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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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Shchemelev AN, Semenov AV, Ostankova YV, Naidenova EV, Zueva EB, Valutite DE, Churina MA, Virolainen PA, Totolian AA. [Genetic diversity of the human immunodeficiency virus (HIV-1) in the Kaliningrad region]. Vopr Virusol 2022; 67:310-321. [PMID: 36097712 DOI: 10.36233/0507-4088-119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
INTRODUCTION As is currently known, the epidemic process in the Kaliningrad Region was mainly associated with the spread of the recombinant form of HIV-1 (CRF03_AB); however, regular HIV importations from other countries and continents has created favorable conditions for emergence and spread of various recombinant forms of the virus.The most complete information on the diversity of recombinant forms in the region is also necessary to understand the structure of drug resistance (DR). The aim of the study was to explore the HIV-1 genetic diversity in the Kaliningrad Region. MATERIALS AND METHODS We studied 162 blood plasma samples obtained from patients from the Kaliningrad Region, both with confirmed virological failure of antiretroviral therapy (ART) and with newly diagnosed HIV infection. For reverse transcription and amplification of HIV genome fragments, diagnostic «AmpliSense HIVResist-Seq». RESULTS AND DISCUSSION The various recombinants between subtypes A and B (74%) were predominant in study group: recombinant was between CRF03_AB and subtype A (33.95%) and CRF03_AB-like (13.58%) were the most common. Among the "pure" subtypes of the virus, subtype A6 (16.67%). The circulation of subtypes B (3.70%) and G (1.23%) was also noted.Ninety-six patients (59.26%) were identified with at least one mutation associated with antiretroviral (ARV) drug resistance. CONCLUSION The observed diversity of subtypes and recombinant forms of the virus implies that the new recombinants are actively emerging in the studied region, both between existing recombinant forms and "pure" subtypes, as well as between "pure" subtypes.
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Affiliation(s)
- A N Shchemelev
- FBSI «Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology» of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)
| | - A V Semenov
- Ekaterinburg Research Institute of Viral Infections of the Federal Research Institute, State Research Center for Virology and Biotechnology "Vector" of the Consumer Rights Protection and Human Welfare (Rospotrebnadzor)
| | - Yu V Ostankova
- FBSI «Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology» of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)
| | - E V Naidenova
- FSSI Russian Research Anti-Plague Institute «Microbe» of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)
| | - E B Zueva
- FBSI «Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology» of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)
| | - D E Valutite
- FBSI «Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology» of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)
| | - M A Churina
- St. Petersburg GBUZ «Botkin Clinical Infectious Diseases Hospital»
| | - P A Virolainen
- FBSI «Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology» of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)
| | - A A Totolian
- FBSI «Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology» of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)
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Bennedbæk M, Zhukova A, Tang MHE, Bennet J, Munderi P, Ruxrungtham K, Gisslen M, Worobey M, Lundgren JD, Marvig RL. Phylogenetic analysis of HIV-1 shows frequent cross-country transmission and local population expansions. Virus Evol 2021; 7:veab055. [PMID: 34532059 PMCID: PMC8438898 DOI: 10.1093/ve/veab055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 05/26/2021] [Accepted: 06/09/2021] [Indexed: 12/03/2022] Open
Abstract
Understanding of pandemics depends on the characterization of pathogen collections from well-defined and demographically diverse cohorts. Since its emergence in Congo almost a century ago, Human Immunodeficiency Virus Type 1 (HIV-1) has geographically spread and genetically diversified into distinct viral subtypes. Phylogenetic analysis can be used to reconstruct the ancestry of the virus to better understand the origin and distribution of subtypes. We sequenced two 3.6-kb amplicons of HIV-1 genomes from 3,197 participants in a clinical trial with consistent and uniform sampling at sites across 35 countries and analyzed our data with another 2,632 genomes that comprehensively reflect the HIV-1 genetic diversity. We used maximum likelihood phylogenetic analysis coupled with geographical information to infer the state of ancestors. The majority of our sequenced genomes (n = 2,501) were either pure subtypes (A-D, F, and G) or CRF01_AE. The diversity and distribution of subtypes across geographical regions differed; USA showed the most homogenous subtype population, whereas African samples were most diverse. We delineated transmission of the four most prevalent subtypes in our dataset (A, B, C, and CRF01_AE), and our results suggest both continuous and frequent transmission of HIV-1 over country borders, as well as single transmission events being the seed of endemic population expansions. Overall, we show that coupling of genetic and geographical information of HIV-1 can be used to understand the origin and spread of pandemic pathogens.
