. ASP generated results 1.3 days faster compared with WGS. These findings suggest using variant assays such as ASP may enhance epidemiological surveillance and IPC measures.
Keywords: SARS-CoV-2; allele-specific PCR; variant assay; variants of concerns; whole genome sequencing.