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Antonova A, Kazennova E, Lebedev A, Ozhmegova E, Kuznetsova A, Tumanov A, Bobkova M. Recombinant Forms of HIV-1 in the Last Decade of the Epidemic in the Russian Federation. Viruses 2023; 15:2312. [PMID: 38140553 PMCID: PMC10748268 DOI: 10.3390/v15122312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Currently, HIV-1 displays a substantial level of genetic diversity on a global scale, partly attributed to its recombinant variants. This study seeks to identify and analyze HIV-1 recombinants in Russia during the last decade of the epidemic. A comprehensive examination was conducted, encompassing 3178 partial pol sequences. Subtyping was achieved through various programs including COMET, the Stanford Database, REGA, jpHMM, RIP, and RDP4 for recombination analysis. The study also involved phylogenetic analysis to trace the origins of the identified recombinants. Primary resistance (PrimDR) prevalence and Drug Resistance Mutations (DRMs) were assessed. The study uncovered an overall proportion of recombinants at 8.7%, with a statistically significant increase in their frequency observed over time (p < 0.001). The Northwestern (18.5%) and Siberian (15.0%) Federal Districts exhibited a high prevalence of recombinants, while the Volga (1.9%) and Ural (2.8%) Federal Districts had a lower prevalence. Among HIV-1 recombinants, a PrimDR prevalence of 11.4% was identified. Notably, significant differences in DRMs were observed, with a higher prevalence of M184V in sub-subtype A6 (p = 0.018) and K103N in CRF63_02A6 (p = 0.002). These findings underscore the increasing HIV-1 genetic diversity and highlight a substantial prevalence of PrimDR among its recombinant forms, emphasizing the necessity for ongoing systematic monitoring.
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Affiliation(s)
- Anastasiia Antonova
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Elena Kazennova
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Aleksey Lebedev
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Ekaterina Ozhmegova
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Anna Kuznetsova
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Aleksandr Tumanov
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Marina Bobkova
- I. Mechnikov Research Institute for Vaccines and Sera, 105064 Moscow, Russia;
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Lai A, Simonetti FR, Brindicci G, Bergna A, Di Giambenedetto S, Sterrantino G, Mussini C, Menzo S, Bagnarelli P, Zazzi M, Angarano G, Galli M, Monno L, Balotta C. Local Epidemics Gone Viral: Evolution and Diffusion of the Italian HIV-1 Recombinant Form CRF60_BC. Front Microbiol 2019; 10:769. [PMID: 31031735 PMCID: PMC6474184 DOI: 10.3389/fmicb.2019.00769] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/26/2019] [Indexed: 12/15/2022] Open
Abstract
The molecular epidemiology of HIV-1 in Italy is becoming increasingly complex, mainly due to the spread of non-B subtypes and the emergence of new recombinant forms. We previously characterized the outbreak of the first Italian circulating recombinant form (CRF60_BC), occurring among young MSM living in Apulia between the years 2009 and 2011. Here we show a 5-year follow-up surveillance to trace the evolution of CRF60_BC and to investigate its further spread in Italy. We collected additional sequences and clinical data from patients harboring CRF60_BC, enrolled at the Infectious Diseases Clinic of the University of Bari. In addition to the 24 previously identified sequences, we retrieved 27 CRF60_BC sequences from patients residing in Apulia, whose epidemiological and clinical features did not differ from those of the initial outbreak, i.e., the Italian origin, young age at HIV diagnosis (median: 24 years; range: 18–37), MSM risk factor (23/25, 92%) and recent infection (from 2008 to 2017). Sequence analysis revealed a growing overall nucleotide diversity, with few nucleotide changes that were fixed over time. Twenty-seven additional sequences were detected across Italy, spanning multiple distant regions. Using a BLAST search, we also identified a CRF60_BC sequence isolated in United Kingdom in 2013. Three patients harbored a unique second generation recombinant form in which CRF60_BC was one of the parental strains. Our data show that CRF60_BC gained epidemic importance, spreading among young MSM in multiple Italian regions and increasing its population size in few years, as the number of sequences identified so far has triplicated since our first report. The observed further divergence of CRF60_BC is likely due to evolutionary bottlenecks and host adaptation during transmission chains. Of note, we detected three second-generation recombinants, further supporting a widespread circulation of CRF60_BC and the increasing complexity of the HIV-1 epidemic in Italy.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | | | - Gaetano Brindicci
- Clinic of Infectious Diseases, University of Bari Aldo Moro, Bari, Italy
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | | | - Gaetana Sterrantino
- Division of Tropical and Infectious Diseases, Careggi Hospital, Florence, Italy
| | - Cristina Mussini
- Clinic of Infectious Diseases, University of Modena and Reggio Emilia, Modena, Italy
| | - Stefano Menzo
- Unit of Virology, Azienda Ospedaliero-Universitaria 'Ospedali Riuniti', Torrette, Italy
| | - Patrizia Bagnarelli
- Unit of Virology, Azienda Ospedaliero-Universitaria 'Ospedali Riuniti', Torrette, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Massimo Galli
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | - Laura Monno
- Clinic of Infectious Diseases, University of Bari Aldo Moro, Bari, Italy
| | - Claudia Balotta
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
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Delgado E, Benito S, Montero V, Cuevas MT, Fernández-García A, Sánchez-Martínez M, García-Bodas E, Díez-Fuertes F, Gil H, Cañada J, Carrera C, Martínez-López J, Sintes M, Pérez-Álvarez L, Thomson MM. Diverse Large HIV-1 Non-subtype B Clusters Are Spreading Among Men Who Have Sex With Men in Spain. Front Microbiol 2019; 10:655. [PMID: 31001231 PMCID: PMC6457325 DOI: 10.3389/fmicb.2019.00655] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 03/15/2019] [Indexed: 11/23/2022] Open
Abstract
In Western Europe, the HIV-1 epidemic among men who have sex with men (MSM) is dominated by subtype B. However, recently, other genetic forms have been reported to circulate in this population, as evidenced by their grouping in clusters predominantly comprising European individuals. Here we describe four large HIV-1 non-subtype B clusters spreading among MSM in Spain. Samples were collected in 9 regions. A pol fragment was amplified from plasma RNA or blood-extracted DNA. Phylogenetic analyses were performed via maximum likelihood, including database sequences of the same genetic forms as the identified clusters. Times and locations of the most recent common ancestors (MRCA) of clusters were estimated with a Bayesian method. Five large non-subtype B clusters associated with MSM were identified. The largest one, of F1 subtype, was reported previously. The other four were of CRF02_AG (CRF02_1; n = 115) and subtypes A1 (A1_1; n = 66), F1 (F1_3; n = 36), and C (C_7; n = 17). Most individuals belonging to them had been diagnosed of HIV-1 infection in the last 10 years. Each cluster comprised viruses from 3 to 8 Spanish regions and also comprised or was related to viruses from other countries: CRF02_1 comprised a Japanese subcluster and viruses from 8 other countries from Western Europe, Asia, and South America; A1_1 comprised viruses from Portugal, United Kingom, and United States, and was related to the A1 strain circulating in Greece, Albania and Cyprus; F1_3 was related to viruses from Romania; and C_7 comprised viruses from Portugal and was related to a virus from Mozambique. A subcluster within CRF02_1 was associated with heterosexual transmission. Near full-length genomes of each cluster were of uniform genetic form. Times of MRCAs of CRF02_1, A1_1, F1_3, and C_7 were estimated around 1986, 1989, 2013, and 1983, respectively. MRCA locations for CRF02_1 and A1_1 were uncertain (however initial expansions in Spain in Madrid and Vigo, respectively, were estimated) and were most probable in Bilbao, Spain, for F1_3 and Portugal for C_7. These results show that the HIV-1 epidemic among MSM in Spain is becoming increasingly diverse through the expansion of diverse non-subtype B clusters, comprising or related to viruses circulating in other countries.