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Affiliation(s)
| | - Anna Zhukova
- Unité Bioinformatique Evolutive, Hub Bioinformatique et Biostatistique, USR3756 (C3BI//DBC), Institut Pasteur and CNRS, 25-28 Rue du Dr Roux, 75015 Paris, France
| | | | | | - Paula Munderi
- MRC Uganda Research Unit on AIDS, UVRI P.O.Box 49, Plot 51-59 Nakiwogo Road, Entebbe-Uganda
| | - Kiat Ruxrungtham
- HIV-NAT, Thai Red Cross AIDS Research Center, and School of Global Health, Faculty Medicine, Chulalongkorn University, Chamchuri 5 Bld. 6th Fl., Phayathai Rd., Wangmai, Pathumwan Bangkok 10330, Thailand
| | - Magnus Gisslen
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Universitetsplatsen 1, 405 30 Gothenburg, Sweden,Department of Infectious Diseases, Region Västra Götaland, Sahlgrenska University Hospital, Universitetsplatsen 1, 405 30 Gothenburg, Sweden
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Biological Sciences West, Rm. 324 Tucson, AZ 85721, USA
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Lebedev A, Pasechnik O, Ozhmegova E, Antonova A, Blokh A, Grezina L, Sandyreva T, Dementeva N, Kazennova E, Bobkova M. Prevalence and spatiotemporal dynamics of HIV-1 Circulating Recombinant Form 03_AB (CRF03_AB) in the Former Soviet Union countries. PLoS One 2020; 15:e0241269. [PMID: 33095842 PMCID: PMC7584246 DOI: 10.1371/journal.pone.0241269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/12/2020] [Indexed: 11/19/2022] Open
Abstract
Background HIV-1 circulating recombinant forms (CRFs) infections has been increasing in Former Soviet Union (FSU) countries in the recent decade. One is the CRF03_AB, which circulated in the region since late 1990s and probably became widespread in northwestern FSU countries. However, there is not much information provided about the dissemination of this recombinant. Here, we examine the prevalence, evolutionary dynamics and dispersion pattern of HIV-1 CRF03_AB recombinant. Methods We analyzed 32 independent studies and 151 HIV-1 CRF03_AB pol sequences isolated from different FSU countries over a period of 22 years. Pooled prevalence was estimated using a random effects model. Bayesian coalescent-based method was used to estimate the evolutionary, phylogeographic and demographic parameters. Results Our meta-analysis showed that the pooled prevalence of CRF03_AB infection in northwestern FSU region was 5.9% [95%CI: 4.1–7.8]. Lithuania (11.6%), Russia (5.9%) and Belarus (2.9%) were the most affected by CRF03_AB. We found that early region wide spread of HIV-1 CRF03_AB originated from one viral clade that arose in the city of Kaliningrad in 1992 [95%HPD: 1990–1995]. Fourteen migration route of this variant were found. The city of Kaliningrad is involved in most of these, confirming its leading role in CRF03_AB spread within FSU. Demographic reconstruction point to this is that CRF03_AB clade seems to have experienced an exponential growth until the mid-2000s and a decrease in recent years. Conclusion These data provide new insights into the molecular epidemiology of CRF03_AB as well as contributing to the fundamental understanding of HIV epidemic in FSU.
