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Lebedev A, Kuznetsova A, Kim K, Ozhmegova E, Antonova A, Kazennova E, Tumanov A, Mamatkulov A, Kazakova E, Ibadullaeva N, Brigida K, Musabaev E, Mustafaeva D, Rakhimova V, Bobkova M. Identifying HIV-1 Transmission Clusters in Uzbekistan through Analysis of Molecular Surveillance Data. Viruses 2022; 14:v14081675. [PMID: 36016298 PMCID: PMC9413238 DOI: 10.3390/v14081675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 11/16/2022] Open
Abstract
The CRF02_AG and sub-subtype A6 are currently the predominant HIV-1 variants in the Republic of Uzbekistan, but little is known about their time-spatial clustering patterns in high-risk populations. We have applied molecular evolution methods and network analyses to better understand the transmission patterns of these subtypes by analyzing 316 pol sequences obtained during the surveillance study of HIV drug resistance. Network analysis showed that about one third of the HIV infected persons were organized into clusters, including large clusters with more than 35 members. These clusters were composed mostly of injecting drug users and/or heterosexuals, with women having mainly high centrality within networks identified in both subtypes. Phylogenetic analyses of the 'Uzbek' sequences, including those publicly available, show that Russia and Ukraine played a role as the main sources of the current subtype A6 epidemic in the Republic. At the same time, Uzbekistan has been a local center of the CRF02_AG epidemic spread in the former USSR since the early 2000s. Both of these HIV-1 variants continue to spread in Uzbekistan, highlighting the importance of identifying transmission networks and transmission clusters to prevent further HIV spread, and the need for HIV prevention and education campaigns in high-risk groups.
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Affiliation(s)
- Aleksey Lebedev
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (A.K.); (K.K.); (E.O.); (A.A.); (E.K.); (A.T.); (M.B.)
- Correspondence:
| | - Anna Kuznetsova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (A.K.); (K.K.); (E.O.); (A.A.); (E.K.); (A.T.); (M.B.)
| | - Kristina Kim
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (A.K.); (K.K.); (E.O.); (A.A.); (E.K.); (A.T.); (M.B.)
| | - Ekaterina Ozhmegova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (A.K.); (K.K.); (E.O.); (A.A.); (E.K.); (A.T.); (M.B.)
| | - Anastasiia Antonova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (A.K.); (K.K.); (E.O.); (A.A.); (E.K.); (A.T.); (M.B.)
| | - Elena Kazennova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (A.K.); (K.K.); (E.O.); (A.A.); (E.K.); (A.T.); (M.B.)
| | - Aleksandr Tumanov
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (A.K.); (K.K.); (E.O.); (A.A.); (E.K.); (A.T.); (M.B.)
| | - Adkhamjon Mamatkulov
- Research Institute of Virology, Tashkent 100194, Uzbekistan; (A.M.); (E.K.); (N.I.); (K.B.); (E.M.)
| | - Evgeniya Kazakova
- Research Institute of Virology, Tashkent 100194, Uzbekistan; (A.M.); (E.K.); (N.I.); (K.B.); (E.M.)
| | - Nargiz Ibadullaeva
- Research Institute of Virology, Tashkent 100194, Uzbekistan; (A.M.); (E.K.); (N.I.); (K.B.); (E.M.)
| | - Krestina Brigida
- Research Institute of Virology, Tashkent 100194, Uzbekistan; (A.M.); (E.K.); (N.I.); (K.B.); (E.M.)
| | - Erkin Musabaev
- Research Institute of Virology, Tashkent 100194, Uzbekistan; (A.M.); (E.K.); (N.I.); (K.B.); (E.M.)
| | - Dildora Mustafaeva
- Republican AIDS Center, The Ministry of Health, Tashkent 100135, Uzbekistan;
| | - Visola Rakhimova
- Center for Development of Profession Qualification of Medical Workers, Tashkent 100007, Uzbekistan;
| | - Marina Bobkova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (A.K.); (K.K.); (E.O.); (A.A.); (E.K.); (A.T.); (M.B.)
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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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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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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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Díez-Fuertes F, Cabello M, Thomson MM. Bayesian phylogeographic analyses clarify the origin of the HIV-1 subtype A variant circulating in former Soviet Union's countries. INFECTION GENETICS AND EVOLUTION 2015; 33:197-205. [PMID: 25952568 DOI: 10.1016/j.meegid.2015.05.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/24/2015] [Accepted: 05/04/2015] [Indexed: 10/23/2022]
Abstract
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.
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Affiliation(s)
- Francisco Díez-Fuertes
- AIDS Immunopathology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain
| | - Marina Cabello
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain; Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Michael M Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain.
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Caplinskas S, Loukachov VV, Gasich EL, Gilyazova AV, Caplinskiene I, Lukashov VV. Distinct HIV type 1 strains in different risk groups and the absence of new infections by drug-resistant strains in Lithuania. AIDS Res Hum Retroviruses 2013. [PMID: 23186249 DOI: 10.1089/aid.2012.0312] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To analyze HIV-1 genotypes in Lithuania and the transmission of drug-resistant viruses, HIV-1 sequences were obtained from 138 individuals, who were diagnosed as HIV-1 infected in 1990-2008 and represented all major risk groups. Subtype A strains, dominating in the former Soviet Union (90% of cases), were found in 60% of individuals, followed by subtype B (22%) and CRF03_AB (12%) strains. The remaining 7% of the strains included variants belonging to subtype C, CRF01_AE, CRF02_AG, more complex recombinant forms, and strains that could not be reliably genotyped. Analysis of virus genotypes per risk group revealed the circulation of distinct HIV-1 strains in different risk groups: subtype A viruses were present in 82% of injecting drug users (IDUs), but less than a half of heterosexually infected individuals and cases with unknown transmission route, and none of men having sex with men (MSM). We observed no mutations causing drug resistance among 27 newly diagnosed HIV-1 cases.
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Affiliation(s)
- Saulius Caplinskas
- Centre for Communicable Diseases and AIDS and Faculty of Social Policy, University of Mykolas Romeris, Vilnius, Lithuania
| | - Vladimir V. Loukachov
- Faculties of Science and Medicine, University of Amsterdam, Amsterdam, The Netherlands
| | - Elena L. Gasich
- Department of Clinical Virology, Republican Research Practical Center for Epidemiology and Microbiology, Minsk, Belarus
| | - Alla V. Gilyazova
- Laboratory of Immunochemistry, D.I. Ivanovsky Institute of Virology, Moscow, Russia
| | - Irma Caplinskiene
- Centre for Communicable Diseases and AIDS and Faculty of Social Policy, University of Mykolas Romeris, Vilnius, Lithuania
| | - Vladimir V. Lukashov
- Laboratory of Immunochemistry, D.I. Ivanovsky Institute of Virology, Moscow, Russia
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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Eremin VF, Gasich EL, Sasinovich SV. A new unique recombinant HIV type 1 isolated from a child born to an HIV-infected mother. AIDS Res Hum Retroviruses 2011; 27:1323-6. [PMID: 21534848 DOI: 10.1089/aid.2011.0112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The new HIV-1 recombinant, with a B(gag) A(pol)A(env) structure, is described. This recombinant virus differs from the classical "Kaliningrad" (AF193276.1) virus with an A(gag) B(pol)B(env) structure. The number of new HIV cases in Belarus has been increasing in the past few years. Within the 12 months of 2010, 1069 new cases of HIV infection were registered. Molecular epidemiological investigations have shown that though HIV-1 subtype A (84.5%) still dominates in HIV/AIDS patients, the quantity of CRFs has also increased to 7.1%. Although cases with the CRF03_AB virus were previously described in patients from Belarus, CRF06_cpx and CRF02_AG are described in Belarus for the first time.
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Affiliation(s)
- Vladimir F. Eremin
- Department of Clinical Virology, Republican Research Practical Center for Epidemiology and Microbiology, Minsk, Belarus
| | - Elena L. Gasich
- Department of Clinical Virology, Republican Research Practical Center for Epidemiology and Microbiology, Minsk, Belarus
| | - Sviataslau V. Sasinovich
- Department of Clinical Virology, Republican Research Practical Center for Epidemiology and Microbiology, Minsk, Belarus
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Skar H, Hedskog C, Albert J. HIV-1 evolution in relation to molecular epidemiology and antiretroviral resistance. Ann N Y Acad Sci 2011; 1230:108-18. [PMID: 21824168 DOI: 10.1111/j.1749-6632.2011.06128.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
HIV/AIDS has become one of the most important infectious diseases with a cumulative number of almost 60 million infections worldwide. The prevalence and epidemiological patterns are unevenly distributed across the globe and also within countries. HIV is one of the fastest evolving organisms known. Several genetically distinct subtypes are present and new circulating recombinant forms are continuously emerging. This review discusses HIV-1 evolution in relation to molecular epidemiology and antiretroviral resistance. Factors and concepts that influence global spread and within-patient evolution of HIV-1 are discussed as well as future perspectives on the use of phylodynamics in HIV epidemiology.
