Detection of drug-resistant HIV minorities in clinical specimens and therapy failure

HIV Med. 2008 Mar;9(3):133-41. doi: 10.1111/j.1468-1293.2007.00529.x. Epub 2008 Jan 21.


Objective: Particularly for therapy-experienced patients, resistance assessment by genotypic or phenotypic methods produces discordances. This study seeks proof that differences may arise from the fact that genotyping produces a single summary sequence whereas replicative phenotyping (rPhenotyping) functionally detects and assigns resistances in mixed HIV populations.

Methods: For validation, defined mixes of wild-type and M184V mutant were analysed by rPhenotyping or standard genotyping. Allele-specific and quantitative polymerase chain reaction (PCR) set detection and quantification limits for minor virus populations in vitro and in authentic clinical samples showing geno-/pheno-discrepant lamivudine resistance.

Results: Allele-specific and real-time PCR methods detected down to 0.3% of mutant M184V. The functional assessment was sensitive enough to reveal <1% of mutant M184V in mixed samples. Also in discordant samples from the diagnostic routine, in which rPhenotyping had identified drug resistance, real-time PCR confirmed minute amounts of mutant M184V.

Conclusion: By utilizing the replication dynamics of HIV under drug pressure, a rPhenotyping format potently reveals relevant therapy-resistant minority species, even of HIV known to possess reduced replicative fitness. With its rapid turnaround of 8 days and its high sensitivity, our rPhenotyping system may be a valuable diagnostic tool for detecting the early emergence of therapy-threatening HIV minorities or the persistence of residual resistant virus.

MeSH terms

  • Alleles
  • Anti-HIV Agents / therapeutic use*
  • Drug Resistance, Viral / genetics*
  • Genotype
  • HIV Infections / drug therapy*
  • HIV Infections / genetics
  • Humans
  • Mutation / genetics
  • Phenotype
  • Reverse Transcriptase Polymerase Chain Reaction / methods
  • Treatment Failure


  • Anti-HIV Agents