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Affiliation(s)
- Aleksey Lebedev
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
- * E-mail:
| | - Oksana Pasechnik
- Departments of Epidemiology, Omsk State Medical University, Omsk, Russia
| | - Ekaterina Ozhmegova
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
| | - Anastasiia Antonova
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
| | - Aleksey Blokh
- Departments of Epidemiology, Omsk State Medical University, Omsk, Russia
| | - Liliya Grezina
- Clinical Diagnostic Laboratory, Yamalo-Nenets Autonomous District Center for Prevention and Control of AIDS and Infectious Diseases, Noyabr'sk, Russia
| | - Tatiana Sandyreva
- Clinical Diagnostic Laboratory, Sverdlovsk Regional Center for Prevention and Control of AIDS and Infectious Diseases, Ekaterinburg, Russia
| | - Natalia Dementeva
- Clinical Diagnostic Laboratory, Saint-Petersburg Center for Prevention and Control of AIDS and Infectious Disease, Saint-Petersburg, Russia
| | - Elena Kazennova
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
| | - Marina Bobkova
- Laboratory of T-Lymphotropic Viruses, Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
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Abstract
PURPOSE OF REVIEW To explore the consequences of policies implemented in the Russian Federation in response to syndemic of HIV-1 and opioid use disorder and compare the responses to the concomitant syndemic in rural America. RECENT FINDINGS The syndemic spread has not been reduced by policies implemented by the Russian government, which continues to underfund harm reduction efforts to reduce HIV transmission, refuses to approve evidence-based opioid agonist treatments for opioid use disorder, and relies on criminal justice and abstinence approaches to control illicit opioids. When effective measures have been undertaken locally, the lessons learned have not been transferred to other parts of the country and local programs have been allowed to wither. As in many parts of rural America, Russia has experienced intertwined epidemics of opioid misuse and HIV-1 that continue to expand. The expansion has been facilitated by adoption of policies that run contrary to medical and public health evidence.
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Affiliation(s)
- Robert Heimer
- Department of Epidemiology of Microbial Diseases and Center for Interdisciplinary Research on AIDS, Yale University School of Public Health, New Haven, CT, 06520-8034, USA.
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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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Vasylyeva TI, Liulchuk M, du Plessis L, Fearnhill E, Zadorozhna V, Babii N, Scherbinska A, Novitsky V, Pybus OG, Faria NR. The Changing Epidemiological Profile of HIV-1 Subtype B Epidemic in Ukraine. AIDS Res Hum Retroviruses 2019; 35:155-163. [PMID: 30430838 PMCID: PMC6360399 DOI: 10.1089/aid.2018.0167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
While HIV-1 subtype B has caused a large epidemic in the Western world, its transmission in Ukraine remains poorly understood. We assessed the genetic diversity of HIV-1 subtype B viruses circulating in Ukraine, characterized the transmission group structure, and estimated key evolutionary and epidemiological parameters. We analyzed 120 HIV-1 subtype B pol sequences (including 46 newly generated) sampled from patients residing in 11 regions of Ukraine between 2002 and 2017. Phylogenies were estimated using maximum likelihood and Bayesian phylogenetic methods. A Bayesian molecular clock coalescent analysis was used to estimate effective population size dynamics and date the most recent common ancestors of identified clades. A phylodynamic birth-death model was used to estimate the effective reproductive number (Re) of these clades. We identified two phylogenetically distinct predominantly Ukrainian (≥75%) clades of HIV-1 subtype B. We found no significant transmission group structure for either clade, suggesting frequent mixing among transmission groups. The estimated dates of origin of both subtype B clades were around early 1970s, similar to the introduction of HIV-1 subtype A into Ukraine. Re was estimated to be 1.42 [95% highest posterior density (HPD) 1.26-1.56] for Clade 1 and 1.69 (95% HPD 1.49-1.84) for Clade 2. Evidently, the subtype B epidemic in the country is no longer concentrated in specific geographical regions or transmission groups. The study results highlight the necessity for strengthening preventive and monitoring efforts to reduce the further spread of HIV-1 subtype B.
