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Nikoloski Z, King EJ, Mossialos E. HIV in the Russian Federation: mortality, prevalence, risk factors, and current understanding of sexual transmission. AIDS 2023; 37:637-645. [PMID: 36729857 PMCID: PMC9994792 DOI: 10.1097/qad.0000000000003441] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/14/2022] [Accepted: 11/18/2022] [Indexed: 02/03/2023]
Abstract
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.
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Affiliation(s)
- Zlatko Nikoloski
- Department of Health Policy, London School of Economics and Political Science, London, UK
| | - Elizabeth J. King
- University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Elias Mossialos
- Department of Health Policy, London School of Economics and Political Science, London, UK
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Lebedev A, Pasechnik O, Ozhmegova E, Antonova A, Blokh A, Grezina L, Sandyreva T, Dementeva N, Kazennova E, Bobkova M. Prevalence and spatiotemporal dynamics of HIV-1 Circulating Recombinant Form 03_AB (CRF03_AB) in the Former Soviet Union countries. PLoS One 2020; 15:e0241269. [PMID: 33095842 PMCID: PMC7584246 DOI: 10.1371/journal.pone.0241269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/12/2020] [Indexed: 11/19/2022] Open
Abstract
Background HIV-1 circulating recombinant forms (CRFs) infections has been increasing in Former Soviet Union (FSU) countries in the recent decade. One is the CRF03_AB, which circulated in the region since late 1990s and probably became widespread in northwestern FSU countries. However, there is not much information provided about the dissemination of this recombinant. Here, we examine the prevalence, evolutionary dynamics and dispersion pattern of HIV-1 CRF03_AB recombinant. Methods We analyzed 32 independent studies and 151 HIV-1 CRF03_AB pol sequences isolated from different FSU countries over a period of 22 years. Pooled prevalence was estimated using a random effects model. Bayesian coalescent-based method was used to estimate the evolutionary, phylogeographic and demographic parameters. Results Our meta-analysis showed that the pooled prevalence of CRF03_AB infection in northwestern FSU region was 5.9% [95%CI: 4.1–7.8]. Lithuania (11.6%), Russia (5.9%) and Belarus (2.9%) were the most affected by CRF03_AB. We found that early region wide spread of HIV-1 CRF03_AB originated from one viral clade that arose in the city of Kaliningrad in 1992 [95%HPD: 1990–1995]. Fourteen migration route of this variant were found. The city of Kaliningrad is involved in most of these, confirming its leading role in CRF03_AB spread within FSU. Demographic reconstruction point to this is that CRF03_AB clade seems to have experienced an exponential growth until the mid-2000s and a decrease in recent years. Conclusion These data provide new insights into the molecular epidemiology of CRF03_AB as well as contributing to the fundamental understanding of HIV epidemic in FSU.
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Affiliation(s)
- Aleksey Lebedev
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
- * E-mail:
| | - Oksana Pasechnik
- Departments of Epidemiology, Omsk State Medical University, Omsk, Russia
| | - Ekaterina Ozhmegova
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
| | - Anastasiia Antonova
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
| | - Aleksey Blokh
- Departments of Epidemiology, Omsk State Medical University, Omsk, Russia
| | - Liliya Grezina
- Clinical Diagnostic Laboratory, Yamalo-Nenets Autonomous District Center for Prevention and Control of AIDS and Infectious Diseases, Noyabr'sk, Russia
| | - Tatiana Sandyreva
- Clinical Diagnostic Laboratory, Sverdlovsk Regional Center for Prevention and Control of AIDS and Infectious Diseases, Ekaterinburg, Russia
| | - Natalia Dementeva
- Clinical Diagnostic Laboratory, Saint-Petersburg Center for Prevention and Control of AIDS and Infectious Disease, Saint-Petersburg, Russia
| | - Elena Kazennova
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
| | - Marina Bobkova
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
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3
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Neshumaev D, Lebedev A, Malysheva M, Boyko A, Skudarnov S, Ozhmegova E, Antonova A, Kazennova E, Bobkova M. Molecular Surveillance of HIV-1 Infection in Krasnoyarsk Region, Russia: Epidemiology, Phylodynamics and Phylogeography. Curr HIV Res 2020; 17:114-125. [PMID: 31210113 DOI: 10.2174/1570162x17666190618155816] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/27/2019] [Accepted: 06/11/2019] [Indexed: 11/22/2022]
Abstract
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.