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Affiliation(s)
- Helena Skar
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden.
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Dilernia DA, Jones LR, Pando MA, Rabinovich RD, Damilano GD, Turk G, Rubio AE, Pampuro S, Gomez-Carrillo M, Salomón H. Analysis of HIV type 1 BF recombinant sequences from South America dates the origin of CRF12_BF to a recombination event in the 1970s. AIDS Res Hum Retroviruses 2011; 27:569-78. [PMID: 20919926 PMCID: PMC3131829 DOI: 10.1089/aid.2010.0118] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 epidemics in South America are believed to have originated in part from the subtype B epidemic initiated in the Caribbean/North America region. However, circulation of BF recombinants in similar proportions was extensively reported. Information currently shows that many BF recombinants share a recombination structure similar to that found in the CRF12_BF. In the present study, analyzing a set of 405 HIV sequences, we identified the most likely origin of the BF epidemic in an early event of recombination. We found that the subtype B epidemics in South America analyzed in the present study were initiated by a founder event that occurred in the early 1970s, a few years after the introduction of these strains in the Americas. Regarding the F/BF recombinant epidemics, by analyzing a subtype F genomic segment within the viral gene gag present in the majority of the BF recombinants, we found evidence of a geographic divergence very soon after the introduction of subtype F strains in South America. Moreover, through analysis of a subtype B segment present in all the CRF12_BF-like recombination structure, we estimated the circulation of the subtype B strain that gave rise to that recombinant structure around the same time period estimated for the introduction of subtype F strains. The HIV epidemics in South America were initiated in part through a founder event driven by subtype B strains coming from the previously established epidemic in the north of the continent. A second introduction driven by subtype F strains is likely to have encountered the incipient subtype B epidemic that soon after their arrival recombined with them, originating the BF epidemic in the region. These results may explain why in South America the majority of F sequences are found as BF recombinants.
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Affiliation(s)
- Dario A. Dilernia
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Capital Federal, Buenos Aires, Argentina
| | - Leandro R. Jones
- División de Biología Molecular, Estación de Fotobiología “Playa Unión,” Rawson, Chubut, Argentina
| | - Maria A. Pando
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Capital Federal, Buenos Aires, Argentina
| | - Roberto D. Rabinovich
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Capital Federal, Buenos Aires, Argentina
| | - Gabriel D. Damilano
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Capital Federal, Buenos Aires, Argentina
| | - Gabriela Turk
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Capital Federal, Buenos Aires, Argentina
| | - Andrea E. Rubio
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Capital Federal, Buenos Aires, Argentina
| | - Sandra Pampuro
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Capital Federal, Buenos Aires, Argentina
| | - Manuel Gomez-Carrillo
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Capital Federal, Buenos Aires, Argentina
| | - Horacio Salomón
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Capital Federal, Buenos Aires, Argentina
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Rumyantseva OA, Olkhovskiy IA, Malysheva MA, Ruzaeva LA, Vasiliev AV, Kazennova EV, Bobkova MR, Lukashov VV. Epidemiological networks and drug resistance of HIV type 1 in Krasnoyarsk region, Russia. AIDS Res Hum Retroviruses 2009; 25:931-6. [PMID: 19689192 DOI: 10.1089/aid.2009.0075] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To study the molecular epidemiology of HIV-1 in Krasnoyarsk region, Russia, where HIV-1 has spread rapidly since 2000, we obtained pol sequences from individuals living in this region (n = 67) as well as in the geographically closely related Altay region (n = 13). In both regions, subtype A viruses specific for the former Soviet Union (IDU-A strains) were dominant (92.5%). Virus sequences clustered according to the geographic origin of the infected individuals rather than to their risk group, demonstrating the role of geographically defined epidemiological networks in the propagation of the HIV-1 epidemic in the region. Six viruses belonged to subtype B. Three of them were phylogenetically (and therefore epidemiologically) closely related to each other, demonstrating that even though IDU-A viruses dominate the epidemic, the spread of other virus strains does occur. Most viruses (75%) had an A62V mutation in reverse transcriptase, specific for HIV-1 strains in Russia. Remarkably, 26 of 47 (55%) patients under HAART with detectable virus loads did not have any known drug-resistant mutation, indicating the need to increase compliance to therapy.
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Affiliation(s)
- Olga A. Rumyantseva
- Krasnoyarsk Regional AIDS Center, Krasnoyarsk, Russia
- D.I. Ivanovsky Institute of Virology, Moscow, Russia
| | | | | | | | | | | | | | - Vladimir V. Lukashov
- D.I. Ivanovsky Institute of Virology, Moscow, Russia
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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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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Paraskevis D, Pybus O, Magiorkinis G, Hatzakis A, Wensing AMJ, van de Vijver DA, Albert J, Angarano G, Åsjö B, Balotta C, Boeri E, Camacho R, Chaix ML, Coughlan S, Costagliola D, De Luca A, de Mendoza C, Derdelinckx I, Grossman Z, Hamouda O, Hoepelman IM, Horban A, Korn K, Kücherer C, Leitner T, Loveday C, MacRae E, Maljkovic-Berry I, Meyer L, Nielsen C, Op de Coul ELM, Ormaasen V, Perrin L, Puchhammer-Stöckl E, Ruiz L, Salminen MO, Schmit JC, Schuurman R, Soriano V, Stanczak J, Stanojevic M, Struck D, Van Laethem K, Violin M, Yerly S, Zazzi M, Boucher CA, Vandamme AM. Tracing the HIV-1 subtype B mobility in Europe: a phylogeographic approach. Retrovirology 2009; 6:49. [PMID: 19457244 PMCID: PMC2717046 DOI: 10.1186/1742-4690-6-49] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2008] [Accepted: 05/20/2009] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The prevalence and the origin of HIV-1 subtype B, the most prevalent circulating clade among the long-term residents in Europe, have been studied extensively. However the spatial diffusion of the epidemic from the perspective of the virus has not previously been traced. RESULTS In the current study we inferred the migration history of HIV-1 subtype B by way of a phylogeography of viral sequences sampled from 16 European countries and Israel. Migration events were inferred from viral phylogenies by character reconstruction using parsimony. With regard to the spatial dispersal of the HIV subtype B sequences across viral phylogenies, in most of the countries in Europe the epidemic was introduced by multiple sources and subsequently spread within local networks. Poland provides an exception where most of the infections were the result of a single point introduction. According to the significant migratory pathways, we show that there are considerable differences across Europe. Specifically, Greece, Portugal, Serbia and Spain, provide sources shedding HIV-1; Austria, Belgium and Luxembourg, on the other hand, are migratory targets, while for Denmark, Germany, Italy, Israel, Norway, the Netherlands, Sweden, Switzerland and the UK we inferred significant bidirectional migration. For Poland no significant migratory pathways were inferred. CONCLUSION Subtype B phylogeographies provide a new insight about the geographical distribution of viral lineages, as well as the significant pathways of virus dispersal across Europe, suggesting that intervention strategies should also address tourists, travellers and migrants.
