Frequent polymorphism at drug resistance sites in HIV-1 protease and reverse transcriptase

Mary Kearney, Sarah Palmer, Frank Maldarelli, Wei Shao, Michael A. Polis, Joann Mican, Diane Rock-Kress, Joseph B. Margolick, John M. Coffin, John W. Mellors

Research output: Contribution to journalArticlepeer-review

68 Scopus citations


BACKGROUND: Failure of antiretroviral therapy may result from the selection of pre-existing, drug-resistant HIV-1 variants, but the frequency and type of such variants have not been defined. OBJECTIVE: We used single genome sequencing (SGS) to characterize the frequency of polymorphism at drug resistance sites in protease (PR) and reverse transcriptase (RT) in plasma samples from antiretroviral naive individuals. METHODS: A total of 2229 pro-pol sequences in 79 plasma samples from 30 patients were analyzed by SGS. A mean of 28 single genome sequences was obtained from each sample. The frequency of mutations at all PR and RT sites was compared to those associated with drug resistance. RESULTS: We detected polymorphism at one or more drug resistance sites in 27 of 30 (90%) patients. Polymorphism at positions 179 and 215 of RT was most common, both occurring in 23% of patients. Most (68%) of other drug resistance sites were polymorphic with an average of 3.2% of genomes per sample containing at least one variant from wild type. Seven drug resistance sites were polymorphic in more than 1% of genomes: PR position 33; RT positions 69, 98, 118, 179, 210, and 215. Although frequencies of synonymous polymorphism were similar at resistance and nonresistance sites, nonsynonymous polymorphism were significantly less common at drug resistance sites, implying stronger purifying selection at these positions. CONCLUSIONS: HIV-1 variants that are polymorphic at drug resistance sites pre-exist frequently as minor species in antiretroviral naive individuals. Standard genotype techniques have grossly underestimated their frequency.

Original languageEnglish (US)
Pages (from-to)497-501
Number of pages5
Issue number4
StatePublished - Feb 2008


  • Drug resistance
  • Drug resistance polymorphisms
  • Minority drug-resistant variants
  • Single genome sequencing (SGS)
  • Treatment-naive patients
  • pro-pol diversity

ASJC Scopus subject areas

  • Immunology and Allergy
  • Immunology
  • Infectious Diseases


Dive into the research topics of 'Frequent polymorphism at drug resistance sites in HIV-1 protease and reverse transcriptase'. Together they form a unique fingerprint.

Cite this