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Affiliation(s)
- Dmitry Neshumaev
- Krasnoyarsk Regional AIDS Centre, Krasnoyarsk, Russian Federation
| | - Aleksey Lebedev
- Gamaleya National Research Center of Epidemiology and Microbiology, Moscow, Russian Federation
| | - Marina Malysheva
- Krasnoyarsk Regional AIDS Centre, Krasnoyarsk, Russian Federation
| | - Anatoly Boyko
- Krasnoyarsk Regional AIDS Centre, Krasnoyarsk, Russian Federation
| | - Sergey Skudarnov
- Krasnoyarsk Regional AIDS Centre, Krasnoyarsk, Russian Federation
| | - Ekaterina Ozhmegova
- Gamaleya National Research Center of Epidemiology and Microbiology, Moscow, Russian Federation
| | - Anastasia Antonova
- Gamaleya National Research Center of Epidemiology and Microbiology, Moscow, Russian Federation
| | - Elena Kazennova
- Gamaleya National Research Center of Epidemiology and Microbiology, Moscow, Russian Federation
| | - Marina Bobkova
- Gamaleya National Research Center of Epidemiology and Microbiology, Moscow, Russian Federation
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4
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King EJ, Niccolai LM, Eritsyan KU, Heimer R, Levina OS. HIV testing among people who inject drugs in Ivanovo and Novosibirsk, Russia. Cent Eur J Public Health 2019; 27:50-53. [PMID: 30927397 DOI: 10.21101/cejph.a4831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Indexed: 11/15/2022]
Abstract
OBJECTIVE HIV testing among people who inject drugs (PWID) in Russia has been documented to be low; however, few studies have been conducted outside of the major metropolitan cities. The aim of this study was to determine how many PWID were aware of their HIV serostatus and what motivators were associated with getting tested for HIV. METHODS Our analysis describes HIV testing behaviours among 593 PWID in Ivanovo and Novosibirsk, Russia. Participants completed a questionnaire and consented to HIV testing. We used logistic regression modelling to determine demographic and behavioural correlates of HIV testing. RESULTS Self-reported history of HIV testing was 52% in Ivanovo and 54% in Novosibirsk. Prior knowledge of serostatus was very low among PWID who tested positive (3 of 102 in Ivanovo and 0 of 11 in Novosibirsk). The most common reason for testing was doctor referral, and the most common locations were government HIV/AIDS centres and prisons. HIV testing was rarely client initiated or led by a personal motivation for being tested. CONCLUSIONS HIV testing in Ivanovo and Novosibirsk is suboptimal, resulting in poor knowledge of HIV serostatus. More programmes to promote HIV testing among PWID are urgently needed in both cities.
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Affiliation(s)
- Elizabeth J King
- Department of Health Behavior and Health Education, University of Michigan School of Public Health, Ann Arbor, Michigan, USA.,Yale School of Public Health and Center for Interdisciplinary Research on AIDS, New Haven, Connecticut, USA
| | - Linda M Niccolai
- Yale School of Public Health and Center for Interdisciplinary Research on AIDS, New Haven, Connecticut, USA
| | | | - Robert Heimer
- Yale School of Public Health and Center for Interdisciplinary Research on AIDS, New Haven, Connecticut, USA
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Kazennova EV, Laga VY, Gromov KB, Sankov MN, Popova ES, Lgumnova EG, Oparina EN, Sorokina TA, Bobkova MR. [Molecular epidemiological analysis of hiv infection in northern seaports of Russia]. Vopr Virusol 2018; 62:154-161. [PMID: 29733164 DOI: 10.18821/0507-4088-2017-62-4-154-161] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 12/13/2016] [Indexed: 11/17/2022]
Abstract
The results of the molecular-epidemiological analysis of HIV-1 variants circulating in Arkhangelsk and Murmansk - northern seaports of Russia - were presented. In these seaports the HIV-1 variants belonging to subtype A1 were predominant (93% in Murmansk, 83% in Arkhangelsk). In addition to these variants, viruses of other subtypes such as B, C, D and recombinant forms CRF02_AG and CRF03_AB were identifed. The heterogeneity of circulating HIV-1 variants was higher in Arkhangelsk than in Murmansk. According to the results of phylogenetic analysis, subtype A1 sequences formed the common branch with nucleotide sequences of IDU-A strains found in other regions of Russia. HIV-1 variants of subtype B sub-clustered with sequences of East European B-variants. The recombinant strains CRF02_AG formed the common branch with HIV-1 sequences from Central Asia republics of the former USSR. Among 124 therapy-naive patients from Arkhangelsk and Murmansk (n = 124) the transmitted resistance was less than 5%.