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Affiliation(s)
- Dimitrios Paraskevis
- Katholieke Universiteit Leuven, Rega Institute for Medical research, Minderbroederstraat 10, B-3000 Leuven, Belgium
- National Retrovirus Reference Center, Department of Hygiene Epidemiology and Medical Statistics, Medical School, University of Athens, M. Asias 75, GR-11527, Athens, Greece
| | - Oliver Pybus
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Gkikas Magiorkinis
- National Retrovirus Reference Center, Department of Hygiene Epidemiology and Medical Statistics, Medical School, University of Athens, M. Asias 75, GR-11527, Athens, Greece
| | - Angelos Hatzakis
- National Retrovirus Reference Center, Department of Hygiene Epidemiology and Medical Statistics, Medical School, University of Athens, M. Asias 75, GR-11527, Athens, Greece
| | - Annemarie MJ Wensing
- University Medical Center Utrecht, Department of Virology, G04.614, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - David A van de Vijver
- Department of Virology, Erasmus MC, University Medical Centre, Postbus 2040 3000 CA Rotterdam, the Netherlands
| | - Jan Albert
- Department of Microbiology, Tumor and Cellbiology, Karolinska Institutet, SE 171 77 Stockholm, Sweden
- Dept of Virology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
| | - Guiseppe Angarano
- University of Foggia, Clinic of Infectious Diseases, Ospedali Riuniti – Via L. Pinto 71100 Foggia, Italy
| | - Birgitta Åsjö
- Center for Research in Virology, University of Bergen, Bergen High Technology Center, N-5020 Bergen, Norway
| | - Claudia Balotta
- University of Milano, Institute of Infectious and Tropical Diseases, Via Festa del Perdono 7, 20122 Milano, Italy
| | - Enzo Boeri
- Diagnostica and Ricerca San Raffaele, Centro San Luigi, I.R.C.C.S. Istituto Scientifico San Raffaele, Milan, Italy
| | - Ricardo Camacho
- Universidade Nova de Lisboa, Laboratorio de Virologia, Rua da Junqueira 96 1349-008 Lisboa, Portugal
| | - Marie-Laure Chaix
- EA 3620, Universite Paris Descartes, Virologie, CHU Necker, Paris France
| | - Suzie Coughlan
- National Virus Reference Laboratory, University College, Dublin, Ireland
| | - Dominique Costagliola
- INSERM U263 et SC4, Faculté de médecine Saint-Antoine, Université Pierre et Marie Curie, 27 rue de Chaligny, F-75571 Paris, France
| | - Andrea De Luca
- Department of Infectious Diseases, Catholic University, L.go A. Gemelli, 8 00168 Rome, Italy
| | | | | | - Zehava Grossman
- National. HIV Reference Lab, Central Virology, Public Health Laboratories, MOH Central Virology, Sheba Medical Center, 2 Ben-Tabai Street, Israel
| | - Osama Hamouda
- Robert Koch Institut (RKI), Nordufer 20, 13353 Berlin, Germany
| | - IM Hoepelman
- University Medical Center Utrecht, Department of Internal Medicine and Infectious Diseases F02.126, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - Andrzej Horban
- Hospital for Infectious Diseases, Center for Diagnosis & Therapy Warsaw 37, Wolska Str. 01-201 Warszawa, Poland
| | - Klaus Korn
- University of Erlangen, Schlossplatz 4, D-91054 Erlangen, Germany
| | | | - Thomas Leitner
- Department of Microbiology, Tumor and Cellbiology, Karolinska Institutet, SE 171 77 Stockholm, Sweden
- Dept of Virology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
| | - Clive Loveday
- ICVC Charity Laboratories, 3d floor, Apollo Centre Desborough Road High Wycombe, Buckinghamshire, HP11 2QW, UK
| | | | - I Maljkovic-Berry
- Department of Microbiology, Tumor and Cellbiology, Karolinska Institutet, SE 171 77 Stockholm, Sweden
- Dept of Virology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
| | | | - Claus Nielsen
- Statens Serum Institut Copenhagen, Retrovirus Laboratory, department of virology, building 87, Division of Diagnostic Microbiology 5, Artillerivej 2300 Copenhagen, Denmark
| | - Eline LM Op de Coul
- Centre for Infectious Disease Control (Epidemiology & Surveillance), National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, the Netherlands
| | - Vidar Ormaasen
- Ullevaal University Hospital, Department of Infectious Diseases Kirkeveien 166, N-0407 Oslo, Norway
| | - Luc Perrin
- Laboratory of Virology, Geneva University Hospital and University of Geneva Medical School, Geneva, Switzerland
| | | | - Lidia Ruiz
- IrsiCaixa Foundation, Hospital Germans Trias i Pujol, Ctra. de Canyet s/n, 08916 Badalona (Barcelona), Spain
| | - Mika O Salminen
- National Public Health Institute, HIV laboratory and department of infectious disease epidemiology, Mannerheimintie 166, FIN-00300 Helsinki, Finland
| | - Jean-Claude Schmit
- Centre Hospitalier de Luxembourg, Retrovirology Laboratory, National service of Infectious Diseases, 4 Rue Barblé, L-1210, Luxembourg
| | - Rob Schuurman
- University Medical Center Utrecht, Department of Virology, G04.614, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | | | - J Stanczak
- Hospital for Infectious Diseases, Center for Diagnosis & Therapy Warsaw 37, Wolska Str. 01-201 Warszawa, Poland
| | - Maja Stanojevic
- University of Belgrade School of Medicine, Institute of Microbiology and Immunology Virology Department, Dr Subotica 1, 11000 Belgrade, Serbia
| | - Daniel Struck
- Centre Hospitalier de Luxembourg, Retrovirology Laboratory, National service of Infectious Diseases, 4 Rue Barblé, L-1210, Luxembourg
| | - Kristel Van Laethem
- Katholieke Universiteit Leuven, Rega Institute for Medical research, Minderbroederstraat 10, B-3000 Leuven, Belgium
| | - M Violin
- University of Milano, Institute of Infectious and Tropical Diseases, Via Festa del Perdono 7, 20122 Milano, Italy
| | - Sabine Yerly
- Laboratory of Virology, Geneva University Hospital and University of Geneva Medical School, Geneva, Switzerland
| | - Maurizio Zazzi
- Section of Microbiology, Department of Molecular Biology, University of Siena, Italy
| | - Charles A Boucher
- University Medical Center Utrecht, Department of Virology, G04.614, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
- Department of Virology, Erasmus MC, University Medical Centre, Postbus 2040 3000 CA Rotterdam, the Netherlands
| | - Anne-Mieke Vandamme
- Katholieke Universiteit Leuven, Rega Institute for Medical research, Minderbroederstraat 10, B-3000 Leuven, Belgium
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Abstract
OBJECTIVES To determine the prevalence of HIV in Hainan island and the molecular epidemiological linkages related to risk factors of viral transmission. METHODS A governmental HIV/AIDS surveillance program, HIV serological study was conducted in volunteers from several high-risk groups between 1991 and 2006 in Hainan province. By phylogenetic reconstruction, we performed a molecular epidemiological tracing in a representative subset of the HIV-1-seropositive individuals diagnosed during this survey. RESULTS Of 499 752 volunteers, 523 (0.1%) accumulated cases of HIV-1 infection (69.2% needle-sharing drug users, 19.3% heterosexually acquired adults, 3.3% receivers of blood transfusion, 0.8% children born from HIV-1-infected mothers, and 7.7% remained unknown) were diagnosed. Among 83 patient samples examined (70 were infected with HIV-1 subtypes CRF01_AE and eight, two, one, one, and one were B', C, CRF08_BC, B, and a new CRF01_AE/B' recombinant, respectively), 66 (79.5%) were segregated into one large cluster (59 sequences) (founder effect) and one small cluster (three sequences) of CRF01_AE, one small cluster (two sequences) of B', and one small cluster (two sequences) of C. Phylogenetic and epidemiological linkages confirmed four heterosexual transmission events and rejected two potential heterosexual transmission suggested by contact tracing. Only two cases of CRF01_AE showed mutations conferring resistance to nucleoside and nonnucleoside reverse transcriptase inhibitors. CONCLUSION The reconstruction of current HIV-1 outbreaks by molecular epidemiological tracing is helpful for identifying epidemic sources and for defining prevention strategies.
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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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15
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Maljkovic Berry I, Ribeiro R, Kothari M, Athreya G, Daniels M, Lee HY, Bruno W, Leitner T. Unequal evolutionary rates in the human immunodeficiency virus type 1 (HIV-1) pandemic: the evolutionary rate of HIV-1 slows down when the epidemic rate increases. J Virol 2007; 81:10625-35. [PMID: 17634235 PMCID: PMC2045441 DOI: 10.1128/jvi.00985-07] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HIV-1 sequences in intravenous drug user (IDU) networks are highly homogenous even after several years, while this is not observed in most sexual epidemics. To address this disparity, we examined the human immunodeficiency virus type 1 (HIV-1) evolutionary rate on the population level for IDU and heterosexual transmissions. All available HIV-1 env V3 sequences from IDU outbreaks and heterosexual epidemics with known sampling dates were collected from the Los Alamos HIV sequence database. Evolutionary rates were calculated using phylogenetic trees with a t test root optimization of dated samples. The evolutionary rate of HIV-1 subtype A1 was found to be 8.4 times lower in fast spread among IDUs in the former Soviet Union (FSU) than in slow spread among heterosexual individuals in Africa. Mixed epidemics (IDU and heterosexual) showed intermediate evolutionary rates, indicating a combination of fast- and slow-spread patterns. Hence, if transmissions occur repeatedly during the initial stage of host infection, before selective pressures of the immune system have much impact, the rate of HIV-1 evolution on the population level will decrease. Conversely, in slow spread, where HIV-1 evolves under the pressure of the immune system before a donor infects a recipient, the virus evolution at the population level will increase. Epidemiological modeling confirmed that the evolutionary rate of HIV-1 depends on the rate of spread and predicted that the HIV-1 evolutionary rate in a fast-spreading epidemic, e.g., for IDUs in the FSU, will increase as the population becomes saturated with infections and the virus starts to spread to other risk groups.
