Temporal trends in the HIV-1 epidemic in Russia: predominance of subtype A

HIV drug resistance among patients experiencing antiretroviral therapy failure in Russia, 2019-2021

Increasing HIV drug resistance is an important public health concern. The current study aimed to assess HIV drug resistance among people who live with HIV (PLWH) experiencing virological failure. Blood samples and epidemiological characteristics were collected in four Siberian regions from PLWH experiencing ART failure. Partial pol gene sequences were obtained for the study individuals. Drug resistance mutations (DRMs) were predicted using the Stanford HIVdb Program. The association of HIV DRM with epidemiological characteristics was estimated using logistic regression analysis. Further analysis was performed for children (0-14 y old) and adults (≥15 y old) separately. In total, 815 (89.4%) patients were included in the final dataset. Overall, 501 (61.5%) patients had DRM detected. NRTI DRM was more common in children, while NRTI+NNRTI DRM was more frequent in adults (P < 0.001). Krasnoyarsk region, male sex and high viral load were positively associated with the presence of DRM in adults, while higher CD4 cell count and PI/INSTI-based ART had a negative association. No association between epidemiological characteristics and DRM was identified in children. The remaining 38.5% of patients with virological failure had no DRM detected; those patients were likely to have insufficient ART adherence. Most (55.5%) patients had HIV CRF63_02A6, followed by sub-subtype A6 (39.2%). This study revealed poor ART adherence as a main factor driving ART failure among PLWH in the Siberian region. DRM was detected in over 60% of PLWH experiencing ART failure. The current results highlight an urgent need for the introduction of special programs focusing on ART adherence improvement.

HIV in the Russian Federation: mortality, prevalence, risk factors, and current understanding of sexual transmission

BACKGROUND

Although HIV infection in the Russian Federation was historically concentrated among marginalized populations (people who inject drugs, sex workers, MSM, and the prison population), recent evidence suggests that it has become a more generalized epidemic. The objective of our research was to explore how these trends in HIV prevalence and HIV-related mortality compare across Russia.

METHODS

We calculated HIV-associated mortality for both male and female individuals in each region (oblast) of the Russian Federation using data from the Russian Fertility and Mortality Database (RusFMD). Using current data on HIV prevalence, we computed the correlation between HIV prevalence and HIV-associated mortality. We also used oblast-level data to examine the associations between HIV prevalence and the risk factors most commonly associated with HIV infection.

RESULTS

Over the past 20 years, the Russian Federation has experienced a rapid increase in HIV-associated mortality in both male and female individuals. Our findings revealed significant heterogeneity, with higher rates of HIV-associated mortality reported in oblasts in the Siberian and Ural Federal Districts. There is a strong correlation (0.8) between HIV-associated mortality and virus prevalence. These findings confirm that there are regional disparities in access and adherence to antiretroviral therapy (ART), as indicated by the low correlation (-0.4) between virus prevalence and access to ART coverage. The results from our modeling analysis revealed that, in addition to the factors most commonly associated with this disease (e.g. intravenous drug use), knowledge about sexual transmission of HIV in the general population has a broad impact on its prevalence at the oblast level.

CONCLUSION

Interventions that reduce HIV prevalence, for example, opioid substitution therapy and needle-sharing programs for people who inject drugs, as well as the increased availability of educational and preventive programs may halt the spread of HIV across the Russian Federation. Similarly, increased access to treatment could help in reducing HIV-related mortality.

[Genetic diversity of capsid protein (p24) in human immunodeficiency virus type-1 (HIV-1) variants circulating in the Russian Federation]

INTRODUCTION

The human immunodeficiency virus (HIV) protein p24 plays an important role in the life cycle of the virus, and also is a target for diagnostic tests and for new antiretroviral drugs and therapeutic vaccines. The most studied variant of HIV-1 in the world is subtype B. In Russia, the most common variant is A6, the spread of recombinant forms (CRF63_02A6, CRF03_A6B) is observed as well as circulation of G and CRF02_AG variants. However, a detailed study of the p24 protein in these variants has not yet been conducted. The aim was to study the features of the p24 protein in HIV-1 variants circulating in Russia and estimate the frequency of occurrence of pre-existing mutations associated with resistance to lenacapavir, the first antiretroviral drug in the class of capsid inhibitors.

MATERIALS AND METHODS

The objects of the study were the nucleotide sequences obtained from the Los Alamos international database and clinical samples from HIV infected patients.

RESULTS AND DISCUSSION

The features of HIV-1 variants circulating in Russia have been determined. V86A, H87Q, I91F are characteristic substitutions in A6 genome. It is shown that the presence of preexisting mutations associated with resistance to lenacapavir is unlikely.

CONCLUSION

Features of the p24 protein in HIV-1 variants circulating in Russia allow them to be distinguished from others variants and among themselves. The prognosis for the use of lenacapavir in Russia is generally favorable. The results obtained could be taken into account in developing and using antiretroviral drugs and therapeutic vaccines.

[Genetic diversity of the human immunodeficiency virus (HIV-1) in the Kaliningrad region]

INTRODUCTION

As is currently known, the epidemic process in the Kaliningrad Region was mainly associated with the spread of the recombinant form of HIV-1 (CRF03_AB); however, regular HIV importations from other countries and continents has created favorable conditions for emergence and spread of various recombinant forms of the virus.The most complete information on the diversity of recombinant forms in the region is also necessary to understand the structure of drug resistance (DR). The aim of the study was to explore the HIV-1 genetic diversity in the Kaliningrad Region.

MATERIALS AND METHODS

We studied 162 blood plasma samples obtained from patients from the Kaliningrad Region, both with confirmed virological failure of antiretroviral therapy (ART) and with newly diagnosed HIV infection. For reverse transcription and amplification of HIV genome fragments, diagnostic «AmpliSense HIVResist-Seq».

RESULTS AND DISCUSSION

The various recombinants between subtypes A and B (74%) were predominant in study group: recombinant was between CRF03_AB and subtype A (33.95%) and CRF03_AB-like (13.58%) were the most common. Among the "pure" subtypes of the virus, subtype A6 (16.67%). The circulation of subtypes B (3.70%) and G (1.23%) was also noted.Ninety-six patients (59.26%) were identified with at least one mutation associated with antiretroviral (ARV) drug resistance.

CONCLUSION

The observed diversity of subtypes and recombinant forms of the virus implies that the new recombinants are actively emerging in the studied region, both between existing recombinant forms and "pure" subtypes, as well as between "pure" subtypes.