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Affiliation(s)
- E V Kazennova
- D.I. Ivanovsky Institute of Virology «Federal Research Center of Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya», Moscow, 123098, Russian Federation
| | - V Yu Laga
- D.I. Ivanovsky Institute of Virology «Federal Research Center of Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya», Moscow, 123098, Russian Federation
| | - K B Gromov
- D.I. Ivanovsky Institute of Virology «Federal Research Center of Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya», Moscow, 123098, Russian Federation
| | - M N Sankov
- D.I. Ivanovsky Institute of Virology «Federal Research Center of Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya», Moscow, 123098, Russian Federation
| | - E S Popova
- Arkhangelsk Clinical Center for Prevention and Control of AIDS and Infectious Diseases, Arkhangelsk, 163000, Russian Federation
| | - E G Lgumnova
- Arkhangelsk Clinical Center for Prevention and Control of AIDS and Infectious Diseases, Arkhangelsk, 163000, Russian Federation
| | - E N Oparina
- Arkhangelsk Clinical Center for Prevention and Control of AIDS and Infectious Diseases, Arkhangelsk, 163000, Russian Federation
| | - T A Sorokina
- Arkhangelsk Clinical Center for Prevention and Control of AIDS and Infectious Diseases, Arkhangelsk, 163000, Russian Federation
| | - M R Bobkova
- D.I. Ivanovsky Institute of Virology «Federal Research Center of Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya», Moscow, 123098, Russian Federation
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Karamov E, Epremyan K, Siniavin A, Zhernov Y, Cuevas MT, Delgado E, Sánchez-Martínez M, Carrera C, Kornilaeva G, Turgiev A, Bacqué J, Pérez-Álvarez L, Thomson MM. HIV-1 Genetic Diversity in Recently Diagnosed Infections in Moscow: Predominance of A FSU, Frequent Branching in Clusters, and Circulation of the Iberian Subtype G Variant. AIDS Res Hum Retroviruses 2018; 34:629-634. [PMID: 29587492 DOI: 10.1089/aid.2018.0055] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 protease-reverse transcriptase sequences from 62 HIV-1-infected individuals recently diagnosed in Moscow were analyzed. Subtype A former Soviet Union (FSU) (AFSU) 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%). AFSU 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 AFSU 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.
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Affiliation(s)
- Eduard Karamov
- Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | - Khoren Epremyan
- Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | - Andrei Siniavin
- Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | - Yury Zhernov
- Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | - María Teresa Cuevas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Mónica Sánchez-Martínez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Cristina Carrera
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Galina Kornilaeva
- Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | - Ali Turgiev
- Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
- Immunomica LLC, Moscow, Russia
| | - Joan Bacqué
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Lucía Pérez-Álvarez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Michael M. Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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7
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Kazennova E, Laga V, Gromov K, Lebedeva N, Zhukova E, Pronin A, Grezina L, Dement'eva N, Shemshura A, Bobkova M. Genetic Variants of HIV Type 1 in Men Who Have Sex with Men in Russia. AIDS Res Hum Retroviruses 2017; 33:1061-1064. [PMID: 28443684 DOI: 10.1089/aid.2017.0078] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The men who have sex with men (MSM) population infected with HIV is poorly studied in Russia because of stigma and discrimination. In the first years of the HIV epidemic, the only HIV genetic variant that circulated among MSM was subtype B, usually acquired abroad. Meanwhile, the massive epidemic of HIV in Russia was caused by a highly homogenic subtype A variant, AFSU (A6), and spread mainly among drug users. In this study, 155 HIV pol sequences from MSM collected during the 2006-2016 period were analyzed. Phylogenetic analysis found that 19.4% of the viral sequences from MSM clustered with HIV genetic variants A6 and BFSU, which were previously identified only among drug users and their heterosexual partners. These data show that the MSM population in Russia is gradually becoming less isolated from the general epidemic process. Urgent measures should be taken to prevent the spread of HIV among the MSM population.
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Affiliation(s)
- Elena Kazennova
- Ivanovsky Institute of Virology, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | - Vita Laga
- Ivanovsky Institute of Virology, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | - Konstantin Gromov
- Ivanovsky Institute of Virology, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | | | | | | | | | | | | | - Marina Bobkova
- Ivanovsky Institute of Virology, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
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Nikolopoulos GK, Kostaki EG, Paraskevis D. Overview of HIV molecular epidemiology among people who inject drugs in Europe and Asia. INFECTION GENETICS AND EVOLUTION 2016; 46:256-268. [PMID: 27287560 DOI: 10.1016/j.meegid.2016.06.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/01/2016] [Accepted: 06/05/2016] [Indexed: 01/14/2023]
Abstract
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 AFSU (also known as IDU-A), BFSU (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.
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Affiliation(s)
- Georgios K Nikolopoulos
- Hellenic Centre for Diseases Control and Prevention, Amarousio, Greece; Hellenic Scientific Society for the Study of AIDS and Sexually Transmitted Diseases, Transmission Reduction Intervention Project-Athens site, Athens, Greece.