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Affiliation(s)
- Irina Maljkovic Berry
- Department of Virology, Swedish Institute for Infectious Disease Control, Solna, Sweden.
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16
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Smolskaya T, Liitsola K, Zetterberg V, Golovanova E, Kevlova N, Konovalova N, Sevastianova K, Brummer-Korvenkontio H, Salminen M. HIV epidemiology in the Northwestern Federal District of Russia: dominance of HIV type 1 subtype A. AIDS Res Hum Retroviruses 2006; 22:1074-80. [PMID: 17147492 DOI: 10.1089/aid.2006.22.1074] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
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.
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Affiliation(s)
- Tatiana Smolskaya
- North-West District AIDS Centre of Russian Federation, Saint-Petersburg Pasteur Institute, Saint-Petersburg, Russia
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Abstract
Human immunodeficiency virus (HIV) is the worldwide disseminated causative agent of acquired immunodeficiency syndrome (AIDS). HIV is a member of the Lentivirus genus of Retroviridae family and is grouped in two types named HIV-1 and HIV-2. These viruses have a notable ability to mutate and adapt to the new conditions of human environment. A large incidence of errors at the transcriptional level results in changes on the genetic bases during the reproductive cycle. The elevated genomic variability of HIV has carried important implications for the diagnosis, treatment and prevention as well as epidemiologic investigations. The present review describes important definitions and geographical distribution of subtypes, circulating recombinant forms and other genomic variations of HIV. The present study aimed at leading students of Biomedical Sciences and public health laboratory staff guidance to general and specific knowledge about the genomic variability of the HIV.
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Affiliation(s)
- Henry I Z Requejo
- Seção de Imunologia, Instituto Adolfo Lutz, Av. Dr. Arnaldo 351, 01246-902 São Paulo, SP, Brazil.
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18
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Abstract
Uma das características mais marcantes do HIV-1 é a imensa diversidade observada entre as cepas que compõem a pandemia de HIV/AIDS. Na última década, a classificação das variantes do vírus em grupos, subtipos e formas recombinantes circulantes (CRF) e a observação de padrões específicos de mutação têm provado serem ferramentas poderosas para os estudos da dinâmica molecular do vírus. O acompanhamento da distribuição mundial da diversidade do HIV-1 tem sido empregado, por exemplo, em programas de vigilância epidemiológica, bem como na reconstrução da história de epidemias regionais. Além disto, a observação de padrões específicos de distribuição espacial do vírus sugere a existência de diferenças na patogenia e transmissibilidade entre os diversos subtipos. A análise molecular das seqüências do vírus também permite a estimativa do tempo de divergência entre as variantes e das forças dinâmicas que modelam as árvores filogenéticas.
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Affiliation(s)
- Mônica Edelenyi Pinto
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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Vázquez de Parga E, Rakhmanova A, Pérez-Alvarez L, Vinogradova A, Delgado E, Thomson MM, Casado G, Sierra M, Muñoz M, Carmona R, Vega Y, Contreras G, Medrano L, Osmanov S, Nájera R. 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. J Med Virol 2005; 77:337-44. [PMID: 16173024 DOI: 10.1002/jmv.20461] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
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.
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Lazouskaya NV, Eremin VF, Adema KW, Gasich EL, Baan E, Lukashov VV. The HIV type 1 epidemic in Belarus: predominance of Eastern European subtype A strains and circulation of subtype B viruses. AIDS Res Hum Retroviruses 2005; 21:830-3. [PMID: 16218809 DOI: 10.1089/aid.2005.21.830] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
To study the molecular epidemiology of HIV-1 in Belarus, where the rapid spread of HIV-1 has been registered since 1996, we obtained HIV-1 sequences from 30 individuals living in five cities in both the main geographic areas of the epidemic (Gomel and Minsk regions) and territories where spreading of the epidemic remains limited (Grodno region). Analysis of env V3 and gag p17/p24 sequences demonstrated that infections in all 12 injecting drug users and 14 of 18 individuals infected through sexual contacts were caused by subtype A viruses that are specific for the epidemic in the former Soviet Union (IDU-A viruses), while the remaining four infections were caused by phylogenetically unrelated to each other subtype B viruses. Extrapolation of these results to the total population of HIV-1-infected individuals in Belarus allowed us to estimate that IDU-A viruses account for nearly 95% of HIV-1 infections in Belarus.
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Affiliation(s)
- Natallia V Lazouskaya
- Department of Clinical Virology, Institute for Epidemiology and Microbiology, 220114 Minsk, Belarus
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Nabatov AA, Masharsky AE, Verevochkin SV, Emelyanov AV, Kozlov AP. Host-dependent serum specificity to the V3 domain of HIV-1. Scand J Immunol 2004; 60:471-6. [PMID: 15541039 DOI: 10.1111/j.0300-9475.2004.01506.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The previous studies of anti-HIV-1 humoral immune response have found the stable individual structural bias in the antibody production that reflects the changes in the immune functional network caused by HIV-1. The correlation between antigen structure, in particular the V3 domain of HIV-1, and the serum specificity to the structure remains unclear. To clarify the role of host individual factors in the serum specificity, we used the slightly modified HIV-1 serotyping methodological approach for the sera of the patients infected with HIV-1 with a different level of genetic similarity. Substantial discrepancy between serum specificities and antigen structure was found. Patients infected with HIV-1 carrying similar and identical V3 sequences had significantly different serum specificities. The opposite situation was often observed as well. The results of the study suggest that the influence of the V3 loop structure in the development of humoral immune response to the V3 loop is substantially modified in a patient-specific manner.
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Affiliation(s)
- A A Nabatov
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
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22
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Roudinskii NI, Sukhanova AL, Kazennova EV, Weber JN, Pokrovsky VV, Mikhailovich VM, Bobkov AF. Diversity of human immunodeficiency virus type 1 subtype A and CRF03_AB protease in Eastern Europe: selection of the V77I variant and its rapid spread in injecting drug user populations. J Virol 2004; 78:11276-87. [PMID: 15452247 PMCID: PMC521816 DOI: 10.1128/jvi.78.20.11276-11287.2004] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
To characterize polymorphisms of the subtype A protease in the former Soviet Union, proviral DNA samples were obtained, with informed consent, from 119 human immunodeficiency virus type 1 (HIV-1)-positive untreated injecting drug users (IDUs) from 16 regions. All individuals studied have never been treated with antiretroviral drugs. The isolates were defined as IDU-A (n = 115) and CRF03_AB (n = 4) by using gag/env HMA/sequencing. The pro region was analyzed by using sequencing and original HIV-ProteaseChip hybridization technology. The mean of pairwise nucleotide distance between 27 pro sequences (23 IDU-A and 4 CRF03_AB) was low (1.38 +/- 0.79; range, 0.00 to 3.23). All sequences contained no primary resistance mutations. However, 13 of 23 (56.5%) subtype A isolates bore the V77I substitution known as the secondary protease mutation. V77I was associated with two synonymous substitutions in triplets 31 and 78, suggesting that all V77I-bearing viruses evolved from a single source in 1997. Hybridization analysis showed that 55 of 115 (47.8%) HIV-1 isolates contained V77I, but this variant was not found in any of 31 DNA samples taken from regions, where the HIV-1 epidemic among IDUs started earlier 1997, as well as in any of four CRF03_AB isolates. The results of analysis of 12 additional samples derived from epidemiologically linked subjects showed that in all four epidemiological clusters the genotype of the donor and the recipients was the same irrespective of the route of transmission. This finding demonstrates the transmission of the V77I mutant variant, which is spreading rapidly within the circulating viral pool in Russia and Kazakhstan. The continued molecular epidemiological and virological monitoring of HIV-1 worldwide thus remains of great importance.