Spatiotemporal dynamics of HIV-1 CRF63_02A6 sub-epidemic

HIV-1 epidemic in Russia is one of the fastest growing in the world reaching 1.14 million people living with HIV-1 (PLWH) in 2021. Since mid-1990s, the HIV-1 epidemic in Russia has started to grow substantially due to the multiple HIV-1 outbreaks among persons who inject drugs (PWID) leading to expansion of the HIV-1 sub-subtype A6 (former Soviet Union (FSU) subtype A). In 2006, a local HIV-1 sub-epidemic caused by the distribution of novel genetic lineage CRF63_02A6 was identified in Siberia. In this study, we used a comprehensive dataset of CRF63_02A6 pol gene sequences to investigate the spatiotemporal dynamic of the HIV-1 CRF63_02A6 sub-epidemic. This study includes all the available CRF63_02A6 HIV-1 pol gene sequences from Los Alamos National Laboratory (LANL) HIV Sequence Database. The HIV-1 subtypes of those sequences were conferred using phylogenetic analysis, and two automated HIV-1 subtyping tools Stanford HIVdb Program and COMET. Ancestral state reconstruction and origin date were estimated using Nextstrain. Evolutionary rate and phylodynamic analysis were estimated using BEAST v 1.10.4. CRF63_02A6 was assigned for 872 pol gene sequences using phylogenetic analysis approach. Predominant number (n = 832; 95.4%) of those sequences were from Russia; the remaining 40 (4.6%) sequences were from countries of Central Asia. Out of 872 CRF63_02A6 sequences, the corresponding genetic variant was assigned for 75.7 and 79.8% of sequences by Stanford and COMET subtyping tools, respectively. Dated phylogenetic analysis of the CRF63_02A6 sequences showed that the virus most likely originated in Novosibirsk, Russia, in 2005. Over the last two decades CRF63_02A6 has been widely distributed across Russia and has been sporadically detected in countries of Central Asia. Introduction of new genetic variant into mature sub-subtype A6 and CRF02_AGFSU epidemics could promote the increase of viral genetic diversity and emergence of new recombinant forms. Further HIV-1 studies are needed due to a continuing rapid virus distribution. Also, the implementation of HIV-1 prevention programs is required to reduce HIV-1 transmission. This study also highlights the discrepancies in HIV-1 subtyping approaches. The reference lists of HIV-1 sequences implemented in widely used HIV-1 automated subtyping tools need to be updated to provide reliable results.

Detection of Patient HIV-1 Drug Resistance Mutations in Russia’s Northwestern Federal District in Patients with Treatment Failure

Highly active antiretroviral therapy (HAART) is currently a combination of three (less frequently four) antiretroviral drugs; these target pathways involved in various stages of HIV replication in the body. Treatment failure is a problem facing doctors and patients using HAART. The most common cause of therapeutic failure is the development of HIV drug resistance. The emergence of resistance is associated with processes involving mutation occurring in the viral genome under the influence of evolutionary factors. Sequencing reactions were performed using the AmpliSens HIV Resist-Seq. Assembly of consensus sequences from fragments obtained during sequencing was carried out using Unipro UGENE softwar. Isolate genotyping was performed using the MEGA-X software with the Neighbor-joining algorithm. According to the analysis, 72.05% of patients had at least one significant mutation associated with drug resistance for the corresponding viral subtype. HIV-1 A6 remains the predominant HIV-1 genetic variant in Russia’s Northwestern Federal District. Among samples with drug resistance mutations, in all cases, mutations associated with pharmacological resistance to two or three drug groups were found. Given the high incidence of resistance mutations in patients on ineffective ART, surveillance of HIV-1 drug resistance, in both ART-receiving and ART-naive individuals, appears necessary. A lack of vigilance and control measures may lead to the spread of primary ART-resistant HIV strains.

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.

Genetic Diversity of HIV-1 in Krasnoyarsk Krai: Area with High Levels of HIV-1 Recombination in Russia

More than a quarter of HIV-infected individuals registered in Russia live in Siberia. Unlike Central Russia where HIV-1 subtype A6 is predominant, in most Siberian regions since 2012, a new HIV-1 CRF63_02A1 genetic variant has spread, with the share of this variant attaining 75-85% among newly identified HIV cases. Krasnoyarsk Krai is considered to be a high-risk territory according to morbidity rate and HIV infection incidence among the population. The current paper aims to study the molecular epidemiologic characteristics of HIV-1 spreading in Krasnoyarsk Krai. Phylogenetic and recombination analyses of pol (PR-RT, IN) and env regions of the virus were used for genotyping 159 HIV-1 isolated in Krasnoyarsk Krai. 57.2% of the isolates belonged to subtype A (A6) specific to Russia, 12.6% to CRF63_02A1, and 0.6% to CRF02_AGСА, and in 29.6% HIV-1 URFs were detected, including URF63/А (23.9%), URFА/В (4.4%), and URF02/А (1.3%). In 6 of 7, HIV-1 URFА/В identical recombination model was detected; the origin of 38 URF63/А was proven to be the result of individual recombination events. Since 2015, a share of the population with newly diagnosed HIV who were infected with HIV-1 URF reached an exceptionally high rate of 38.6%. As distinct from adjacent Siberian regions, the HIV-1 CRF63_02A1 prevalence rate in Krasnoyarsk Krai is within 16%; however, the increased contribution of new HIV-1 into the regional epidemic development was observed due to the recombination of viruses of subtypes А, В, and CRF63_02A1. The difference between the described molecular epidemiologic picture in Krasnoyarsk Krai and in adjacent areas is likely caused by differences in predominant routes of HIV transmission and by more recent HIV-1 CRF63_02A1 transmission in the PWID group, which had a high prevalence of HIV-1 subtype A by the time of the new virus transmission, resulting in increased possibility of coinfection with various HIV-1 genetic variants.

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.

Reconstruction of the Genetic History and the Current Spread of HIV-1 Subtype A in Germany

HIV-1 non-B infections have been increasing in Europe for several years. In Germany, subtype A belongs to the most abundant non-B subtypes showing an increasing prevalence of 8.3% among new infections in 2016. Here we trace the origin and examine the current spread of the German HIV-1 subtype A epidemic. Bayesian coalescence and birth-death analyses were performed with 180 German HIV-1 pol sequences and 528 related and publicly available sequences to reconstruct the population dynamics and fluctuations for each of the transmission groups. Our reconstructions indicate two distinct sources of the German subtype A epidemic, with an Eastern European and an Eastern African lineage both cocirculating in the country. A total of 13 German-origin clusters were identified; among these, 6 clusters showed recent activity. Introductions leading to further countrywide spread originated predominantly from Eastern Africa when introduced before 2005. Since 2005, however, spreading introductions have occurred exclusively within the Eastern European clade. Moreover, we observed changes in the main route of subtype A transmission. The beginning of the German epidemic (1985 to 1995) was dominated by heterosexual transmission of the Eastern African lineage. Since 2005, transmissions among German men who have sex with men (MSM) have been increasing and have been associated with the Eastern European lineage. Infections among people who inject drugs dominated between 1998 and 2005. Our findings on HIV-1 subtype A infections provide new insights into the spread of this virus and extend the understanding of the HIV epidemic in Germany.IMPORTANCE HIV-1 subtype A is the second most prevalent subtype worldwide, with a high prevalence in Eastern Africa and Eastern Europe. However, an increase of non-B infections, including subtype A infections, has been observed in Germany and other European countries. There has simultaneously been an increased flow of refugees into Europe and especially into Germany, raising the question of whether the surge in non-B infections resulted from this increased immigration or whether German transmission chains are mainly involved. This study is the first comprehensive subtype A study from a western European country analyzing in detail its phylogenetic origin, the impact of various transmission routes, and its current spread. The results and conclusions presented provide new and substantial insights for virologists, epidemiologists, and the general public health sector. In this regard, they should be useful to those authorities responsible for developing public health intervention strategies to combat the further spread of HIV/AIDS.

