SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays

Area of Science:

• * Molecular Virology
• * Infectious Disease Epidemiology
• * Genetic Analysis

Background:

• * Rapid and cost-effective detection of SARS-CoV-2 variants is crucial for effective public health responses.
• * Traditional sequencing methods for variant identification are often time-consuming and expensive.
• * Development of alternative molecular assays is needed for timely surveillance and control.

Purpose of the Study:

• * To evaluate the performance of the TaqMan SARS-CoV-2 mutation panel genotyping assay.
• * To assess its capability in detecting and differentiating common SARS-CoV-2 variants.
• * To establish its utility as a screening method alternative to sequencing.

Main Methods:

• * Utilized 150 SARS-CoV-2 positive samples collected between March and July.
• * Employed ThermoFisher TaqMan SARS-CoV-2 mutation panel assay targeting single nucleotide polymorphisms (SNPs).
• * Validated assay performance using synthetic RNA controls and compared results with sequencing for nine samples.

Main Results:

• * The TaqMan assay accurately identified all validation controls, including B.1.1.7, B.1.351, P.1, and B.1.617.1.
• * Among 150 samples, the assay identified prevalent variants: B.1.617.2 (Delta, 46%), B.1.1.7 (Alpha, 32.7%), P.1/P.2 (Gamma/Zeta, 5.4%), B.1.351 (Beta, 1.3%), B.1.427/B.1.429 (Epsilon, 1.3%), and B.1.526 (Iota, 2%).
• * Genotyping results for B.1.617.2, B.1.1.7, and B.1.526 variants showed concordance with sequencing data.

Conclusions:

• * The TaqMan SARS-CoV-2 mutation panel assay effectively detects and differentiates common SARS-CoV-2 variants, including Delta, Alpha, Iota, Beta, Gamma, Zeta, Kappa, and Epsilon.
• * This molecular genotyping assay is suitable for widespread use in surveillance programs.
• * The assay provides a valuable tool for epidemic control and prevention efforts by enabling rapid variant tracking.