| | - Evangelia-Georgia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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9
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Lai A, Bozzi G, Franzetti M, Binda F, Simonetti FR, De Luca A, Micheli V, Meraviglia P, Bagnarelli P, Di Biagio A, Monno L, Saladini F, Zazzi M, Zehender G, Ciccozzi M, Balotta C. HIV-1 A1 Subtype Epidemic in Italy Originated from Africa and Eastern Europe and Shows a High Frequency of Transmission Chains Involving Intravenous Drug Users. PLoS One 2016; 11:e0146097. [PMID: 26752062 PMCID: PMC4709132 DOI: 10.1371/journal.pone.0146097] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 12/14/2015] [Indexed: 12/04/2022] Open
Abstract
Background Subtype A accounts for only 12% of HIV-1 infections worldwide but predominates in Russia and Former Soviet Union countries of Eastern Europe. After an early propagation via heterosexual contacts, this variant spread explosively among intravenous drug users. A distinct A1 variant predominates in Greece and Albania, which penetrated directly from Africa. Clade A1 accounts for 12.5% of non-B subtypes in Italy, being the most frequent after F1 subtype. Aim Aim of this study was to investigate the circulation of A1 subtype in Italy and trace its origin and diffusion through phylogenetic and phylodynamic approaches. Results The phylogenetic analysis of 113 A1 pol sequences included in the Italian ARCA database, indicated that 71 patients (62.8%) clustered within 5 clades. A higher probability to be detected in clusters was found for patients from Eastern Europe and Italy (88.9% and 60.4%, respectively) compared to those from Africa (20%) (p < .001). Higher proportions of clustering sequences were found in intravenous drug users with respect to heterosexuals (85.7% vs. 59.3%, p = .056) and in women with respect to men (81.4% vs. 53.2%, p < .006). Subtype A1 dated phylogeny indicated an East African origin around 1961. Phylogeographical reconstruction highlighted 3 significant groups. One involved East European and some Italian variants, the second encompassed some Italian and African strains, the latter included the majority of viruses carried by African and Italian subjects and all viral sequences from Albania and Greece. Conclusions Subtype A1 originated in Central Africa and spread among East European countries in 1982. It entered Italy through three introduction events: directly from East Africa, from Albania and Greece, and from the area encompassing Moldavia and Ukraine. As in previously documented A1 epidemics of East European countries, HIV-1 A1 subtype spread in Italy in part through intravenous drug users. However, Eastern European women contributed to the penetration of such variant, probably through sex work.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
- * E-mail:
| | - Giorgio Bozzi
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
| | - Marco Franzetti
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
| | - Francesca Binda
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
| | - Francesco R. Simonetti
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
| | - Andrea De Luca
- Division of Infectious Diseases, Siena University Hospital, Siena, Italy
| | - Valeria Micheli
- Laboratory of Microbiology, ‘L. Sacco’ Hospital, Milan, Italy
| | - Paola Meraviglia
- 2nd Division of Infectious Diseases, ‘L. Sacco’ Hospital, Milan, Italy
| | - Patrizia Bagnarelli
- Department of Biomedical Science, Section of Microbiology, Laboratory of Virology, University Politecnica delle Marche, Ancona, Italy
| | | | - Laura Monno
- Division of Infectious Disease, University of Bari, Bari, Italy
| | | | - Maurizio Zazzi
- Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
| | - Massimo Ciccozzi
- Epidemiology Unit, Department of Infectious, Parasite and Immune-Mediated Diseases, Italian Institute of Health, Rome, Italy
| | - Claudia Balotta
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
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10
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Nikolaitchik O, Keele B, Gorelick R, Alvord WG, Mazurov D, Pathak VK, Hu WS. High recombination potential of subtype A HIV-1. Virology 2015; 484:334-340. [PMID: 26164392 PMCID: PMC6258064 DOI: 10.1016/j.virol.2015.06.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Revised: 05/28/2015] [Accepted: 06/09/2015] [Indexed: 01/18/2023]
Abstract
Recombination can assort polymorphic alleles to increase diversity in the HIV-1 population. To better understand the recombination potential of subtype A HIV-1, we generated viruses containing sequences from two variants circulating in Russia and analyzed the polymerase gene (pol) of the recombinants after one round of HIV-1 replication using single-genome sequencing. We observed that recombination occurred throughout pol and could easily assort alleles containing mutations that conferred resistance to currently approved antivirals. We measured the recombination rate in various regions of pol including a G-rich region that has been previously proposed to be a recombination hot spot. Our study does not support a recombination hot spot in this G-rich region. Importantly, of the 58 proviral sequences containing crossover event(s) in pol, we found that each sequence was a unique genotype indicating that recombination is a powerful genetic mechanism in assorting the genomes of subtype A HIV-1 variants.
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Affiliation(s)
- Olga Nikolaitchik
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Brandon Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Robert Gorelick
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - W Gregory Alvord
- Data Management Services, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Dmitriy Mazurov
- Institute of Immunology, Kashirskoe shosse 24-2, Moscow 115478, Russia
| | - Vinay K Pathak
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Wei-Shau Hu
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA.
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11
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Heimer R, Levina OS, Osipenko V, Ruiz MS, Sergeyev B, Sirotkin AV, Vyshemirskaya I. Impact of incarceration experiences on reported HIV status and associated risk behaviours and disease comorbidities. Eur J Public Health 2015; 25:1089-94. [PMID: 26381650 DOI: 10.1093/eurpub/ckv157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The Russian human immunodeficiency virus (HIV) epidemic among people who inject drugs (PWID) originated in Kaliningrad, but research into risk behaviours among PWID has been lacking. The potential for heterosexual spread has not been analysed. METHODS A sample of PWID was accrued using two methods. A questionnaire was administered to assess HIV-related risk behaviours for parenteral and sexual transmission, sociodemographic factors, HIV knowledge and attitudes about sexual risks. Data were analysed focusing on the role of imprisonment, factors associated with awareness of being HIV infected and condom use. RESULTS More than a quarter of the sample reported having been diagnosed with HIV infection, with higher prevalence among women and those with a history of incarceration. More than half reported having been diagnosed with hepatitis C virus infection. Those reporting being HIV positive were less likely to distribute used syringes to other PWID and more likely to have used a condom the last time they had sex. A history of incarceration was associated with higher rates of receptive syringe sharing among those not having ever received an HIV-positive diagnosis and a lower likelihood of believing that condoms are needed when having sex with a casual partner. CONCLUSION Although extensive HIV testing has alerted many PWID to their HIV-positive status, which is associated with less distributive syringe sharing and higher likelihood of condom use, substantial risk for parenteral and especially sexual HIV transmission remains. More active prevention programs will be required to control the heterosexual spread of HIV.