[Genetic diversity of human immunodeficiency viruses and antiretroviral therapy]

The lecture is devoted to the analysis of the state-of-the-art of the impact of genetic diversity of human immunodeficiency (HIV) viruses on the pattern of infection and the efficiency of antiretroviral therapy (ART). It provides brief information on the origin and evolution of HIV and on the current classification of their genetic variants. The molecular epidemiological situation of HIV infection in Russia and nearby states and the major molecular HIV variants that are dominant in these countries, as well as their origin and prevalence trends are characterized. How the diversity of HIV can affect the efficiency of diagnosis, the transmission of the virus, and the pattern of HIV pathogenesis are briefly reviewed. The comparative data available in the world's scientific literature on these topics are given. More detailed attention is given to the possible causes of varying therapeutic effects against different HIV subtypes, as well as to the specific features of the formation and phenotyping manifestation of ART drug resistance mutations. There is evidence for the necessity of forming a unified follow-up system for treated HIV-infected patients during ART scaling, including in an effort to evaluate the impact of the specific features of the HIV genome on the efficiency of treatment regimens used in Russia.

HIV-1 Genetic Diversity in Recently Diagnosed Infections in Moscow: Predominance of AFSU, Frequent Branching in Clusters, and Circulation of the Iberian Subtype G Variant

HIV-1 protease-reverse transcriptase sequences from 62 HIV-1-infected individuals recently diagnosed in Moscow were analyzed. Subtype A former Soviet Union (FSU) (A_FSU) variant was the predominant clade (62.9%), followed by subtype B (22.6%), unique recombinants (6.5%), subtype G (6.5%), and CRF01_AE (1.6%). A_FSU predominated among people who inject drugs (88.9%) and heterosexually acquired infections (77.8%), while subtype B was the most prevalent genetic form among men who have sex with men (44%), although A_FSU was also frequent in this population (36%). Forty-eight (77.4%) viruses branched within intrasubtype clusters, three of which, of subtype B, had a majority of viruses collected outside of FSU. The four subtype G viruses identified in this study belonged to the Portuguese-Spanish (Iberian) variant and, together with three from databases, formed a Russian cluster closely related to viruses from Denmark. This is the first report of the circulation of the Iberian subtype G variant in Russia.

HIV-1 Epidemiology, Genetic Diversity, and Primary Drug Resistance in the Tyumen Oblast, Russia

Introduction. Specific molecular epidemic features of HIV infection in Tyumen Oblast (TO), Russia, were studied. Methods. The genome sequences encoding HIV-1 protease-reverse transcriptase, integrase, and major envelope protein were examined for 72 HIV-1 specimens isolated from the TO resident infected in 2000-2015. Results. The recorded prevalence of HIV-1 subtype A (A1) is 93.1%; HIV-1 subtype B continues to circulate in MSM risk group (1.4%). Solitary instances of HIV-1 recombinant forms, CRF63_02A1 (1.4%) and CRF03_AB (1.4%), were detected as well as two cases of HIV-1 URF63_A1 (2.8%). Phylogenetic analysis showed no HIV-1 clustering according to the duration of infection and risk groups but revealed different epidemic networks confirming that HIV infection spread within local epidemic foci. A high incidence of CXCR4-tropic HIV-1 variants and a higher rate of secondary mutations influencing the virus fitness (K20R, L10V, and I) are observed among the virus specimens isolated from newly infected individuals. Conclusions. The current HIV-1 epidemic in TO develops within the local epidemic networks. Similar to the previous period, HIV-1 subtype A is predominant in TO with sporadic cases of importation of HIV-1 recombinant forms circulating in adjacent areas.

Molecular epidemiology of HIV-1 infection in Europe: An overview

Human Immunodeficiency Virus type 1 (HIV-1) is characterised by vast genetic diversity. Globally circulating HIV-1 viruses are classified into distinct phylogenetic strains (subtypes, sub-subtypes) and several recombinant forms. Here we describe the characteristics and evolution of European HIV-1 epidemic over time through a review of published literature and updated queries of existing HIV-1 sequence databases. HIV-1 in Western and Central Europe was introduced in the early-1980s in the form of subtype B, which is still the predominant clade. However, in Eastern Europe (Former Soviet Union (FSU) countries and Russia) the predominant strain, introduced into Ukraine in the mid-1990s, is subtype A (A_FSU) with transmission mostly occurring in People Who Inject Drugs (PWID). In recent years, the epidemic is evolving towards a complex tapestry with an increase in the prevalence of non-B subtypes and recombinants in Western and Central Europe. Non-B epidemics are mainly associated with immigrants, heterosexuals and females but more recently, non-B clades have also spread amongst groups where non-B strains were previously absent - non-immigrant European populations and amongst men having sex with men (MSM). In some countries, non-B clades have spread amongst the native population, for example subtype G in Portugal and subtype A in Greece, Albania and Cyprus. Romania provides a unique case where sub-subtype F1 has predominated throughout the epidemic. In contrast, HIV-1 epidemic in FSU countries remains more homogeneous with A_FSU clade predominating in all countries. The differences between the evolution of the Western epidemic and the Eastern epidemic may be attributable to differences in transmission risk behaviours, lifestyle and the patterns of human mobility. The study of HIV-1 epidemic diversity provides a useful tool by which we can understand the history of the pandemic in addition to allowing us to monitor the spread and growth of the epidemic over time.

Overview of HIV molecular epidemiology among people who inject drugs in Europe and Asia

HIV strains continuously evolve, tend to recombine, and new circulating variants are being discovered. Novel strains complicate efforts to develop a vaccine against HIV and may exhibit higher transmission efficiency and virulence, and elevated resistance to antiretroviral agents. The United Nations Joint Programme on HIV/AIDS (UNAIDS) set an ambitious goal to end HIV as a public health threat by 2030 through comprehensive strategies that include epidemiological input as the first step of the process. In this context, molecular epidemiology becomes invaluable as it captures trends in HIV evolution rates that shape epidemiological pictures across several geographical areas. This review briefly summarizes the molecular epidemiology of HIV among people who inject drugs (PWID) in Europe and Asia. Following high transmission rates of subtype G and CRF14_BG among PWID in Portugal and Spain, two European countries, Greece and Romania, experienced recent HIV outbreaks in PWID that consisted of multiple transmission clusters including subtypes B, A, F1, and recombinants CRF14_BG and CRF35_AD. The latter was first identified in Afghanistan. Russia, Ukraine, and other Former Soviet Union (FSU) states are still facing the devastating effects of epidemics in PWID produced by A_FSU (also known as IDU-A), B_FSU (known as IDU-B), and CRF03_AB. In Asia, CRF01_AE and subtype B (Western B and Thai B) travelled from PWID in Thailand to neighboring countries. Recombination hotspots in South China, Northern Myanmar, and Malaysia have been generating several intersubtype and inter-CRF recombinants (e.g. CRF07_BC, CRF08_BC, CRF33_01B etc.), increasing the complexity of HIV molecular patterns.

Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity

Given the dynamic changes in HIV-1 complexity and diversity, next-generation sequencing (NGS) has the potential to revolutionize strategies for effective HIV global surveillance. In this study, we explore the utility of metagenomic NGS to characterize divergent strains of HIV-1 and to simultaneously screen for other co-infecting viruses. Thirty-five HIV-1-infected Cameroonian blood donor specimens with viral loads of >4.4 log₁₀ copies/ml were selected to include a diverse representation of group M strains. Random-primed NGS libraries, prepared from plasma specimens, resulted in greater than 90% genome coverage for 88% of specimens. Correct subtype designations based on NGS were concordant with sub-region PCR data in 31 of 35 (89%) cases. Complete genomes were assembled for 25 strains, including circulating recombinant forms with relatively limited data available (7 CRF11_cpx, 2 CRF13_cpx, 1 CRF18_cpx, and 1 CRF37_cpx), as well as 9 unique recombinant forms. HPgV (formerly designated GBV-C) co-infection was detected in 9 of 35 (25%) specimens, of which eight specimens yielded complete genomes. The recovered HPgV genomes formed a diverse cluster with genotype 1 sequences previously reported from Ghana, Uganda, and Japan. The extensive genome coverage obtained by NGS improved accuracy and confidence in phylogenetic classification of the HIV-1 strains present in the study population relative to conventional sub-region PCR. In addition, these data demonstrate the potential for metagenomic analysis to be used for routine characterization of HIV-1 and identification of other viral co-infections.

Enhanced HIV-1 surveillance using molecular epidemiology to study and monitor HIV-1 outbreaks among intravenous drug users (IDUs) in Athens and Bucharest

BACKGROUND

A significant increase in HIV-1 diagnoses was reported among Injecting Drug Users (IDUs) in the Athens (17-fold) and Bucharest (9-fold) metropolitan areas starting 2011.

METHODS

Molecular analyses were conducted on HIV-1 sequences from IDUs comprising 51% and 20% of the diagnosed cases among IDUs during 2011-2013 for Greece and Romania, respectively. Phylodynamic analyses were performed using the newly developed birth-death serial skyline model which allows estimating of important epidemiological parameters, as implemented in BEAST programme.

RESULTS

Most infections (>90%) occurred within four and three IDU local transmission networks in Athens and Bucharest, respectively. For all Romanian clusters, the viral strains originated from local circulating strains, whereas in Athens, the local strains seeded only two of the four sub-outbreaks. Birth-death skyline plots suggest a more explosive nature for sub-outbreaks in Bucharest than in Athens. In Athens, two sub-outbreaks had been controlled (Re<1.0) by 2013 and two appeared to be endemic (Re∼1). In Bucharest one outbreak continued to expand (Re>1.0) and two had been controlled (Re<1.0). The lead times were shorter for the outbreak in Athens than in Bucharest.

CONCLUSIONS

Enhanced molecular surveillance proved useful to gain information about the origin, causal pathways, dispersal patterns and transmission dynamics of the outbreaks that can be useful in a public health setting.

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.

Bayesian phylogeographic analyses clarify the origin of the HIV-1 subtype A variant circulating in former Soviet Union's countries

The HIV-1 subtype A variant dominating the HIV-1 epidemics in former Soviet Union (FSU) countries (A(FSU)) represents one of the major clades of the HIV-1 pandemic. This variant was reported to have begun spreading among injecting drug users (IDUs) in the Ukrainian city of Odessa in late 1994. Two competing hypotheses have been proposed on the ancestral origin of the A(FSU) variant, locating it either in the Democratic Republic of Congo (DRC) or in the Republic of Guinea (RG). The studies supporting these hypotheses employed phylogenetic analyses to identify HIV-1 sequences collected outside FSU countries ancestrally related to A(FSU). A different approach, based on Bayesian phylogenetic inference and coalescent-based population genetics, has been employed here to elucidate the ancestry of this HIV-1 variant and to improve our knowledge on its spread in FSU countries. The analyses were carried out using env (C2-V3-C3) and p24(gag) fragments of the HIV-1 genome. The inferred migration for the HIV-1 A(FSU) variant revealed only one significantly supported migration pathway from Africa to Eastern Europe, supporting the hypothesis of its origin in the DRC and estimating the upper limit of the migration of the ancestral virus from Africa around 1970. The support for an origin in the RG was negligible. The results supported the main role of Odessa as the epicenter of the A(FSU) epidemic, dating the tMRCA of the A(FSU) variant around 1984, ten years before its explosive expansion among IDUs. The estimated origin of the AFSU subcluster responsible for the IDU outbreak was also located in Odessa, with the estimated tMRCA around 1993. Statistically supported migration routes from Odessa to other cities of Ukraine, Russia, Kazakhstan, Uzbekistan and Belarus were also inferred by the Bayesian phylogeographic analysis. These results shed new light on the origin and spread of the HIV-1 A(FSU) variant.

A rapid expansion of HIV-1 CRF63_02A1 among newly diagnosed HIV-infected individuals in the Tomsk Region, Russia

The prevalence of HIV infection in different Russian regions is nonuniform. In the Tomsk region (TR), 2020 HIV new infection cases were recorded in 2013, the morbidity having increased 5.9-fold as compared to 2012. In total, 64 blood plasma samples from primary HIV cases have been examined. HIV-specific fragments of the pol gene have been obtained for 61 samples (of protease for 58 and of integrase for 23) and of the env gene V3 region for 40 samples. Phylogenetic analysis of the determined HIV-1 sequences has detected CRF63_02A1 in 55 (90.2%) cases, whereas HIV subtype A1, characteristic of Russia, has been observed in only three (4.9%) patients. Three (4.9%) cases contain CRF63_02A1/A recombinant variants. This article demonstrates that a drastic activation of the epidemic in the Tomsk region is accompanied by a rapid spreading of the recently described HIV-1 CRF63_02A1, which we detected in the Novosibirsk region outbreak of 2008.

A uniquely prevalent nonnucleoside reverse transcriptase inhibitor resistance mutation in Russian subtype A HIV-1 viruses

BACKGROUND

The subtype A variant in the Former Soviet Union (A(FSU)) causes most of Russia's HIV-1 infections. However, the spectrum of drug-resistance mutations (DRMs) in antiretroviral experienced patients with this variant has not been studied.

METHODS

Between 2010 and 2013, genotypic resistance testing was performed on plasma samples from 366 antiretroviral-experienced patients in Siberia.

RESULTS

Three-hundred patients (82%) had subtype A(FSU) and 55 (15%) had CRF02_AG viruses. The pattern of DRMs was consistent with patient antiretroviral history with one exception. G190S was the most common nonnucleoside reverse transcriptase inhibitor (NNRTI) resistance mutation, occurring in 55 (33%) subtype A(FSU) viruses from 167 NNRTI-experienced patients compared with none of 37 CRF02_AG viruses from NNRTI-experienced patients (P < 0.001). The next most common subtype A(FSU) NNRTI-resistance mutation, K103N, occurred in 25 (15%) viruses. Wild-type glycine (G) at position 190 is encoded by GGC in more than 99% of published A(FSU) strains. By contrast, G190 is encoded by GGA or GGG in 97% of other subtypes and in subtype A strains outside of the FSU. Therefore, G190S results from a single G→A transition: G (GGC) → S (AGC) almost exclusively in subtype A(FSU) viruses.

