title: Bridging epidemiology with population genetics in a low incidence MSM-driven HIV-1 subtype B epidemic in Central Europe.
abstract: BACKGROUND
  The HIV-1 epidemic in Slovenia, a small Central European country, has some characteristics that make it an ideal model to study HIV-1 transmission. The epidemic is predominantly affecting men who have sex with men infected with subtype B (89% of all patients), has a low prevalence (less than 1/1000) and is growing slowly. The aim of the present study was to analyze in detail the evolutionary history and the determinants of transmission.
  
  
  METHODS
  A total of 223 partial pol gene sequences from therapy naïve individuals were included, representing 52% of all patients newly diagnosed in 13 years (2000-2012) and analyzed together with genetically similar worldwide sequences, selected in a BLAST search.
  
  
  RESULTS
  Combined analysis (maximum likelihood and Bayesian) of HIV-1 transmission chains revealed 8 major clusters (n ≥ 10 patients), 1 group of 4 patients, 2 trios and 12 transmission pairs, thus leaving only 43 (19.3%) Slovenian patients infected with subtype B without a local epidemiological link, indicating a predominance of local transmission of HIV-1 infection. Bayesian analysis performed on a full set of sequences estimated several introductions of HIV-1 into Slovenia, with the most recent common ancestor (tMRCA) of the earliest Slovenian cluster dated to the late 1980s, although tMRCAs obtained from separate independent analysis of each cluster showed considerably more recent estimates. These findings indicate inconsistencies in molecular clock estimation, which we further explored. We hypothesize that these inconsistent dating estimates across the tree could be caused by an evolutionary rate acceleration of HIV-1 after entering the Slovenia epidemic that is not taken into account by the molecular clock model. It could be caused by a lower transmission rate in this setting, as demonstrated by the low epidemic growth rate estimated by Bayesian skyline plot analysis.
  
  
  CONCLUSIONS
  HIV-1 subtype B was introduced into Slovenia at several time points from the late 80s onward. The majority of patients had a local transmission link, indicating a closed HIV community. The observed slower epidemic rate suggests that individuals with a long-lasting infection are the driving force of the epidemic in this region.
authors.affiliation: Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia. maja.lunar@mf.uni-lj.si.
authors.forename: Maja M
authors.initials: MM
authors.lastname: Lunar
authors.affiliation: KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, B-3000, Leuven, Belgium. annemie.vandamme@uzleuven.be.|Unidade de Microbiologia e Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal. annemie.vandamme@uzleuven.be.
authors.forename: Anne-Mieke
authors.initials: AM
authors.lastname: Vandamme
authors.affiliation: Department of Infectious Diseases, University Medical Center Ljubljana, Ljubljana, Slovenia. janez.tomazic@kclj.si.
authors.forename: Janez
authors.initials: J
authors.lastname: Tomažič
authors.affiliation: Department of Infectious Diseases, University Medical Center Ljubljana, Ljubljana, Slovenia. primoz.karner@guest.arnes.si.
authors.forename: Primož
authors.initials: P
authors.lastname: Karner
authors.affiliation: Department of Infectious Diseases, University Medical Center Ljubljana, Ljubljana, Slovenia. tomaz.vovko@kclj.si.
authors.forename: Tomaž D
authors.initials: TD
authors.lastname: Vovko
authors.affiliation: Department of Infectious Diseases, University Medical Center Ljubljana, Ljubljana, Slovenia. blaz.pecavar@gmail.com.
authors.forename: Blaž
authors.initials: B
authors.lastname: Pečavar
authors.affiliation: Department of Infectious Diseases, University Medical Center Ljubljana, Ljubljana, Slovenia. gabi.volcansek@gmail.com.
authors.forename: Gabriele
authors.initials: G
authors.lastname: Volčanšek
authors.affiliation: Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia. mario.poljak@mf.uni-lj.si.
authors.forename: Mario
authors.initials: M
authors.lastname: Poljak
authors.affiliation: Unidade de Saúde Pública Internacional e Bioestatística e Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal. ana.abecasis@gmail.com.
authors.forename: Ana B
authors.initials: AB
authors.lastname: Abecasis
mesh_terms: D000328:Adult; D016000:Cluster Analysis; D058872:Epidemics; D005060:Europe / Q000453:epidemiology; D005260:Female; D015751:Genes, pol; D005828:Genetics, Population; D015658:HIV Infections / Q000453:epidemiology* / Q000235:genetics* / Q000635:transmission / Q000821:virology; D015497:HIV-1 / Q000145:classification / Q000235:genetics; D018451:Homosexuality, Male / Q000706:statistics & numerical data*; D006801:Humans; D015994:Incidence; D008297:Male; D008875:Middle Aged; D010802:Phylogeny; D015995:Prevalence; D017524:Slovenia / Q000453:epidemiology