title: Phylodynamic and Phylogeographic Profiles of Subtype B HIV-1 Epidemics in South Spain.
abstract: BACKGROUND
  Since 1982, HIV-1 epidemics have evolved to different scenarios in terms of transmission routes, subtype distribution and characteristics of transmission clusters. We investigated the evolutionary history of HIV-1 subtype B in south Spain.
  
  
  METHODS
  We studied all newly diagnosed HIV-1 subtype B patients in East Andalusia during the 2005-2012 period. For the analysis, we used the reverse transcriptase and protease sequences from baseline resistance, and the Trugene® HIV Genotyping kit (Siemens, Barcelona, Spain). Subtyping was done with REGA v3.0. The maximum likelihood trees constructed with RAxML were used to study HIV-1 clustering. Phylogeographic and phylodynamic profiles were studied by Bayesian inference methods with BEAST v1.7.5 and SPREAD v1.0.6.
  
  
  RESULTS
  Of the 493 patients infected with HIV-1 subtype B, 234 grouped into 55 clusters, most of which were small (44 clusters ≤ 5 patients, 31 with 2 patients, 13 with 3). The rest (133/234) were grouped into 11 clusters with ≥ 5 patients, and most (82%, 109/133) were men who have sex with men (MSM) grouped into 8 clusters. The association with clusters was more frequent in Spanish (p = 0.02) men (p< 0.001), MSM (p<0.001) younger than 35 years (p = 0.001) and with a CD4+ T-cell count above 350 cells/ul (p<0.001). We estimated the date of HIV-1 subtype B regional epidemic diversification around 1970 (95% CI: 1965-1987), with an evolutionary rate of 2.4 (95%CI: 1.7-3.1) x 10-3 substitutions/site/year. Most clusters originated in the 1990s in MSMs. We observed exponential subtype B HIV-1 growth in 1980-1990 and 2005-2008. The most significant migration routes for subtype B went from inland cities to seaside locations.
  
  
  CONCLUSIONS
  We provide the first data on the phylodynamic and phylogeographic profiles of HIV-1 subtype B in south Spain. Our findings of transmission clustering among MSMs should alert healthcare managers to enhance preventive measures in this risk group in order to prevent future outbreaks.
authors.affiliation: Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario e Instituto de Investigación IBS, Granada, Spain.
authors.forename: Santiago
authors.initials: S
authors.lastname: Pérez-Parra
authors.affiliation: Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario e Instituto de Investigación IBS, Granada, Spain.
authors.forename: Natalia
authors.initials: N
authors.lastname: Chueca
authors.affiliation: Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario e Instituto de Investigación IBS, Granada, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Álvarez
authors.affiliation: Servicio de Infecciosas, Hospital Virgen de las Nieves, Granada, Spain.
authors.forename: Juan
authors.initials: J
authors.lastname: Pasquau
authors.affiliation: Servicio de Infecciosas, Hospital Ciudad de Jaén, Jaén, Spain.
authors.forename: Mohamed
authors.initials: M
authors.lastname: Omar
authors.affiliation: Servicio de Medicina Interna, Hospital de Torrecárdenas, Almería, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Collado
authors.affiliation: Servicio de Infecciosas, Hospital Universitario San Cecilio, Granada, Spain.
authors.forename: David
authors.initials: D
authors.lastname: Vinuesa
authors.affiliation: Servicio de Infecciosas, Hospital de Poniente, Almería, Spain.
authors.forename: Ana B
authors.initials: AB
authors.lastname: Lozano
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.
authors.forename: Gonzalo
authors.initials: G
authors.lastname: Yebra
authors.affiliation: Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario e Instituto de Investigación IBS, Granada, Spain.
authors.forename: Federico
authors.initials: F
authors.lastname: García
mesh_terms: D000328:Adult; D001499:Bayes Theorem; D018791:CD4 Lymphocyte Count; D015496:CD4-Positive T-Lymphocytes / Q000166:cytology; D003710:Demography; D005260:Female; D005838:Genotype; D015658:HIV Infections / Q000175:diagnosis / Q000453:epidemiology* / Q000635:transmission / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D018451:Homosexuality, Male; D006801:Humans; D016013:Likelihood Functions; D008297:Male; D008875:Middle Aged; D010802:Phylogeny; D017423:Sequence Analysis, RNA; D013030:Spain / Q000453:epidemiology; D054302:pol Gene Products, Human Immunodeficiency Virus / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D054302:pol Gene Products, Human Immunodeficiency Virus