CONCLUSION

The predisposition of subtype A(FSU) to G190S is concerning because G→A is the most common HIV-1 mutation and because G190S causes higher levels of nevirapine and efavirenz resistance than K103N. This study exemplifies the need for characterizing the genetic mechanisms of resistance in diverse populations and warrants studies to verify that NRTI/NNRTI regimens are as efficacious in treating subtype A(FSU) as viruses belonging to other subtypes.

Short communication: Molecular epidemiology, phylogeny, and phylodynamics of CRF63_02A1, a recently originated HIV-1 circulating recombinant form spreading in Siberia

The HIV-1 epidemic in Russia is dominated by the former Soviet Union subtype A (A(FSU)) variant, but other genetic forms are circulating in the country. One is the recently described CRF63_02A1, derived from recombination between a CRF02_AG variant circulating in Central Asia and A(FSU), which has spread in the Novosibirsk region, Siberia. Here we phylogenetically analyze pol and env segments from 24 HIV-1 samples from the Novosibirsk region collected in 2013, with characterization of three new near full-length genome CRF63_02A1 sequences, and estimate the time of the most recent common ancestor (tMRCA) and the demographic growth of CRF63_02A1 using a Bayesian method. The analyses revealed that CRF63_02A1 is highly predominant in the Novosibirsk region (81.2% in pol sequences) and is transmitted both among injecting drug users and by heterosexual contact. Similarity searches with database sequences combined with phylogenetic analyses show that CRF63_02A1 is circulating in East Kazakhstan and the Eastern area of Russia bordering China. The analyses of near full-length genome sequences show that its mosaic structure is more complex than reported, with 18 breakpoints. The tMRCA of CRF63_02A1 was estimated around 2006, with exponential growth in 2008-2009 and subsequent stabilization. These results provide new insights into the molecular epidemiology, phylogeny, and phylodynamics of CRF63_02A1.

Short communication: molecular epidemiology of HIV type 1 infection in Kazakhstan: CRF02_AG prevalence is increasing in the southeastern provinces

To analyze HIV-1 genetic variants in Kazakhstan, HIV-1 sequences were obtained from 205 antiretroviral-treated (ART) and naive patients in 2009-2013. Samples were collected in the most populous cities and provinces of Kazakhstan. On the basis of phylogenetic analyses of partial pol sequences, subtype A variant intravenous drug user (IDU)-A (which is dominant in the former Soviet Union) was found in 60.0% of the individuals, followed by CRF02_AG (34.6%); the rest of the samples were subtype B, CRF03_AB, CRF63_02A1, and CRF07_BC. The proportion of CRF02_AG has increased significantly since 2001-2003, when it was less than 5%. The majority of the CRF02_AG cases were found in Almaty, the former capital and the most populous city in Kazakhstan. The IDU-A variant dominated in the industrial regions of northern and central Kazakhstan and some other regions. Both dominant HIV-1 genetic variants were almost equally represented in the two main transmission groups: IDUs and heterosexuals. The analysis of drug-resistant mutations found a low prevalence of drug resistance in 165 therapy-naive individuals (3.0%). Thus, in the beginning of the second decade of the 2000s, the HIV epidemic in Kazakhstan is driven by two main genetic variants: IDU-A and CRF02_AG.

HIV-1 genetic diversity in Russia: CRF63_02A1, a new HIV type 1 genetic variant spreading in Siberia

One of the factors determining a high degree of heterogeneity in the HIV population is recombination-based variation, which leads to the emergence of the virus variants with a mosaic genome. An example is CRF63_02A1, an HIV-1 variant currently spreading in the Siberian region of Russia. To prove that this HIV-1 variant is a new circulating recombinant form that had emerged as a result of repeated recombination between CRF02_AG and subtype A, we have isolated seven full-length HIV genomes and theoretically analyzed them, that is, reconstructed the phylogenetic relationships, determined recombination breakpoints and regions, and compared them with the regions known for CRF02_AG.

Consensus HIV-1 subtype A integrase and its raltegravir-resistant variants: design and characterization of the enzymatic properties

Model studies of the subtype B and non-subtype B integrases are still required to compare their susceptibility to antiretroviral drugs, evaluate the significance of resistance mutations and identify the impact of natural polymorphisms on the level of enzymatic reactivity. We have therefore designed the consensus integrase of the HIV-1 subtype A strain circulating in the former Soviet Union territory (FSU-A) and two of its variants with mutations of resistance to the strand transfer inhibitor raltegravir. Their genes were synthesized, and expressed in E coli; corresponding His-tagged proteins were purified using the affinity chromatography. The enzymatic properties of the consensus integrases and their sensitivity to raltegravir were examined in a series of standard in vitro reactions and compared to the properties of the integrase of HIV-1 subtype B strain HXB2. The consensus enzyme demonstrated similar DNA-binding properties, but was significantly more active than HXB-2 integrase in the reactions of DNA cleavage and integration. All integrases were equally susceptible to inhibition by raltegravir and elvitegravir, indicating that the sporadic polymorphisms inherent to the HXB-2 enzyme have little effect on its susceptibility to drugs. Insensitivity of the mutated enzymes to the inhibitors of strand transfer occurred at a cost of a 30-90% loss of the efficacies of both 3'-processing and strand transfer. This is the first study to describe the enzymatic properties of the consensus integrase of HIV-1 clade A and the effects of the resistance mutations when the complex actions of sporadic sequence polymorphisms are excluded.

HIV-1 autologous antibody neutralization associates with mother to child transmission

The HIV-1 characteristics associated with mother to child transmission (MTCT) are still poorly understood and if known would indicate where intervention strategies should be targeted. In contrast to horizontally infected individuals, exposed infants possess inherited antibodies (Abs) from their mother with the potential to protect against infection. We investigated the HIV-1 gp160 envelope proteins from seven transmitting mothers (TM) whose children were infected either during gestation or soon after delivery and from four non-transmitting mothers (NTM) with similar viral loads and CD4 counts. Using pseudo-typed viruses we tested gp160 envelope glycoproteins for TZM-bl infectivity, CD4 and CCR5 interactions, DC-SIGN capture and transfer and neutralization with an array of common neutralizing Abs (NAbs) (2F5, 2G12, 4E10 and b12) as well as mother and infant plasma. We found no viral correlates associated with HIV-1 MTCT nor did we find differences in neutralization with the panel of NAbs. We did, however, find that TM possessed significantly higher plasma neutralization capacities than NTM (P = 0.002). Furthermore, we found that in utero (IU) TM had a higher neutralization capacity than mothers transmitting either peri-partum (PP) or via breastfeeding (BF) (P = 0.002). Plasma from children infected IU neutralized viruses carrying autologous gp160 viral envelopes as well as those from their corresponding mothers whilst plasma from children infected PP and/or BF demonstrated poor neutralizing capacity. Our results demonstrate heightened autologous NAb responses against gp120/gp41 can associate with a greater risk of HIV-1 MTCT and more specifically in those infants infected IU. Although the number of HIV-1 transmitting pairs is low our results indicate that autologous NAb responses in mothers and infants do not protect against MTCT and may in fact be detrimental when considering IU HIV-1 transmissions.

