title: Constrained patterns of covariation and clustering of HIV-1 non-nucleoside reverse transcriptase inhibitor resistance mutations.
abstract: OBJECTIVE
  We characterized pairwise and higher order patterns of non-nucleoside reverse transcriptase inhibitor (NNRTI)-selected mutations because multiple mutations are usually required for clinically significant resistance to second-generation NNRTIs.
  
  
  METHODS
  We analysed viruses from 13 039 individuals with sequences containing at least one of 52 published NNRTI-selected mutations, including 1133 viruses from individuals who received efavirenz but no other NNRTI and 1510 viruses from individuals who received nevirapine but no other NNRTI. Of the 17 reported etravirine resistance-associated mutations (RAMs), Y181C/I/V, L100I, K101P and M230L were considered major based on published in vitro susceptibility data.
  
  
  RESULTS
  Efavirenz preferentially selected for 16 mutations, including L100I (14% versus 0.1%, P < 0.001), K101P (3.3% versus 0.4%, P < 0.001) and M230L (2.8% versus 1.3%, P = 0.004), whereas nevirapine preferentially selected for 12 mutations, including Y181C/I/V (48% versus 6.9%, P < 0.001). Twenty-nine pairs of NNRTI-selected mutations covaried significantly, including Y181C with seven other mutations (A98G, K101E/H, V108I, G190A/S and H221Y), L100I with K103N, and K101P with K103S. Two pairs (Y181C + V179F and Y181C + G190S) were predicted to confer >10-fold decreased etravirine susceptibility. Seventeen percent of sequences had three or more NNRTI-selected mutations, mostly in clusters of covarying mutations. Many clusters had Y181C plus a non-major etravirine RAM; few had more than one major etravirine RAM.
  
  
  CONCLUSIONS
  Although major etravirine RAMs rarely occur in combination, 2 of 29 pairs of covarying mutations were associated with >10-fold decreased etravirine susceptibility. Viruses with three or more NNRTI-selected mutations often contained Y181C in combination with one or more minor etravirine RAMs; however, phenotypic and clinical correlates for most of these higher order combinations have not been published.
authors.affiliation: Division of Infectious Diseases, Department of Medicine, Stanford University, 300 Pasteur Drive, Grant S-146, Stanford, CA 94305, USA. ereuman@stanford.edu
authors.forename: Elizabeth C
authors.initials: EC
authors.lastname: Reuman
authors.forename: Soo-Yon
authors.initials: SY
authors.lastname: Rhee
authors.forename: Susan P
authors.initials: SP
authors.lastname: Holmes
authors.forename: Robert W
authors.initials: RW
authors.lastname: Shafer
mesh_terms: D000480:Alkynes; D019943:Amino Acid Substitution / Q000235:genetics; D019380:Anti-HIV Agents / Q000494:pharmacology* / Q000627:therapeutic use; D048588:Benzoxazines / Q000494:pharmacology / Q000627:therapeutic use; D003521:Cyclopropanes; D004252:DNA Mutational Analysis; D024921:Drug Resistance, Multiple, Viral; D005260:Female; D015658:HIV Infections / Q000821:virology*; D054303:HIV Reverse Transcriptase / Q000235:genetics*; D015497:HIV-1 / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008297:Male; D020125:Mutation, Missense; D019829:Nevirapine / Q000494:pharmacology / Q000627:therapeutic use; D009570:Nitriles; D011724:Pyridazines / Q000494:pharmacology; D011743:Pyrimidines; D018894:Reverse Transcriptase Inhibitors / Q000494:pharmacology* / Q000627:therapeutic use
chemical_list: D000480:Alkynes; D019380:Anti-HIV Agents; D048588:Benzoxazines; D003521:Cyclopropanes; D009570:Nitriles; D011724:Pyridazines; D011743:Pyrimidines; D018894:Reverse Transcriptase Inhibitors; C451734:etravirine; D019829:Nevirapine; C514824:reverse transcriptase, Human immunodeficiency virus 1; D054303:HIV Reverse Transcriptase; C098320:efavirenz
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