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Affiliation(s)
| | - Mariia Liulchuk
- L.V. Gromashevskij Institute of Epidemiology and Infectious Diseases of National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Louis du Plessis
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Esther Fearnhill
- Institute for Global Health, University College London, United Kingdom
| | - Victoriia Zadorozhna
- L.V. Gromashevskij Institute of Epidemiology and Infectious Diseases of National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Nataliia Babii
- L.V. Gromashevskij Institute of Epidemiology and Infectious Diseases of National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Alla Scherbinska
- L.V. Gromashevskij Institute of Epidemiology and Infectious Diseases of National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Vladimir Novitsky
- Department of Immunology and Infectious diseases, Harvard TH Chan School of Public Health, Boston, Massachusetts
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Nuno R. Faria
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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Recordon-Pinson P, Alves BM, Tumiotto C, Bellecave P, Bonnet F, Neau D, Soares EA, Soares MA, Fleury H. A New HIV-1 Circulating Recombinant Form (CRF98_cpx) Between CRF06_cpx and Subtype B Identified in Southwestern France. AIDS Res Hum Retroviruses 2018; 34:1005-1009. [PMID: 29947242 DOI: 10.1089/aid.2018.0122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
During a recent study on the sequencing data of our database between 2012 and 2016 in Southwestern France, we observed that eight patients harbored what seemed to be the same virus. Indeed, routine genotyping at the time of HIV diagnosis showed that protease and reverse transcriptase were related to CRF06_cpx and subtype B, respectively. The integrase sequences (available for three patients) were clustering with CRF06_cpx and envelope (Env) gp120 sequences (available for two patients) with subtype B. Since such a recombinant has not been recorded in the Los Alamos database, we decided to characterize the full-length genome of this virus. The data suggest the identification of a new circulating recombinant form (CRF) between CRF06_cpx and subtype B, the structure of which is very complex with multiple breakpoints. We will refer this CRF as CRF98_cpx.
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Affiliation(s)
| | | | - Camille Tumiotto
- CNRS MFP-UMR 5234, Bordeaux, France
- Department of Biology and Pathology, University Hospital of Bordeaux, Bordeaux, France
| | - Pantxika Bellecave
- Department of Biology and Pathology, University Hospital of Bordeaux, Bordeaux, France
| | - Fabrice Bonnet
- Department of Internal Medicine, University Hospital of Bordeaux, Bordeaux, France
| | - Didier Neau
- Department of Infectious and Tropical Diseases, University Hospital of Bordeaux, Bordeaux, France
| | | | | | - Hervé Fleury
- CNRS MFP-UMR 5234, Bordeaux, France
- Department of Biology and Pathology, University Hospital of Bordeaux, Bordeaux, France
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Karamov E, Epremyan K, Siniavin A, Zhernov Y, Cuevas MT, Delgado E, Sánchez-Martínez M, Carrera C, Kornilaeva G, Turgiev A, Bacqué J, Pérez-Álvarez L, Thomson MM. HIV-1 Genetic Diversity in Recently Diagnosed Infections in Moscow: Predominance of A FSU, Frequent Branching in Clusters, and Circulation of the Iberian Subtype G Variant. AIDS Res Hum Retroviruses 2018; 34:629-634. [PMID: 29587492 DOI: 10.1089/aid.2018.0055] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 protease-reverse transcriptase sequences from 62 HIV-1-infected individuals recently diagnosed in Moscow were analyzed. Subtype A former Soviet Union (FSU) (AFSU) variant was the predominant clade (62.9%), followed by subtype B (22.6%), unique recombinants (6.5%), subtype G (6.5%), and CRF01_AE (1.6%). AFSU predominated among people who inject drugs (88.9%) and heterosexually acquired infections (77.8%), while subtype B was the most prevalent genetic form among men who have sex with men (44%), although AFSU was also frequent in this population (36%). Forty-eight (77.4%) viruses branched within intrasubtype clusters, three of which, of subtype B, had a majority of viruses collected outside of FSU. The four subtype G viruses identified in this study belonged to the Portuguese-Spanish (Iberian) variant and, together with three from databases, formed a Russian cluster closely related to viruses from Denmark. This is the first report of the circulation of the Iberian subtype G variant in Russia.
