The South American human immunodeficiency virus type 1 (HIV-1) epidemic is 
driven by several subtypes (B, C, and F1) and circulating and unique recombinant 
forms derived from those subtypes. Those variants are heterogeneously 
distributed around the continent in a country-specific manner. Despite some 
inconsistencies mainly derived from sampling biases and analytical constrains, 
most of studies carried out in the area agreed in pointing out specificities in 
the evolutionary dynamics of the circulating HIV-1 lineages. In this paper, we 
covered the theoretical basis, and the application of bioinformatics methods to 
reconstruct the HIV spatial-temporal dynamics, unveiling relevant information to 
understand the origin, geographical dissemination and the current molecular 
scenario of the HIV epidemic in the continent, particularly in the countries of 
Southern Cone.