Analytical Agreement of the GeneXpert HIV-1 Viral Load Assay Compared with the Abbott Alinity m HIV-1 Assay

Background/Objectives: Early and accurate quantification of Human Immunodeficiency Virus type 1 (HIV-1) viral load is essential for monitoring antiretroviral therapy and guiding clinical management. Although conventional real-time polymerase chain reaction (PCR) platforms provide reliable viral load measurement, they often require centralized laboratories and longer turnaround times. Cartridge-based systems such as the GeneXpert HIV-1 Viral Load assay offer a simplified testing workflow and may facilitate decentralized molecular testing. This study aimed to evaluate the qualitative and quantitative agreement between the GeneXpert HIV-1 Viral Load assay and the Abbott Alinity m HIV-1 assay. Methods: A total of 102 residual clinical Ethylenediaminetetraacetic acid (EDTA) plasma specimens were analyzed using both the GeneXpert HIV-1 Viral Load assay and the Abbott Alinity m HIV-1 assay. Qualitative agreement was evaluated using positive percent agreement (PPA), negative percent agreement (NPA), overall agreement, and Cohen’s κ coefficient. Quantitative agreement among specimens with paired quantifiable viral load results was assessed using Pearson’s correlation and Bland–Altman analyses. Results: Overall qualitative agreement between the two assays was 95.1%, with a PPA of 92.6%, an NPA of 100.0%, and a Cohen’s κ coefficient of 0.894, indicating almost perfect agreement. Among the 57 specimens with paired quantifiable viral load results, a very strong positive correlation was observed (Pearson’s r = 0.9972; 95% CI: 0.9952–0.9984; p < 0.001). Bland–Altman analysis demonstrated a minimal mean bias of −0.018 log10 IU/mL, with 95% limits of agreement ranging from −0.175 to 0.139 log10 International Units per milliliter (IU/mL). All paired quantitative differences were within the clinically accepted agreement threshold of ±0.5 log10 IU/mL. Conclusions: The GeneXpert HIV-1 Viral Load assay demonstrated excellent qualitative and quantitative agreement with the Abbott Alinity m HIV-1 assay. These findings support the potential use of the GeneXpert HIV-1 Viral Load assay as an alternative testing platform for routine HIV-1 viral load monitoring in appropriate clinical settings.