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Affiliation(s)
- Eduard Karamov
- Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | - Khoren Epremyan
- Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | - Andrei Siniavin
- Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | - Yury Zhernov
- Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | - María Teresa Cuevas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Mónica Sánchez-Martínez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Cristina Carrera
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Galina Kornilaeva
- Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
| | - Ali Turgiev
- Laboratory of Immunochemistry, Gamaleya Center for Epidemiology and Microbiology, Moscow, Russia
- Immunomica LLC, Moscow, Russia
| | - Joan Bacqué
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Lucía Pérez-Álvarez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Michael M. Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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Sharma AL, Singh TR, Devi KR, Singh LS. Molecular epidemiology of HIV-1 among the HIV infected people of Manipur, Northeastern India: Emergence of unique recombinant forms. J Med Virol 2016; 89:989-999. [PMID: 27869320 DOI: 10.1002/jmv.24738] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/12/2016] [Accepted: 11/17/2016] [Indexed: 11/10/2022]
Abstract
According to the Joint National Programme on HIV/AIDS (UNAIDS), the northeastern region of India has the highest HIV prevalence in the country. This study was conducted to determine the current HIV-1 molecular epidemiology of Manipur, a state in northeast India. Blood samples from HIV-1 seropositive subjects were collected between June 2011 and February 2014. The partial regions of HIV-1 genes; pol and tat-vpu-env were independently amplified, sequenced, analyzed, and genotyped. Based on all sequences generated from 110 samples using pol and/or tat-vpu-env gene, the overall HIV-1 genotypes distribution of Manipur was as follows: 65.45% (72/110) subtype C, 32.73% (36/110) unique recombinant forms (URFs), and 1.82% (2/110) subtype B. The distribution of HIV-1 genotypes among the risk groups was: heterosexual: 58.33% (35/60) subtype C, 38.33% (23/60) URFs, and 3.34% (2/60) subtype B; intravenous drug users (IDUs): 85.36% (35/41) subtype C, 9.76% (4/41) URFs, and 4.88% (2/41) subtype B; mother to child (MTC): 50% (3/6) URFs and 50% (3/6) subtype C and blood transfusion: 100% (3/3) subtype C. The findings for the first time revealed the emergence of URFs of HIV-1 in Manipur which is predominant among the sexual and MTC risk groups as compared to IDUs. Taking together, this study illustrated that Manipur is the "recombinant hotspot of HIV" of India. The results will provide the clinical importance for continuous monitoring of HIV-infections in order to design appropriate prevention measures to limit the spread of new HIV infections.
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Affiliation(s)
| | - Thiyam Ramsing Singh
- Cancer and Molecular Biology Division, Department of Biotechnology, Manipur University, Imphal, Manipur, India
| | - Khuraijam Ranjana Devi
- Department of Microbiology, Regional Institute of Medical Sciences, Imphal, Manipur, India
| | - Lisam Shanjukumar Singh
- Cancer and Molecular Biology Division, Department of Biotechnology, Manipur University, Imphal, Manipur, India
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11
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Foley BT, Leitner T, Paraskevis D, Peeters M. Primate immunodeficiency virus classification and nomenclature: Review. INFECTION GENETICS AND EVOLUTION 2016; 46:150-158. [PMID: 27789390 DOI: 10.1016/j.meegid.2016.10.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 12/25/2022]
Abstract
The International Committee for the Taxonomy and Nomenclature of Viruses does not rule on virus classifications below the species level. The definition of species for viruses cannot be clearly defined for all types of viruses. The complex and interesting epidemiology of Human Immunodeficiency Viruses demands a detailed and informative nomenclature system, while at the same time it presents challenges such that many of the rules need to be flexibly applied or modified over time. This review outlines the nomenclature system for primate lentiviruses and provides an update on new findings since the last review was written in 2000.