Consensus HIV-1 FSU-A integrase gene variants electroporated into mice induce polyfunctional antigen-specific CD4+ and CD8+ T cells

Our objective is to create gene immunogens targeted against drug-resistant HIV-1, focusing on HIV-1 enzymes as critical components in viral replication and drug resistance. Consensus-based gene vaccines are specifically fit for variable pathogens such as HIV-1 and have many advantages over viral genes and their expression-optimized variants. With this in mind, we designed the consensus integrase (IN) of the HIV-1 clade A strain predominant in the territory of the former Soviet Union and its inactivated derivative with and without mutations conferring resistance to elvitegravir. Humanized IN gene was synthesized; and inactivated derivatives (with 64D in the active site mutated to V) with and without elvitegravir-resistance mutations were generated by site-mutagenesis. Activity tests of IN variants expressed in E coli showed the consensus IN to be active, while both D64V-variants were devoid of specific activities. IN genes cloned in the DNA-immunization vector pVax1 (pVaxIN plasmids) were highly expressed in human and murine cell lines (>0.7 ng/cell). Injection of BALB/c mice with pVaxIN plasmids followed by electroporation generated potent IFN-γ and IL-2 responses registered in PBMC by day 15 and in splenocytes by day 23 after immunization. Multiparametric FACS demonstrated that CD8+ and CD4+ T cells of gene-immunized mice stimulated with IN-derived peptides secreted IFN-γ, IL-2, and TNF-α. The multi-cytokine responses of CD8+ and CD4+ T-cells correlated with the loss of in vivo activity of the luciferase reporter gene co-delivered with pVaxIN plasmids. This indicated the capacity of IN-specific CD4+ and CD8+ T-cells to clear IN/reporter co-expressing cells from the injection sites. Thus, the synthetic HIV-1 clade A integrase genes acted as potent immunogens generating polyfunctional Th1-type CD4+ and CD8+ T cells. Generation of such response is highly desirable for an effective HIV-1 vaccine as it offers a possibility to attack virus-infected cells via both MHC class I and II pathways.

Implications of HIV diversity for the HIV-1 pandemic

HIV-1 genetic variability within individuals and populations plays a central role in the HIV pandemic. Multiple zoonotic transmissions of SIV to humans have resulted in distinct HIV lineages in humans which have further diversified within the population over time. High rates of mutation and recombination during HIV reverse transcription create a genetic diversity in the host which is subject to selection pressures by the immune response and antiretroviral treatment. The global distribution of HIV genetic variants and the impact of HIV diversity on pathogenesis, transmission and clinical management are reviewed. Finally, the key role of escape mutations in the immune response to HIV is discussed as well as the major challenge which HIV-1 diversity poses to HIV vaccine development.

Isolation, characterization, and sequence analysis of a novel HIV type 1 subtype A1 strain from Russia

A new syncytia-inducing human immunodeficiency virus type 1 (HIV-1) strain designated PokA79 was first isolated from a peripheral blood mononuclear cells (PBMC) pool from 24 HIV-1-infected patients from Russia and adapted to growth in MT2, MT4, and U937 cell cultures. The full-length genome of this isolate was amplified by RT-two-round PCR and sequenced. The obtained sequence belongs to the A1 subtype and clustered with other A1 former Soviet Union (FSU) strains. Full-length genome analysis showed that some of the PokA79 genes contain insertions and frame shifts, and the gp120 V3 loop has the three amino acid insertion inside its apex, which is rare for subtype A1 sequences. Nonidentical insertions of the same size are also present in the V3 apex region of several HIV-1 sequences from Central Africa.

Genetic characterization of an isolate of HIV type 1 AG recombinant form circulating in Siberia, Russia

Before 2008, HIV-1 subtype A was the predominant genetic variant in the Novosibirsk oblast of Russia as well as in most parts of this country. However, a rapid spread of the recombinant HIV-1 02_AG form has been reported in Novosibirsk since 2009. We have analyzed the genome of the 10.RU.6637 isolate, a HIV-1 02_AG recombinant form, which represents a monophyletic cluster of the HIV-1 variants widespread in this region. Phylogenetic analysis has shown that the Siberian 10.RU.6637 isolate displays the highest sequence identity to the HIV-1 subtype AG forms circulating in Uzbekistan. However, recombination analysis of 10.RU.6637 has demonstrated that this isolate is a recombinant form between HIV-1 subtype A and CRF02_AG, differing in its genetic structure from both the CRF02_AG reference sequences and the Central Asian variants of HIV-1 02_AG.

Molecular typing of the recently expanding subtype B HIV-1 epidemic in Romania: evidence for local spread among MSMs in Bucharest area

HIV-1 subtype B is predominant in Europe except in some countries from Eastern Europe which are characterized by a high prevalence of non-B subtypes and circulating recombinant forms (CRFs). Romania is a particular case: the HIV-1 epidemic started with subtype F1 which is still the most prevalent. Previous studies have shown an increasing prevalence of subtype B which is the second most frequent one among the newly diagnosed individuals, followed by subtype C and several CRFs as well as unique recombinant forms (URFs). Our objective was to analyze in detail the characteristics (way of dispersal, association with transmission risk groups) of the subtype B infections in Romania by means of phylogenetic analysis. Among all the individuals sampled during 2003-2010, 71 out of 1127 patients (6.3%) have been identified to be infected with subtype B strains. The most frequent route of infection identified in HIV-1 subtype B patients in Romania was MSM transmission (39.6%), followed by the heterosexual route (35.2%). Many of the patients acquired the infection abroad, mainly in Western European countries. Phylogenetic analysis indicated the existence of a local transmission network (monophyletic clade) including 14 patients, mainly MSM living in the Bucharest area. We estimate the origin of the local transmission network that dates at the beginning of the 90s; the introduction of the F1 and C subtypes occurred earlier. The rest of the sequences were intermixed with reference strains sampled across Europe suggesting that single infection were not followed by subsequent dispersal within the local population. Although HIV-1 subtype B epidemic in Romania is recent, there is evidence for local spread among the MSMs, in addition to multiple introductions.

Identification of a current hot spot of HIV type 1 transmission in Mongolia by molecular epidemiological analysis

We investigated the current molecular epidemiological status of HIV-1 in Mongolia, a country with very low incidence of HIV-1 though with rapid expansion in recent years. HIV-1 pol (1065 nt) and env (447 nt) genes were sequenced to construct phylogenetic trees. The evolutionary rates, molecular clock phylogenies, and other evolutionary parameters were estimated from heterochronous genomic sequences of HIV-1 subtype B by the Bayesian Markov chain Monte Carlo method. We obtained 41 sera from 56 reported HIV-1-positive cases as of May 2009. The main route of infection was men who have sex with men (MSM). Dominant subtypes were subtype B in 32 cases (78%) followed by subtype CRF02_AG (9.8%). The phylogenetic analysis of the pol gene identified two clusters in subtype B sequences. Cluster 1 consisted of 21 cases including MSM and other routes of infection, and cluster 2 consisted of eight MSM cases. The tree analyses demonstrated very short branch lengths in cluster 1, suggesting a surprisingly active expansion of HIV-1 transmission during a short period with the same ancestor virus. Evolutionary analysis indicated that the outbreak started around the early 2000s. This study identified a current hot spot of HIV-1 transmission and potential seed of the epidemic in Mongolia. Comprehensive preventive measures targeting this group are urgently needed.

