title: Mining for pairs: shared clinic visit dates identify steady HIV-positive partnerships.
abstract: Here we examined the hypothesis that some stable HIV-infected partnerships can be found in cohort studies, as the patients frequently attend the clinic visits together.
  
  
  
  Using mathematical approximations and shuffling to derive the probabilities of sharing a given number of visits by chance, we identified and validated couples that may represent either transmission pairs or serosorting couples in a stable relationship.
  
  
  
  We analysed 434 432 visits for 16 139 Swiss HIV Cohort Study patients from 1990 to 2014. For 89 pairs, the number of shared visits exceeded the number expected. Of these, 33 transmission pairs were confirmed on the basis of three criteria: an extensive phylogenetic tree, a self-reported steady HIV-positive partnership, and risk group affiliation. Notably, 12 of the validated transmission pairs (36%; 12 of 33) were of a mixed ethnicity with a large median age gap [17.5 years; interquartile range (IQR) 11.8-22 years] and these patients harboured HIV-1 of predominantly non-B subtypes, suggesting imported infections.
  
  
  
  In the context of the surge in research interest in HIV transmission pairs, this simple method widens the horizons of research on within-pair quasi-species exchange, transmitted drug resistance and viral recombination at the biological level and targeted prevention at the public health level.
authors.affiliation: Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.|Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland.
authors.forename: A
authors.initials: A
authors.lastname: Marzel
authors.affiliation: Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.|Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland.
authors.forename: M
authors.initials: M
authors.lastname: Shilaih
authors.affiliation: Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.|Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland.
authors.forename: T
authors.initials: T
authors.lastname: Turk
authors.affiliation: Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.|Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland.
authors.forename: N K
authors.initials: NK
authors.lastname: Campbell
authors.affiliation: Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.
authors.forename: W-L
authors.initials: WL
authors.lastname: Yang
authors.affiliation: Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland.
authors.forename: J
authors.initials: J
authors.lastname: Böni
authors.affiliation: Laboratory of Virology, Geneva University Hospital, Geneva, Switzerland.
authors.forename: S
authors.initials: S
authors.lastname: Yerly
authors.affiliation: Molecular Virology, Department of Biomedicine-Petersplatz, University of Basel, Basel, Switzerland.
authors.forename: T
authors.initials: T
authors.lastname: Klimkait
authors.affiliation: Division of Immunology and Allergy, University Hospital Lausanne, Lausanne, Switzerland.
authors.forename: V
authors.initials: V
authors.lastname: Aubert
authors.affiliation: Department of Infectious Diseases, Berne University Hospital and University of Berne, Berne, Switzerland.
authors.forename: H
authors.initials: H
authors.lastname: Furrer
authors.affiliation: Division of Infectious Diseases, Geneva University Hospital, Geneva, Switzerland.
authors.forename: A
authors.initials: A
authors.lastname: Calmy
authors.affiliation: Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland.
authors.forename: M
authors.initials: M
authors.lastname: Battegay
authors.affiliation: Service of Infectious Diseases, Lausanne University Hospital, Lausanne, Switzerland.
authors.forename: M
authors.initials: M
authors.lastname: Cavassini
authors.affiliation: Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland.
authors.forename: E
authors.initials: E
authors.lastname: Bernasconi
authors.affiliation: Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital, St. Gallen, Switzerland.
authors.forename: P
authors.initials: P
authors.lastname: Schmid
authors.affiliation: Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.|Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland.
authors.forename: K J
authors.initials: KJ
authors.lastname: Metzner
authors.affiliation: Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.|Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland.
authors.forename: H F
authors.initials: HF
authors.lastname: Günthard
authors.affiliation: Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.|Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland.
authors.forename: R D
authors.initials: RD
authors.lastname: Kouyos
mesh_terms: D000553:Ambulatory Care / Q000706:statistics & numerical data; D015331:Cohort Studies; D057225:Data Mining / Q000379:methods*; D005260:Female; D015658:HIV Infections / Q000188:drug therapy* / Q000208:ethnology / Q000821:virology; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D018452:Homosexuality, Female / Q000208:ethnology; D018451:Homosexuality, Male / Q000208:ethnology; D006801:Humans; D008297:Male; D010802:Phylogeny; D057566:Self Report; D012747:Sexual Partners / Q000145:classification*; D059039:Standard of Care
keywords: 
  HIV
  ; cohort studies; data mining; epidemiology; phylogeny; transmission