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Affiliation(s)
- Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Sonia Benito
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Vanessa Montero
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - María Teresa Cuevas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Aurora Fernández-García
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain.,CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Mónica Sánchez-Martínez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Elena García-Bodas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Francisco Díez-Fuertes
- AIDS Immunopathogenesis Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Horacio Gil
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain.,European Program for Public Health Microbiology Training, European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Javier Cañada
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Carrera
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Martínez-López
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Marcos Sintes
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Lucía Pérez-Álvarez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Michael M Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
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Daw MA, El-Bouzedi A, Ahmed MO, Dau AA. Molecular and epidemiological characterization of HIV-1 subtypes among Libyan patients. BMC Res Notes 2017; 10:170. [PMID: 28454556 PMCID: PMC5410017 DOI: 10.1186/s13104-017-2491-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 04/24/2017] [Indexed: 12/31/2022] Open
Abstract
Background The epidemiological and clinical aspects of human immunodeficiency virus subtypes are of great interest worldwide. These subtypes are rarely studied in North African countries. Libya is a large country with the longest coast on the Mediterranean Sea, facing the Southern European countries. Studies on the characterization of HIV-1 subtypes are limited in Libya. This study aimed to determine the magnitude of the HIV problem among the Libyan population and to better understand the genetic diversity and the epidemiologic dynamics of HIV 1, as well as to correlate that with the risk factors involved. Methods A total of 159 HIV-1 strains were collected from 814 HIV positive patients from the four Libyan regions during a 16-year period (1995–2010). To determine the HIV-1 subtypes, genetic analysis and molecular sequencing were carried out using provirus polygene. Epidemiologic and demographic information was obtained from each participant and correlated with HIV-1 subtypes using logistic regression. Results The overall prevalence of HIV among Libyans ranged from 5 to 10 per 100,000 during the study period. It was higher among intravenous drug users (IVDUs) (53.9%), blood recipients (25.9%) and heterosexuals (17.6%) than by vertical transmission (2.6%). Prevalence was higher among males aged 20–40 years (M:F 1:6, P > 0.001). Among the 159 strains of HIV-1 available for typing, 117 strains (73.6%) were subtype B, 29 (18.2%) were CRF02_AG, and 13 (8.2%) were subtype A. HIV-1 subtype B was the most prevalent all over the country, and it was more prevalent in the Northern region, particularly among IVDUs (P < 0.001). GRF02_AG was common in the Eastern region, particularly among blood recipients while subtype A emerged in the Western region, particularly among IVDUs. Conclusions HIV-1 infection is emerging in Libya with a shifting prevalence of subtypes associated with the changing epidemiology of HIV-1 among risk groups. A genetic analysis of HIV-1 strains demonstrated low subtype heterogeneity with the evolution of subtype B, and CRF_20 AG, as well as HIV-1 subtype A. Our study highlights the importance of expanded surveillance programs to control HIV infection and the necessity of introducing public health strategies to target the risk groups, particularly IVDUs.
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Affiliation(s)
- Mohamed A Daw
- Department of Medical Microbiology, Faculty of Medicine, University of Tripoli, CC 82668, Tripoli, Libya. .,, Tripoli, Libya. .,Department of Medical Microbiology and Immunology, Faculty of Medicine, University of Tripoli, Tripoli, Libya.
| | - Abdallah El-Bouzedi
- Department of Laboratory Medicine, Faculty of Biotechnology, University of Tripoli, CC 82668, Tripoli, Libya
| | - Mohamed O Ahmed
- Department of Microbiology and Parasitology, Faculty of Veterinary, University of Tripoli, CC 82668, Tripoli, Libya
| | - Aghnyia A Dau
- Department of Surgery, Tripoli Medical Centre, Faculty of Medicine, University of Tripoli, CC 82668, Tripoli, Libya
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5
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Magiorkinis G, Angelis K, Mamais I, Katzourakis A, Hatzakis A, Albert J, Lawyer G, Hamouda O, Struck D, Vercauteren J, Wensing A, Alexiev I, Åsjö B, Balotta C, Gomes P, Camacho RJ, Coughlan S, Griskevicius A, Grossman Z, Horban A, Kostrikis LG, Lepej SJ, Liitsola K, Linka M, Nielsen C, Otelea D, Paredes R, Poljak M, Puchhammer-Stöckl E, Schmit JC, Sönnerborg A, Staneková D, Stanojevic M, Stylianou DC, Boucher CAB, Nikolopoulos G, Vasylyeva T, Friedman SR, van de Vijver D, Angarano G, Chaix ML, de Luca A, Korn K, Loveday C, Soriano V, Yerly S, Zazzi M, Vandamme AM, Paraskevis D. The global spread of HIV-1 subtype B epidemic. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2016; 46:169-179. [PMID: 27262355 PMCID: PMC5157885 DOI: 10.1016/j.meegid.2016.05.041] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/25/2016] [Accepted: 05/31/2016] [Indexed: 01/04/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) was discovered in the early 1980s when the virus had already established a pandemic. For at least three decades the epidemic in the Western World has been dominated by subtype B infections, as part of a sub-epidemic that traveled from Africa through Haiti to United States. However, the pattern of the subsequent spread still remains poorly understood. Here we analyze a large dataset of globally representative HIV-1 subtype B strains to map their spread around the world over the last 50years and describe significant spread patterns. We show that subtype B travelled from North America to Western Europe in different occasions, while Central/Eastern Europe remained isolated for the most part of the early epidemic. Looking with more detail in European countries we see that the United Kingdom, France and Switzerland exchanged viral isolates with non-European countries than with European ones. The observed pattern is likely to mirror geopolitical landmarks in the post-World War II era, namely the rise and the fall of the Iron Curtain and the European colonialism. In conclusion, HIV-1 spread through specific migration routes which are consistent with geopolitical factors that affected human activities during the last 50years, such as migration, tourism and trade. Our findings support the argument that epidemic control policies should be global and incorporate political and socioeconomic factors.
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Affiliation(s)
| | - Konstantinos Angelis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | - Ioannis Mamais
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | | | - Angelos Hatzakis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Glenn Lawyer
- Department of Computational Biology, Max Planck Institute for Informatics, Saarbrücken, Germany
| | | | - Daniel Struck
- Centre de Recherche Public de la Sante, Luxembourg, Luxembourg
| | - Jurgen Vercauteren
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Annemarie Wensing
- Department of Virology, University Medical Center, Utrecht, The Netherlands
| | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | | | - Perpétua Gomes
- Molecular Biology Lab, LMCBM, SPC, HEM, Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - Ricardo J Camacho
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | | | | | | | | | | | - Snjezana J Lepej
- Department of Molecular Diagnostics and Flow Cytometry, University Hospital for Infectious Diseases "Dr. F. Mihaljevic", Zagreb, Croatia
| | - Kirsi Liitsola
- National Institute of Health and Welfare, Helsinki, Finland
| | - Marek Linka
- National Reference Laboratory of AIDS, National Institute of Health, Prague, Czech Republic
| | | | - Dan Otelea
- National Institute for Infectious Diseases "Prof. Dr. Matei Bals", Bucharest, Romania
| | | | - Mario Poljak
- Slovenian HIV/AIDS Reference Centre, University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia
| | | | | | - Anders Sönnerborg
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden; Divisions of Infectious Diseases and Clinical Virology, Karolinska Institute, Stockholm, Sweden
| | | | - Maja Stanojevic
- University of Belgrade Faculty of Medicine, Belgrade, Serbia
| | | | | | - Georgios Nikolopoulos
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | | | - Samuel R Friedman
- Institute of Infectious Diseases Research, National Development and Research Institutes, Inc., New York, USA
| | - David van de Vijver
- Eijkman Winkler Institute, Department of Virology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Andrea de Luca
- Institute of Clinical Infectious Diseases, Catholic university, Rome, Italy
| | - Klaus Korn
- University of Erlangen, Erlangen, Germany
| | - Clive Loveday
- International Clinical Virology Centre, Buckinghamshire, England, United Kingdom
| | | | | | | | - Anne-Mieke Vandamme
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece.
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Multiple introductions and onward transmission of non-pandemic HIV-1 subtype B strains in North America and Europe. Sci Rep 2016; 6:33971. [PMID: 27653834 PMCID: PMC5032033 DOI: 10.1038/srep33971] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/06/2016] [Indexed: 12/28/2022] Open
Abstract
Most HIV-1 subtype B infections in North America and Europe seem to have resulted from the expansion of a single pandemic lineage (BPANDEMIC) disseminated from the United States (US). Some non-pandemic subtype B strains of Caribbean origin (BCAR) may have also reached North America and Europe, but their epidemiological relevance in those regions remains largely unknown. Here we analyze a total of 20,045 HIV-1 subtype B pol sequences from the US, Canada, and Europe, to estimate the prevalence and to reconstruct the spatiotemporal dynamics of dissemination of HIV-1 BCAR strains in those regions. We find that BCAR strains were probably disseminated from the Caribbean into North America and Europe at multiple times since the early 1970s onwards. The BCAR strains reached the US, Canada and at least 16 different European countries, where they account for a very low fraction (<5%) of subtype B infections, with exception of the Czech Republic (7.7%). We also find evidence of the onward transmission of BCAR clades in the US, Canada, the Czech Republic, Germany, Italy, Spain and the UK, as well as short-distance spreading of BCAR lineages between neighboring European countries from Central and Western Europe, and long-distance dissemination between the US and Europe.
