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

Reconstructing the Temporal Origin and the Transmission Dynamics of the HIV Subtype B Epidemic in St. Petersburg, Russia

The HIV/AIDS epidemic in Russia is among the fastest growing in the world. HIV epidemic burden is non-uniform in different Russian regions and diverse key populations. An explosive epidemic has been documented among people who inject drugs (PWID) starting from the mid-1990s, whereas presently, the majority of new infections are linked to sexual transmission. Nationwide, HIV sub-subtype A6 (previously called A_FSU) predominates, with the increasing presence of other subtypes, namely subtype B and CRF063_02A. This study explores HIV subtype B sequences from St. Petersburg, collected from 2006 to 2020, in order to phylogenetically investigate and characterize transmission clusters, focusing on their evolutionary dynamics and potential for further growth, along with a socio-demographic analysis of the available metadata. In total, 54% (107/198) of analyzed subtype B sequences were found grouped in 17 clusters, with four transmission clusters with the number of sequences above 10. Using Bayesian MCMC inference, tMRCA of HIV-1 subtype B was estimated to be around 1986 (95% HPD 1984-1991), whereas the estimated temporal origin for the four large clusters was found to be more recent, between 2001 and 2005. The results of our study imply a complex pattern of the epidemic spread of HIV subtype B in St. Petersburg, Russia, still in the exponential growth phase, and in connection to the men who have sex with men (MSM) transmission, providing a useful insight needed for the design of public health priorities and interventions.

Molecular Epidemiology of HIV-1 in Oryol Oblast, Russia

The HIV/AIDS epidemic in Russia is growing, with approximately 100,000 people infected annually. Molecular epidemiology can provide insight into the structure and dynamics of the epidemic. However, its applicability in Russia is limited by the weakness of genetic surveillance, as viral genetic data are only available for <1 per cent of cases. Here, we provide a detailed description of the HIV-1 epidemic for one geographic region of Russia, Oryol Oblast, by collecting and sequencing viral samples from about a third of its known HIV-positive population (768 out of 2,157 patients). We identify multiple introductions of HIV-1 into Oryol Oblast, resulting in eighty-two transmission lineages that together comprise 66 per cent of the samples. Most introductions are of subtype A (315/332), the predominant HIV-1 subtype in Russia, followed by CRF63 and subtype B. Bayesian analysis estimates the effective reproduction number R_e for subtype A at 2.8 [1.7–4.4], in line with a growing epidemic. The frequency of CRF63 has been growing more rapidly, with the median R_e of 11.8 [4.6–28.7], in agreement with recent reports of this variant rising in frequency in some regions of Russia. In contrast to the patterns described previously in European and North American countries, we see no overrepresentation of males in transmission lineages; meanwhile, injecting drug users are overrepresented in transmission lineages. This likely reflects the structure of the HIV-1 epidemic in Russia dominated by heterosexual and, to a smaller extent, people who inject drugs transmission. Samples attributed to men who have sex with men (MSM) transmission are associated with subtype B and are less prevalent than expected from the male-to-female ratio for this subtype, suggesting underreporting of the MSM transmission route. Together, our results provide a high-resolution description of the HIV-1 epidemic in Oryol Oblast, Russia, characterized by frequent interregional transmission, rapid growth of the epidemic, and rapid displacement of subtype A with the recombinant CRF63 variant.

People Living With HIV in St. Petersburg, Russia: Gender and Exposure Group Differences in HIV Care Engagement, Psychosocial Health, Substance Use, and Transmission Risk Behavior

This study examined psychosocial and health needs of persons living with HIV (PLWH) in Russia. The study combined baseline datasets from two social network samples of PLWH in St. Petersburg (N = 872). Samples were recruited between 2014 and 2018 by enrolling a PLWH seed who was either out-of-care or treatment nonadherent as well as network members surrounding each seed, assessing each participant's HIV care, transmission risk, substance use, and mental health characteristics. Almost one-quarter of participants said they were never offered antiretroviral therapy (ART), and-among those offered ART-one-quarter refused or discontinued therapy and 45% were <95% ART-adherent. Almost half of participants had detectable viral load, and many reported continued condomless intercourse with potentially nonconcordant serostatus partners or needle sharing. Over 46% of participants had elevated scores on measures of depression, hopelessness, state anxiety, or poor social support. Study findings illustrate unmet needs of PLWH in Russia.

