The HIV-1 subtype A epidemic affecting injecting drug users (IDU) in former Soviet Union (FSU) countries started dramatically in Odessa, southern Ukraine, in 1995, and is caused by a variant of monophyletic origin, often designated IDU-A. We phylogenetically analyzed one near full-length genome and two partial sequences of three HIV-1 subtype A viruses collected in St. Petersburg, Russia, heterosexually transmitted in 1992–1994. The sequences branched basally to the IDU-A clade, together with eight viruses from Odessa collected in 1993, all presumably acquired heterosexually, and two viruses from the Democratic Republic of Congo. Of all other FSU sequences in databases, only those from three recently collected viruses, one from Ukraine and two from northwestern Russia, at least one of them acquired heterosexually, branched basally to the IDU-A cluster. The results indicate that the FSU IDU-A variant derives from a strain that initially propagated heterosexually in Ukraine and originated in central Africa.

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 1 of 4 strongly supported subclusters. The largest comprised 63% A_FSU 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% A_FSU 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.