HIV is an RNA retrovirus that infects CD4 cells; HIV-1 is the dominant global subtype while HIV-2 is less common (endemic in parts of West Africa) and typically has lower plasma viremia and slower clinical progression, with important diagnostic and treatment implications because many HIV-1 assays do not reliably detect HIV-2.
Quantitative HIV-1 RNA (viral load) testing is performed with sensitive RT-PCR platforms (e.g., COBAS, RealTime, Alinity, Aptima) and is essential for diagnosis in specific settings, monitoring response to ART, and guiding treatment decisions; assay variability occurs across platforms (gene targets, input volume, subtype detection) so plasma HIV RNA should be measured on the same analytical method for a patient to ensure valid comparisons.
Due to high HIV replication and mutation rates, drug resistance emerges commonly. Genotypic assays detect specific resistance mutations in protease, reverse transcriptase, and integrase genes and are generally preferred for initial and most clinical resistance testing because they are more available, less costly, and faster; phenotypic assays measure actual viral susceptibility and are useful when complex mutation patterns are suspected or for multidrug resistance assessment.
Next-generation sequencing (NGS) methods (targeted viral NGS or proviral DNA NGS) can detect low-level variants and may increase detection of resistance mutations compared with Sanger sequencing, provide utility for testing from proviral DNA when plasma RNA is low or undetectable, and have demonstrated analytic concordance with Sanger in many settings but may require interpretation considerations for minority variants and laboratory validation.