Molecular Surveillance of HIV-1 Infection in Krasnoyarsk Region, Russia: Epidemiology, Phylodynamics and Phylogeography

BACKGROUND

The information about the dynamics of the viral population and migration events that affect the epidemic in different parts of the Russia is insufficient. Possibly, the huge size of the country and limited transport accessibility to certain territories may determine unique traits of the HIV-1 evolutionary history in different regions.

OBJECTIVE

The aim of this study was to explore the genetic diversity of HIV-1 in the Krasnoyarsk region and reconstruct spatial-temporal dynamics of the infection in the region.

METHODS

The demographic and virologic data from 281 HIV-infected individuals in Krasnoyarsk region collected during 2011-2016 were analyzed. The time to the most recent common ancestor, evolutionary rates, population growth, and ancestral geographic movements was estimated using Bayesian coalescent-based methods.

RESULTS

The study revealed moderate diversity of the HIV-1 subtypes found in the region, which included A6 (92.3%), CRF063_02A (4.3%), B (1.1%), and unique recombinants (2.5%). Phylogenetic reconstruction revealed that the A6 subtype was introduced into Krasnoyarsk region by one viral lineage, which arose around 1996.9 (1994.5-1999.5). The phylogeography analysis pointed to Krasnoyarsk city as the geographical center of the epidemic, which further spread to central neighboring districts of the region. At least two epidemic growth phases of subtype A6 were identified which included exponential growth in early-2000s followed by the decline in the mid/late 2010s.

CONCLUSION

This study demonstrates a change in the genetic diversity of HIV-1 in the Krasnoyarsk region. At the beginning of the epidemic, subtype A6 prevailed, subtypes B and CRF063_02A appeared in the region later.

Human Immunodeficiency Virus-1 Diversity in the Moscow Region, Russia: Phylodynamics of the Most Common Subtypes

This study analyzes the HIV-1 subtype diversity and its phylodynamics in Moscow region, which is the most densely populated area of Russia characterized by high rates of internal and external migration. The demographic and viral data from 896 HIV-infected individuals collected during 2011–2016 were analyzed. The study revealed broad diversity in the HIV-1 subtypes found in Moscow, which included A6 (85.1%), B (7.6%), CRF02_AG (1.2%) and URF_A6/B recombinants (4.2%). Other HIV-1 subtypes were detected as single cases. While A6 was most prevalent (>86.0%) among heterosexuals, injecting drug users and cases of mother-to-child transmission of HIV, subtype B (76.3%) was more common in men who have sex with men. Phylogenetic reconstruction revealed that the A6 sequences were introduced into the epidemic cluster that arose approximately around 1998. Within the subtype B, six major epidemic clusters were identified, each of which contained strains associated with only one or two dominant transmission routes. The date of origin of these clusters varied between 1980 and 1993, indicating that the HIV-1 B epidemic began much earlier than the HIV-1 A6 epidemic. Reconstruction of the demographic history of subtypes A6 and B identified at least two epidemic growth phases, which included an initial phase of exponential growth followed by a decline in the mid/late 2010s. Thus, our results indicate an increase in HIV-1 genetic diversity in Moscow region. They also help in understanding the HIV-1 temporal dynamics as well as the genetic relationships between its circulating strains.

HIV PREVALENCE AMONG VULNERABLE GROUPS IN RUSSIA - RESULTS OF AN INTEGRATED BIO-BEHAVIORAL SURVEY

Aim. Of the study is to assess HIV prevalence in the vulnerable groups namely injecting drug users (IDU), sex workers (SW), and men who have sex with men (MSM) in some of the largest Russian regiоnal capitals mostly affected by HIV infection. Materials and methods. The study involved 3744 persons from vulnerable groups enrolled by respondent-driven sampling (RDS) or time-location sampling (TLS). The study was undertaken in seven regions of the Russian Federation: Moscow, St.-Petersburg, Yekaterinburg, Krasnoyarsk, Kemerovo, Tomsk and Perm. All participants were interviewed using specially designed questionnaire and then tested for HIV. The retrospective cohort method was applied to evaluate the number of new HIV cases among respondents. Results. HIV prevalence in IDUs ranged from 48.10% [95% confidence interval (CI)=42.20.54.10%] in Krasnoyarsk and 75.20% [95%CI=69.90.80.60%] in Kemerovo. HIV prevalence among sex workers varied from 2.32% [95%CI=0.49.4.17%] in St. Petersburg to 15.01% [95%CI=11.46.18.56%] in Perm. HIV prevalence among MSM ranged from 7.10% [95%CI=4.10.10.10%] in Moscow to 22.80% [95%CI=17.90.27.70%] in St.-Petersburg. Conclusion. The number of new HIV infections estimated by the retrospective cohort method indicated rapid spread of HIV infection among IDUs in all cities except St.-Petersburg, relatively high HIV growth rates among MSM ranging from 1.6% per year [95%CI=0.1... 3.1%] to 4.6% per year [95%CI=0.0... 11%] and 12.3% annual HIV growth rate [95%CI=0.0... 28.3%] among sex workers. Generally, the situation in the studied groups remained adverse and called for more intensive prevention activities in vulnerable populations.