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Affiliation(s)
- Robert Heimer
- 1 Department of Epidemiology of Microbial Diseases and the Center for Interdisciplinary Research on AIDS, Yale University School of Public Health, New Haven, CT 06520, USA
| | | | | | - Monica S Ruiz
- 4 Department of Prevention and Community Health, Milkin Institute School of Public Health, The George Washington University, Washington, DC, USA
| | - Boris Sergeyev
- 5 Office of the Nordic Council of Ministers, Kaliningrad, RF
| | - Aleksander V Sirotkin
- 6 International Laboratory for Applied Network Research, National Research University Higher School of Economics, St. Petersburg, RF
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12
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Gashnikova NM, Bogachev VV, Baryshev PB, Totmenin AV, Gashnikova MP, Kazachinskaya AG, Ismailova TN, Stepanova SA, Chernov AS, Mikheev VN. A rapid expansion of HIV-1 CRF63_02A1 among newly diagnosed HIV-infected individuals in the Tomsk Region, Russia. AIDS Res Hum Retroviruses 2015; 31:456-60. [PMID: 25738513 DOI: 10.1089/aid.2014.0375] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
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.
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Affiliation(s)
- Natalya M Gashnikova
- 1 Department of Retroviruses, State Research Center of Virology and Biotechnology Vector , Koltsovo, Russia
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13
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Shcherbakova NS, Shalamova LA, Delgado E, Fernández-García A, Vega Y, Karpenko LI, Ilyichev AA, Sokolov YV, Shcherbakov DN, Pérez-Álvarez L, Thomson MM. Short communication: Molecular epidemiology, phylogeny, and phylodynamics of CRF63_02A1, a recently originated HIV-1 circulating recombinant form spreading in Siberia. AIDS Res Hum Retroviruses 2014; 30:912-9. [PMID: 25050828 DOI: 10.1089/aid.2014.0075] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
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.
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Affiliation(s)
- Nadezhda S. Shcherbakova
- Department of Bioengineering, State Research Center of Virology and Biotechnology “Vector,” Koltsovo, Novosibirsk, Russia
| | - Lyudmila A. Shalamova
- Department of Zoonotic Infections and Influenza, State Research Center of Virology and Biotechnology “Vector,” Koltsovo, Novosibirsk, Russia
| | - Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Aurora Fernández-García
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Yolanda Vega
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Larissa I. Karpenko
- Laboratory of Recombinant Vaccine, State Research Center of Virology and Biotechnology “Vector,” Koltsovo, Novosibirsk, Russia
| | - Alexander A. Ilyichev
- Department of Bioengineering, State Research Center of Virology and Biotechnology “Vector,” Koltsovo, Novosibirsk, Russia
| | - Yuri V. Sokolov
- Center for Prevention and Control of AIDS and Infectious Diseases, Koltsovo, Novosibirsk, Russia
| | | | - Lucía Pérez-Álvarez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Michael M. Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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14
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Kazennova E, Laga V, Lapovok I, Glushchenko N, Neshumaev D, Vasilyev A, Bobkova M. HIV-1 genetic variants in the Russian Far East. AIDS Res Hum Retroviruses 2014; 30:742-52. [PMID: 24773167 DOI: 10.1089/aid.2013.0194] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A molecular analysis of HIV-1 subtypes and recombinants circulating in cities in the Russian Far East was performed. The study included samples from 201 outpatients from Vladivostok, Khabarovsk, and Blagoveshchensk. In most parts of Russia, patients are infected with HIV-1 subtype A, known as the IDU-A variant. Subtype B, including the IDU-B variant, is rare in Russia but widespread in the Ukraine, and the CRF02_AG is prevalent in Central Asian countries and Siberia, Russia. One of the challenges of this study in the Far East was to determine whether the molecular landscape of HIV infection in this region is influenced by the bordering countries, including China and Japan, where a distinct set of HIV subtypes is circulating, such as B', C, and CRF01_AE. The distribution of HIV-1 genetic variants in the cities studied was as follows: subtype A (IDU-A), 55.7%; subtype B, 25.3% (IDU-B variant-24.3%); subtype C, 10.0%; CRF02_AG, 1.5%; and CRF63_02A1, 7.5%. A phylogenetic analysis confirmed the relationship of subtype A viruses with the IDU-A variant predominating in Ukraine, Russia and other former Soviet Union (FSU) countries, of subtype B viruses with IDU-B in the Ukraine and of CRF02_AG variants with variants in Uzbekistan, Russia, and other former USSR countries. Subtype C sequences were not uniform, and most clustered between each other and HIV-1 sequences originating from Africa; there was only one sample possibly related to Chinese variants. Thus, despite close cultural and commercial relationships among Russia, China, and Japan, the distribution of HIV-1 subtypes in the Russian Far East is still primarily influenced by contacts with the countries of the former USSR.