Epidemiologic links between drug use and HIV epidemics: an international perspective

Injecting use of heroin has been the highest risk substance use behavior for HIV since the beginning of the pandemic. These risks extend beyond individual levels to networks of drugs users and to wider social contexts that have been referred to collectively as the risk environment. Investigations of individual, network, and risk environment level associations with heroin availability, use, and subsequent spread among injecting drug users (IDUs) have been conducted in multiple settings, but much less is known about the world's center of illicit opium production and heroin exports-Afghanistan. Recent outbreaks of injecting drug use and of HIV infection attributed to IDUs in several African countries suggest that heroin use is expanding into new regions. This article explores the epidemiology of HIV among drug users in several risk environments, the epidemiology of heroin and its associations with HIV outbreaks among IDUs in Central Asia and the Commonwealth of Independent States, and the drug use and IDUs outbreaks now emerging in Africa. The dearth of targeted, evidence-and human rights-based responses to these epidemics is explored as a structural driver of HIV spread in these settings.

Evolution of HIV-1 in India

Nearly 25 years after the discovery of the human immunodeficiency virus type 1 (HIV-1) effective control of the AIDS pandemic remains elusive. At the root of this challenge is the evolution of this virus to elude immune control. Error-prone nature of replication and retro-transcription is the hallmark of this virus. This fidelity of replication in HIV-1 is due to the absence of proof-reading/repair and post-replicative error correction mechanisms that normally operate during replication of DNA viruses. Advances in sequencing technology and expanded disease surveillance have allowed researchers to characterize the variation in HIV-1 around the world and within individual patient overtime. Although HIV-1 has been classified into distinct subtypes, the classification does not reflect dynamic genetic evolution of HIV-1 through which new strains are constantly emerging. The resultant viral diversity has implications for differential rates of disease progression in different geographical areas, differential responses to antiretroviral therapy (including the development of resistance), and vaccine development. In this review evolution of HIV-1 in India is discussed.

Male sex workers in Moscow, Russia: a pilot study of demographics, substance use patterns, and prevalence of HIV-1 and sexually transmitted infections

The Russian federation has been undergoing a concentrated epidemic of HIV-1 with high rates of infection among injecting drug users. Less is known about the relative risk and contribution to the country's HIV epidemic by other at-risk populations including sex workers and men who have sex with men. The goals of this project were to explore demographic characteristics, substance use patterns, and estimate the prevalence of sexually transmitted infections (STIs) and high-risk behaviors among male sex workers (MSW) in Moscow and to assess the feasibility of prospective cohort recruitment and retention among this population. Research design was a longitudinal study of 50 men with a six-month follow-up period. Participants were recruited through venue-based and snowball sampling methods. Results revealed an HIV prevalence at baseline of 16%; one MSW seroconverted during the follow-up period, yielding an incidence estimate of 4.8/100PY (95%CI 0.0-11.2). Twenty-four percentage were diagnosed with at least one STI: 12% had syphilis; 8% had Human Papilloma Virus (HPV); and 4% had Herpes Simplex Virus (HSV)-2. Three (6%) of the study participants had evidence of previous Hepatitis C Virus (HCV) exposure at baseline. Retention rates were poor with higher retention significantly associated with older men (OR: 13.1, 95% CI 3.3-52.5). This was the first study to evaluate baseline demographics, substance use patterns, and prevalence of infectious disease among MSW in Moscow. Identification and recruitment of this population appears to be feasible, but retention a challenge. While the sample size in the current study was small, the results also suggested that this is a population at considerable high risk for HIV. MSW in Moscow may be an important at-risk population in the Russian HIV epidemic and further research is urgently required to address their needs and explore prevention strategies.

Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections

Since DNA sequencing techniques first became available almost 30 years ago, the amount of nucleic acid sequence data has increased enormously. Phylogenetics, which is widely applied to compare and analyze such data, is particularly useful for the analysis of genes from rapidly evolving viruses. It has been used extensively to describe the molecular epidemiology and transmission of the human immunodeficiency virus (HIV), the origins and subsequent evolution of the severe acute respiratory syndrome (SARS)-associated coronavirus (SCoV), and, more recently, the evolving epidemiology of avian influenza as well as seasonal and pandemic human influenza viruses. Recent advances in phylogenetic methods can infer more in-depth information about the patterns of virus emergence, adding to the conventional approaches in viral epidemiology. Examples of this information include estimations (with confidence limits) of the actual time of the origin of a new viral strain or its emergence in a new species, viral recombination and reassortment events, the rate of population size change in a viral epidemic, and how the virus spreads and evolves within a specific population and geographical region. Such sequence-derived information obtained from the phylogenetic tree can assist in the design and implementation of public health and therapeutic interventions. However, application of many of these advanced phylogenetic methods are currently limited to specialized phylogeneticists and statisticians, mainly because of their mathematical basis and their dependence on the use of a large number of computer programs. This review attempts to bridge this gap by presenting conceptual, technical, and practical aspects of applying phylogenetic methods in studies of influenza, HIV, and SCoV. It aims to provide, with minimal mathematics and statistics, a practical overview of how phylogenetic methods can be incorporated into virological studies by clinical and laboratory specialists.

Short communication: Molecular epidemiology of HIV type 1 in the Republic of Dagestan, Russian Federation: virtually uniform circulation of subtype A, former Soviet Union variant, with predominance of the V77I(PR) subvariant

We examine the distribution of viral genetic forms and the presence of antiretroviral drug resistance mutations in HIV-1 infections in the Republic of Dagestan, in the North Caucasus area of Russia, where a recent large increase in HIV-1 infections has been documented. Samples were collected from 41 HIV-1-infected individuals from Dagestan, most of them from the cities of Derbent (n = 21) and Mahachkala (n = 18). Thirty six were injecting drug users and five were infected by heterosexual contact. None was on antiretroviral drug treatment. HIV-1 protease and a segment of reverse transcriptase were amplified by RT-PCR from plasma RNA and sequenced, and phylogenetic trees were constructed via maximum likelihood. Forty (97.6%) of 41 samples were of subtype A, former Soviet Union variant (A(FSU)), of which 27 (67.5%) clustered with the subvariant containing the V77I substitution in protease (V77I(PR)). Within this cluster, 13 viruses formed a local subcluster, 10 of which were from Derbent. Four viruses clustered with the A(SP2) subcluster, recently identified in St. Petersburg, two with a virus from Georgia and one with a virus from Azerbaijan. No mutations associated with antiretroviral drug resistance were detected. The results, therefore, show the relationship of the HIV-1 epidemic in Dagestan with that of other areas of Russia and of neighboring countries, and reveal the spread of the A(FSU) V77I(PR) variant in the North Caucasus area.

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.

Characterization of an emerging heterosexual HIV epidemic in Russia

BACKGROUND

The Russian Federation is currently experiencing one of the fastest growing HIV epidemics worldwide. The objective was to identify sexual risk factors for recent heterosexually-acquired HIV infections.

METHODS

A case-control study of recent HIV infection was conducted in the regions of Altaiskiy Krai, Krasnoyarskiy Krai, Saratov Oblast, and Tverskaya Oblast. Data from 166 participants who did not report recent injection drug use were analyzed (19 male cases, 22 male controls, 67 female cases, 58 female controls). Independent risk factors for HIV infection are reported as adjusted odds ratios (AOR) with 95% confidence intervals (CI).

