Adaptation of pathogens, either to on-going immune pressures within individual hosts or following transmission to new hosts of the same or different species, can result in infectious outbreaks that constitute major threats for public health [9] [10] [11] [12] . The human immunodeficiency virus (HIV) is an extremely recombinogenic pathogen in which recombination has been implicated in key aspects of viral pathogenesis such as immune evasion [13] , transmissibility [14] , the evolution of antiretroviral resistance [15, 16] and cross-species transmission [9, 12] . Indeed, the remarkable genetic flexibility of HIV is underlined by its large genetic diversity. The HIV-1 population is subdivided into three groups, named M, N and O, with group M (which is responsible for the vast majority of the infections worldwide) being further subdivided into nine subtypes (named A, B, C, D, F, G, H, J and K) [17] .