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Affiliation(s)
| | - Vita Laga
- Ivanovsky Institute of Virology, Moscow, Russia
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15
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Cepeda JA, Niccolai LM, Eritsyan K, Heimer R, Levina O. Moderate/heavy alcohol use and HCV infection among injection drug users in two Russian cities. Drug Alcohol Depend 2013; 132:571-9. [PMID: 23642314 PMCID: PMC3770791 DOI: 10.1016/j.drugalcdep.2013.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 03/26/2013] [Accepted: 04/03/2013] [Indexed: 01/12/2023]
Abstract
BACKGROUND In Russia, injection drug use and transmission of blood-borne pathogens such as human immunodeficiency virus (HIV) and hepatitis C virus (HCV) are inextricably linked, however the burden of alcohol use remains unexplored among injection drug users (IDUs). METHODS Individuals who were 18 years of age and older and had injected drugs in the previous 30 days were recruited in the cities of Novosibirsk and Ivanovo by respondent driven sampling. Consenting individuals were administered a quantitative survey instrument and provided blood samples for serological testing. RESULTS In Novosibirsk and Ivanovo, 29% and 35% of respondents were categorized as moderate/heavy drinkers, respectively. Individuals reported problems related to alcohol use that affected their physical health (23%), family (55%), and induced financial hardships (43%). In the multivariate analysis, we found that methamphetamine injection in the past 12 months was a strong and significant correlate of moderate/heavy drinking in Novosibirsk (aOR=5.63 95% CI: [1.01-31.47]) and Ivanovo (aOR=3.81 95% CI: [2.20-6.62]). There was poor agreement between self-reported HCV status and HCV test results (κ=-0.05 and 0.26 in Novosibirsk and Ivanovo, respectively). IDUs who correctly knew their HCV seropositive status in Novosibirsk and IDUs who correctly knew their HCV seronegative status in Ivanovo were significantly more likely to be moderate/heavy drinkers. CONCLUSION Alcohol use is problematic among IDUs who are at high risk for HCV. Future interventions should target IDUs who are moderate/heavy drinkers in order to prevent liver complications resulting from HCV infection.
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Affiliation(s)
- Javier A Cepeda
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases and Center for Interdisciplinary Research on AIDS, New Haven, CT, USA.
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16
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Siljic M, Salemovic D, Jevtovic D, Pesic-Pavlovic I, Zerjav S, Nikolic V, Ranin J, Stanojevic M. Molecular typing of the local HIV-1 epidemic in Serbia. INFECTION GENETICS AND EVOLUTION 2013; 19:378-85. [PMID: 23797143 DOI: 10.1016/j.meegid.2013.06.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 06/05/2013] [Accepted: 06/12/2013] [Indexed: 01/08/2023]
Abstract
Worldwide HIV-1 pandemic is becoming increasingly complex, with growing heterogeneity of subtypes and recombinant viruses. Previous studies have documented HIV-1 subtype B as the predominant one in Serbia, with limited presence and genetic diversity of non B subtypes. In recent years, MSM transmission has become the most frequently reported risk for HIV infection among newly diagnosed patients in Serbia, but very little is known of the network structure and dynamics of viral transmission in this and other risk groups. To gain insight about the HIV-1 subtypes distribution pattern as well as characteristics of HIV-1 transmission clusters in Serbia, we analyzed the genetic diversity of the pol gene segment in 221 HIV-1-infected patients sampled during 2002-2011. Subtype B was found to still be the most prevalent one in Serbia, accounting for over 90% of samples, while greater diversity of other subtypes was found than previously reported, including subtypes G, C, A, F, CRF01 and CRF02. In total, 41.3% of analyzed subtype B sequences were found associated in transmission clusters/network, that are highly related with MSM transmission route.
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Affiliation(s)
- Marina Siljic
- Institute of Microbiology and Immunology, University of Belgrade Faculty of Medicine, Belgrade, Serbia
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17
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Vinogradova A, Gafurova E, Muñoz-Nieto M, Rakhmanova A, Osmanov S, Thomson MM. 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. AIDS Res Hum Retroviruses 2010; 26:395-400. [PMID: 20377421 DOI: 10.1089/aid.2009.0205] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
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.
