Despite high concordance, distinct mutational and phenotypic drug resistance profiles in human immunodeficiency virus type 1 RNA are observed in gastrointestinal mucosal biopsy specimens and peripheral blood mononuclear cells compared with plasma

The gastrointestinal mucosa is a major lymphoid tissue reservoir for human immunodeficiency virus (HIV) replication. Genotypic and phenotypic resistan ce patterns of HIV type 1 (HIV-1) RNA isolated from colonic mucosa were com pared with those from the plasma and peripheral blood mononuclear cells (PB MC) of 7 patients. Genotyping was performed using full-sequence analysis, a nd phenotyping was performed using a recombinant virus assay. Mutations in the reverse-transcriptase (kappa=.84) and protease (kappa=.73) genes were h ighly concordant among compartments. Similarly, phenotypic resistance patte rns were highly concordant among compartments (intraclass correlation coeff icient, .91). In 5 instances among 3 patients, a different genotypic result was observed between plasma and the other tissue compartments. Mixtures of wild-type and mutated HIV-1 RNA were present in the mucosa and PBMC but no t in the plasma. Despite significant concordance among compartments, mucosa l- and PBMC-derived viral RNA showed instances of discordance with plasma-d erived virus that may suggest compartmentalization of virus.