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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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8
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Junqueira DM, Almeida SEDM. HIV-1 subtype B: Traces of a pandemic. Virology 2016; 495:173-84. [PMID: 27228177 DOI: 10.1016/j.virol.2016.05.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/01/2016] [Accepted: 05/03/2016] [Indexed: 11/18/2022]
Abstract
Human migration is a major process that shaped the origin and dissemination of HIV. Within HIV-1, subtype B (HIV-1B) is the most disseminated variant and it is assumed to be the causative agent in approximately 11% of all cases of HIV worldwide. Phylogenetic studies have revealed that HIV-1B emerged in Kinshasa (Africa) and was introduced into the Caribbean region via Haiti in or around 1966 by human migration. After localized dispersion, the virus was brought to the United States of America via homosexual/bisexual contact around 1969. Inside USA, the incidence of HIV-1B infection increased exponentially and it became established in the population, affecting not only homosexual individuals but also heterosexual individuals and injecting drug users. Soon after, the virus was disseminated and became established in other regions, including Europe, Asia, Latin America, and Australia. Recent studies suggest that, in addition to this pandemic clade, several lineages have emerged from Haiti and reached other Caribbean and Latin American countries via short-distance dissemination. Different subtype B genetic variants have also been detected in these epidemics. Four genetic variants have been described to date: subtype B', which mainly circulates in Thailand and other Asian countries; a specific variant mainly found in Trinidad and Tobago; the GPGS variant, which is primarily detected in Korea; and the GWGR variant, which is mainly detected in Brazil. This paper reviews the evolution of HIV-1B and its impact on the human population.
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Affiliation(s)
- Dennis Maletich Junqueira
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Fundação Estadual de Produção e Pesquisa em Saúde (FEPPS), Avenida Ipiranga, 5400 - Jd Botânico, Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Avenida Bento Gonçalves, 9800 - Agronomia, Porto Alegre, RS, Brazil; Centro Universitário Ritter dos Reis - UniRitter, Departamento de Ciências da Saúde, Avenida Orfanotrófio, 555 - Teresópolis, Porto Alegre, RS, Brazil.
| | - Sabrina Esteves de Matos Almeida
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Fundação Estadual de Produção e Pesquisa em Saúde (FEPPS), Avenida Ipiranga, 5400 - Jd Botânico, Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Avenida Bento Gonçalves, 9800 - Agronomia, Porto Alegre, RS, Brazil; Instituto de Ciências da Saúde, Universidade FEEVALE, Rodovia RS 239, 2755 - Vila Nova, Novo Hamburgo, RS, Brazil.
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9
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Esbjörnsson J, Mild M, Audelin A, Fonager J, Skar H, Bruun Jørgensen L, Liitsola K, Björkman P, Bratt G, Gisslén M, Sönnerborg A, Nielsen C, Medstrand P, Albert J. HIV-1 transmission between MSM and heterosexuals, and increasing proportions of circulating recombinant forms in the Nordic Countries. Virus Evol 2016; 2:vew010. [PMID: 27774303 PMCID: PMC4989887 DOI: 10.1093/ve/vew010] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Increased knowledge about HIV-1 transmission dynamics in different transmission groups and geographical regions is fundamental for assessing and designing prevention efforts against HIV-1 spread. Since the first reported cases of HIV infection during the early 1980s, the HIV-1 epidemic in the Nordic countries has been dominated by HIV-1 subtype B and MSM transmission. HIV-1 pol sequences and clinical data of 51 per cent of all newly diagnosed HIV-1 infections in Sweden, Denmark, and Finland in the period 2000-2012 (N = 3,802) were analysed together with a large reference sequence dataset (N = 4,537) by trend analysis and phylogenetics. Analysis of the eight dominating subtypes and CRFs in the Nordic countries (A, B, C, D, G, CRF01_AE, CRF02_AG, and CRF06_cpx) showed that the subtype B proportion decreased while the CRF proportion increased over the study period. A majority (57 per cent) of the Nordic sequences formed transmission clusters, with evidence of mixing both geographically and between transmission groups. Detailed analyses showed multiple occasions of transmissions from MSM to heterosexuals and that active transmission clusters more often involved single than multiple Nordic countries. The strongest geographical link was between Denmark and Sweden. Finally, Denmark had a larger proportion of heterosexual domestic spread of HIV-1 subtype B (75 per cent) compared with Sweden (49 per cent) and Finland (57 per cent). We describe different HIV-1 transmission patterns between countries and transmission groups in a large geographical region. Our results may have implications for public health interventions in targeting HIV-1 transmission networks and identifying where to introduce such interventions.
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Affiliation(s)
- Joakim Esbjörnsson
- Department of Microbiology Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- REGA Institute, Katholieke Universiteit, Leuven, Belgium
| | - Mattias Mild
- Department of Microbiology, Public Health Agency of Sweden, Stockholm, Sweden
| | - Anne Audelin
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Helena Skar
- Department of Science and Technology, Linköping University, Campus Norrköping, Norrköping, Sweden
| | - Louise Bruun Jørgensen
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Kirsi Liitsola
- Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki, Finland
| | - Per Björkman
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Göran Bratt
- Department of Clinical Science and Education, Venhälsan, Stockholm South General Hospital, Stockholm, Sweden
| | - Magnus Gisslén
- Department of Infectious Diseases, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Anders Sönnerborg
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
- Division of Clinical Microbiology, Karolinska Institute, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Claus Nielsen
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - SPREAD/ESAR Programme
- Department of Microbiology Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- REGA Institute, Katholieke Universiteit, Leuven, Belgium
- Department of Microbiology, Public Health Agency of Sweden, Stockholm, Sweden
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
- Department of Science and Technology, Linköping University, Campus Norrköping, Norrköping, Sweden
- Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki, Finland
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
- Department of Clinical Science and Education, Venhälsan, Stockholm South General Hospital, Stockholm, Sweden
- Department of Infectious Diseases, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
- Division of Clinical Microbiology, Karolinska Institute, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Patrik Medstrand
- Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Jan Albert
- Department of Microbiology Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
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10
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van der Kuyl AC, Bakker M, Jurriaans S, Back NKT, Pasternak AO, Cornelissen M, Berkhout B. Translational HIV-1 research: from routine diagnostics to new virology insights in Amsterdam, the Netherlands during 1983-2013. Retrovirology 2013; 10:93. [PMID: 23985078 PMCID: PMC3765835 DOI: 10.1186/1742-4690-10-93] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 08/21/2013] [Indexed: 02/07/2023] Open
Abstract
An HIV-1 diagnostic laboratory was established in the Academic Medical Center (AMC) of the University of Amsterdam after the discovery of human immunodeficiency virus (HIV) as the cause of the acquired immunodeficiency syndrome (AIDS). The first AIDS patients were diagnosed here in 1981 and since 1983 we have tested the samples of 50992 patients using a variety of assays that greatly improved over the years. We will describe some of the basic results from this diagnostic laboratory and then focus on the spin-off in terms of the development of novel virus assays to detect super-infections and ultra-sensitive assays to measure the intracellular HIV-1 RNA load. We also review several original research findings in the field of HIV-1 virology that stem from initial observations made in the diagnostic unit. This includes the study of genetic defects in the HIV-1 genome and time trends of the replication fitness over 30 years of viral evolution, but also the description of novel HIV-1 variants in difficult-to-diagnose clinical specimen.
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Affiliation(s)
- Antoinette C van der Kuyl
- Laboratory of Experimental Virology, Academic Medical Center of the University of Amsterdam, Amsterdam, the Netherlands.