Characterization of the Transmitted Virus in an Ongoing HIV-1 Epidemic Driven by Injecting Drug Use

Understanding features of the HIV-1 transmission process has the potential to inform biological interventions for prevention. We have examined the transmitted virus in a cohort of people who inject drugs and who are at risk of HIV-1 infection through blood contamination when injecting in a group. This study focused on seven newly infected participants in St. Petersburg, Russia, who were in acute or early infection. We used end-point dilution polymerase chain reaction to amplify single viral genomes to assess the complexity of the transmitted virus. We also used deep sequencing to further assess the complexity of the virus. We interpret the results as indicating that a single viral variant was transmitted in each case, consistent with a model where the exposure to virus during transmission was limited. We also looked at phenotypic properties of the viral Env protein in isolates from acute and chronic infection. Although differences were noted, there was no consistent pattern that distinguished the transmitted variants. Similarly, despite the reduced genetic heterogeneity of the more recent subtype A HIV-1 epidemic in St. Petersburg, we did not see reduced variance in the neutralization properties compared to isolates from the more mature subtype C HIV-1 epidemic. Finally, in looking at members of injecting groups related to the acute HIV-1 infection/early subjects, we found examples of sequence linkage consistent with ongoing and rapid spread of HIV-1 in these groups. These studies emphasize the dynamic nature of this epidemic and reinforce the idea that improved prevention methods are needed.

Polydrug Use and Heterogeneity in HIV Risk Among People Who Inject Drugs in Estonia and Russia: A Latent Class Analysis

Non-medical drug injection is a major risk factor for HIV infection in Russia and Estonia. Multiple drug use (polydrug) has further been associated with increased harms. We compared HIV, injecting and sexual risk associated with polydrug use among people who injected drugs (PWID) in 2012–2013 in Kohtla-Järve (Estonia, n = 591) and St Petersburg (Russia, n = 811). Using latent class analysis, we identified five (poly)drug classes, the largest consisting of single-drug injectors among whom an opioid was the sole drug injected (56% of PWID). The four remaining polydrug classes included polydrug-polyroute injectors who injected and used opiates and stimulants (9%), opiate-stimulant poly-injectors who injected amphetamine-type-stimulants with a primary opiate (7%) and opiate-opioid poly-injectors who injected opioids and opiates (16%). Non-injection stimulant co-users were injectors who also used non-injection stimulants (12%). In multivariable multinomial regressions, all four polydrug classes were associated with greater injection risks than single-drug injection, while opiate-stimulant and opiate-opioid poly-injection were also associated with having multiple sex partners. Riskier behaviours among polydrug-injectors suggest increased potential for transmission of blood-borne and sexually-transmitted infections. In addition to needles/syringes provision, services tailored to PWID drug and risk profiles, could consider drug-appropriate treatment and sexual risk reduction strategies to curb HIV transmission.

A Cohort Approach to Real-Time Detection of Acute HIV Infections Among People Who Inject Drugs in St. Petersburg, Russia

To detect acute HIV infections (AHIs) in real time among people who inject drugs (PWID) in St. Petersburg, Russia and to test the feasibility of this approach. Prospective cohort study. One hundred seronegative or acutely HIV-infected at screening PWID were enrolled and followed until the end of the 12-month pilot period. Each participant was evaluated, tested, and counseled for HIV monthly. Two HIV tests were used: HIV antibody and HIV RNA PCR. If diagnosed with AHI, participants were followed weekly for a month; then, monthly for 3 months; and then, quarterly for the duration of the follow-up period. HIV risk behavior was assessed at each study visit. Most enrolled PWID were 30-39 years old, male, completed high school or more, not employed full-time, heroin users, and frequently shared injection paraphernalia. AHI prevalence at screening was 1.8% [95% confidence interval (CI): 0.4, 5.5]. Three participants with AHI at enrollment represented 3% (95% CI: 0.6, 8.5) of the 100 participants who consented to enroll. Among the HIV-uninfected participants (n = 97), the AHI incidence over time was 9.3 per 100 person-years. Persons with AHI were more likely to report alcohol intoxication within the prior 30 days. This was the first study to detect AHI using a cohort approach. The approach proved to be feasible: recruitment, retention, AHI detection, and virological endpoints were successfully reached. A cost analysis in a real-world setting would be required to determine if this strategy could be brought to scale. The study revealed continued high HIV incidence rate among PWID in St. Petersburg, Russia and the importance of prevention and treatment programs for this group.

