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.

Molecular epidemiology of HIV-1 infection in Europe: An overview

“…Of particular note is Galicia in Northwest Spain where PWID viruses, the G and CRF14_BG clades were found to have originated from Portugal (Thomson et al, 2001;Thomson and Najera, 2007). Furthermore, an outbreak of subtype F1 was detected in northwest Spain (mostly in Galicia) including sequences from other Western European countries that were found to have originated from Southern America (Delgado et al, 2015;Paraskevis et al, 2015a).…”

Identification of a large, fast-expanding HIV-1 subtype B transmission cluster among MSM in Valencia, Spain

“…In Spain, MSMs have been associated with significantly higher levels of local clustering than other risk groups [ 11 , 12 ]. Also, Delgado et al [ 13 ] recently detected a large HIV-1 subtype F cluster affecting tens of MSM from different Spanish regions, indicating a fast and uncontrolled transmission among recently infected MSM who were unaware of their HIV status.…”

High prevalence and diversity of HIV-1 non-B genetic forms due to immigration in southern Spain: A phylogeographic approach

“…We herein detected the presence of one patient from our cohort related to a fast spreading cluster among Spanish MSM infected with subtype F in Galicia (NW Spain) [ 43 ], a transmission cluster which, as Delgado et al . suggest, would probably be closely linked to viruses that circulate in Eastern Europe [ 42 ]. These authors [ 53 ] have also described a subtype A cluster that is being transmitted among individuals in different areas of Spain.…”