Highly diversified multiply drug-resistant HIV-1 quasispecies in PBMCs: a case report

Patterns of drug resistance mutations showed that the viral populations in PBMCs were more heterogeneous than in plasma. Extensive analysis of HIV from infected PBMCs in this patient showed that high-level diversity existed among 109 cloned PR-RT sequences and that the majority of mutations were related to drug resistance. Moreover, the PBMCs included archival species that reflected the treatment history of the patient while those in plasma were mainly related to the most recent treatment. Some of the proviral clones contained single or multiple mutations in various combinations. Approximately eighteen percent of the proviral clones derived from infected PBMCs were defective, i.e. 5.5% contained single nucleotide deletions (frameshift mutations) and 12.8% encoded in-frame stop codons (nonsense mutations). Amino acid substitutions in PR and the polymerase region of RT occurred in 12–15% of cases but were much less frequent in the RNase H region of RT, which might not have been under drug selection pressure.Selective drug pressure can yield multiple drug-resistant quasispecies that include archival and replication-incompetent species in PBMC reservoirs.HIV quasispecies within infected individuals can rapidly adapt to hosts [1-7] due, in part, to variations in replicative fitness that enable some viruses to grow faster than others[3,8]. This is of obvious clinical relevance, since viral genetic changes can result in alterations in receptor usage, escape from drug and host immune pressure, and can impact on viral pathogenesis[9]. HIV-1 may also evolve separately in different physiological compartments, e.g., peripheral blood mononuclear cells (PBMCs) vs. the central nervous system[10]. Here, we report on an individual who failed multiple antiviral therapies (ART), including use of nucleoside and non-nucleoside RT inhibitors (NRTIs and NNRTIs) and protease inhibitors (PIs). After initiating therapy elsewhere with undisclosed regimens, the patient was treated in 1999 at t