A Robust, Highly Multiplexed Mass Spectrometry Assay to Identify SARS-CoV-2 Variants

Area of Science:

• Virology
• Molecular Diagnostics
• Public Health

Background:

• Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants necessitate accurate identification for effective surveillance and patient management.
• Whole-genome sequencing (WGS) is the gold standard but is not always clinically accessible.
• Existing molecular variant panels often lack comprehensive evaluation and target limitations.

Purpose of the Study:

• To evaluate the diagnostic performance of the Agena MassARRAY SARS-CoV-2 Variant Panel v3 for identifying SARS-CoV-2 variants.
• To assess the assay's accuracy against WGS using clinical specimens.

Main Methods:

• Analysis of 391 SARS-CoV-2 clinical RNA specimens from New York City and Bogotá.
• Utilized the Agena MassARRAY SARS-CoV-2 Variant Panel v3, a highly multiplexed molecular assay.
• Compared assay results with whole-genome sequencing (WGS) for variant identification.

Main Results:

• The assay demonstrated near-perfect agreement with WGS for 9 of 11 variant calls (κ ≥ 0.856) and 25 of 30 targets (κ ≥ 0.820).
• Achieved high diagnostic sensitivity (≥93.67%) for contemporary variants like Iota, Alpha, Delta, and Omicron (BA.1).
• Showed high diagnostic specificity for all tested variants (≥96.15%) and targets (≥94.34%).
• Identified distinct target patterns potentially useful for detecting novel variants, including Omicron BA.2.

Conclusions:

• The Agena MassARRAY SARS-CoV-2 Variant Panel v3 is a robust and accurate tool for identifying diverse SARS-CoV-2 variants.
• The assay's performance supports its utility in clinical microbiology laboratories for surveillance and patient care.
• Distinct variant signatures can aid in identifying emerging SARS-CoV-2 strains, complementing WGS.