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Affiliation(s)
- Nikita I Roudinskii
- Laboratory of T-Lymphotropic Viruses, D. I. Ivanovsky Institute of Virology, 16 Gamaleya Street, Moscow 123098, Russia
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Bobkov AF, Kazennova EV, Selimova LM, Khanina TA, Ryabov GS, Bobkova MR, Sukhanova AL, Kravchenko AV, Ladnaya NN, Weber JN, Pokrovsky VV. Temporal trends in the HIV-1 epidemic in Russia: predominance of subtype A. J Med Virol 2004; 74:191-6. [PMID: 15332265 DOI: 10.1002/jmv.20177] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
During the period 1996-1997, three highly homogeneous variants of HIV-1 were identified, circulating among injecting drug users (IDUs) in the former Soviet Union republics. One of these belonged to HIV-1 genetic subtype A (IDU-A), another belonged to HIV-1 genetic subtype B (IDU-B) and the third was a recombinant between the first two variants (CRF03_AB). However, since 1997, the HIV-1 epidemic has affected an increasing number of geographic regions in Russia. This study was undertaken to survey the prevailing genetic variants and to estimate the current proportions of these three HIV-1 genetic subtypes in Russia. Blood samples were taken in 1999-2003 from 1090 HIV-infected individuals and analysed by gag/env HMA. The IDU-A variant was found to be the majority variant (89.7-100%) in 44 of 45 regions of the Russian Federation studied. The IDU-A variant was also found to spreading rapidly through heterosexual transmission in 1999-2003 (30/34, 88%). CRF03_AB predominates in the Kaliningrad region only (28/29, 96.6%). The IDU-B variant is currently of minor importance in the IDU epidemic but other European subtype B variants predominate among men having sex with men (18/18, 100%). Sequence analysis of the env V3 encoding regions derived from HIV-1 infected individuals in Yekaterinburg (the main centre of the HIV-1 epidemic in Russia in 2002-2003) showed that the IDU-A variant is still highly homogeneous. The mean pairwise nucleotide distance (n = 9) was 2.89 +/- 1.14 (range 1.36-6.14). However, the mean genetic distance between each sequence within the samples collected from the Yekaterinburg IDU-A variant subset and the IDU-A consensus is 2.51 +/- 1.06 (range 1.36-4.66) and considerably higher than in South Russia in 1996 (0.79 +/- 0.51, range 0.38-1.90). The current HIV-1 epidemic in Russia is almost entirely caused by a highly homogeneous A-subtype strain, which will influence vaccine development strategies and must be taken into account in the quality control of molecular tests for the diagnosis of HIV-1.
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Bobkov AF, Kazennova EV, Sukhanova AL, Bobkova MR, Pokrovsky VV, Zeman VV, Kovtunenko NG, Erasilova IB. An HIV type 1 subtype A outbreak among injecting drug users in Kazakhstan. AIDS Res Hum Retroviruses 2004; 20:1134-6. [PMID: 15585106 DOI: 10.1089/aid.2004.20.1134] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Kazakhstan experienced the start of the HIV-1 outbreak among intravenous drug users (IDUs) in 1997. To characterize genetically HIV-1 strains circulating in this country, peripheral blood mononuclear cells (PBMCs) DNA samples (1999-2002) derived from HIV-infected IDUs and their sexual partners in Pavlodar (n = 19), Shymkent (n = 6), and Qaraghandy (n = 18) regions were analyzed by the gag/env heteroduplex mobility assay (HMA). The 366-bp proviral env gene fragments encoding the gp120 C2-V3 region obtained from 16 individuals were sequenced. The results of HMA revealed that all 43 HIV-1 strains studied belonged to gag/env subtype A. The nucleotide sequence analysis showed a marked genetic homogeneity with the mean genetic distance being 3.63 +/- 2.39 (range 0.00-12.13). The mean genetic distance between each sequence within the Kazakhstan set and the East-European IDU subtype A consensus was 2.94 +/- 1.92 (range 0.79-8.48). The data presented thus confirm the spreading of the same IDU subtype A virus in the former Soviet Union.
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Tovanabutra S, Beyrer C, Sakkhachornphop S, Razak MH, Ramos GL, Vongchak T, Rungruengthanakit K, Saokhieo P, Tejafong K, Kim B, De Souza M, Robb ML, Birx DL, Jittiwutikarn J, Suriyanon V, Celentano DD, McCutchan FE. The changing molecular epidemiology of HIV type 1 among northern Thai drug users, 1999 to 2002. AIDS Res Hum Retroviruses 2004; 20:465-75. [PMID: 15186520 DOI: 10.1089/088922204323087705] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
CRF01_AE and subtype B have dominated the HIV-1 epidemic in Thailand since 1989. We reported a new circulating recombinant form of HIV-1, CRF15_01B, as well as other unique CRF01_AE/B recombinants among prevalent HIV infections in Thailand. We sought to study this challenging molecular picture through assessment of subtypes among recent HIV-1 seroconverters in northern Thai drug users. A total of 847 HIV-1 seronegative drug users (342 IDU and 505 non-IDU) were enrolled, from 1999 to 2002, in a prospective study; 39 HIV-1 incident cases were identified and characteristics were collected. The overall HIV-1 incidence rate was 2.54/100PY, but it was 10.0/100PY among male IDU. HIV was strongly associated with injection history; 38 of 39 seroconverters gave a history of IDU. A near full-length genome of HIV-1 was recovered by PCR amplification and sequenced from peripheral mononuclear cell extracted DNA of 38 seroconverters. Phylogenetic analysis revealed that 33 (86.8%) were CRF01_AE and 5 (13.2%) were CRF01_AE/B recombinants. These recombinants had different structure but shared some common breakpoints, indicating an ongoing recombination process. Recombinant infection increased with year of sampling (0 to 57.1%). The molecular epidemiology of HIV-1 among drug users in northern Thailand has thus entered a new era. CRF01_AE remains predominant while pure subtype B is becoming rare, and now a substantial component of the epidemic. These findings support the need for CRF01_AE and subtype B components in clade-matched vaccine strategies for Thai phase III trials. Ongoing molecular surveillance of circulating HIV-1 strains is imperative for the evaluation of HIV vaccine efficacy.
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Affiliation(s)
- Sodsai Tovanabutra
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai, Thailand.
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26
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Balode D, Ferdats A, Dievberna I, Viksna L, Rozentale B, Kolupajeva T, Konicheva V, Leitner T. Rapid epidemic spread of HIV type 1 subtype A1 among intravenous drug users in Latvia and slower spread of subtype B among other risk groups. AIDS Res Hum Retroviruses 2004; 20:245-9. [PMID: 15018713 DOI: 10.1089/088922204773004978] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To investigate the rapid HIV epidemic in Latvia, 97 newly detected individuals were sampled in 2000-2001. To establish the molecular epidemiology we sequenced the env V3 and gag p17 regions of the HIV genome and compared them with reference sequences using phylogenetic analyses. As expected, the vast majority (n = 88; 91%) were intravenous drug users (IDUs) from the Riga region. Also, the majority of the investigated individuals (n = 93; 96%) were found to carry a subtype A1 virus that may have entered the Latvian IDU population several times. In addition, one IDU was infected with CRF03_AB and three other individuals, who had been infected through sexual contacts, carried subtype B virus. Thus, subtype A1 dominates the Latvian epidemic and is strongly associated with the IDU risk group. Although some spread of subtype A1 has occurred in the heterosexual group, subtype B dominates among homosexually and heterosexually infected individuals.
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Affiliation(s)
- Dace Balode
- Department of Virology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
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27
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Yu XF, Wang X, Mao P, Wang S, Li Z, Zhang J, Garten R, Kong W, Lai S. Characterization of HIV type 1 heterosexual transmission in Yunnan, China. AIDS Res Hum Retroviruses 2003; 19:1051-5. [PMID: 14686326 DOI: 10.1089/088922203322588422] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The earliest HIV-1 epidemic in China started in Yunnan province, which continues to be one of the most severe areas affected. While HIV-1 infections are spreading rapidly among injection drug users (IDUs) in China, sexual transmission of HIV-1 has also been confirmed, threatening the general population. Recent survey data indicated that heterosexual transmission of HIV-1 in Yunnan was steadily increasing. Diverse HIV-1 strains, including subtype B, C, CRF01, and CRF08, are circulating among individuals who acquired HIV through sexual contacts. Multiple HIV-1 subtypes, including subtypes B, C, and CRF08, were also detected among IDUs. In comparison with other IDU cohorts, intersubject env sequence variation was much higher amongIDUs in Yunnan. Growing evidence suggests that unprotected sex continues to occur at high rates among IDUs and their sex partners. Intervention strategies are urgently needed to target individuals at high risk for HIV heterosexual transmission and injection drug use. The complex pattern of HIV-1 distribution in the high-risk populations in Yunnan may have important implications for HIV transmission as well as vaccine development and evaluation.
