title: Phylogeny and Phylogeography of a Recent HIV-1 Subtype F Outbreak among Men Who Have Sex with Men in Spain Deriving from a Cluster with a Wide Geographic Circulation in Western Europe.
abstract: We recently reported the rapid expansion of an HIV-1 subtype F cluster among men who have sex with men (MSM) in the region of Galicia, Northwest Spain. Here we update this outbreak, analyze near full-length genomes, determine phylogenetic relationships, and estimate its origin. For this study, we used sequences of HIV-1 protease-reverse transcriptase and env V3 region, and for 17 samples, near full-length genome sequences were obtained. Phylogenetic analyses were performed via maximum likelihood. Locations and times of most recent common ancestors were estimated using Bayesian inference. Among samples analyzed by us, 100 HIV-1 F1 subsubtype infections of monophyletic origin were diagnosed in Spain, including 88 in Galicia and 12 in four other regions. Most viruses (n = 90) grouped in a subcluster (Galician subcluster), while 7 from Valladolid (Central Spain) grouped in another subcluster. At least 94 individuals were sexually-infected males and at least 71 were MSM. Seventeen near full-length genomes were uniformly of F1 subsubtype. Through similarity searches and phylogenetic analyses, we identified 18 viruses from four other Western European countries [Switzerland (n = 8), Belgium (n = 5), France (n = 3), and United Kingdom (n = 2)] and one from Brazil, from samples collected in 2005-2011, which branched within the subtype F cluster, outside of both Spanish subclusters, most of them corresponding to recently infected individuals. The most probable geographic origin and age of the Galician subcluster was Ferrol, Northwest Galicia, around 2007, while the Western European cluster probably emerged in Switzerland around 2002. In conclusion, a recently expanded HIV-1 subtype F cluster, the largest non-subtype B cluster reported in Western Europe, continues to spread among MSM in Spain; this cluster is part of a larger cluster with a wide geographic circulation in diverse Western European countries.
authors.affiliation: HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
authors.forename: Elena
authors.initials: E
authors.lastname: Delgado
authors.affiliation: HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
authors.forename: María Teresa
authors.initials: MT
authors.lastname: Cuevas
authors.affiliation: HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
authors.forename: Francisco
authors.initials: F
authors.lastname: Domínguez
authors.affiliation: HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
authors.forename: Yolanda
authors.initials: Y
authors.lastname: Vega
authors.affiliation: HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
authors.forename: Marina
authors.initials: M
authors.lastname: Cabello
authors.affiliation: HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
authors.forename: Aurora
authors.initials: A
authors.lastname: Fernández-García
authors.affiliation: Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-InBIO), Vairão, Portugal.
authors.forename: Marcos
authors.initials: M
authors.lastname: Pérez-Losada
authors.affiliation: Department of Internal Medicine, Complejo Hospitalario Universitario de A Coruña, A Coruña, Spain.
authors.forename: María Ángeles
authors.initials: MÁ
authors.lastname: Castro
authors.affiliation: HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
authors.forename: Vanessa
authors.initials: V
authors.lastname: Montero
authors.affiliation: HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
authors.forename: Mónica
authors.initials: M
authors.lastname: Sánchez
authors.affiliation: Infectious Diseases Unit, Department of Internal Medicine, Complejo Hospitalario Universitario Arquitecto Marcide, Ferrol, A Coruña, Spain.
authors.forename: Ana
authors.initials: A
authors.lastname: Mariño
authors.affiliation: Infectious Diseases Unit, Department of Internal Medicine, Complejo Hospitalario Universitario Arquitecto Marcide, Ferrol, A Coruña, Spain.
authors.forename: Hortensia
authors.initials: H
authors.lastname: Álvarez
authors.affiliation: Department of Microbiology, Complejo Hospitalario Universitario Arquitecto Marcide, Ferrol, A Coruña, Spain.
authors.forename: Patricia
authors.initials: P
authors.lastname: Ordóñez
authors.affiliation: Department of Internal Medicine, Complejo Hospitalario Universitario de Vigo, Vigo, Pontevedra, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Ocampo
authors.affiliation: Department of Internal Medicine, Complejo Hospitalario Universitario de Vigo, Vigo, Pontevedra, Spain.
authors.forename: Celia
authors.initials: C
authors.lastname: Miralles
authors.affiliation: Department of Microbiology, Complejo Hospitalario Universitario de Vigo, Vigo, Pontevedra, Spain.
authors.forename: Sonia
authors.initials: S
authors.lastname: Pérez-Castro
authors.affiliation: Infectious Disesases Unit, Hospital Universitario Lucus Augusti, Lugo, Spain.
authors.forename: María José
authors.initials: MJ
authors.lastname: López-Álvarez
authors.affiliation: Department of Internal Medicine, Complejo Hospitalario Universitario de Ourense, Ourense, Spain.
authors.forename: Raúl
authors.initials: R
authors.lastname: Rodríguez
authors.affiliation: Department of Microbiology, Complejo Hospitalario Provincial de Pontevedra, Pontevedra, Spain.
authors.forename: Matilde
authors.initials: M
authors.lastname: Trigo
authors.affiliation: Department of Internal Medicine, Complejo Hospitalario Provincial de Pontevedra, Pontevedra, Spain.
authors.forename: Julio
authors.initials: J
authors.lastname: Diz-Arén
authors.affiliation: Department of Internal Medicine, Hospital Clínico Universitario de Valladolid, Valladolid, Spain.
authors.forename: Carmen
authors.initials: C
authors.lastname: Hinojosa
authors.affiliation: Department of Internal Medicine, Hospital Universitario Río Hortega, Valladolid, Spain.
authors.forename: Pablo
authors.initials: P
authors.lastname: Bachiller
authors.affiliation: Department of Clinical Microbiology and Infection Control, Hospital Universitario de Basurto, Bilbao, Vizcaya, Spain.
authors.forename: Silvia
authors.initials: S
authors.lastname: Hernáez-Crespo
authors.affiliation: Department of Clinical Microbiology and Infection Control, Hospital Universitario de Basurto, Bilbao, Vizcaya, Spain.
authors.forename: Ramón
authors.initials: R
authors.lastname: Cisterna
authors.affiliation: Department of Microbiology, Hospital Infanta Cristina, Badajoz, Spain.
authors.forename: Eugenio
authors.initials: E
authors.lastname: Garduño
authors.affiliation: HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
authors.forename: Lucía
authors.initials: L
authors.lastname: Pérez-Álvarez
authors.affiliation: HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
authors.forename: Michael M
authors.initials: MM
authors.lastname: Thomson
mesh_terms: D023241:Antiretroviral Therapy, Highly Active; D001499:Bayes Theorem; D004196:Disease Outbreaks; D024882:Drug Resistance, Viral; D005060:Europe / Q000453:epidemiology; D005838:Genotype; D015658:HIV Infections / Q000188:drug therapy / Q000453:epidemiology* / Q000635:transmission / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000187:drug effects / Q000235:genetics*; D018451:Homosexuality, Male; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D010802:Phylogeny; D058974:Phylogeography; D015995:Prevalence; D013030:Spain / Q000453:epidemiology