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11
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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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12
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Transmission of risk-group specific HIV-1 strains among Dutch drug users for more than 20 years and their replacement by nonspecific strains after switching to low-harm drug practices. J Acquir Immune Defic Syndr 2013; 62:234-8. [PMID: 23117501 DOI: 10.1097/qai.0b013e318279734d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES To characterize HIV-1 epidemiological networks of men having sex with men (MSM) and drug users (DUs) in the Netherlands for >30 years. DESIGN AND METHODS Previously, we demonstrated different origin of the HIV-1 epidemics in Dutch MSM and DUs. To achieve the study objectives, risk group-specific genetic markers in the pol gene were examined in 315 participants of the Amsterdam Cohort Studies on HIV/AIDS who were registered as HIV-1 infected in 1981-2011. RESULTS Phylogenetic analysis demonstrated circulation of distinct virus strains in the 2 networks, with 98% of viruses of MSM clustering together and apart from strains of 73% DUs. Nine genetic markers that significantly distinguished virus strains specific for DUs were identified, of which 3 were ≥90% conserved. Over the total observation period, only 6% of viruses (4 of MSM and 14 of DUs) clustered with those of the other risk group. Among these sequences, the 3 most conserved genetic markers of that other risk group were 87% conserved.All 4 cases of DU-specific viruses among MSM occurred in 1980s-early 1990s. Viruses nonspecific for DUs were causing new infections among DUs at the rate of 20% till 2002 and replaced DU-specific strains among new infections thereafter, coinciding with switching of DUs to low-harm drug practices. CONCLUSIONS Dutch MSM and DUs have remained separate epidemiological networks for decades, despite their geographical and behavioral overlap. Switching to low-harm drug practices among DUs resulted in new infections caused by HIV-1 strains originating from other risk groups.
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13
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Ciccozzi M, Lai A, Ebranati E, Gabanelli E, Galli M, Mugosa B, Vratnica Z, Vujoševic D, Lauševic D, Ciotti M, Cella E, Lo Presti A, Zehender G. Phylogeographic reconstruction of HIV type 1B in Montenegro and the Balkan region. AIDS Res Hum Retroviruses 2012; 28:1280-4. [PMID: 22364163 DOI: 10.1089/aid.2011.0138] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Human immunodeficiency virus (HIV) is one of the most genetically variable human viruses as it is characterized by high rates of mutation, viral replication, and recombination. Phylodynamics is a powerful means of describing the behavior of an infection as a combination of evolutionary and ecological processes. Only a few studies of HIV-1 molecular epidemiology have so far been carried out in the Balkans. In this study, we used Bayesian methods to reconstruct the phylogeography and phylodynamics of HIV-1B in Montenegro and some other Balkan countries on the basis of pol gene sequences retrieved from a public database. The phylogenetic analysis showed that 43% of the isolates grouped in accordance with their geographic area, whereas the majority were interspersed in the tree, thus confirming the multiple introductions of HIV-1B in the Balkans. The Bayesian phylogeographic analysis suggested that HIV-1B entered the Balkans in the early 1970s probably through Greece and other Mediterranean tourist/travel destinations (such as Slovenia). Other Balkan countries, such as Bulgaria and Serbia, may have played an important role in spreading the infection to the entire Eastern Mediterranean area, and possibly to Northeast Europe. This suggests that the Balkans may have played a role as a "gateway" between Western and Eastern Europe.
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Affiliation(s)
- Massimo Ciccozzi
- Epidemiology Unit, Department of Infectious, Parasitic and Immune-Mediated Diseases, Italian Institute of Health, Rome, Italy
| | - Alessia Lai
- Department of Clinical Sciences, L. Sacco Hospital, Section of Infectious Diseases and Immunopathology, University of Milan, Milan, Italy
| | - Erika Ebranati
- Department of Clinical Sciences, L. Sacco Hospital, Section of Infectious Diseases and Immunopathology, University of Milan, Milan, Italy
| | - Elena Gabanelli
- Department of Clinical Sciences, L. Sacco Hospital, Section of Infectious Diseases and Immunopathology, University of Milan, Milan, Italy
| | - Massimo Galli
- Department of Clinical Sciences, L. Sacco Hospital, Section of Infectious Diseases and Immunopathology, University of Milan, Milan, Italy
| | - Boban Mugosa
- Institute of Public Health, Podgorica, Montenegro
| | | | | | | | - Marco Ciotti
- Laboratory of Molecular Virology, Foundation Polyclinic Tor Vergata, Rome, Italy
| | - Eleonora Cella
- Epidemiology Unit, Department of Infectious, Parasitic and Immune-Mediated Diseases, Italian Institute of Health, Rome, Italy
| | - Alessandra Lo Presti
- Epidemiology Unit, Department of Infectious, Parasitic and Immune-Mediated Diseases, Italian Institute of Health, Rome, Italy
| | - Gianguglielmo Zehender
- Department of Clinical Sciences, L. Sacco Hospital, Section of Infectious Diseases and Immunopathology, University of Milan, Milan, Italy
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14
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Rusine J, Jurriaans S, van de Wijgert J, Cornelissen M, Kateera B, Boer K, Karita E, Mukabayire O, de Jong M, Ondoa P. Molecular and phylogeographic analysis of human immuno-deficiency virus type 1 strains infecting treatment-naive patients from Kigali, Rwanda. PLoS One 2012; 7:e42557. [PMID: 22905148 PMCID: PMC3419187 DOI: 10.1371/journal.pone.0042557] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 07/09/2012] [Indexed: 01/18/2023] Open
Abstract
This study aimed at describing the genetic subtype distribution of HIV-1 strains circulating in Kigali and their epidemiological link with the HIV-1 strains from the five countries surrounding Rwanda. One hundred and thirty eight pol (RT and PR) sequences from 116 chronically- and 22 recently-infected antiretroviral therapy (ART)-naïve patients from Kigali were generated and subjected to HIV drug resistance (HIV-DR), phylogenetic and recombinant analyses in connection with 366 reference pol sequences from Rwanda, Burundi, Kenya, Democratic Republic of Congo, Tanzania and Uganda (Los Alamos database). Among the Rwandan samples, subtype A1 predominated (71.7%), followed by A1/C recombinants (18.1%), subtype C (5.8%), subtype D (2.9%), one A1/D recombinant (0.7%) and one unknown subtype (0.7%). Thirteen unique and three multiple A1/C recombinant forms were identified. No evidence for direct transmission events was found within the Rwandan strains. Molecular characteristics of HIV-1 were similar between chronically and recently-infected individuals and were not significantly associated with demographic or social factors. Our report suggests that the HIV-1 epidemic in Kigali is characterized by the emergence of A1/C recombinants and is not phylogenetically connected with the HIV-1 epidemic in the five neighboring countries. The relatively low level of transmitted HIV-DR mutations (2.9%) reported here indicates the good performance of the ART programme in Rwanda. However, the importance of promoting couples' counseling, testing and disclosure during HIV prevention strategies is highlighted.
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Affiliation(s)
- John Rusine
- National Reference Laboratory, Kigali, Rwanda
| | - Suzanne Jurriaans
- Laboratory of Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | - Janneke van de Wijgert
- Department of Global Health, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | - Marion Cornelissen
- Laboratory of Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | - Brenda Kateera
- Department of Global Health, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
- The Infectious Diseases Network for Treatment and Research in Africa (INTERACT) Project, Kigali, Rwanda
- Royal Tropical Institute (KIT), Biomedical Research, Epidemiology Unit, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | - Kimberly Boer
- Department of Global Health, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
- The Infectious Diseases Network for Treatment and Research in Africa (INTERACT) Project, Kigali, Rwanda
- Royal Tropical Institute (KIT), Biomedical Research, Epidemiology Unit, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | | | | | - Menno de Jong
- Laboratory of Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | - Pascale Ondoa
- Department of Global Health, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
- * E-mail:
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15
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Abstract
The HIV epidemic in higher-income nations is driven by receptive anal intercourse, injection drug use through needle/syringe sharing, and, less efficiently, vaginal intercourse. Alcohol and noninjecting drug use increase sexual HIV vulnerability. Appropriate diagnostic screening has nearly eliminated blood/blood product-related transmissions and, with antiretroviral therapy, has reduced mother-to-child transmission radically. Affected subgroups have changed over time (e.g., increasing numbers of Black and minority ethnic men who have sex with men). Molecular phylogenetic approaches have established historical links between HIV strains from central Africa to those in the United States and thence to Europe. However, Europe did not just receive virus from the United States, as it was also imported from Africa directly. Initial introductions led to epidemics in different risk groups in Western Europe distinguished by viral clades/sequences, and likewise, more recent explosive epidemics linked to injection drug use in Eastern Europe are associated with specific strains. Recent developments in phylodynamic approaches have made it possible to obtain estimates of sequence evolution rates and network parameters for epidemics.
