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

Juan Ángel Patiño-Galindo,David Navarro,Fernando González-Candelas,María José Galindo,Ignacio Alastrué,Enrique Ortega,María Alma Bracho,Manoli Torres-Puente,Concepción Gimeno,Amparo Juan,Zhefeng Meng

doi:10.1371/journal.pone.0171062

Abstract

We describe and characterize an exceptionally large HIV-1 subtype B transmission cluster occurring in the Comunidad Valenciana (CV, Spain). A total of 1806 HIV-1 protease-reverse transcriptase (PR/RT) sequences from different patients were obtained in the CV between 2004 and 2014. After subtyping and generating a phylogenetic tree with additional HIV-1 subtype B sequences, a very large transmission cluster which included almost exclusively sequences from the CV was detected (n = 143 patients). This cluster was then validated and characterized with further maximum-likelihood phylogenetic analyses and Bayesian coalescent reconstructions. With these analyses, the CV cluster was delimited to 113 patients, predominately men who have sex with men (MSM). Although it was significantly located in the city of Valencia (n = 105), phylogenetic analyses suggested this cluster derives from a larger HIV lineage affecting other Spanish localities (n = 194). Coalescent analyses estimated its expansion in Valencia to have started between 1998 and 2004. From 2004 to 2009, members of this cluster represented only 1.46% of the HIV-1 subtype B samples studied in Valencia (n = 5/143), whereas from 2010 onwards its prevalence raised to 12.64% (n = 100/791). In conclusion, we have detected a very large transmission cluster in the CV where it has experienced a very fast growth in the recent years in the city of Valencia, thus contributing significantly to the HIV epidemic in this locality. Its transmission efficiency evidences shortcomings in HIV control measures in Spain and particularly in Valencia.

Highlights

By means of phylogenetic analysis, we have identified an exceptionally large HIV-1 transmission cluster mainly localized in the city of Valencia and which is characterized by a rapid and recent expansion among men who have sex with men (MSM)
A potential transmission cluster was found in the initial HIV-1B tree obtained with FastTree (Fig 2), and it was further validated with a ML tree obtained with 633 additional, non-redundant sequences retrieved in a BLAST search and additional controls as detailed in Material and Methods
The Comunidad Valenciana (CV)-cluster included 105 sequences from patients living in the city of Valencia and its metropolitan area and 6 from patients living in other localities from the CV

Summary

Introduction

Molecular epidemiology analyses have revealed the vulnerability of MSM to HIV infection in different ways, such as the frequent detection of transmission clusters affecting this risk group [6,7,8,9,10], and the estimation of shorter times between infections compared to those of HTs and IDUs [11]. By means of phylogenetic analysis, we have identified an exceptionally large HIV-1 transmission cluster mainly localized in the city of Valencia (third largest city in Spain and the capital of the CV, with a metropolitan area of >1,500,000 inhabitants) and which is characterized by a rapid and recent expansion among MSM.

Results

Conclusion