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

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 

Below:  Distribution of viruses of the subtype F cluster sequenced by us according to city of sample collection

Below:  Prevalence of infections with viruses of the subtype F cluster in 2009–2012 among all new HIV-1 diagnoses and among new HIV-1 diagnoses in MSM in Galicia and A Coruña city (Northwest Galicia)

Below:  Bootscan analysis of the near full-length genome sequence of X3364.

The analysis was done with Simplot v.3.5.1, using a window of 500 nucleotides, moving in 50 nucleotide increments. Phylogenetic trees were constructed using the neighbor-joining algorithm based on Kimura 2-parameter distances, with Tv:Ti ratios estimated from the dataset.

Below:  Bayesian skyline plot of the population growth of the subtype F cluster.

The black line represents the median estimate of the effective number of infections through time (logarithmic scale) and the shaded area represents the 95% HPD credibility interval. The horizontal axis represents calendar years

Full article at:  http://goo.gl/lTucgu

By:   

Elena Delgado, María Teresa Cuevas, Francisco Domínguez, Yolanda Vega, Marina Cabello, Aurora Fernández-García, Vanessa Montero, Mónica Sánchez, Lucía Pérez-Álvarez, Michael M Thomson

HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain

Marcos Pérez-Losada

Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-InBIO), Vairão, Portugal

María Ángeles Castro

Department of Internal Medicine, Complejo Hospitalario Universitario de A Coruña, A Coruña, Spain

Ana Mariño, Hortensia Álvarez

Infectious Diseases Unit, Department of Internal Medicine, Complejo Hospitalario Universitario Arquitecto Marcide, Ferrol, A Coruña, Spain

Patricia Ordóñez

Department of Microbiology, Complejo Hospitalario Universitario Arquitecto Marcide, Ferrol, A Coruña, Spain

Antonio Ocampo, Celia Miralles

Department of Internal Medicine, Complejo Hospitalario Universitario de Vigo, Vigo, Pontevedra, Spain

Sonia Pérez-Castro

Department of Microbiology, Complejo Hospitalario Universitario de Vigo, Vigo, Pontevedra, Spain

María José López-Álvarez

Infectious Disesases Unit, Hospital Universitario Lucus Augusti, Lugo, Spain

Raúl Rodríguez

Department of Internal Medicine, Complejo Hospitalario Universitario de Ourense, Ourense, Spain

Matilde Trigo

Department of Microbiology, Complejo Hospitalario Provincial de Pontevedra, Pontevedra, Spain

Julio Diz-Arén

Department of Internal Medicine, Complejo Hospitalario Provincial de Pontevedra, Pontevedra, Spain

Carmen Hinojosa

Department of Internal Medicine, Hospital Clínico Universitario de Valladolid, Valladolid, Spain

Pablo Bachiller

Department of Internal Medicine, Hospital Universitario Río Hortega, Valladolid, Spain

Silvia Hernáez-Crespo, Ramón Cisterna

Department of Clinical Microbiology and Infection Control, Hospital Universitario de Basurto, Bilbao, Vizcaya, Spain

Eugenio Garduño

Department of Microbiology, Hospital Infanta Cristina, Badajoz, Spain

 

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