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Affiliation(s)
| | | | - Mercedes Muñoz-Nieto
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Aza Rakhmanova
- Department of Infectious Diseases, Botkin's Infectious Diseases Hospital, St. Petersburg, Russia
| | | | - Michael M. Thomson
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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18
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Fernández-García A, Cuevas MT, Vinogradova A, Rakhmanova A, Pérez-Álvarez L, de Castro RO, Osmanov S, Thomson MM. Near full-length genome characterization of a newly identified HIV type 1 subtype F variant circulating in St. Petersburg, Russia. AIDS Res Hum Retroviruses 2009; 25:1187-91. [PMID: 19943791 DOI: 10.1089/aid.2009.0140] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
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.
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Affiliation(s)
| | - María Teresa Cuevas
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | | | - Aza Rakhmanova
- Department of Infectious Diseases, Botkin's Infectious Diseases Hospital, St. Petersburg, Russia
| | - Lucía Pérez-Álvarez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | | | | | - Michael M. Thomson
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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Molecular epidemiology of HIV-1 in St Petersburg, Russia: predominance of subtype A, former Soviet Union variant, and identification of intrasubtype subclusters. J Acquir Immune Defic Syndr 2009; 51:332-9. [PMID: 19363451 DOI: 10.1097/qai.0b013e31819c1757] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
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.
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20
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Giuliani M, Montieri S, Palamara G, Latini A, Alteri C, Perno C, Santoro M, Rezza G, Ciccozzi M. Non-B HIV type 1 subtypes among men who have sex with men in Rome, Italy. AIDS Res Hum Retroviruses 2009; 25:157-64. [PMID: 19108689 DOI: 10.1089/aid.2008.0175] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
An increase in the circulation of HIV-1 non-B subtypes has been observed in recent years in Western European countries. Due to the lack of data on the circulation of HIV-1 non-B subtypes among European HIV-1-infected men who have sex with men (MSM), a biomolecular study was conducted in Rome, Italy. HIV-1 partial pol gene sequences from 111 MSM individuals (76 drug naive and 35 drug experienced) were collected during the years 2004-2006. All these sequences were analyzed using the REGA HIV-1 Subtyping Tool, and aligned using CLUSTAL X followed by manual editing using the Bioedit software. A BLAST search for non-B subtype sequences was also performed. Twenty-six (23.4%) MSM were not Italians. Eight individuals (7.2%) were diagnosed as HIV infected before 1991, 20 (18.0%) between 1991 and 1999, and 83 (74.8%) from 2000 to 2006. Fifteen (15/111, 13.5%) individuals were infected with the non-B subtype. The percentage of infection with HIV-1 non-B subtypes was 8.2% (7/85) among Italian MSM and 30.8% (8/26) among the non-Italians (OR = 4.95 95% IC: 1.40-17.87). Individuals infected with the non-B subtype were significantly younger than those infected with the HIV-1 B subtype (28 years vs. 34 years, p = 0.003). The CRFs were more prevalent (8.1%) than pure subtypes (5.4%), which were distributed as follows: subtype C (2.6%), subtype A1 (1.7%), and subtype F1 (0.9%). Major mutations conferring resistance to antiretroviral drugs (ARV) were not found among HIV-1 non-B subtype drug-naive patients but were found in two ARV-experienced individuals. The data show that viral diversity is likely increasing in a population group that had been previously characterized by the circulation of HIV-1 subtype B.
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Affiliation(s)
- M. Giuliani
- Reparto Epidemiologia, Dipartimento Malattie Infettive, Parassitarie e Immunomediate (MIPI), Istituto Superiore di Sanità, Rome, Italy
- S. C. Dermatologia Infettiva, Istituto Dermatovenereologico S. Gallicano (IRCCS), Rome, Italy
| | - S. Montieri
- Reparto Epidemiologia, Dipartimento Malattie Infettive, Parassitarie e Immunomediate (MIPI), Istituto Superiore di Sanità, Rome, Italy
| | - G. Palamara
- S. C. Dermatologia Infettiva, Istituto Dermatovenereologico S. Gallicano (IRCCS), Rome, Italy
| | - A. Latini
- S. C. Dermatologia Infettiva, Istituto Dermatovenereologico S. Gallicano (IRCCS), Rome, Italy
| | - C. Alteri
- Dipartimento di Medicina Sperimentale e Scienze Biochimiche, Università degli Studi di Roma, Tor Vergata, Rome, Italy
| | - C.F. Perno
- Dipartimento di Medicina Sperimentale e Scienze Biochimiche, Università degli Studi di Roma, Tor Vergata, Rome, Italy
| | - M.M. Santoro
- Dipartimento di Medicina Sperimentale e Scienze Biochimiche, Università degli Studi di Roma, Tor Vergata, Rome, Italy
| | - G. Rezza
- Reparto Epidemiologia, Dipartimento Malattie Infettive, Parassitarie e Immunomediate (MIPI), Istituto Superiore di Sanità, Rome, Italy
| | - M. Ciccozzi
- Reparto Epidemiologia, Dipartimento Malattie Infettive, Parassitarie e Immunomediate (MIPI), Istituto Superiore di Sanità, Rome, Italy
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Ding N, Guo D, Zhang C. Reidentification of the recombination map of CRF03_AB: evidence for a new additional mosaic a subtype segment. AIDS Res Hum Retroviruses 2008; 24:1337-9. [PMID: 18844466 DOI: 10.1089/aid.2008.0112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Na Ding
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Dongmei Guo
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Chiyu Zhang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China
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22