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Affiliation(s)
- Xiao-Fang Yu
- Department of Molecular Microbiology and Immunology, Johns Hopkins Univesity Bloomberg School of Public Health, Baltimore, Maryland 21205, USA.
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Masharsky AE, Klimov NA, Kozlov AP. Molecular cloning and analysis of full-length genome of HIV type 1 strains prevalent in countries of the former Soviet Union. AIDS Res Hum Retroviruses 2003; 19:933-9. [PMID: 14601597 DOI: 10.1089/088922203322493139] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The HIV-1 epidemic among injecting drug users (IDUs) in countries of the former Soviet Union (FSU) was caused mainly by two HIV-1 variants: subtype A and CRF03-AB. To date only three full-length HIV-I genomes from the FSU have been sequenced: one subtype A from Byelorussia and two CRF03-AB from Russia. We report the full-length genome cloning and analysis of two more HIV-1 strains from the FSU countries (98UA0116 of subtype A and 98BY10443 of CRF03-AB). Isolate 98UA0116 is the second cloned and sequenced full-length HIV-1 genome of subtype A lineage from the FSU, which may be a novel subsubtype within sub-type A. Isolate 98BY10443 is the third full-length HIV-1 genome of CRF03-AB in the world to be cloned and sequenced. Additionally, it is the first CRF03-AB strain discovered in Byelorussia. Cloned genomic sequences of the FSU HIV-1 isolates are being used for the development of a region-specific HIV-1 vaccine.
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Affiliation(s)
- Alexei E Masharsky
- The Biomedical Center, Pudozhskaja st. 7, 197110 St. Petersburg, Russia.
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29
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Tovanabutra S, Watanaveeradej V, Viputtikul K, De Souza M, Razak MH, Suriyanon V, Jittiwutikarn J, Sriplienchan S, Nitayaphan S, Benenson MW, Sirisopana N, Renzullo PO, Brown AE, Robb ML, Beyrer C, Celentano DD, McNeil JG, Birx DL, Carr JK, McCutchan FE. A new circulating recombinant form, CRF15_01B, reinforces the linkage between IDU and heterosexual epidemics in Thailand. AIDS Res Hum Retroviruses 2003; 19:561-7. [PMID: 12908933 DOI: 10.1089/088922203322230923] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 subtype B and CRF01_AE have been in circulation in Thailand and Southeast Asia for more than a decade. Initially separated by risk group, the two strains are increasingly intermixed, and two recombinant strains of essentially reciprocal structure have been recently reported. Here we identify additional CRF_01B recombinants and provide the evidence that HIV-1 strains now pass freely between the two high-risk populations. HIV isolates that showed discordance between CRF01_AE and subtype B in multi-region genotyping assays were selected for the study. They were drawn from 3 different cohorts in Thailand representing different risk behaviors and demographic characteristics: a drug user cohort in the north, a family planning clinic attendee cohort in the southeast, and a cohort study of the mucosal virology and immunology of HIV-1 infection in Thailand. The DNA from these isolates was PCR amplified to recover the full HIV-1 genome and subjected to sequencing and phylogenetic analysis. We establish that one particular CRF_01B recombinant, with the external envelope of subtype B and the rest of the genome from CRF01_AE, is circulating widely in Thailand. Termed CRF15_01B (also referred to as CRF15), the strain was primarily heterosexually transmitted, although injecting drug use (IDU) also played a role. In aggregate data from the studies, CRF15 constituted 1.7% of all HIV-1 infections (95% confidence interval 0.5-4.4%) and was dispersed widely in the country. The previously separate heterosexual and IDU epidemics have apparently been bridged by a new CRF. The entry of CRF15 into the mainstream of the epidemic signals new complexity in the long stable molecular picture in Thailand. These recombinants must be considered in ongoing or projected efficacy evaluations of HIV-1 vaccines and antiviral therapies.
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Affiliation(s)
- Sodsai Tovanabutra
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai, Thailand.
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Nabatov AA, Kravchenko ON, Lyulchuk MG, Shcherbinskaya AM, Lukashov VV. Simultaneous introduction of HIV type 1 subtype A and B viruses into injecting drug users in southern Ukraine at the beginning of the epidemic in the former Soviet Union. AIDS Res Hum Retroviruses 2002; 18:891-5. [PMID: 12201913 DOI: 10.1089/08892220260190380] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The vast majority of HIV-1 strains from the epidemic in the former Soviet Union (FSU) belong to subtype A (IDU-A) and CRF03_AB (IDU-A/B), for which IDU-A is one of parental strains; no epidemic by another parental virus, belonging to subtype B (IDU-B), has yet been identified. To characterize viruses present during the early stage of the epidemic in southern Ukraine, where the first outbreaks in the FSU were registered, we obtained partial env and pol sequences from IDUs from Odessa and Nikolaev and compared them with viruses from other outbreaks. All viruses from Odessa belonged to the IDU-A type, which is in accord with previous studies. At the same time, we found that the outbreak in Nikolaev was caused by IDU-B viruses, indicating that this outbreak is the result of an independent virus introduction. Phylogenetic analysis of viruses from the FSU supported the epidemiological data suggesting that the HIV-1 epidemic in the FSU started in southern Ukraine.
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Affiliation(s)
- Alexey A Nabatov
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
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32
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Yu XF, Liu W, Chen J, Kong W, Liu B, Zhu Q, Liang F, McCutchan F, Piyasirisilp S, Lai S. Maintaining low HIV type 1 env genetic diversity among injection drug users infected with a B/C recombinant and CRF01_AE HIV type 1 in southern China. AIDS Res Hum Retroviruses 2002; 18:167-70. [PMID: 11839150 DOI: 10.1089/08892220252779719] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 outbreaks in Guangxi Province, southern China were initiated from two separate border cities in 1996 and 1997. Drug users in Pingxiang City, which borders Vietnam, were infected with CRF01_AE HIV-1, and drug users in Baise City, which borders Yunan Province, were infected with a novel B/C recombinant HIV-1. Since 1997, HIV-1 has been rapidly spreading in Guangxi, including its capital city Nanning. Survey data indicated that HIV-1 prevalence among IDUs in new outbreak regions increased 8 to 42% within 1 year. The B/C recombinants obtained from five separate regions in Guangxi, which span a 4-year time frame, were remarkable for their low intersubject env V3 diversity, less than 0.2%. Similarly, the CRF01_AE from IDUs over a 3-year time frame had low intersubject env V3 diversity of less than 1.6%. Different patterns of sequence variations in the V3 and V4 regions were observed for the B/C recombinant and the CRF01_AE HIV1. The rapid spreading of homogeneous HIV-1 strains in Guangxi may have important implications for HIV transmission as well as vaccine development and evaluation.
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Affiliation(s)
- Xiao-Fang Yu
- Department of Molecular Microbiology and Immunology, Johns Hopkins University School of Hygiene and Public Health, Baltimore, Maryland 21205, USA.
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Foley B, Donegan E, Silitonga N, Wignall FS, Busch MP, Delwart EL. Importation of multiple HIV type 1 strains into West Papua, Indonesia (Irian Jaya). AIDS Res Hum Retroviruses 2001; 17:1655-9. [PMID: 11779353 DOI: 10.1089/088922201753342068] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 from 16 sexually transmitted disease clinic patients in Timika, West Papua, Indonesia was amplified by RT-PCR and subtyped by a combination of envelope and gag region heteroduplex mobility analysis (HMA) and direct PCR DNA sequencing. HMA showed the presence of 14 subtype E (CRF01_AE) and 2 subtype B HIV-1. Phylogenetic analysis of a 540-bp V3-V4 region of gp120 showed that 9 of 10 CRF01_AE variants clustered tightly with a median distance of 1.3% (range, 0.5 to 2.2%) whereas 1 CRF01_AE variant diverged significantly from the others (median distance, 10.7%; range, 10.1 to 11.8%). One subtype B virus envelope was typical of United States/European strains whereas the other appeared to be related to Thai subtype B' variants. These results reflect the independent introduction of multiple HIV-1 strains into West Papua, with the rapid spread in the majority of infected patients tested of a single strain of HIV-1E (CRF01_AE).