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Affiliation(s)
- Sten H Vermund
- Institute for Global Health and Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
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16
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Paraschiv S, Otelea D, Batan I, Baicus C, Magiorkinis G, Paraskevis D. Molecular typing of the recently expanding subtype B HIV-1 epidemic in Romania: evidence for local spread among MSMs in Bucharest area. INFECTION GENETICS AND EVOLUTION 2012; 12:1052-7. [PMID: 22430050 PMCID: PMC3778987 DOI: 10.1016/j.meegid.2012.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 02/21/2012] [Accepted: 03/04/2012] [Indexed: 02/04/2023]
Abstract
HIV-1 subtype B is predominant in Europe except in some countries from Eastern Europe which are characterized by a high prevalence of non-B subtypes and circulating recombinant forms (CRFs). Romania is a particular case: the HIV-1 epidemic started with subtype F1 which is still the most prevalent. Previous studies have shown an increasing prevalence of subtype B which is the second most frequent one among the newly diagnosed individuals, followed by subtype C and several CRFs as well as unique recombinant forms (URFs). Our objective was to analyze in detail the characteristics (way of dispersal, association with transmission risk groups) of the subtype B infections in Romania by means of phylogenetic analysis. Among all the individuals sampled during 2003-2010, 71 out of 1127 patients (6.3%) have been identified to be infected with subtype B strains. The most frequent route of infection identified in HIV-1 subtype B patients in Romania was MSM transmission (39.6%), followed by the heterosexual route (35.2%). Many of the patients acquired the infection abroad, mainly in Western European countries. Phylogenetic analysis indicated the existence of a local transmission network (monophyletic clade) including 14 patients, mainly MSM living in the Bucharest area. We estimate the origin of the local transmission network that dates at the beginning of the 90s; the introduction of the F1 and C subtypes occurred earlier. The rest of the sequences were intermixed with reference strains sampled across Europe suggesting that single infection were not followed by subsequent dispersal within the local population. Although HIV-1 subtype B epidemic in Romania is recent, there is evidence for local spread among the MSMs, in addition to multiple introductions.
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Affiliation(s)
- Simona Paraschiv
- Molecular Diagnostics Laboratory, Prof. Dr. Matei Bals National Institute for Infectious Diseases, Str. Calistrat Grozovici, Nr. 1, Sector 2, 021105 Bucharest, Romania
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17
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Dynamics of two separate but linked HIV-1 CRF01_AE outbreaks among injection drug users in Stockholm, Sweden, and Helsinki, Finland. J Virol 2010; 85:510-8. [PMID: 20962100 DOI: 10.1128/jvi.01413-10] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Detailed phylogenetic analyses were performed to characterize an HIV-1 outbreak among injection drug users (IDUs) in Stockholm, Sweden, in 2006. This study investigated the source and dynamics of HIV-1 spread during the outbreak as well as associated demographic and clinical factors. Seventy Swedish IDUs diagnosed during 2004 to 2007 were studied. Demographic, clinical, and laboratory data were collected, and the V3 region of the HIV-1 envelope gene was sequenced to allow detailed phylogenetic analyses. The results showed that the Stockholm outbreak was caused by a CRF01_AE variant imported from Helsinki, Finland, around 2003, which was quiescent until the outbreak started in 2006. Local Swedish subtype B variants continued to spread at a lower rate. The number of new CRF01_AE cases over a rooted phylogenetic tree accurately reflected the transmission dynamics and showed a temporary increase, by a factor of 12, in HIV incidence during the outbreak. Virus levels were similar in CRF01_AE and subtype B infections, arguing against differences in contagiousness. Similarly, there were no major differences in other baseline characteristics. Instead, the outbreak in Stockholm (and Helsinki) was best explained by an introduction of HIV into a standing network of previously uninfected IDUs. The combination of phylogenetics and epidemiological data creates a powerful tool for investigating outbreaks of HIV and other infectious diseases that could improve surveillance and prevention.
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18
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Lai A, Riva C, Marconi A, Balestrieri M, Razzolini F, Meini G, Vicenti I, Rosi A, Saladini F, Caramma I, Franzetti M, Rossini V, Galli A, Galli M, Violin M, Zazzi M, Balotta C. Changing patterns in HIV-1 non-B clade prevalence and diversity in Italy over three decades. HIV Med 2010; 11:593-602. [PMID: 20408891 DOI: 10.1111/j.1468-1293.2010.00832.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
BACKGROUND HIV-1 non-B subtypes have recently entered Western Europe following immigration from other regions. The distribution of non-B clades and their association with demographic factors, over the entire course of the HIV-1 epidemic, have not been fully investigated in Italy. METHODS We carried out a phylogenetic analysis of HIV-1 pol sequences derived from 3670 patients followed at 50 Italian clinical centres over nearly three decades. RESULTS Overall, 417 patients (11.4%) carried non-B subtypes. The prevalence of non-B strains increased from 2.6% in 1980-1992 to 18.9% in 1993-2008 (P<0.0001) in a subset of 2479 subjects with a known year of diagnosis. A multivariate analysis on a subset of 1364 patients for whom relevant demographic data were available indicated that African ethnicity, heterosexual route of infection and year of diagnosis were independently associated with non-B HIV-1 infection (P ≤ 0.0001). All pure subtypes, except for clade K, and seven circulating recombinant forms were detected, accounting for 56.6 and 34.1% of the non-B infections, respectively. The F1 subtype was the most prevalent non-B clade among Europeans and was acquired heterosexually in half of this patient population. Unique recombinant forms accounted for 9.4% of the non-B sequences and showed a B/F1 recombination pattern in one-third of cases. CONCLUSIONS The circulation of non-B clades has significantly increased in Italy in association with demographic changes. Spread of the F1 subtype and B/F recombinants appears to predominate, which may result in a redistribution of the relative proportions of the different strains, and this could lead to overlapping epidemics. Thus, the HIV-1 landscape in Italy may in future be distinct from that of the rest of Europe.
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Affiliation(s)
- A Lai
- Section of Infectious Diseases and Immunopathology, Department of Clinical Sciences, L Sacco Hospital, University of Milan, Milan, Italy.
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19
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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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Skar H, Sylvan S, Hansson HB, Gustavsson O, Boman H, Albert J, Leitner T. Multiple HIV-1 introductions into the Swedish intravenous drug user population. INFECTION GENETICS AND EVOLUTION 2008; 8:545-52. [PMID: 18472306 DOI: 10.1016/j.meegid.2008.03.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2007] [Revised: 03/25/2008] [Accepted: 03/27/2008] [Indexed: 10/22/2022]
Abstract
In 2001, an increase of HIV-1 diagnoses among intravenous drug users (IVDU) was reported in Sweden. In nearby countries, Finland, Russia and the Baltic states, recent outbreaks had been described. Since there was a concern that these outbreaks would carry over to Sweden a study was initiated to determine the factors leading to the Swedish increase of HIV-1 diagnosed IVDUs. HIV-1 env V3 sequences were obtained from 97 patients enrolled in ongoing epidemiological studies encompassing the years 1987--2004 with a focus on 2001--2002. The sequences were used for maximum likelihood and Bayesian inference of the molecular epidemiology. Among the virus spreading in 2001--2002, we found that four different subtypes/CRFs were present in the Swedish IVDU population (A, B, CRF01_AE and CRF06_cpx). Subtype B constituted 85% of the infections, established by 12 independent introductions into the IVDU population. The worrisome increase in 2001 was mainly not a result of import of the outbreaks in nearby countries, but rather a higher detection rate of secondary cases due to efficient epidemiological tracing of the generally slow spread of established forms of subtype B in the IVDU community. However, a few of the non-subtype B cases were linked to the outbreaks in Finland, Estonia and Latvia. Because HIV-1 outbreaks can easily be exported from one country to another amongst IVDUs, this prompts continued surveillance in the Baltic Sea Region.
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Affiliation(s)
- Helena Skar
- Department of Virology, Swedish Institute for Infectious Disease Control, SE-17182 Solna, Sweden
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21
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Esteves A, Parreira R, Piedade J, Venenno T, Franco M, Germano de Sousa J, Patrício L, Brum P, Costa A, Canas-Ferreira WF. Spreading of HIV-1 subtype G and envB/gagG recombinant strains among injecting drug users in Lisbon, Portugal. AIDS Res Hum Retroviruses 2003; 19:511-7. [PMID: 12892060 DOI: 10.1089/088922203766774568] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We have evaluated the genetic diversity of HIV-1 strains infecting injecting drug users (IDUs) in Lisbon, Portugal. Heteroduplex mobility assay and/or phylogenetic analysis revealed that env (C2V3C3 or gp41) subtype B is present in 63.7% of the 135 viral samples studied, followed by subtypes G (23.7%), A (6.7%), F (5.2%), and D (0.7%). Similar analysis of gag (p24/p7) performed on 91 of the specimens demonstrated that 49.5% of the infections were caused by subtype G viruses; other gag subtypes identified were B (39.5%), F (3.3%), A and D (1.1.% each), and the recombinant circulating form CRF02_AG (5.5%). Discordant env/gag sub-types were detected in 34.1% of the strains and may reflect the presence of dual infections and/or recombinant viruses. The presumptive B/G recombinant form was highly predominant (21 of 31). The genetic pattern of HIV-1 subtype B and G strains is suggestive of multiple introductions and recombination episodes and of a longstanding presence of both subtypes in the country. C2V3C3 amino acid sequences from IDU-derived subtype G viruses presented highly significant signatures, which distinguish the variants from this transmission group. The unusually high prevalence of subtype G sequences (34.1%), independent of the geographic origin of the infected individuals, makes this IDU HIV-1 epidemic unique.
