title: Ambiguous nucleotide calls from population-based sequencing of HIV-1 are a marker for viral diversity and the age of infection.
abstract: BACKGROUND
  The time passed since the infection of a human immunodeficiency virus (HIV)-infected individual (the age of infection) is an important but often only poorly known quantity. We assessed whether the fraction of ambiguous nucleotides obtained from bulk sequencing as done for genotypic resistance testing can serve as a proxy of this parameter.
  
  
  METHODS
  We correlated the age of infection and the fraction of ambiguous nucleotides in partial pol sequences of HIV-1 sampled before initiation of antiretroviral therapy (ART). Three groups of Swiss HIV Cohort Study participants were analyzed, for whom the age of infection was estimated on the basis of Bayesian back calculation (n = 3,307), seroconversion (n = 366), or diagnoses of primary HIV infection (n = 130). In addition, we studied 124 patients for whom longitudinal genotypic resistance testing was performed while they were still ART-naïve.
  
  
  RESULTS
  We found that the fraction of ambiguous nucleotides increased with the age of infection with a rate of .2% per year within the first 8 years but thereafter with a decreasing rate. We show that this pattern is consistent with population-genetic models for realistic parameters. Finally, we show that, in this highly representative population, a fraction of ambiguous nucleotides of >.5% provides strong evidence against a recent infection event <1 year prior to sampling (negative predictive value, 98.7%).
  
  
  CONCLUSIONS
  These findings show that the fraction of ambiguous nucleotides is a useful marker for the age of infection.
authors.affiliation: Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland. rkouyos@princeton.edu
authors.forename: Roger D
authors.initials: RD
authors.lastname: Kouyos
authors.forename: Viktor
authors.initials: V
authors.lastname: von Wyl
authors.forename: Sabine
authors.initials: S
authors.lastname: Yerly
authors.forename: Jürg
authors.initials: J
authors.lastname: Böni
authors.forename: Philip
authors.initials: P
authors.lastname: Rieder
authors.forename: Beda
authors.initials: B
authors.lastname: Joos
authors.forename: Patrick
authors.initials: P
authors.lastname: Taffé
authors.forename: Cyril
authors.initials: C
authors.lastname: Shah
authors.forename: Philippe
authors.initials: P
authors.lastname: Bürgisser
authors.forename: Thomas
authors.initials: T
authors.lastname: Klimkait
authors.forename: Rainer
authors.initials: R
authors.lastname: Weber
authors.forename: Bernard
authors.initials: B
authors.lastname: Hirschel
authors.forename: Matthias
authors.initials: M
authors.lastname: Cavassini
authors.forename: Andri
authors.initials: A
authors.lastname: Rauch
authors.forename: Manuel
authors.initials: M
authors.lastname: Battegay
authors.forename: Pietro L
authors.initials: PL
authors.lastname: Vernazza
authors.forename: Enos
authors.initials: E
authors.lastname: Bernasconi
authors.forename: Bruno
authors.initials: B
authors.lastname: Ledergerber
authors.forename: Sebastian
authors.initials: S
authors.lastname: Bonhoeffer
authors.forename: Huldrych F
authors.initials: HF
authors.lastname: Günthard
mesh_terms: D000328:Adult; D015331:Cohort Studies; D005260:Female; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008297:Male; D008875:Middle Aged; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA; D013557:Switzerland; D013997:Time Factors; D054302:pol Gene Products, Human Immunodeficiency Virus / Q000235:genetics
chemical_list: D054302:pol Gene Products, Human Immunodeficiency Virus