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Affiliation(s)
- B Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87501, USA
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34
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Chen MY, Lee CN. Molecular epidemiology of HIV-1: an example of Asia. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2001; 49:417-36. [PMID: 11013770 DOI: 10.1016/s1054-3589(00)49033-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Affiliation(s)
- M Y Chen
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
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35
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Bobkov A, Kazennova E, Khanina T, Bobkova M, Selimova L, Kravchenko A, Pokrovsky V, Weber J. An HIV type 1 subtype A strain of low genetic diversity continues to spread among injecting drug users in Russia: study of the new local outbreaks in Moscow and Irkutsk. AIDS Res Hum Retroviruses 2001; 17:257-61. [PMID: 11177409 DOI: 10.1089/088922201750063188] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
An explosive epidemic of human immunodeficiency virus type 1 (HIV-1) has been documented among injecting drug users (IDUs) in the former Soviet Union republics. In 1999, the two largest local IDU outbreaks of HIV-1 infection in the Russian Federation were registered in the Moscow and Irkutsk regions, where 13,004 HIV-1 cases were identified (44% of the total number of HIV-1 infections in Russia in 1999). To study the prevailing genetic variants and to estimate the genetic diversity of HIV-1 in these outbreaks, 60 samples from Moscow (n = 36) and from Irkutsk (n = 24) were analyzed using the gag/env heteroduplex mobility assay, and the env gp120 V3 encoding regions obtained from 23 individuals were sequenced. Both virus populations were highly homogeneous (the means of pairwise nucleotide distance were 1.75 +/- 0.83 and 2.35 +/- 1.59 for Irkutsk and Moscow, respectively), and similar to the subtype A viruses obtained earlier from IDUs in the former Soviet Union. The subtype A HIV-1 variant thus dominates in the largest HIV-1 outbreaks among IDUs in the Russian Federation.
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Affiliation(s)
- A Bobkov
- Laboratory of T-Lymphotropic Viruses, Ivanovsky Institute of Virology, Moscow 123098, Russia.
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36
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Bobkova MR, Kazennova EV, Selimova LM, Buravtsova EV, Lister S, Prilipov AG, Weber JN, Pokrovsky VV, Bobkov AF. Serological approaches to subtyping of HIV-1 in injecting drug users in Russia: evidence of subtype homogeneity at the main sites of the epidemic. Int J STD AIDS 2001. [DOI: 10.1177/095646240101200107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The aim of this study was to develop and evaluate a simple V3 peptide-based enzyme immunoassay (PEIA) for large-scale serotyping of HIV-1 specimens derived from injecting drug users (IDUs) in the Russian Federation. Two synthetic peptides were evaluated, named P1 (RKSIHIGPGRAFYATGD) and P2 (RTSVRIGPGQVFYKTGD), in an PEIA on 63 HIV-1 IDUs sera for which genotypes had been determined by heteroduplex mobility assay (HMA) and sequencing. The sensitivities of P1 (subtype B) and P2 (subtype A) were 87% and 75% respectively. Specificity of the assay was 100% for both peptides, with 100% predictive values of a monoreactive positive test for both peptides. Using the PEIA with peptides P1 and P2, we have serotyped 375 of 477 serum samples derived from IDUs in 4 main sites of the HIV-1 epidemic in Russia. The results demonstrated a high level of subtype homogeneity in all regions studied. In 3 of 4 territories, Tver' (n=345), and Rostov-on-Don (n=61) regions, and Krasnodar Kray (n=27), 100% of typable sera were found to belong to env subtype A. On the other hand, all specimens serotyped in the Kaliningrad region (n=38) belonged to env subtype B, and there is strong evidence that the recombinant gagAenvB virus which has caused the largest outbreak of HIV-1 in Russia is located in this region. At the present time another parental strain with gagBenvB genotype is of minor importance in the IDUs HIV-1 epidemic in Russia.
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Affiliation(s)
| | | | | | | | - Simon Lister
- Imperial College School of Medicine, St Mary's Hospital, London W2 1NY, UK
| | | | - Jonathan N Weber
- Imperial College School of Medicine, St Mary's Hospital, London W2 1NY, UK
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Piyasirisilp S, McCutchan FE, Carr JK, Sanders-Buell E, Liu W, Chen J, Wagner R, Wolf H, Shao Y, Lai S, Beyrer C, Yu XF. A recent outbreak of human immunodeficiency virus type 1 infection in southern China was initiated by two highly homogeneous, geographically separated strains, circulating recombinant form AE and a novel BC recombinant. J Virol 2000; 74:11286-95. [PMID: 11070028 PMCID: PMC113233 DOI: 10.1128/jvi.74.23.11286-11295.2000] [Citation(s) in RCA: 248] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
New outbreaks of human immunodeficiency virus type 1 (HIV-1) among injecting drug users (IDUs) are spreading in China along heroin trafficking routes. Recently, two separate HIV-1 epidemics among IDUs were reported in Guangxi, Southern China, where partial sequencing of the env gene showed subtype C and circulating recombinant form (CRF) AE. We evaluated five virtually full-length HIV-1 genome sequences from IDUs in Guangxi to determine the genetic diversity and the presence of intersubtype recombinants. Sequence analysis showed two geographically separated, highly homogeneous HIV-1 strains. B/C intersubtype recombinants were found in three IDUs from Baise City, in a mountainous region near the Yunnan-Guangxi border. These were mostly subtype C, with portions of the capsid and reverse transcriptase (RT) genes from subtype B. The subtype B portion of the capsid was located in the N-terminal domain, which has been shown to influence virus core maturation, virus infectivity, and binding to cyclophilin A, whereas the subtype B portion of RT was located in the palm subdomain, which is the active site of the enzyme. These BC recombinants differed from a BC recombinant found in Xinjiang Province in northwestern China. CRF AE strains were found in IDUs from Nanning, the capital of Guangxi, and in IDUs from Pingxiang City near the China-Vietnam border. The AE and BC recombinants were both remarkable for their low interpatient diversity, less than 1% for the full genome. Rapid spread of HIV-1 among IDUs may foster the emergence of highly homogeneous strains, including novel recombinants in regions with multiple subtypes.
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Affiliation(s)
- S Piyasirisilp
- Department of Molecular Microbiology and Immunology, The Johns Hopkins School of Hygiene and Public Health, Baltimore, Maryland 21205, USA
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Liitsola K, Ristola M, Holmström P, Salminen M, Brummer-Korvenkontio H, Simola S, Suni J, Leinikki P. An outbreak of the circulating recombinant form AECM240 HIV-1 in the Finnish injection drug user population. AIDS 2000; 14:2613-5. [PMID: 11101077 DOI: 10.1097/00002030-200011100-00028] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- K Liitsola
- Department of Infectious Disease Epidemiology, National Public Health Institute, Helsinki, Finland
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Foley B, Pan H, Buchbinder S, Delwart EL. Apparent founder effect during the early years of the San Francisco HIV type 1 epidemic (1978-1979). AIDS Res Hum Retroviruses 2000; 16:1463-9. [PMID: 11054259 DOI: 10.1089/088922200750005985] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV-1 envelope sequence variants were RT-PCR amplified from serum samples cryopreserved in San Francisco in 1978-1979. The HIV-1 subtype B env V3-V5 sequences from four homosexual men clustered phylogenetically, with a median nucleotide distance of 2.8%, reflecting a recent common origin. These early U.S. HIV-1 env variants mapped close to the phylogenetic root of the subtype B tree while env variants collected in the United States throughout the 1980s and 1990s showed, on average, increasing genetic diversity and divergence from the subtype B consensus sequence. These results indicate that the majority of HIV-1 currently circulating in the United States may be descended from an initial introduction and rapid spread during the mid- to late 1970s of subtype B viruses with limited variability (i.e., a founder effect). As expected from the starburst-shaped phylogeny of HIV-1 subtype B, contemporary U.S. strains were, on average, more closely related at the nucleic acid and amino acid levels to the earlier 1978-1979 env variants than to each other. The growing levels of HIV-1 genetic diversity, one of multiple obstacles in designing a protective vaccine, may therefore be mitigated by using epidemic founding variants as antigenic strains for protection against contemporary strains.
