Molecular epidemiology of HIV-1 in St Petersburg, Russia: predominance of subtype A, former Soviet Union variant, and identification of intrasubtype subclusters.
OBJECTIVE
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 (AFSU), was the predominant clade (89.3%); other clades were subtypes B (9.7%) and F1 (1%). AFSU 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 AFSU variant, most sequences (93.5%) branched within 1 of 4 strongly supported subclusters. The largest comprised 63% AFSU viruses and was uncommon outside St Petersburg. A second subcluster (17.4% AFSU 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 AFSU 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 AFSU viruses in St Petersburg and point to a few phylogenetically identifiable introductions as the origin of most current HIV-1 AFSU infections in the city.
Thomson
Michael M
MM
Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain. mthomson@isciii.es
Vinogradova
Anna
A
Delgado
Elena
E
Rakhmanova
Aza
A
Yakovlev
Aleksey
A
Cuevas
María T
MT
Muñoz
Mercedes
M
Pinilla
Milagros
M
Vega
Yolanda
Y
Pérez-Alvarez
Lucía
L
Osmanov
Saladin
S
Nájera
Rafael
R
D001483:Base Sequence; D014644:Genetic Variation; D015658:HIV Infections / Q000453:epidemiology* / Q000821:virology; D015497:HIV-1 / Q000145:classification* / Q000235:genetics*; D006801:Humans; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D015995:Prevalence; D012426:Russia / Q000453:epidemiology; D054302:pol Gene Products, Human Immunodeficiency Virus / Q000235:genetics*
D054302:pol Gene Products, Human Immunodeficiency Virus