Molecular Epidemiology of HIV-1 in St Petersburg, Russia: Predominance of Subtype A, Former Soviet Union Variant, and Identification of Intrasubtype Subclusters

Objectives: To examine HIV-1 genetic diversity in St. Petersburg. Methods: Partial HIV-1 pol sequences from 102 plasma samples collected in 2006 were analyzed with a Bayesian phylogeny inference method. Results: Subtype A, former Soviet Union (FSU) variant (A(FSU)), was the predominant clade (89.3%); other clades were subtypes B (9.7%) and F1 (1%). A(FSU) was predominant both among injecting drug users (98.2%) and heterosexually infected individuals (91.4%), whereas subtype B was more prevalent among homosexual men (75%). Within the A(FSU) variant, most sequences (93.5%) branched within I of 4 strongly supported subclusters. The largest comprised 63% AFSU viruses and was uncommon outside St Petersburg. A second subcluster (17.4% A(FSU) viruses) corresponds to the variant with the V77I substitution in protease, which is widely circulating in different FSU countries. Two minor subclusters comprised 8.7% and 6.5% AFSU viruses, respectively There was no correlation between risk exposure and A(FSU) subclusters. Six of 8 subtype B sequences, 4 of them from homosexual men, grouped in a monophyletic subcluster. Conclusions: The results of this study show a great predominance of A(FSU) viruses in St Petersburg and point to a few phylogenetically identifiable introductions as the origin of most current HIV-1 A(FSU) infections in the city.