Cycle Threshold Probability Score for Immediate and Sensitive Detection of B.1.351 SARS-CoV-2 Lineage

Area of Science:

• Virology
• Molecular Diagnostics
• Public Health

Background:

• Detecting SARS-CoV-2 variants of concern is crucial for maintaining vaccine effectiveness.
• Immune escape properties of certain variants necessitate rapid identification.
• The B.1.351 lineage (South African variant) poses a significant public health challenge.

Purpose of the Study:

• To evaluate the Allplex SARS-CoV-2 Assay for screening the B.1.351 variant.
• To investigate the utility of delayed N gene amplification as a screening marker.
• To assess the diagnostic performance of a derived probability score for B.1.351 detection.

Main Methods:

• Analysis of amplification curves (E/N/S-RdRP targets) from 397 RT-PCR positive samples.
• Whole-genome sequencing for variant genotyping.
• Logistic regression modeling to develop a B.1.351 probability score (VOC.V2 score).
• Validation of the screening test in an independent cohort.

Main Results:

• A characteristic delayed N vs E gene amplification was observed for B.1.351.
• The VOC.V2 probability score, based on N and E gene cycle thresholds, demonstrated strong predictive capability (AUC=0.94).
• The score achieved high sensitivity (98.7%) and negative predictive value (99.6%) at a cutoff of 0.12.

Conclusions:

• Delayed N vs E gene amplification in the Allplex assay is a reliable indicator for B.1.351 screening.
• This assay provides a fast and highly sensitive method for identifying this SARS-CoV-2 variant.
• The findings support the use of this assay for rapid surveillance of B.1.351.