The rate of epidemiological and virological changes during the transition from nascent to concentrated HIV epidemic stage in the former Soviet Union countries

Two Independent HIV Epidemics in Saint Petersburg, Russia Revealed by Molecular Epidemiology

The HIV epidemic in Russia, one of the world's fastest growing, has been concentrated mostly among people who inject drugs (PWID). We sought to explore the epidemiology of the epidemic in St. Petersburg by sampling from the highest risk groups of PWID and men who have sex with men (MSM) and use viral sequencing data to better understand the nature of the city's epidemic. Serological testing confirmed an HIV prevalence among PWID in excess of 40%. All but 1 of 110 PWID whose blood samples were tested for genetic diversity were infected by subtype A virus, specifically by the AFSU strain. The remaining person was infected with a CRF-06cpx recombinant. Analysis of pairwise genetic distance among all PWID studied revealed an average of 3.1% sequence divergence, suggesting clonal introduction of the AFSU strain and/or constraints on sequence divergence. The HIV prevalence was less than 10% among MSM. All 17 sequences from HIV-infected MSM were found to be a clade B virus with a much higher average sequence diversity of 15.7%. These findings suggest two independent epidemics with little overlap between the two highest at-risk populations, which will require different HIV prevention approaches.

High percentage of recent HIV infection leading to onward transmission in Odessa, Ukraine associated with young adults

The proportion of new HIV diagnoses between May and December 2009 across Odessa recently-infected was estimated using the BED-CEIA assay. Logistic regression models were used to explore factors associated with testing as recent. Of 1,313 newly-diagnosed individuals, 321 (24 %) were classified as recent. Recent infection was less likely among older adults [odds ratio (OR) = 0.70 per 10-year increase, 95 % CI 0.60-0.82]. Compared to men residing in Odessa city, women in rural Odessa and non-resident men were more likely to be recently-infected (OR 1.85, 1.26-2.71 and 2.83, 1.15-6.97, respectively). Reason for test was not associated with recent infection. In sensitivity analysis, after excluding individuals tested due to clinical indications, the proportion recently-infected and the association with age remained virtually unchanged. Our findings suggest a high risk of onward transmission, particularly in younger age groups. These findings highlight the need for tailored prevention strategies and ongoing RITA testing to monitor and evaluate effectiveness of prevention programmes.

Distinct HIV type 1 strains in different risk groups and the absence of new infections by drug-resistant strains in Lithuania

To analyze HIV-1 genotypes in Lithuania and the transmission of drug-resistant viruses, HIV-1 sequences were obtained from 138 individuals, who were diagnosed as HIV-1 infected in 1990-2008 and represented all major risk groups. Subtype A strains, dominating in the former Soviet Union (90% of cases), were found in 60% of individuals, followed by subtype B (22%) and CRF03_AB (12%) strains. The remaining 7% of the strains included variants belonging to subtype C, CRF01_AE, CRF02_AG, more complex recombinant forms, and strains that could not be reliably genotyped. Analysis of virus genotypes per risk group revealed the circulation of distinct HIV-1 strains in different risk groups: subtype A viruses were present in 82% of injecting drug users (IDUs), but less than a half of heterosexually infected individuals and cases with unknown transmission route, and none of men having sex with men (MSM). We observed no mutations causing drug resistance among 27 newly diagnosed HIV-1 cases.

Transmission of risk-group specific HIV-1 strains among Dutch drug users for more than 20 years and their replacement by nonspecific strains after switching to low-harm drug practices

OBJECTIVES

To characterize HIV-1 epidemiological networks of men having sex with men (MSM) and drug users (DUs) in the Netherlands for >30 years.

DESIGN AND METHODS

Previously, we demonstrated different origin of the HIV-1 epidemics in Dutch MSM and DUs. To achieve the study objectives, risk group-specific genetic markers in the pol gene were examined in 315 participants of the Amsterdam Cohort Studies on HIV/AIDS who were registered as HIV-1 infected in 1981-2011.