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Affiliation(s)
- Aida Esteves
- Unidade de Virologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal.
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22
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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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23
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Abstract
To study the evolutionary relationships among astroviruses, all available sequences for members of the family Astroviridae were collected. Phylogenetic analysis distinguished two deep-rooted groups: one comprising mammalian astroviruses, with ovine astrovirus being an outlier, and the other comprising avian astroviruses. All virus species as well as serotypes of human astroviruses represented individual lineages within the tree. All human viruses clustered together and separately from non-human viruses, which argue for their common evolutionary origin and against ongoing animal-to-human transmissions. The branching order of mammalian astroviruses was exactly the opposite of that of their host species, suggesting at least two cross-species transmissions involving pigs, cats and humans, possibly through intermediate hosts. Analysis of synonymous (Ds) versus non-synonymous (Da) distances revealed that negative selection is dominating in the evolution of astroviruses, with the Ds:Da ratios being up to 46 for the comparisons of the most closely related viruses. Phylogenetic analyses of all open reading frames (ORFs) based on Ds resulted in the loss of tree structures, with virus species--and in ORF2, even serotypes of human astroviruses--branching out from virtually a single node, suggesting their ancient separation. The strong selection against non-synonymous substitutions, the low number of which is, therefore, not proof of a recent separation between lineages, together with the position of the oldest available human astrovirus strain (1971) far from the common node of its serotype 4, suggest that intraserotype diversification originates from an earlier date.
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Affiliation(s)
- Vladimir V Lukashov
- Amsterdam Institute of Viral Genomics, 1105 BA Amsterdam, The Netherlands2
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands1
| | - Jaap Goudsmit
- Amsterdam Institute of Viral Genomics, 1105 BA Amsterdam, The Netherlands2
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands1
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Nguyen L, Hu DJ, Choopanya K, Vanichseni S, Kitayaporn D, van Griensven F, Mock PA, Kittikraisak W, Young NL, Mastro TD, Subbarao S. Genetic analysis of incident HIV-1 strains among injection drug users in Bangkok: evidence for multiple transmission clusters during a period of high incidence. J Acquir Immune Defic Syndr 2002; 30:248-56. [PMID: 12045688 DOI: 10.1097/00042560-200206010-00014] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
During 1995-1996, 1,209 HIV-1-negative injection drug users (IDUs) attending methadone treatment clinics operated by the Bangkok Metropolitan Administration in Bangkok, Thailand, were enrolled in a prospective cohort study. Through 1998, 133 of these IDUs had seroconverted to HIV-1; 130 of these seroconverters were included in this study. HIV-1 CRF01_AE and subtype B strains accounted for 79% and 21% of the incident infections, respectively. To examine phylogenetic relationships among these incident HIV-1 strains, we used several phylogenetic inference methodologies to analyze the env (C2-V4) sequences in blood samples collected soon after seroconversion. These analyses consistently revealed eight phylogenetic clusters comprising 21 incident strains (bootstrap method, >80%; six CRF01_AE and two subtype B clusters). Two factors were found to be associated with the eight clusters. The first factor was temporal: seven of the eight clusters comprised 17 sequences from IDUs whose estimated dates of seroconversion were within a period of high incidence from July 1996 through January 1997. The second factor was a possible geographic association: four clusters were observed among IDUs who had attended the same methadone treatment clinics. These phylogenetic clusters likely represent subgroups within larger HIV transmission networks among IDUs in Bangkok. Despite prevention efforts, the incidence of HIV-1 infection among the Bangkok IDU population continues to be high. A better understanding of transmission networks and factors associated with such networks can help guide prevention efforts.
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Affiliation(s)
- Lily Nguyen
- Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
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Abebe A, Lukashov VV, Rinke De Wit TF, Fisseha B, Tegbaru B, Kliphuis A, Tesfaye G, Negassa H, Fontanet AL, Goudsmit J, Pollakis G. Timing of the introduction into Ethiopia of subcluster C' of HIV type 1 subtype C. AIDS Res Hum Retroviruses 2001; 17:657-61. [PMID: 11375063 DOI: 10.1089/088922201300119770] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Viruses circulating in Ethiopia during the 1990s cluster with main subtype C, but a significant subcluster, C', was noted in multiple analyses. This subcluster of subtype C(C') was in a fifty-fifty equilibrium with the main subtype C (Abebe et al., AIDS Res Hum Retroviruses 2000;16:1909-1914). To analyze genetic diversification within the subcluster of HIV-1 subtype C designated C' in the course of the epidemic in Ethiopia, we analyzed 165 env gp120 V3 sequences obtained between 1988 and 1999. We observed a highly significant positive correlation between sampling years of individual sequences and their synonymous distances to the reconstructed common ancestor of the HIV-1 subtype C' subcluster. The extrapolation of the regression line of synonymous distances back to the date when no synonymous heterogeneity was present among the Ethiopian HIV-1 C' population allowed us to estimate 1982 (95% CI, 1980-1983) as the year of the onset of HIV-1 C' genetic diversification and expansion in Ethiopia. These results are in agreement with retrospective epidemiological and serological data, which demonstrated the absence of an HIV-1 epidemic in the Ethiopian population before the 1980s.
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Affiliation(s)
- A Abebe
- Ethiopian-Netherlands AIDS Research Project (ENARP), Ethiopian Health and Nutrition Research Institute (EHNRI), Addis Ababa, Ethiopia.
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Lukashov VV, Goudsmit J. Evolutionary relationships among parvoviruses: virus-host coevolution among autonomous primate parvoviruses and links between adeno-associated and avian parvoviruses. J Virol 2001; 75:2729-40. [PMID: 11222696 PMCID: PMC115897 DOI: 10.1128/jvi.75.6.2729-2740.2001] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The current classification of parvoviruses is based on virus host range and helper virus dependence, while little data on evolutionary relationships among viruses are available. We identified and analyzed 472 sequences of parvoviruses, among which there were (virtually) full-length genomes of all 41 viruses currently recognized as individual species within the family Parvoviridae. Our phylogenetic analysis of full-length genomes as well as open reading frames distinguished three evolutionary groups of parvoviruses from vertebrates: (i) the human helper-dependent adeno-associated virus (AAV) serotypes 1 to 6 and the autonomous avian parvoviruses; (ii) the bovine, chipmunk, and autonomous primate parvoviruses, including human viruses B19 and V9; and (iii) the parvoviruses from rodents (except for chipmunks), carnivores, and pigs. Each of these three evolutionary groups could be further subdivided, reflecting both virus-host coevolution and multiple cross-species transmissions in the evolutionary history of parvoviruses. No parvoviruses from invertebrates clustered with vertebrate parvoviruses. Our analysis provided evidence for negative selection among parvoviruses, the independent evolution of their genes, and recombination among parvoviruses from rodents. The topology of the phylogenetic tree of autonomous human and simian parvoviruses matched exactly the topology of the primate family tree, as based on the analysis of primate mitochondrial DNA. Viruses belonging to the AAV group were not evolutionarily linked to other primate parvoviruses but were linked to the parvoviruses of birds. The two lineages of human parvoviruses may have resulted from independent ancient zoonotic infections. Our results provide an argument for reclassification of Parvovirinae based on evolutionary relationships among viruses.
