RESUMO
There is scarce data on circulation of genetic subtypes of HIV-1 in South Sudan due to decades of civil war. In this study, phylogenetic analysis of 10 strains collected from HIV-1-infected South Sudanese patients was performed. Partial pol and env viral gene analysis classified sequences as subtype C (n = 4), subtype D (n = 4), and partially unclassifiable recombinants (n = 2), interspersed within the phylogenetic tree with those from other African countries. These results indicate an exchange of viral strains between South Sudan and both neighboring and distant territories. The movements of populations across Sudan's borders during the civil war have probably played an important role in circulation of subtypes not only in South Sudan but also in other African states.