Diagnostic Performance Evaluation of the GXT96 X3 Extraction System with the FluoroType® SARS-CoV-2 varID Q Assay for SARS-CoV-2 Detection and Mutation Screening

Background: The continued evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) created ongoing challenges for molecular diagnostics and variant surveillance. Assays capable of maintaining diagnostic sensitivity across emerging variants while providing variant-related information remain essential for clinical and public health applications. This study evaluated the performance of the GXT96 X3 extraction kit in combination with the FluoroType® SARS-CoV-2 varID Q version 1.0 assay (Hain LifeScience SA (Pty) Ltd., South Africa) for the detection, semi-quantitative assessment, and variant characterization of SARS-CoV-2 under laboratory conditions. Methods: A total of 220 samples were evaluated, including residual nasopharyngeal clinical specimens (n = 183), reference materials, and cultured SARS-CoV-2 virus dilutions. Residual specimens collected during multiple COVID-19 waves in South Africa (wild-type, Beta, Delta, and Omicron) were compared against standard-of-care (SOC) molecular assays used for routine diagnosis. RNA extraction was performed using the automated GXT96 X3 platform, followed by amplification on the FluoroCycler® XT using the FluoroType® SARS-CoV-2 varID Q assay targeting RdRp and N genes, with additional spike gene mutation detection for variant detection. Diagnostic accuracy, agreement (Cohen’s kappa), precision, linearity, and limit of detection (LoD) were assessed. Results: The assay demonstrated a sensitivity of 98.4% (95% CI: 94.2–99.8) and specificity of 100% (95% CI: 95.9–100.0) compared with SOC assays, with an overall agreement of κ = 0.981. Precision analysis showed acceptable reproducibility with a standard deviation of ≤1.49 and a coefficient of variation of ≤3.83%. Regression analysis demonstrated linearity across the dilution series (R2 = 0.9882 for RdRp and 0.994 for N genes). The LoD was ≤100 copies/mL for the RdRp gene and 250 copies/mL for the N gene. Variant-associated spike mutations corresponded broadly with epidemiological wave patterns observed in South Africa. Conclusions: Under the evaluated laboratory conditions, the GXT96 X3 extraction platform combined with the FluoroType® SARS-CoV-2 varID Q assay demonstrated high diagnostic accuracy and reproducibility for SARS-CoV-2 detection across a range of viral loads with additional spike gene mutation detection as an adjunct feature.