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Affiliation(s)
- V V Lukashov
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
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27
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Op de Coul EL, Prins M, Cornelissen M, van der Schoot A, Boufassa F, Brettle RP, Hernández-Aguado L, Schiffer V, McMenamin J, Rezza G, Robertson R, Zangerle R, Goudsmit J, Coutinho RA, Lukashov VV. Using phylogenetic analysis to trace HIV-1 migration among western European injecting drug users seroconverting from 1984 to 1997. AIDS 2001; 15:257-66. [PMID: 11216936 DOI: 10.1097/00002030-200101260-00017] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To reconstruct the epidemiological relationships of the HIV epidemics among injecting drug users (IDU) in western Europe. METHODS HIV env V3 sequences of and epidemiological data were obtained from 145 IDU who seroconverted in three sequential periods: 1984-1988, 1989-1992 and 1993-1997. The sequences were phylogenetically analysed and examined for signature patterns characteristic of northern European IDU, including the conserved GGC codon in the V3 loop. RESULTS Subpopulations of genetically related HIV strains were observed in Italy, France, Scotland and Spain, in contrast to the Netherlands, Austria and Switzerland. This difference between the two groups of countries suggests that the HIV epidemics amongst IDU in the latter group was caused by multiple virus introductions. In Edinburgh and the surrounding area, most IDU were infected with the same GGC strain over the 12-year study period. The epidemic among IDU in north-western Europe started with GGC viruses, whereas in south-western Europe non-GGC viruses predominated. This geographical separation has faded during the course of the epidemic, most likely because of virus exchange among IDU populations.
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Affiliation(s)
- E L Op de Coul
- Division of Public Health and Environment, Municipal Health Service, Amsterdam, The Netherlands
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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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Casado C, Urtasun I, Saragosti S, Chaix ML, de Rossi A, Cattelan AM, Dietrich U, López-Galíndez C. Different distribution of HIV type 1 genetic variants in European patients with distinct risk practices. AIDS Res Hum Retroviruses 2000; 16:299-304. [PMID: 10710219 DOI: 10.1089/088922200309403] [Citation(s) in RCA: 15] [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 use of two genetic markers has permitted the analysis of the distribution of two different human immunodeficiency virus type 1 (HIV-1) variants in patients of the homosexual (HO) and intravenous drug user (IDU) groups in distinct European countries. In Germany, Holland, and Italy the variants circulating in each risk group of HO and IDU patients were genetically distinguishable according to the genetic markers used. In contrast, in France and Spain, the same variant has been recovered from patients with different risk practices. These data highlight the diversity of the HIV-1 epidemic in Europe and the different patterns of HIV-1 variant distribution in European countries.
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Affiliation(s)
- C Casado
- Centro Nacional de Biología Fundamental, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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30
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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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31
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Stoeckli TC, Steffen-Klopfstein I, Erb P, Brown TM, Kalish ML. Molecular epidemiology of HIV-1 in Switzerland: evidence for a silent mutation in the C2V3 region distinguishing intravenous drug users from homosexual men. Swiss HIV Cohort Study. J Acquir Immune Defic Syndr 2000; 23:58-67. [PMID: 10708057 DOI: 10.1097/00126334-200001010-00008] [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: 11/25/2022]
Abstract
OBJECTIVES To study the molecular epidemiology of HIV-1 strains found in Switzerland and to determine possible genetic linkages among strains sorted by risk group or geographic region. DESIGN A cross-sectional, clinic-based survey of HIV-1 molecular sequences and linked patient history from Swiss people. METHODS Specimens were collected from 215 HIV-1-infected people in HIV outpatient clinics of four tertiary referral centers (Lausanne, St. Gallen, Zurich, and Basel) between May and August 1996, mainly from homosexual men, injecting drug users (IDU), and heterosexually infected people. In addition, specimens collected between 1991 and 1995 in the HIV outpatient clinic at University of Geneva were included into this survey. These specimens were collected primarily for an ongoing, prospective cohort (Swiss HIV Cohort Study). Direct C2V3C3 sequences of the env gene were determined from 158 samples of peripheral blood mononuclear cells. Genetic data were analyzed with the available patient history on each specimen. RESULTS As found in other previous studies in Europe, primarily subtype B viruses were identified, whereas seven (4%) of 158 were non-subtype B: one subtype D, four subtype A, and two subtype E. Five of seven non-B subtypes occurred in immigrants from African or Asian countries and all seven were found exclusively in individuals who had been infected by heterosexual contact. No significant clustering of strains within different study sites or risk groups was found. A silent mutation (LAI env 834) occurred significantly more often in IDU than in homosexual men (p<.001). CONCLUSIONS Although the lack of significant clustering of strains by risk group or geographic region may result from early introduction of subtype B viruses in Switzerland, the strong association of a silent mutation with IDU suggests that, early in the epidemic, there was a unique founder virus among IDUs. The HIV epidemic in Switzerland is still predominantly caused by subtype B viruses.
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Affiliation(s)
- T C Stoeckli
- Division of AIDS, STD, and TB Laboratory Research, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
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Molecular Epidemiology of HIV-1 in Switzerland: Evidence for a Silent Mutation in the C2V3 Region Distinguishing Intravenous Drug Users From Homosexual Men. J Acquir Immune Defic Syndr 2000. [DOI: 10.1097/00042560-200001010-00008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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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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Günthard HF, Frost SD, Leigh-Brown AJ, Ignacio CC, Kee K, Perelson AS, Spina CA, Havlir DV, Hezareh M, Looney DJ, Richman DD, Wong JK. Evolution of envelope sequences of human immunodeficiency virus type 1 in cellular reservoirs in the setting of potent antiviral therapy. J Virol 1999; 73:9404-12. [PMID: 10516049 PMCID: PMC112975 DOI: 10.1128/jvi.73.11.9404-9412.1999] [Citation(s) in RCA: 158] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/1999] [Accepted: 07/09/1999] [Indexed: 11/20/2022] Open
Abstract
In human immunodeficiency virus (HIV)-infected patients treated with potent antiretroviral therapy, the persistence of latently infected cells may reflect the long decay half-life of this cellular reservoir or ongoing viral replication at low levels with continuous replenishment of the population or both. To address these possibilities, sequences encompassing the C2 and V3 domains of HIV-1 env were analyzed from virus present in baseline plasma and from viral isolates obtained after 2 years of suppressive therapy in six patients. The presence of sequence changes consistent with evolution was demonstrated for three subjects and correlated with less complete suppression of viral replication, as indicated by the rapidity of the initial virus load decline or the intermittent reappearance of even low levels of detectable viremia. Together, these results provide evidence for ongoing replication. In the remaining three patients, virus recovered after 2 years of therapy was either genotypically contemporary with or ancestral to virus present in plasma 2 years before, indicating that virus recovery had indeed resulted from activation of latently infected cells.
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Adwan G, Papa A, Kouidou S, Alexiou S, Malissiovas N, Ntoutsos I, Kiosses B, Antoniadis A. HIV type 1 sequences with GGC substitution in injecting drug users in Greece. AIDS Res Hum Retroviruses 1999; 15:679-80. [PMID: 10331447 DOI: 10.1089/088922299310980] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- G Adwan
- Department of Microbiology, School of Medicine, Aristotelian University of Thessaloniki, Greece
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Goudsmit J, Lukashov VV, van Ameijden EJ, Zorgdrager F, van den Burg R, Cornelissen M. Impact of sexual versus parenteral transmission events on the evolution of the gag and env genes of HIV type 1. AIDS Res Hum Retroviruses 1998; 14:1483-6. [PMID: 9824326 DOI: 10.1089/aid.1998.14.1483] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- J Goudsmit
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, The Netherlands
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Lukashov VV, Karamov EV, Eremin VF, Titov LP, Goudsmit J. Extreme founder effect in an HIV type 1 subtype A epidemic among drug users in Svetlogorsk, Belarus. AIDS Res Hum Retroviruses 1998; 14:1299-303. [PMID: 9764916 DOI: 10.1089/aid.1998.14.1299] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- V V Lukashov
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, The Netherlands
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Novitsky VA, Montano MA, Essex M. Molecular epidemiology of an HIV-1 subtype A subcluster among injection drug users in the Southern Ukraine. AIDS Res Hum Retroviruses 1998; 14:1079-85. [PMID: 9718124 DOI: 10.1089/aid.1998.14.1079] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Phylogenetic characterization of primary isolates from 17 HIV-1-infected individuals within a recent epidemic in the city of Odessa, Ukraine was conducted. The isolates were drawn from two time periods, 1993 and 1996. The 1996 isolates coincided with the first apparent expansion of HIV-1 among injection drug users (IDU). Multi-locus phylogenetic analysis indicated that HIV-1 gag, env, tat, and long terminal repeat (LTR) sequences all conformed to the HIV-1 classification of a subcluster within subtype A. There was no evidence for intersubtype recombinants among these isolates. A number of potential signature sequences, particularly within env, were identified in these two time periods, possibly suggesting a selective pressure on viral evolution among IDU. Results of this study are consistent with a recent introduction and subsequent independent evolution of an HIV-1 subtype A subcluster among IDU in the Southern Ukraine. This study demonstrates a congruence of multi-locus phylogenetic analysis, and suggests that non-B genetic subtypes, such as HIV-1 subtype A, may become relevant to the study of IDU transmission in the future.
