HIV can be found in blood plasma, peripheral blood mononuclear cells (PBMCs), bodily fluids and human tissue. Most discussions refer to HIV that exists in the blood plasma and PBMCs. However, viral populations in other bodily tissues (compartments) may serve as reservoirs of resistant virus, and sexual transmission depends on virus in the semen and vaginal tissues.

Antiretroviral drugs themselves reach different concentrations in different bodily compartments: AZT and 3TC have been found at higher concentrations in semen than in blood ^[1], while PIs do not always appear to reach adequate concentrations in semen ^[2].

A small number of studies have looked for drug-resistant HIV in different tissue compartments. In people treated during the era of single and two-drug therapy, a mixture of wild-type and resistant virus can often by isolated from various cellular reservoirs even after successful suppression of HIV with triple drug therapy ^[3] [4].

High similarity has been found between resistance profiles in the blood and in the gut tissue. In cases where blood contained 100% mutant virus, gut tissue showed a mix of mutant and wild-type virus ^[5].

Another study found that HIV variants in the blood plasma and the cerebrospinal fluid (CSF), the fluid around the brain, do not differ in untreated people during the early stages of HIV infection. However, differences have been found between resistance patterns in blood plasma and the central nervous system in people with longer-term infection ^[6][7].

Several studies have found varying resistance patterns in the blood and genital tract in women ^[8][9][10], and between the blood and semen in men ^{[11][12][13][14]}.

In addition, two men treated during primary infection had resistant virus in their blood, but undetectable virus in their semen ^[15].

Another group found that drug-resistant HIV in the vagina was likely to be associated with macrophages, thus increasing the risk of transmission of drug-resistant virus and reported that virus in blood and vaginal cells may have similar rates of evolution towards resistance ^[16].