Tenofovir is a nucleotide reverse transcriptase inhibitor (NRTI). After phosphorylation to its active form (tenofovir diphosphate), it competes with deoxyadenosine triphosphate for incorporation into the growing DNA chain by the viral reverse transcriptase. Because it lacks a 3'-hydroxyl group, its incorporation results in chain termination, thus inhibiting the synthesis of double-stranded proviral DNA from the viral RNA template.

HIV entry is a two-step process involving two envelope glycoproteins. First, the surface glycoprotein gp120 binds to the CD4 receptor and a coreceptor (CCR5 or CXCR4). This binding event induces a conformational change that exposes the transmembrane glycoprotein gp41. The newly exposed gp41 protein then inserts into the host cell membrane and refolds, pulling the viral and host membranes together and mediating their fusion. p24 is the capsid protein, and p17 is the matrix protein.

The long terminal repeats (LTRs) are created during reverse transcription and are found at both ends of the integrated provirus. The 5' LTR acts as a powerful promoter for viral gene expression. It contains binding sites for host cell transcription factors, such as NF-κB and Sp1, as well as for the viral Tat protein. The activation state of the T-cell influences the availability of these transcription factors, which in turn regulates the transcription of the proviral DNA by the host's RNA polymerase II.

Control of latent Toxoplasma gondii infection relies heavily on cell-mediated immunity. CD4+ T-helper cells, specifically the Th1 subset, are critical for this process. Th1 cells produce interferon-gamma (IFN-γ), which is the principal cytokine responsible for activating macrophages to kill intracellular tachyzoites. With a CD4 count of 75 cells/mm³, this patient has a profound defect in Th1 function, allowing for the reactivation of latent toxoplasmosis and the development of encephalitis.

Most HIV protease inhibitors, including atazanavir, are potent inhibitors of the cytochrome P450 system, particularly the CYP3A4 isoenzyme. Simvastatin and many other statins are extensively metabolized by CYP3A4. Co-administration of a protease inhibitor with simvastatin can block its metabolism, leading to significantly increased plasma concentrations and a heightened risk of dose-dependent adverse effects like myopathy and rhabdomyolysis.

Maraviroc is a CCR5 antagonist, also known as an entry inhibitor. It blocks the binding of the HIV gp120 protein to the CCR5 coreceptor. This interaction is a necessary step for the entry of macrophage-tropic (M-tropic) HIV strains, which are typically dominant in early infection. By blocking this coreceptor, maraviroc prevents the virus from entering host cells like macrophages and CD4+ T-cells.

Raltegravir is an integrase strand transfer inhibitor (INSTI). It binds to and inhibits the viral enzyme integrase, which is responsible for covalently inserting the proviral DNA (synthesized by reverse transcriptase) into the host cell's chromosome. This step is critical for establishing a permanent, latent infection. By blocking integration, raltegravir effectively halts the viral replication cycle.

HIV protease is a viral enzyme essential for the late stages of replication. It cleaves the Gag and Gag-Pol polyproteins into their individual functional components (e.g., p24 capsid, p17 matrix, reverse transcriptase, integrase). Inhibition of protease prevents this maturation step. As a result, immature, non-infectious virions are assembled and released from the cell, effectively stopping the spread of the virus.

The p24 protein is the viral capsid protein, a core component of the HIV virion. It is produced in large quantities during the initial burst of viral replication in acute infection. p24 antigen can be detected in the blood as early as 10-14 days post-infection, before the development of detectable anti-HIV antibodies. Fourth-generation assays detect both p24 antigen and HIV antibodies, shortening the diagnostic 'window period' compared to older antibody-only tests.

HIV tropism is determined by the coreceptor it uses in addition to CD4. Macrophage-tropic (M-tropic or R5) strains use the CCR5 coreceptor, found on macrophages, dendritic cells, and memory T cells. T-cell-tropic (T-tropic or X4) strains use the CXCR4 coreceptor, found primarily on naive T-lymphocytes. A switch from CCR5 to CXCR4 usage (a 'tropism switch') often occurs late in disease and is associated with accelerated CD4+ T-cell depletion and disease progression.