title: Mapping natural polymorphisms of hepatitis C virus NS3/4A protease and antiviral resistance to inhibitors in worldwide isolates.
abstract: BACKGROUND
  Several inhibitors for the hepatitis C virus (HCV) NS3/4A protease are under development. Although previous studies identified viral resistance mutations, there is little information on the natural variability of proteases from the different viral subtypes. Here, we aimed to determine both the natural variability and presence of resistance or compensatory mutations to new protease inhibitors (PI) in NS3/4A proteases from worldwide HCV isolates.
  
  
  METHODS
  A comprehensive analysis was performed in 380 HCV NS3 sequences (275 genotype 1; 105 other genotypes) from public HCV databases (EuHCVdb and Los Alamos). Amino acid polymorphism and signature patterns were deduced in the protease domain, including all sites associated with resistance to the PIs BILN-2061, Telaprevir (VX-950), Boceprevir (SCH-503034), SCH-6 and ITMN-191.
  
  
  RESULTS
  Few of the residues in the catalytic triad or in substrate/metal-binding sites were polymorphic, and were identified in only 4/380 isolates. However, a relevant polymorphism was found in sites associated either with resistance to PI (V36, 1170 and D168) or with compensatory mutations (171, T72, Q86 and 1153). Furthermore, some unique genotype-specific signature patterns associated with resistance to PI were also identified.
  
  
  CONCLUSIONS
  We describe for the first time the relevant natural polymorphisms of the HCV NS3/4A protease in worldwide isolates. Although the prevalence of major resistance mutations is very low, many compensatory sites are naturally polymorphic among proteases from several HCV subtypes. These data will help to determine whether HCV resistance is likely to be selected with new PIs and will aid the design of genotypic resistance testing.
authors.affiliation: Public Health Department, Generalitat Valenciana, Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), E-46071 Valencia, Spain. F.Xavier.Lopez@uv.es
authors.forename: F Xavier
authors.initials: FX
authors.lastname: López-Labrador
authors.forename: Andrés
authors.initials: A
authors.lastname: Moya
authors.forename: Fernando
authors.initials: F
authors.lastname: Gonzàlez-Candelas
mesh_terms: D000595:Amino Acid Sequence; D000998:Antiviral Agents / Q000494:pharmacology; D002219:Carbamates / Q000494:pharmacology; D002352:Carrier Proteins / Q000737:chemistry / Q000235:genetics*; D024882:Drug Resistance, Viral / Q000235:genetics*; D014943:Global Health; D016174:Hepacivirus / Q000187:drug effects / Q000201:enzymology / Q000235:genetics / Q000302:isolation & purification; D006526:Hepatitis C / Q000821:virology; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins; D047028:Macrocyclic Compounds / Q000494:pharmacology; D008826:Microbial Sensitivity Tests / Q000379:methods; D008969:Molecular Sequence Data; D009842:Oligopeptides / Q000494:pharmacology; D011110:Polymorphism, Genetic; D011392:Proline / Q000031:analogs & derivatives / Q000494:pharmacology; D011480:Protease Inhibitors / Q000494:pharmacology*; D011804:Quinolines / Q000494:pharmacology; D016415:Sequence Alignment; D013844:Thiazoles / Q000494:pharmacology; D017361:Viral Nonstructural Proteins / Q000737:chemistry / Q000235:genetics*; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics*; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
chemical_list: D000998:Antiviral Agents; D002219:Carbamates; D002352:Carrier Proteins; D047908:Intracellular Signaling Peptides and Proteins; D047028:Macrocyclic Compounds; D009842:Oligopeptides; D011392:Proline; D011480:Protease Inhibitors; D011804:Quinolines; D013844:Thiazoles; D017361:Viral Nonstructural Proteins; D014764:Viral Proteins; C479555:BILN 2061; C084422:NS3 protein, hepatitis C virus; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases; C455041:NS4A cofactor peptide, Hepatitis C virus; C486464:telaprevir; C512204:N-(3-amino-1-(cyclobutylmethyl)-2,3-dioxopropyl)-3-(2-((((1,1-dimethylethyl)amino)carbonyl)amino)-3,3-dimethyl-1-oxobutyl)-6,6-dimethyl-3-azabicyclo(3.1.0)hexan-2-carboxamide