Molecular epidemiology of HIV-1 subtype A in former Soviet Union countries

While in other parts of the world it is on decline, incidence of HIV infection continues to rise in the former Soviet Union (FSU) countries. The present study was conducted to investigate the patterns and modes of HIV transmission in FSU countries. We performed phylogenetic analysis of publicly available 2705 HIV-1 subtype A pol sequences from thirteen FSU countries: Armenia, Azerbaijan, Belarus, Estonia, Georgia, Kazakhstan, Kyrgyzstan, Latvia, Lithuania, Moldova, Russia, Ukraine and Uzbekistan. Our analysis showed that the clusters from FSU countries were intermixed, indicating a possible role of transmigration in HIV transmission. Injection drug use was found to be the most frequent mode of transmission, while the clusters from PWID and heterosexual transmission were intermixed, indicating bridging of HIV infection across populations. To control the expanding HIV epidemic in this region, harm reduction strategies should be focused on three modes of transmission, namely, cross-border migration, injection drug use and heterosexual.

Differences in risk behaviours and HIV status between primary amphetamines and opioid injectors in Estonia and Russia

BACKGROUND AND OBJECTIVE

People who inject drugs (PWID) account for over half of new HIV infections in Eastern Europe and central Asia, where opioids continue to be the dominant illicit drugs injected. Stimulants including amphetamines (ATS) have been associated with HIV infection risk in several settings. We sought to examine whether primary ATS injection was associated with greater HIV risk, compared to opioid injection in two European locales with significant HIV epidemics.

METHODS

PWID in Kohtla-Järve and St. Petersburg were recruited using respondent-driven sampling in 2012-2013. Survey data on demographic characteristics, service use, injecting and sexual risk behaviours and HIV-status (and HCV in Kohtla-Järve) were compared between primary opioid and ATS injectors using logistic regression models.

RESULTS

Of 591 injectors recruited in Kohtla-Järve and 811 in St. Petersburg, 195 (33%) and 27 (4%) primarily injected ATS in each city. In both cities, ATS injectors were younger than opioid injectors, initiated injection later, injected less frequently and were more likely to have been paid for sex. In both cities, PWID had high levels of multiple sex partners. In Kohtla-Järve, ATS-injectors had lower odds of back-loading and greater odds of polydrug use than opioid-injectors. In St. Petersburg, where over half of PWID reported unsafe sharing practices, ATS-injectors were less likely to report these practices. ATS-injection was negatively associated with being HIV positive in Kohtla-Järve (aOR = 0.6; 95%CI: 0.5-0.8) and St. Petersburg (aOR = 0.3; 95%CI: 0.1-0.7). ATS-injection was negatively associated with HCV-reactivity in Kohtla-Järve (aOR = 0.5; 95%CI: 0.3-0.6).

CONCLUSIONS

In both locations, primary ATS injection was associated with lower injecting risk behaviours, lower odds of HIV and being paid for sex compared to opioid injection. Interventions targeting the characteristics and needs of ATS injectors are needed to increase contact with services and reduce sexual and injecting risk. Harm reduction services, including sexual risk reduction, need to be expanded for all PWID in St. Petersburg.

Food Insecurity, HIV Disease Progression and Access to Care Among HIV-Infected Russians not on ART

Food insecurity (FI) has been associated with HIV disease progression among people on antiretroviral therapy (ART), presumably a consequence of poor medication adherence. We assessed whether there is a longitudinal association between FI and two primary outcomes reflecting on HIV disease progression (i.e., CD4 count and time to ART initiation) among people not on ART. Analyses used linear mixed effects and Cox models controlling for confounders. In this cohort (n = 310) FI was common (53%). Most (71.3%) reported past month heavy alcohol use and 37.1% reported past month injection drug use. Only 50 participants initiated ART during the study and mean time to ART was 128 days (SD 120). There were no significant differences in CD4 cell count between the groups with mild/moderate FI or severe FI versus those with no FI [adjusted mean difference, mild/moderate insecurity versus no FI -32.5 (95% CI -94.3, 29.3); severe versus no FI -45.5 (95% CI -124.1, 33.0); global p = 0.42]. We found no significant association between FI and longer time to ART initiation (p = 0.36). Food security is a desirable goal for overall health and shown beneficial for those on ART, however it does not appear to be associated with HIV disease progression among those with high prevalence of substance use and not yet on ART.