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Affiliation(s)
- B Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87501, USA
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Liitsola K, Holm K, Bobkov A, Pokrovsky V, Smolskaya T, Leinikki P, Osmanov S, Salminen M. An AB recombinant and its parental HIV type 1 strains in the area of the former Soviet Union: low requirements for sequence identity in recombination. UNAIDS Virus Isolation Network. AIDS Res Hum Retroviruses 2000; 16:1047-53. [PMID: 10933619 DOI: 10.1089/08892220050075309] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In the former Soviet Union (SU) increasing numbers of HIV-1 infections among injecting drug users (IDU) have been reported, especially in the Ukraine. The main subtype transmitted among the IDUs seems to be subtype A, but limited numbers of subtype B cases have also been reported. In Kaliningrad, Russia, an AB recombinant strain was earlier shown to be responsible for the local outbreak. Here we describe the genetic relationship of HIV-1 strains circulating among IDUs in the former SU. For subtype A and the AB recombinant strains nearly full-length genomes were sequenced, and for one subtype B strain the entire envelope gene was cloned. The relationship between the AB recombinant strain and the subtype A and subtype B strains and the mosaic structure of the recombinant was studied by phylogenetic analysis. Ukrainian A and B strains were shown to be the probable parental viruses of the Kaliningrad AB recombinant strain. In the envelope gene the recombination breakpoint could also be precisely mapped to a region of similarity of only 14 base pairs. This suggests that only short stretches of absolute sequence identity may be needed for efficient RNA recombination between HIV-1 subtypes.
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Affiliation(s)
- K Liitsola
- Department of Infectious Disease Epidemiology, National Public Health Institute, Helsinki, Finland.
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Bobkov AF, Lukashov VV, Goudsmit J, Weber JN. Silent mutation in the V3 region characteristic of HIV type 1 env subtype B strains from injecting drug users in the former Soviet Union. AIDS Res Hum Retroviruses 2000; 16:291-4. [PMID: 10710217 DOI: 10.1089/088922200309386] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
New independent states of the former Soviet Union are facing a rapidly growing epidemic of HIV-1 among injecting drug users (IDUs). This epidemic is caused by three HIV-1 populations, one belonging to HIV-1 subtype A (IDU-A), another to subtype B (IDU-B), and the third being a recombinant of the IDU-A and IDU-B viruses (IDU-A/B, gagA/envB). Each of these populations is characterized by a high level of genetic homogeneity. We identified a unique synonymous nucleotide substitution in the first isoleucine codon at the IHIGPGR motif (ATT), which was observed in the env subtype B V3 sequences derived from IDUs in Russia and the Ukraine. This substitution was observed in none of 179 sequences obtained from IDUs in western Europe, northern America, and Asia. Molecular epidemiological analysis of HIV-1 strains based on this sequence pattern could be useful for tracing the origin and spread of the IDU-B viruses to other countries and risk groups.
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Affiliation(s)
- A F Bobkov
- D.I. Ivanovsky Institute of Virology, Moscow, Russia.
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Oelrichs RB, Shrestha IL, Anderson DA, Deacon NJ. The explosive human immunodeficiency virus type 1 epidemic among injecting drug users of Kathmandu, Nepal, is caused by a subtype C virus of restricted genetic diversity. J Virol 2000; 74:1149-57. [PMID: 10627525 PMCID: PMC111449 DOI: 10.1128/jvi.74.3.1149-1157.2000] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An explosive epidemic of human immunodeficiency virus type 1 (HIV-1) has been documented among the injecting drug user population of Kathmandu, Nepal, whose seropositivity rate has risen from 0 to 40% between 1995 and 1997. By using Catrimox to preserve whole-blood RNA at ambient temperature for transportation, HIV-1 envelope V3-V4 sequences were obtained from 36 patients in this group. Analysis of the sequences indicated a homogenous epidemic of subtype C virus, with at least two independent introductions of the virus into the population. Viral diversity was restricted within two transmission subclusters, with the majority of variation occurring in V4. Calculation of the synonymous-to-nonsynonymous mutation ratio (Ks:Ka) across this region showed that significant evolutionary pressure had been experienced during the rapid horizontal spread of the virus in this population, most strongly directed to the region between V3 and V4.
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Affiliation(s)
- R B Oelrichs
- AIDS Molecular Biology Unit, Macfarlane Burnet Centre for Medical Research, Fairfield, Victoria 3078, Australia.
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Lukashov VV, Huismans R, Rakhmanova AG, Lisitsina ZN, Akhtyrskaya NA, Vlasov NN, Melnick OB, Goudsmit J. Circulation of subtype A and gagA/envB recombinant HIV type 1 strains among injecting drug users in St. Petersburg, Russia, correlates with geographical origin of infections. AIDS Res Hum Retroviruses 1999; 15:1577-83. [PMID: 10580409 DOI: 10.1089/088922299309874] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Countries of the former Soviet Union are experiencing an emerging HIV-1 epidemic due to a rapid expansion of HIV-1 among injecting drug users (IDUs). To study the molecular epidemiology of HIV-1 among IDUs in St. Petersburg, Russia, virus sequences were obtained from 22 individuals. Phylogenetic analysis of the env and gag regions revealed circulation of two major HIV-1 populations, one belonging to HIV-1 subtype A, and another being a recombinant of subtype A and B viruses (gagA/envB). Both virus populations were highly homogeneous, with a mean pairwise genetic distance of <2%, and similar to viruses obtained earlier from IDUs in other regions of the former Soviet Union. Distribution of the two major HIV-1 genotypes in St. Petersburg correlated with geographical origin of infections. In one individual, a virus type previously unseen among IDUs was found, which demonstrates the possibility that new viruses are entering this risk group.
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Affiliation(s)
- V V Lukashov
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, The Netherlands
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Dehne KL, Grund JPC, Khodakevich L, Kobyshcha Y. The HIV/AIDS Epidemic among Drug Injectors in Eastern Europe: Patterns, Trends and Determinants. JOURNAL OF DRUG ISSUES 1999. [DOI: 10.1177/002204269902900402] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Our objective is to describe recent patterns and trends in HIV and injecting drug use and to explore possible determinants of the epidemics in eastern Europe. The available data confirm a rapid spread of HIV among injecting drug users (IDUs) in the newly independent states (NIS) and suggest that all successor states of the former Soviet Union are now threatened by such epidemics, while central and southeast Europe have so far been spared from large-scale outbreaks and seem at lower risk. The future course of the epidemic in the NIS will largely depend on trends in drug injecting and on the success of harm reduction programs. Furthermore, there is potential for the further spread of HIV, via heterosexual intercourse, into the general population.
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Plantier JC, Damond F, Lasky M, Sankalé JL, Apetrei C, Peeters M, Buzelay L, M'Boup S, Kanki P, Delaporte E, Simon F, Barin F. V3 serotyping of HIV-1 infection: correlation with genotyping and limitations. JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES AND HUMAN RETROVIROLOGY : OFFICIAL PUBLICATION OF THE INTERNATIONAL RETROVIROLOGY ASSOCIATION 1999; 20:432-41. [PMID: 10225224 DOI: 10.1097/00042560-199904150-00004] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
HIV-1 V3 serotyping is a classification of immunodeficiency viruses based on antibody binding to V3 peptides that allows obtaining information on circulating subtypes that could be important for population-based epidemiologic studies. Recently, several laboratories have developed V3 enzyme-immunoassays (EIAs) using V3 peptides of subtypes A to E. In the present study, the utility of including additional peptides of subtypes F to H to the EIA was evaluated on a panel of 203 well-characterized serum samples from patients with diverse geographic origins (22 countries) and known HIV-1 genotype (79 A, 61 B, 21 C, 7 D, 7 E, 21 F, 6 G, 1 H). The results indicate a high predictive value (ppv) for serotypes B (> or =0.86), D (1) and E (0.88), and confirm the difficulty of predicting genotype A or C based on serotype A or C. Results also indicate that inclusion of the F peptide in the V3 EIAs may be useful (ppv = 0.61), but introduction of peptides G and H failed to demonstrate significant sensitivity or specificity for these subtypes. Correlation between serotyping and amino-acid sequences of the V3 region from 103 samples allowed the identification of key amino-acids that appear essential for subtype-specific seroreactivity.
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Affiliation(s)
- J C Plantier
- Laboratoire de Virologie, Université François Rabelais, Tours, France
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