title: Whole genome pyrosequencing of rare hepatitis C virus genotypes enhances subtype classification and identification of naturally occurring drug resistance variants.
abstract: BACKGROUND
  Infection with hepatitis C virus (HCV) is a burgeoning worldwide public health problem, with 170 million infected individuals and an estimated 20 million deaths in the coming decades. While 6 main genotypes generally distinguish the global geographic diversity of HCV, a multitude of closely related subtypes within these genotypes are poorly defined and may influence clinical outcome and treatment options. Unfortunately, the paucity of genetic data from many of these subtypes makes time-consuming primer walking the limiting step for sequencing understudied subtypes.
  
  
  METHODS
  Here we combined long-range polymerase chain reaction amplification with pyrosequencing for a rapid approach to generate the complete viral coding region of 31 samples representing poorly defined HCV subtypes.
  
  
  RESULTS
  Phylogenetic classification based on full genome sequences validated previously identified HCV subtypes, identified a recombinant sequence, and identified a new distinct subtype of genotype 4. Unlike conventional sequencing methods, use of deep sequencing also facilitated characterization of minor drug resistance variants within these uncommon or, in some cases, previously uncharacterized HCV subtypes.
  
  
  CONCLUSIONS
  These data aid in the classification of uncommon HCV subtypes while also providing a high-resolution view of viral diversity within infected patients, which may be relevant to the development of therapeutic regimens to minimize drug resistance.
authors.affiliation: Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. rnewman@broadinstitute.org
authors.forename: Ruchi M
authors.initials: RM
authors.lastname: Newman
authors.forename: Thomas
authors.initials: T
authors.lastname: Kuntzen
authors.forename: Brian
authors.initials: B
authors.lastname: Weiner
authors.forename: Andrew
authors.initials: A
authors.lastname: Berical
authors.forename: Patrick
authors.initials: P
authors.lastname: Charlebois
authors.forename: Carla
authors.initials: C
authors.lastname: Kuiken
authors.forename: Donald G
authors.initials: DG
authors.lastname: Murphy
authors.forename: Peter
authors.initials: P
authors.lastname: Simmonds
authors.forename: Phil
authors.initials: P
authors.lastname: Bennett
authors.forename: Niall J
authors.initials: NJ
authors.lastname: Lennon
authors.forename: Bruce W
authors.initials: BW
authors.lastname: Birren
authors.forename: Michael C
authors.initials: MC
authors.lastname: Zody
authors.forename: Todd M
authors.initials: TM
authors.lastname: Allen
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Henn
mesh_terms: D000998:Antiviral Agents / Q000627:therapeutic use; D001483:Base Sequence; D024882:Drug Resistance, Viral / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics; D016679:Genome, Viral / Q000235:genetics; D005838:Genotype; D016174:Hepacivirus / Q000145:classification / Q000187:drug effects / Q000235:genetics*; D006526:Hepatitis C / Q000188:drug therapy / Q000821:virology; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny
chemical_list: D000998:Antiviral Agents
keywords: Hepatitis C virus; drug resistance mutations; pyrosequencing; subtype classification; viral diversity