Research Article: The Use of Bioinformatics for Studying HIV Evolutionary and Epidemiological History in South America

Date Published: November 15, 2011

Publisher: Hindawi Publishing Corporation

Author(s): Gonzalo Bello, Marcelo A. Soares, Carlos G. Schrago.


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.

Partial Text

Human immunodeficiency virus (HIV), the causative agent of AIDS, is classified into types, groups, subtypes and subsubtypes according to its genetic diversity [1]. HIV type 1 (HIV-1) is widely disseminated worldwide and can be further divided into four genetic groups: group M (major or main), group O (outlier), and group N (new or non-M non-O), and the most recently characterized group P [1, 2]. While HIV-1 groups N, P, and O are restricted to countries of Central Africa, notably to Cameroon, HIV-1 group M is the responsible for the AIDS pandemic, accounting for over 90% of worldwide HIV infections [3]. HIV-2 is restricted to countries of West Africa, where it also represents a minority of viral infections and is decreasing in prevalence over time [4]. Nine pure subtypes of HIV-1 group M are currently known (A–D, F–H, J, and K). Some subtypes are further divided into subsubtypes, like subtypes F (F1 and F2) and A (A1, A2, and A3). Subtypes and sub-subtypes can form additional mosaic forms though recombination of different strains inside dually or multiply infected individuals [5]. Some of these recombinant forms may further achieve epidemic relevance, giving rise to known circulating recombinant forms (CRF). To date, at least 49 CRF are recognized in diverse parts of the world (

South America follows the HIV molecular epidemiology commonly seen in the Americas, with HIV-1B being the most prevalent. However, a number of regional specificities are also observed. Brazil, the largest country of the continent, and which accounts for roughly two thirds of the infections, has likely the highest reported diversity. In addition to HIV-1B, other subtypes such as F1, C, and a number of B/F and B/C recombinants cocirculate [7–11]. In other South American countries, HIV-1B has been mostly reported, with the exception of Argentina and Uruguay, where a large number of B/F recombinants circulate at high proportion [12–16].




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