Predictors of HIV Risk Behaviors Among a National Sample of Russian Men Who Have Sex with Men

Russia has one of the fastest growing HIV epidemics in the world and is at the point of transitioning from injection drug use to sexual transmissions. We sought to identify factors associated with unprotected sex among men who have sex with men (MSM) in Russia, separately for Moscow, St. Petersburg and the rest of the country. Multivariable data from a national cross-sectional study (n = 5035) demonstrate that significant correlates of unprotected anal intercourse (UAI) with a non-steady partner across all areas were visiting sex-related venues (AOR range 1.35-1.96) and access to condoms (AOR range 0.37-0.52). In Moscow and St. Petersburg, being HIV-positive was correlated with UAI (AOR 2.13 and 2.69). The dynamics of the HIV epidemic among MSM in Russia appear to be both similar, and different, across various areas and factors associated with unprotected sex should be seen as part of an environment of exogenous factors impacting MSM's sexual behaviors.

Implementation of methadone therapy for opioid use disorder in Russia - a modeled cost-effectiveness analysis

BACKGROUND

Opioid agonist therapy using methadone, an effective treatment of opioid use disorders (OUD) for people who inject drugs (PWID), is recommended by the World Health Organization as essential to curtail the growing HIV epidemic. Yet, despite increasing prevalence of OUD and HIV, methadone therapy has not yet been implemented in Russia. The aim of this modeling study was to estimate the cost-effectiveness of methadone therapy for Russian adults with a diagnosed OUD.

METHODS/DESIGN

We modeled the projected program implementation costs and estimated disability-adjusted life years (DALYs) averted over a 10-year period, associated with the provision of methadone therapy for a hypothetical, unreplenished cohort of Russian adults with an OUD (n = 249,000), in comparison to the current therapies at existing addiction treatment facilities. Our model compared four distinct scenarios of treatment coverage in the cohort ranging from 3.1 to 55%.

RESULTS

Providing methadone therapy to as few as 3.1% of adults with an OUD amounted to an estimated almost 50,000 DALYs averted over 10 years at a cost of just over USD 17 million. Further expanding service coverage to 55% resulted in an estimated almost 900,000 DALYs averted, at a cost of about USD 308 million.

CONCLUSION

Our study indicated that implementing opioid agonist therapy with methadone to treat OUD at existing facilities in Russia is highly cost-effective.

Correlates of Lifetime History of Purchasing Sex Services by Men in Saint Petersburg and Leningrad Oblast, Russia

Commercial sex workers (CSWs) in the Russian Federation are at high risk of HIV infection and transmission as a result of unsafe sexual and injecting behaviors. Their clients might be at increased risk of acquiring HIV; however, little is known about the population of men purchasing sex services. This study aims to investigate factors associated with a history of purchasing sex services by men in Saint Petersburg and Leningrad Oblast, Russian Federation. Data were collected as part of a cross-sectional study offering free anonymous rapid HIV testing in Saint Petersburg and Leningrad Oblast in 2014; in total, 3565 men aged 18 years and older provided information about their behaviors associated with risk of acquiring HIV during face-to-face interviews. Prevalence of CSW use in our study was 23.9%. Multivariable analyses using log-binomial regression were stratified by self-reported HIV testing during the 12 months preceding the study interview. In both strata, older age, multiple sex partners, and a history of sex with an injection drug user (IDU) were associated with an elevated prevalence ratio (PR) for history of purchasing sex services, although the strength of the association differed by strata. Among men who reported recent HIV testing, condom use (PR = 1.22, 90% confidence interval (CI) 1.0, 1.48) was associated with a history of purchasing sex services, and among men who did not report recent HIV testing, having a consistent sex partner was associated with purchasing sex services (PR = 1.23, 90% CI 1.1, 1.37). The high prevalence of CSW service use and associations found in this study raise serious concerns about potential for sexual HIV transmission and should be investigated more closely.