title: Analysis of a local HIV-1 epidemic in portugal highlights established transmission of non-B and non-G subtypes.
abstract: The existing data support Portugal as the western European country with the highest HIV-1 subtype diversity. However, detailed phylogenetic studies of Portuguese HIV-1 epidemics are still scarce. Thus, our main goal was to analyze the phylodynamics of a local HIV-1 infection in the Portuguese region of Minho. Molecular epidemiological analysis was applied to data from 289 HIV-1-infected individuals followed at the reference hospital of the province of Minho, Portugal, at which isolated viruses had been sequenced between 2000 and 2012. Viruses of the G (29.1%) and B (27.0%) subtypes were the most frequent, followed by recombinant forms (17.6%) and the C (14.5%), F1 (7.3%), and A1 (4.2%) subtypes. Multinomial logistic regression revealed that the odds of being infected with the A1 and F1 subtypes increased over the years compared with those with B, G, or C subtypes or recombinant viruses. As expected, polyphyletic patterns suggesting multiple and old introductions of the B and G subtypes were found. However, transmission clusters of non-B and non-G viruses among native individuals were also found, with the dates of the most recent common ancestor estimated to be in the early 2000s. Our study supports that the HIV-1 subtype diversity in the Portuguese region of Minho is high and has been increasing in a manner that is apparently driven by factors other than immigration and international travel. Infections with A1 and F1 viruses in the region of Minho are becoming established and are mainly found in sexually transmitted clusters, reinforcing the need for more efficacious control measures targeting this infection route.
authors.affiliation: Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal ICVS/3B PT Government Associate Laboratory, Braga/Guimarães, Portugal Hospital de Braga, Braga, Portugal.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Carvalho
authors.affiliation: Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal ICVS/3B PT Government Associate Laboratory, Braga/Guimarães, Portugal.
authors.forename: Patrício
authors.initials: P
authors.lastname: Costa
authors.affiliation: Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal ICVS/3B PT Government Associate Laboratory, Braga/Guimarães, Portugal.
authors.forename: Vera
authors.initials: V
authors.lastname: Triunfante
authors.affiliation: Hospital de Braga, Braga, Portugal.
authors.forename: Fernando
authors.initials: F
authors.lastname: Branca
authors.affiliation: Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal ICVS/3B PT Government Associate Laboratory, Braga/Guimarães, Portugal.
authors.forename: Fernando
authors.initials: F
authors.lastname: Rodrigues
authors.affiliation: Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal ICVS/3B PT Government Associate Laboratory, Braga/Guimarães, Portugal.
authors.forename: Catarina L
authors.initials: CL
authors.lastname: Santos
authors.affiliation: Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal ICVS/3B PT Government Associate Laboratory, Braga/Guimarães, Portugal.
authors.forename: Margarida
authors.initials: M
authors.lastname: Correia-Neves
authors.affiliation: Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal ICVS/3B PT Government Associate Laboratory, Braga/Guimarães, Portugal.
authors.forename: Margarida
authors.initials: M
authors.lastname: Saraiva
authors.affiliation: Institute of Health Sciences, Universidade Católica Portuguesa (Portuguese Catholic University, UCP), Porto, Portugal.
authors.forename: Henrique
authors.initials: H
authors.lastname: Lecour
authors.affiliation: Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal ICVS/3B PT Government Associate Laboratory, Braga/Guimarães, Portugal.
authors.forename: António G
authors.initials: AG
authors.lastname: Castro
authors.affiliation: Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal ICVS/3B PT Government Associate Laboratory, Braga/Guimarães, Portugal.
authors.forename: Jorge
authors.initials: J
authors.lastname: Pedrosa
authors.affiliation: Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal ICVS/3B PT Government Associate Laboratory, Braga/Guimarães, Portugal nosorio@ecsaude.uminho.pt.
authors.forename: Nuno S
authors.initials: NS
authors.lastname: Osório
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D015331:Cohort Studies; D058872:Epidemics; D005260:Female; D014644:Genetic Variation; D005838:Genotype; D015658:HIV Infections / Q000453:epidemiology* / Q000635:transmission / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008297:Male; D008875:Middle Aged; D017720:Molecular Epidemiology; D010802:Phylogeny; D011174:Portugal / Q000453:epidemiology; D015995:Prevalence; D017422:Sequence Analysis, DNA; D055815:Young Adult