We aimed to characterize the HIV-1 epidemic of the Belgian and Colombian cohorts using an integrated approach that includes socio-demographic information, clinical data, and viral sequences, analyzed with statistical and phylogenetic approaches. ; Andrea-Clemencia Pineda-Peña was supported by a Doctoral Research Training Program ‘‘Francisco Jose de Caldas’’ by the Departamento Administrativo de Ciencia, Tecnología e Innovación, COLCIENCIAS, Republic of Colombia and ERACOL academic exchange in medicine and the health sciences, between Europe and Latin America. The research was supported in part by the European Community’s Seventh Framework Programme (FP7/2007–2013) under the project ‘‘Collaborative HIV and Anti-HIV Drug Resistance Network (CHAIN)’’ grant agreement n° 223131 and ERC grant agreement no. 260864; by the Fonds voor Wetenschappelijk Onderzoek – Flanders (FWO) grant G.0611.09 and grant G069214N; by the AIDS Reference Laboratory of Leuven that receives support from the Belgian Ministry of Social Affairs through a fund within the Health Insurance System; by the University of Leuven (Program Financing no. PF/10/018. The computational resources and services used in this work were provided by the Hercules Foundation and the Flemish Government – department EWI-FWO Krediet aan Navorsers (Theys, KAN2012 1.5.249.12). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscripts.