title: Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis.
abstract: BACKGROUND
  The HIV-1 subtype B epidemic amongst men who have sex with men (MSM) is resurgent in many countries despite the widespread use of effective combination antiretroviral therapy (cART). In this combined mathematical and phylogenetic study of observational data, we aimed to find out the extent to which the resurgent epidemic is the result of newly introduced strains or of growth of already circulating strains.
  
  
  RESULTS
  As of November 2011, the ATHENA observational HIV cohort of all patients in care in the Netherlands since 1996 included HIV-1 subtype B polymerase sequences from 5,852 patients. Patients who were diagnosed between 1981 and 1995 were included in the cohort if they were still alive in 1996. The ten most similar sequences to each ATHENA sequence were selected from the Los Alamos HIV Sequence Database, and a phylogenetic tree was created of a total of 8,320 sequences. Large transmission clusters that included ≥10 ATHENA sequences were selected, with a local support value ≥ 0.9 and median pairwise patristic distance below the fifth percentile of distances in the whole tree. Time-varying reproduction numbers of the large MSM-majority clusters were estimated through mathematical modeling. We identified 106 large transmission clusters, including 3,061 (52%) ATHENA and 652 Los Alamos sequences. Half of the HIV sequences from MSM registered in the cohort in the Netherlands (2,128 of 4,288) were included in 91 large MSM-majority clusters. Strikingly, at least 54 (59%) of these 91 MSM-majority clusters were already circulating before 1996, when cART was introduced, and have persisted to the present. Overall, 1,226 (35%) of the 3,460 diagnoses among MSM since 1996 were found in these 54 long-standing clusters. The reproduction numbers of all large MSM-majority clusters were around the epidemic threshold value of one over the whole study period. A tendency towards higher numbers was visible in recent years, especially in the more recently introduced clusters. The mean age of MSM at diagnosis increased by 0.45 years/year within clusters, but new clusters appeared with lower mean age. Major strengths of this study are the high proportion of HIV-positive MSM with a sequence in this study and the combined application of phylogenetic and modeling approaches. Main limitations are the assumption that the sampled population is representative of the overall HIV-positive population and the assumption that the diagnosis interval distribution is similar between clusters.
  
  
  CONCLUSIONS
  The resurgent HIV epidemic amongst MSM in the Netherlands is driven by several large, persistent, self-sustaining, and, in many cases, growing sub-epidemics shifting towards new generations of MSM. Many of the sub-epidemics have been present since the early epidemic, to which new sub-epidemics are being added.
authors.affiliation: HIV Monitoring Foundation, Amsterdam, the Netherlands.
authors.forename: Daniela
authors.initials: D
authors.lastname: Bezemer
authors.affiliation: Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom.
authors.forename: Anne
authors.initials: A
authors.lastname: Cori
authors.affiliation: Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom.
authors.forename: Oliver
authors.initials: O
authors.lastname: Ratmann
authors.affiliation: HIV Monitoring Foundation, Amsterdam, the Netherlands.
authors.forename: Ard
authors.initials: A
authors.lastname: van Sighem
authors.affiliation: Red Cross Blood Bank Foundation, Willemstad, Curaçao.
authors.forename: Hillegonda S
authors.initials: HS
authors.lastname: Hermanides
authors.affiliation: Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands; Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, the Netherlands.
authors.forename: Bas E
authors.initials: BE
authors.lastname: Dutilh
authors.affiliation: HIV Monitoring Foundation, Amsterdam, the Netherlands.
authors.forename: Luuk
authors.initials: L
authors.lastname: Gras
authors.affiliation: Department of Zoology, University of Oxford, Oxford, United Kingdom.
authors.forename: Nuno
authors.initials: N
authors.lastname: Rodrigues Faria
authors.affiliation: HIV Monitoring Foundation, Amsterdam, the Netherlands.
authors.forename: Rob
authors.initials: R
authors.lastname: van den Hengel
authors.affiliation: Red Cross Blood Bank Foundation, Willemstad, Curaçao.
authors.forename: Ashley J
authors.initials: AJ
authors.lastname: Duits
authors.affiliation: HIV Monitoring Foundation, Amsterdam, the Netherlands; Department of Global Health, Academic Medical Center, Amsterdam, the Netherlands; Amsterdam Institute for Global Health and Development, Amsterdam, the Netherlands.
authors.forename: Peter
authors.initials: P
authors.lastname: Reiss
authors.affiliation: Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom.
authors.forename: Frank
authors.initials: F
authors.lastname: de Wolf
authors.affiliation: Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom.
authors.forename: Christophe
authors.initials: C
authors.lastname: Fraser
mesh_terms: D000328:Adult; D017677:Age Distribution; D001483:Base Sequence; D015331:Cohort Studies; D058872:Epidemics; D062665:Epidemiological Monitoring; D015658:HIV Infections / Q000453:epidemiology* / Q000635:transmission; D015497:HIV-1 / Q000235:genetics; D018451:Homosexuality, Male / Q000706:statistics & numerical data*; D006801:Humans; D016013:Likelihood Functions; D008297:Male; D008390:Markov Chains; D008962:Models, Theoretical; D009010:Monte Carlo Method; D009426:Netherlands / Q000453:epidemiology; D010802:Phylogeny