RESULTS

Risk factors were unprotected sex with an HIV-positive/status unknown regular partner (among women only: AOR 5.4, 95% CI 2.1-13); a regular sexual partner who was an injection drug user (AOR 3.6, 95% CI 1.5-8.5); 5 or more sexual partners (among men only: AOR 2.7, 95% CI 0.66-11); unprotected sex with a partner who had a diagnosed sexually transmitted infection (STI) or signs/symptoms of an STI (AOR 6.4, 95% CI 1.1-38); and undiagnosed signs/symptoms of an STI (AOR 3.4, 95% CI 1.5-7.6).

CONCLUSIONS

These data provide evidence of bridging between the injecting and noninjecting populations. Concomitant STI seem to have a major role in fueling the Russian HIV epidemic.

New insights into the origin of the HIV type 1 subtype A epidemic in former Soviet Union's countries derived from sequence analyses of preepidemically transmitted viruses

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.

HIV epidemiology in the Northwestern Federal District of Russia: dominance of HIV type 1 subtype A

A rapidly advancing epidemic of HIV-1 infection has been documented among injecting drug users (IDUs) in Russia. The Northwestern Federal District was the first of the seven Russian Federal Districts involved in a drug-related HIV epidemic through an outbreak in Kaliningrad in 1996. The Northwestern Federal District has a high HIV prevalence rate having reached 252 per 100,000 by the end of 2003, exceeding the Russian average (180) by 1.4 times. The epidemic peaked in 2001. Since then the annual number of new cases has decreased, probably reflecting saturation among at least some IDU populations. However, at the same time, the heterosexual spread of HIV has become more prominent. To study the genetic epidemiology of HIV-1, samples were collected from 150 individuals covering a wide geographical area and different transmission groups in the Northwestern Federal District. Phylogenetic analysis revealed that an Eastern European subtype A HIV-1 strain similar to those reported earlier among IDUs in other regions of Russia accounted for 80% of HIV-1 infections and was the predominant subtype in six out of seven administrative territories studied both among IDUs and heterosexually infected persons. As an exception to the dominant role of the Eastern European subtype A strain, the CRF03-AB strain was found to be dominant in the city of Cherepovets located in the north central European Russian territory of Vologda Oblast. This is the first report of the CRF03-AB strain causing an outbreak outside the Kaliningrad region.

Full-length genomic sequencing and analysis of four HIV type 1 subtype B isolates circulating in the territory of Russia

We describe four full-length genomic sequences of HIV-1 subtype B isolates from Russia. These full-length HIV-1 genomes were amplified by nested polymerase chain reaction and sequenced. The sequences obtained were subjected to neighbor-joining phylogenetic analysis using a Kimura two-parameter model and to detailed sequence analysis. Comparison of the sequences obtained with 68 near full-length HIV-1 subtype B sequences from different geographic regions of the world revealed that isolates from Russia did not cluster significantly with other subtype B genomes. Sequences AY819715 and AY751407 significantly formed one cluster, which indicates their close similarity. The HIV-1 genomes obtained from Russia did not form a distinct homogeneous group inside subtype B. Their genetic diversity probably reflects the result of multiple introduction events of different subtype B strains to Russia. Sequences AY819715 and AY751406 possess some features of viruses from long-term survivors, such as specific extensions of the Env V2 region.

HIV diversity, molecular epidemiology, and the role of recombination

The magnitude of the HIV pandemic and its extensive genetic variation may earn it a unique place among infectious agents. A high mutation rate and a rampant recombination are driving HIV's evolution. Nine subtypes and a variety of recombinant forms of HIV now exist. The source of recombinant forms is the multiple infection of target cells, which becomes highly significant when individuals become infected with two or more divergent strains. In the current paper, we re-examine the role of dual infection and recombination in the generation of HIV-1 diversity, both in individuals and on a global scale. The current molecular epidemiology of HIV-1 is reviewed, emphasizing the latest reports from regional epidemics.

Analysis of drug resistance-associated mutations in treatment-naïve individuals infected with different genetic forms of HIV-1 circulating in countries of the former Soviet Union

There are few data on drug resistance-associated mutations in the former Soviet Union since, studies have usually been focused on the env or gag genes for subtype information. This study examines the prevalence and patterns of resistance-associated mutations to reverse transcriptase and protease inhibitors (RTI, PRI) in 278 HIV-1-infected treatment-naïve subjects from countries of Eastern Europe, and defines characteristic polymorphisms of RT and PR sequences in HIV-1 subtype A viruses. Blood samples were collected between 1997 and 2004. Plasma RNA was used for PR-RT amplification by reverse transcription coupled with nested PCR and sequencing. Phylogenetic analysis was done with neighbor-joining trees and bootscanning. Analysis of drug resistance mutations, with Stanford University HIV Drug Resistance Database's algorithm, resulted in an overall prevalence of 12.9% resistance to RTI and 3.9% to PRI. The most frequent substitutions in the RT region were at positions 62 and 236. V77I substitution in PR was found in 47.8% of samples. Polymorphisms in subtype A sequences were identified. This is the first study reporting the prevalence and patterns of both PRI and RTI resistance-associated mutations in naïve HIV-1 infected patients from the former Soviet Union. These data underline the importance of genotypic resistance testing of chronically HIV-1-infected patients before initiating treatment, in order to select the most suitable drug regimen.

CDC international HIV prevention research activities among injection drug users in Thailand and Russia

The Centers for Disease Control and Prevention (CDC) has participated in collaborative HIV prevention research activities in injection drug users (IDUs) with the Bangkok Metropolitan Administration (BMA) in Bangkok, Thailand, from 1995 to the present and with the Orel AIDS Center in Orel Oblast, Russia, from 2001 to 2003. Studies in Bangkok have included an HIV prevention trial preparatory cohort from 1995 to 1998, a seroconverter cohort from 1998 to the present, a phase III trial of the AIDSVAX B/E gp120 HIV vaccine from 1999 to 2003, and a phase II/III HIV prophylaxis trial with tenofovir scheduled to begin in 2005. Activities in Orel included a review of HIV surveillance data in 2001, focus group discussions and a case-control study with HIV-infected and -uninfected IDUs in 2001, a cross-sectional study with the female sex partners of male IDUs in 2002, and a community outreach intervention in 2002-2003. In Bangkok, 1,209 IDUs were enrolled in the preparatory cohort which revealed an HIV incidence of 5.8% per 100 person-years; 133 HIV-infected IDUs have been followed in the seroconverter cohort with >85% follow-up and HIV and tuberculosis care provided; 2,546 IDUs were enrolled in the HIV vaccine efficacy trial which was successfully completed with a follow-up rate of >95%, although the vaccine was not shown to be effective at reducing HIV incidence; and 1,600 IDUs will be enrolled in the daily tenofovir HIV prophylaxis trial in 2005. In Orel, initial focus group discussions and epidemiologic studies revealed low HIV knowledge and high rates of unsafe injecting and sexual practices among IDUs and their female sex partners; and educational campaigns and the community outreach intervention were developed and implemented. A steady decline in new HIV infections in IDUs was then observed in Orel in 2002-2003. CDC has participated in the conduct of successful collaborative HIV prevention research activities in Thailand and Russia over the past decade. The establishment of long-term relationships with in-country public health and community partners has been instrumental in the success of these efforts.