RESULTS

Phylogenetic analysis demonstrated circulation of distinct virus strains in the 2 networks, with 98% of viruses of MSM clustering together and apart from strains of 73% DUs. Nine genetic markers that significantly distinguished virus strains specific for DUs were identified, of which 3 were ≥90% conserved. Over the total observation period, only 6% of viruses (4 of MSM and 14 of DUs) clustered with those of the other risk group. Among these sequences, the 3 most conserved genetic markers of that other risk group were 87% conserved.All 4 cases of DU-specific viruses among MSM occurred in 1980s-early 1990s. Viruses nonspecific for DUs were causing new infections among DUs at the rate of 20% till 2002 and replaced DU-specific strains among new infections thereafter, coinciding with switching of DUs to low-harm drug practices.

CONCLUSIONS

Dutch MSM and DUs have remained separate epidemiological networks for decades, despite their geographical and behavioral overlap. Switching to low-harm drug practices among DUs resulted in new infections caused by HIV-1 strains originating from other risk groups.

Estimates of HIV incidence among drug users in St. Petersburg, Russia: continued growth of a rapidly expanding epidemic

BACKGROUND

Russia has one of the world's fastest growing HIV epidemics and it has been largely concentrated among injection drug users (IDU). St Petersburg, Russia's second largest city, is one of the country's regions that has been most affected by the HIV epidemic. To monitor the current epidemic situation, we sought to estimate recent HIV incidence among IDU in St Petersburg.

METHODS

In a cross-sectional study of 691 IDU recruited during 2005-08, HIV incidence was estimated by two methods: a retrospective cohort analysis and BED capture enzyme immunoassay (EIA) results. Socio-demographic and behavioural correlates of incident infections and spatial patterns were examined.

RESULTS

In the retrospective cohort analysis, the incidence rate was estimated to be 14.1/100 person-years [95% confidence interval (CI) 10.7-17.6]. Using results of BED EIA and two correction formulas for known misclassification, incidence estimates were 23.9 (95% CI 17.8-30.1) and 25.5 (95% CI 18.9-32.0) per 100 person-years. Independent correlates of being recently infected included current unemployment (P = 0.004) and not having injected drugs in the past 30 days (P = 0.03). HIV incident cases were detected in all but one district in the city, with focal areas of transmission observed to be expanding.

CONCLUSIONS

High HIV incidence among IDU in St Petersburg attests to continued growth of the epidemic. The need for expansion of HIV prevention interventions targeted to vulnerable populations throughout the city is urgent. These results also suggest that the BED EIA may over-estimate incidence even after correction for low specificity.

Near full-length genome characterization of a newly identified HIV type 1 subtype F variant circulating in St. Petersburg, Russia

We report the near full-length genome characterization of an HIV-1 subtype F virus (D88_845) collected in St. Petersburg, Russia, from a 25-year-old Russian woman perinatally infected in 1982. In a Bayesian phylogenetic analysis, the genome sequence branched basally to the subsubtype F1 clade. In partial sequences, D88_845 clustered with 13 other subtype F sequences from Russia, corresponding to gag (n = 2), pol (n = 3), and env (n = 8) segments. At least 11 of these sequences are from samples collected in St. Petersburg from heterosexually infected Russian individuals. In each of these segments, the Russian viruses formed a monophyletic cluster that branched as a sister clade of the F1 subsubtype. One sequence from Belgium branched with D88_845 with a posterior probability of 0.99. This is the first report on the identification and near full-length genome characterization of the subtype F variant circulating in St. Petersburg, which is closely related to, but distinct from, the F1 subsubtype.

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 (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.

The feasibility of HIV vaccine efficacy trials among Russian injection drug users

IDU exposure remains a primary driver of the Russian HIV epidemic, and recent incidence data provide little evidence that this epidemic is slowing. While there are multiple important challenges that need to be further explored before starting vaccine trials, most importantly access to evidence-based drug treatment services for trial participants, the current context of high HIV incidence and low genetic diversity of HIV strains, suggests the need for intensified prevention strategies and supports the feasibility of mounting efficacy trials of HIV vaccines among IDUs in the Russian Federation.