• HIV-1 resistance;
  • genotype;
  • proviral DNA;
  • viral RNA


Blood and concurrent rectal biopsy samples of human immunodeficiency virus type 1 (HIV-1)-positive highly active antiretroviral therapy (HAART)-treated patients were tested for genotypic resistance by direct sequencing of reverse transcriptase (RT) and protease (PR) regions to compare the patterns of resistance in these compartments. Fourteen subjects (five with undetectable plasma viral load (pVL) and nine persistently viremic) were studied. Four of five patients with undetectable pVL also had undetectable mucosal HIV RNA; sequence analyses from proviral DNA (PBMCs and rectal biopsy) were obtained with none or few resistance-associated mutations and no alteration of susceptibility profile. All viremic patients, and one with negative pVL, had detectable levels of mucosal HIV RNA (1.93–4.21 log10 copies/mg); sequences of HIV RNA (plasma and/or rectal biopsy) were also obtained, and multiple mutations generally compatible with current/past medications were detected. Overall, 40 HIV-1 PR and 42 RT sequences were analyzed, yielding a total of 42 PR and 47 RT sequence pairs (plasma/tissue-RNA; plasma-RNA/tissue-DNA; PBMC/tissue-DNA; tissue-DNA/RNA; tissue-RNA/PBMC-DNA; PBMC-DNA/plasma-RNA), which almost always differed at the total amino acid level (median percentage discordance 8.08% in the PR, 4.8% in RT). The median percentage of resistance position discordance equaled 88.8% (IQR = 20–100) in the PR and 74.55% (IQR = 31.75–100%) in the RT pairs, respectively. Different resistance levels were detected by means of a computer-assisted interpretation of mutational profiles. The results support the multiform evolution of HIV genotype in various body compartments and emphasize the participation of intestinal mucosa in HIV genotype selection. Samples from diverse tissues should be used for resistance evaluation to obtain a complete picture of drug resistance for antiretroviral-treated patients. J. Med. Virol. 70: 1–9, 2003. © 2003 Wiley-Liss, Inc.