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Salemi M, Goodenow MM, Montieri S, de Oliveira T, Santoro MM, Beshkov D, Alexiev I, Elenkov I, Elenkov I, Yakimova T, Varleva T, Rezza G, Ciccozzi M. The HIV type 1 epidemic in Bulgaria involves multiple subtypes and is sustained by continuous viral inflow from West and East European countries. AIDS Res Hum Retroviruses 2008; 24:771-9. [PMID: 18544022 DOI: 10.1089/aid.2007.0181] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Little is known about the HIV-1 epidemic in Balkan countries. To fill the gap, we investigated the viral genetic diversity in Bulgaria, by sequencing and phylogenetic characterization of 86 plasma samples collected between 2002 and 2006 from seropositive individuals diagnosed within 1986-2006. Analysis of pol gene sequences assigned 51% of the samples to HIV-1 subtype B and 27% to subtype A1. HIV-1 subtype C, F, G, H, and a few putative recombinant forms were also found. Phylogenetic and molecular clock analysis showed a continuous exchange of subtype A and B between Bulgaria and Western as well as other Eastern European countries. At least three separate introductions of HIV-1 subtype A and four of HIV-1 subtype B have occurred within the past 25 years in Bulgaria. The central geographic location of Bulgaria, the substantial genetic heterogeneity of the epidemic with multiple subtypes, and the significant viral flow observed to and from the Balkan countries have the potential to modify the current HIV-1 epidemiological structure in Europe and highlight the importance of more extensive and continuous monitoring of the epidemic in the Balkans.
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Affiliation(s)
- Marco Salemi
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida 32610
| | - Maureen M. Goodenow
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida 32610
| | - Stefania Montieri
- Epidemiology Unit, Department of Infectious Parasitic and Immunomediate Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Tulio de Oliveira
- MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of Western Cape, Cape Town, South Africa
| | | | - Danail Beshkov
- National HIV Confirmatory Laboratory—National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivailo Alexiev
- National HIV Confirmatory Laboratory—National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - Ivan Elenkov
- Faculty of Biology, University of Sofia, Sofia, Bulgaria
| | - Tsvetana Yakimova
- Ministry of Health, Program of “Prevention and Control of HIV/AIDS,” Sofia, Bulgaria
| | - Tonka Varleva
- Ministry of Health, Program of “Prevention and Control of HIV/AIDS,” Sofia, Bulgaria
| | - Giovanni Rezza
- Epidemiology Unit, Department of Infectious Parasitic and Immunomediate Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Massimo Ciccozzi
- Epidemiology Unit, Department of Infectious Parasitic and Immunomediate Diseases, Istituto Superiore di Sanità, Rome, Italy
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23
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Thomson MM, de Parga EV, Vinogradova A, Sierra M, Yakovlev A, Rakhmanova A, Delgado E, Casado G, Muñoz M, Carmona R, Vega Y, Pérez-Álvarez L, Contreras G, Medrano L, Osmanov S, Nájera R. 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. AIDS Res Hum Retroviruses 2007; 23:1599-604. [PMID: 18160020 DOI: 10.1089/aid.2007.0166] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
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.
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Affiliation(s)
- Michael M. Thomson
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Elena Vázquez de Parga
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | | | - María Sierra
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Aleksey Yakovlev
- Department of Infectious Diseases, Botkins Infectious Diseases Hospital, St. Petersburg, Russia
| | - Aza Rakhmanova
- Department of Infectious Diseases, Botkins Infectious Diseases Hospital, St. Petersburg, Russia
| | - Elena Delgado
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Gema Casado
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Mercedes Muñoz
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Rocío Carmona
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Yolanda Vega
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Lucía Pérez-Álvarez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Gerardo Contreras
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Leandro Medrano
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | | | - Rafael Nájera
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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Beyrer C, Baral S, Shaboltas A, Dukhovlinova E, Masharsky A, Verevochkin S, Latkin C, Heimer R, Hoffman I, Kozlov A. The feasibility of HIV vaccine efficacy trials among Russian injection drug users. Vaccine 2007; 25:7014-6. [PMID: 17707960 PMCID: PMC3747029 DOI: 10.1016/j.vaccine.2007.07.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2007] [Accepted: 07/16/2007] [Indexed: 11/23/2022]
Abstract
IDU exposure remains a primary driver of the Russian HIV epidemic, and recent incidence data provide little evidence that this epidemic is slowing. While there are multiple important challenges that need to be further explored before starting vaccine trials, most importantly access to evidence-based drug treatment services for trial participants, the current context of high HIV incidence and low genetic diversity of HIV strains, suggests the need for intensified prevention strategies and supports the feasibility of mounting efficacy trials of HIV vaccines among IDUs in the Russian Federation.
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Affiliation(s)
- Chris Beyrer
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD 21205, USA.
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