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Affiliation(s)
- V A Novitsky
- Harvard AIDS Institute, Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, USA
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Op de Coul EL, Lukashov VV, van Doornum GJ, Goudsmit J, Coutinho RA. Multiple HIV-1 subtypes present amongst heterosexuals in Amsterdam 1988-1996: no evidence for spread of non-B subtypes. AIDS 1998; 12:1253-5. [PMID: 9677181 DOI: 10.1097/00002030-199810000-00024] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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40
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Estable MC, Merzouki A, Arella M, Sadowski IJ. Distinct clustering of HIV type 1 sequences derived from injection versus noninjection drug users in Vancouver, Canada. AIDS Res Hum Retroviruses 1998; 14:917-9. [PMID: 9671221 DOI: 10.1089/aid.1998.14.917] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- M C Estable
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
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Bobkov A, Kazennova E, Selimova L, Bobkova M, Khanina T, Ladnaya N, Kravchenko A, Pokrovsky V, Cheingsong-Popov R, Weber J. A sudden epidemic of HIV type 1 among injecting drug users in the former Soviet Union: identification of subtype A, subtype B, and novel gagA/envB recombinants. AIDS Res Hum Retroviruses 1998; 14:669-76. [PMID: 9618078 DOI: 10.1089/aid.1998.14.669] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The former Soviet Union republics have experienced an explosive human immunodeficiency virus type 1 (HIV-1) epidemic among injecting drug users (IDUs), consisting mainly of subtype A viruses originated from a point source (Bobkov et al.: AIDS Res Hum Retroviruses 1997;13:1195-1201). To determine whether new HIV-1 subtypes have entered the IDU population, 46 samples derived from IDUs in Russia (n = 39) and the Ukraine (n = 7) were genotyped by heteroduplex mobility assay (HMA). It was shown that 83% of IDU HIV-1 strains found in both countries belong to genetic subtype A. However, env subtype B was also found in 17% of cases. The sequence data showed a marked intrasubtype homogeneity of HIV-1 (the average means of interpatient genetic distance were 1.1 and 1.7% [in the gag gene] or 1.8 and 2.3% [in the env gene] for subtype A and subtype B, respectively), confirming the hypothesis of a point source of virus for each subtype variant. Moreover, recombinant gagA/envB variants originating from those two strains were also found in two samples collected in the Kaliningrad region of Russia. In conclusion, our results suggest that two strains of HIV-1 belonging to different genetic subtypes, A and B, as well as gagA/envB recombinants between genomes of these strains, are now circulating simultaneously among IDUs in the former Soviet Union.
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Affiliation(s)
- A Bobkov
- The D.I. Ivanovsky Institute of Virology, Moscow, Russia
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Lukashov VV, Op de Coul EL, Coutinho RA, Goudsmit J. HIV-1 strains specific for Dutch injecting drug users in heterosexually infected individuals in The Netherlands. AIDS 1998; 12:635-41. [PMID: 9583604 DOI: 10.1097/00002030-199806000-00013] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVE To study the molecular epidemiology of HIV-1 subtype B amongst heterosexually infected individuals in The Netherlands. DESIGN The study population comprised 54 individuals infected by subtype B viruses through heterosexual contacts. Serum samples were collected between 1988 and 1996. METHODS Sequences of the gp120 V3 region were obtained from serum samples and analysed by using the signature pattern and phylogenetic methods. RESULTS In 22 (41%) out of 54 subtype B sequences from heterosexually infected individuals, the synonymous nucleotide substitution in the second glycine codon at the tip of the V3 loop (the GGC pattern), previously identified as specific for Dutch injecting drug users (IDU), was found. The other previously described IDU sequence patterns were observed significantly more often among GGC- than among non-GGC-containing sequences. In addition, we identified another amino-acid change specific for the GGC sequences. In the phylogenetic and principal coordinate analyses, the GGC sequences from heterosexually infected individuals clustered separately from the non-GGC sequences and together with the IDU consensus sequence. Both the nonsynonymous and particularly the synonymous distances amongst the GGC sequences were significantly lower than amongst the non-GGC sequences. CONCLUSIONS Our data provide evidence for a common origin of the viruses in Dutch IDU and the GGC viruses in heterosexuals. We suggest that a considerable proportion of the viruses in heterosexually infected individuals in The Netherlands may have originated from Dutch IDU.
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Affiliation(s)
- V V Lukashov
- Department of Human Retrovirology, Academic Medical Centre, University of Amsterdam, The Netherlands
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Lukashov VV, Goudsmit J. Evolution of the human immunodeficiency virus type 1 subtype-specific V3 domain is confined to a sequence space with a fixed distance to the subtype consensus. J Virol 1997; 71:6332-8. [PMID: 9261350 PMCID: PMC191906 DOI: 10.1128/jvi.71.9.6332-6338.1997] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) strains can be separated into genetic subtypes based on phylogenetic analysis of the envelope gene. Once it had been shown that population-wide intrasubtype genetic variation of HIV-1 strains increases in the course of the AIDS epidemic, it remained uncertain whether HIV-1 subtypes are phenotypic entities spreading as distinct virus populations. To examine this, we applied Eigen's concepts of sequence geometry and fitness topography to the analysis of intrasubtype evolution of the gp120 V3 domain of HIV-1 subtypes A, B, C, and D in the course of the global AIDS epidemic. We observed that despite the high evolution rate of HIV-1, the nonsynonymous distances to the subtype consensus of sequences obtained early in the epidemic are similar to those obtained more than 10 years later, in contrast to the synonymous distances, which increased steadily over time. For HIV-1 subtype B, we observed that the evolution rate of the individual sequences is independent of their distance from the subtype B consensus, but for the individual sequences most distant from the consensus evolution away from the consensus is constrained. As a result, individual HIV-1 genomes fluctuate within a sequence space with fixed distance to the subtype consensus. Our findings suggest that the evolution of the V3 domain of HIV-1 subtypes A, B, C, and D is confined to an area in sequence space within a fixed distance to the consensus of a respective subtype. This in turn indicates that each HIV-1 subtype is a distinct viral quasispecies that is well adapted to the present environment, able to maintain its identity in the V3 region over time, and unlikely to merge during progression of the AIDS epidemic.
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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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Lukashov VV, Goudsmit J. Founder virus population related to route of virus transmission: a determinant of intrahost human immunodeficiency virus type 1 evolution? J Virol 1997; 71:2023-30. [PMID: 9032334 PMCID: PMC191287 DOI: 10.1128/jvi.71.3.2023-2030.1997] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We and others have shown that in individual human immunodeficiency virus type 1 (HIV-1) infection, the adaptive evolution of HIV-1 is influenced by host immune competence. In this study, we tested the hypothesis that in addition to selective forces operating within the host, transmission bottlenecks have an impact on HIV-1 intrahost evolution. Therefore, we studied the intrahost evolution of the V3 region of the external glycoprotein gp120 of HIV-1 during the 3- and 5-year periods following seroconversion after parenteral versus sexual (male-to-male) transmission in 41 participants of the Amsterdam prospective cohorts of homosexual men (n = 31) and intravenous drug users (IVDUs; n = 10) who were AIDS free and had comparable numbers of CD4+ cells. We observed that HIV-1 strains in homosexual men accumulated over 5 years more nonsynonymous substitutions within the V3 loop than HIV-1 strains in IVDUs as a result of lower rates of nonsynonymous evolution in both the initial 3-year period from seroconversion and the following 2-year period as well as a larger proportion of nonsynonymous back substitutions in IVDUs. The mean numbers of synonymous substitutions did not differ between the two risk groups. Since HIV-1 strains in IVDUs could be distinguished from the viruses of homosexual men based on several nucleotide substitutions of which the most conserved is a synonymous substitution at the tip of the V3 loop (GGC pattern), we studied whether the founder virus population itself has an impact on the intrahost evolution of HIV-1. The mean number of nonsynonymous substitutions accumulated over 5 years within the V3 loop was lower in 10 IVDUs infected by the HIV-1 strains with the GGC signature than in 4 IVDUs infected by HIV-1 strains lacking this pattern, while the mean numbers of synonymous substitutions were similar in the two groups.
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Affiliation(s)
- V V Lukashov
- Department of Human Retrovirology, University of Amsterdam, The Netherlands
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