title: Protease sequences from HIV-1 group M subtypes A-H reveal distinct amino acid mutation patterns associated with protease resistance in protease inhibitor-naive individuals worldwide. HIV Variant Working Group.
abstract: BACKGROUND
  Although numerous mutations that confer resistance to protease inhibitors (PRI) have been mapped for HIV-1 subtype B, little is known about such substitutions for the non-B viruses, which globally cause the most infections.
  
  
  OBJECTIVE
  To determine the prevalence of PRI-associated mutations in PRI-naive individuals worldwide.
  
  
  METHODS
  Using the polymerase chain reaction, protease sequences were amplified from 301 individuals infected with HIV-1 subtypes A (79), B (95), B' (19), C (12), D (26), A/E (23), F (26), A/G (11), and H (3) and unclassifiable HIV-1 (7). Amplified DNA was directly sequenced and translated to amino acids to analyze PRI-associated major and accessory mutations.
  
  
  RESULTS
  Of the 301 sequences, 85% contained at least one codon change giving substitution at 10, 20, 30, 36, 46, 63, 71, 77, or 82 associated with PRI resistance; the frequency of these substitutions was higher among non-B (91%) than B (75%) viruses (P < 0.0005). Of these, 25% carried dual and triple substitutions. Two major drug resistance-conferring mutations, either 20M or 30N, were identified in only three specimens, whereas drug resistance accessory mutations were found in 252 isolates. These mutations gave distinct prevalence patterns for subtype B, 63P (62%) > 77I (19%) > 10I/V/R (6%) = 361 (6%) = 71T/V (6%) > 20R (2%), and non-B strains, 36I (83%) > 63P (17%) > 10I/V/R (13%) > 20R (10%) > 77I (2%), which differed statistically at positions 20, 36, 63, 71, and 77.
  
  
  CONCLUSIONS
  The high prevalence of PRI-associated substitutions represent natural polymorphisms occurring in PRI-naive patients infected with HIV-1 strains of subtypes A-H. The significance of distinct mutation patterns identified for subtype B and non-B strains warrants further clinical evaluation. A global HIV-1 protease database is fundamental for the investigation of novel PRI.
authors.affiliation: Division of AIDS, STD, and TB Laboratory Research, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
authors.forename: D
authors.initials: D
authors.lastname: Pieniazek
authors.forename: M
authors.initials: M
authors.lastname: Rayfield
authors.forename: D J
authors.initials: DJ
authors.lastname: Hu
authors.forename: J
authors.initials: J
authors.lastname: Nkengasong
authors.forename: S Z
authors.initials: SZ
authors.lastname: Wiktor
authors.forename: R
authors.initials: R
authors.lastname: Downing
authors.forename: B
authors.initials: B
authors.lastname: Biryahwaho
authors.forename: T
authors.initials: T
authors.lastname: Mastro
authors.forename: A
authors.initials: A
authors.lastname: Tanuri
authors.forename: V
authors.initials: V
authors.lastname: Soriano
authors.forename: R
authors.initials: R
authors.lastname: Lal
authors.forename: T
authors.initials: T
authors.lastname: Dondero
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D002219:Carbamates; D003062:Codon; D004352:Drug Resistance, Microbial / Q000235:genetics; D005663:Furans; D014943:Global Health; D016333:HIV Protease / Q000145:classification / Q000235:genetics*; D017320:HIV Protease Inhibitors / Q000494:pharmacology*; D015497:HIV-1 / Q000145:classification / Q000187:drug effects* / Q000201:enzymology / Q000235:genetics; D006801:Humans; D019469:Indinavir / Q000494:pharmacology; D008969:Molecular Sequence Data; D009154:Mutation; D019888:Nelfinavir / Q000494:pharmacology; D010802:Phylogeny; D019438:Ritonavir / Q000494:pharmacology; D019258:Saquinavir / Q000494:pharmacology; D013449:Sulfonamides / Q000494:pharmacology
chemical_list: D002219:Carbamates; D003062:Codon; D005663:Furans; D017320:HIV Protease Inhibitors; D013449:Sulfonamides; C095108:amprenavir; D019469:Indinavir; D016333:HIV Protease; D019888:Nelfinavir; D019258:Saquinavir; D019438:Ritonavir