Diagnostic Accuracy of Next-Generation Sequencing: Prevalence of HIV-1 Drug Resistance and Associated Factors Among Adults on Integrase Inhibitors with Virologic Failure

Emerging evidence indicates a high rate (>10%) of drug resistance (DR) associated with integrase strand transfer inhibitors (INSTIs) in developed countries, although there is limited information on DR during INSTI treatment in Uganda. With the increased use of INSTIs as standard first-line treatment, monitoring for DR using next-generation sequencing (NGS) has become essential. NGS can detect the lower-frequency variants that may be missed by traditional Sanger sequencing (SS). This study evaluates the diagnostic accuracy of next-generation sequencing (NGS) compared to Sanger sequencing for detecting HIV-1 INSTI resistance mutations and estimates the prevalence and factors associated with drug resistance among adults with virologic failure on INSTI-based regimens in Uganda. Utilizing the Illumina MiSeq platform for NGS, data was analyzed using STATA V.18 and a logistic regression model at 5% level of significance. This study demonstrates that NGS achieved 100% sensitivity, specificity, positive predictive value, negative predictive value, and overall accuracy in detecting major mutations. NGS identified INSTI DRMs in 4% of adults at a ≥20% threshold and was able to detect both high- and low-abundance variants, which could have important implications for clinical outcomes. This study emphasizes the need for HIVDR testing before antiretroviral therapy (ART) initiation, given the increasing use of INSTIs. We recommend that healthcare providers adopt more sensitive diagnostics such as NGS and use detailed resistance profiles to tailor antiretroviral therapies. This approach is critical for effectively managing and preventing drug-resistant HIV strains.