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Affiliation(s)
- Brian T Foley
- Theoretical Biology and Biophysics Group, T-6 Mail Stop K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, T-6 Mail Stop K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Dimitrios Paraskevis
- National and Kapodistrian University of Athens, Department of Hygiene, Epidemiology and Medical Statistics, Medical School, Athens, Greece
| | - Martine Peeters
- UMI233-TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France; IBC, Computational Biology Institute, 34095 Montpellier, France
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12
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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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13
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Bessong PO, Iweriebor B. A putative HIV-1 subtype C/CRF11_cpx unique recombinant from South Africa. SPRINGERPLUS 2016; 5:285. [PMID: 27047711 PMCID: PMC4779448 DOI: 10.1186/s40064-016-1924-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 02/22/2016] [Indexed: 12/03/2022]
Abstract
The HIV epidemic in South Africa is overwhelmingly driven by HIV-1 subtype C viruses. The HIV gag, pol, env (C2-V5) and nef sequences of virus 08MB26ZA, obtained from a 47 year old woman, were studied by phylogenetic analysis, REGA and the jumping Profile Hidden Markov Model (jPHMM) tools. The pol gene was further analyzed for recombination by Simplot. The pol and env sequences were examined for genetic drug resistance mutations and predicted co-receptor usage respectively. There was agreement in the assignment of the gag sequence as pure HIV-1 subtype C by phylogenetic, REGA and jPHMM analyses. The pol sequence clustered with CRF11_cpx and in the J-clade by phylogenetic analysis; and to a CRF11_cpx/subtype C recombinant by REGA. The assignment of pol to CRF11_cpx and subtype C was confirmed by Simplot. The recombinant was of the R5 biotype, with no important drug resistance mutations in the pol region. The epidemiologic and biologic significance of the virus are unknown. The finding suggests that complex viruses are being introduced into South Africa with potential implications for diagnosis. This is apparently the first report from South Africa of a putative unique recombinant involving CRF11_cpx and subtype C genomes.
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Affiliation(s)
- Pascal Obong Bessong
- HIV/AIDS and Global Health Research Programme, Room FF172 Life Sciences Building, Department of Microbiology, University of Venda, Thohoyandou, 0950 South Africa
| | - Benson Iweriebor
- Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
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14
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Lai A, Bozzi G, Franzetti M, Binda F, Simonetti FR, De Luca A, Micheli V, Meraviglia P, Bagnarelli P, Di Biagio A, Monno L, Saladini F, Zazzi M, Zehender G, Ciccozzi M, Balotta C. HIV-1 A1 Subtype Epidemic in Italy Originated from Africa and Eastern Europe and Shows a High Frequency of Transmission Chains Involving Intravenous Drug Users. PLoS One 2016; 11:e0146097. [PMID: 26752062 PMCID: PMC4709132 DOI: 10.1371/journal.pone.0146097] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 12/14/2015] [Indexed: 12/04/2022] Open
Abstract
Background Subtype A accounts for only 12% of HIV-1 infections worldwide but predominates in Russia and Former Soviet Union countries of Eastern Europe. After an early propagation via heterosexual contacts, this variant spread explosively among intravenous drug users. A distinct A1 variant predominates in Greece and Albania, which penetrated directly from Africa. Clade A1 accounts for 12.5% of non-B subtypes in Italy, being the most frequent after F1 subtype. Aim Aim of this study was to investigate the circulation of A1 subtype in Italy and trace its origin and diffusion through phylogenetic and phylodynamic approaches. Results The phylogenetic analysis of 113 A1 pol sequences included in the Italian ARCA database, indicated that 71 patients (62.8%) clustered within 5 clades. A higher probability to be detected in clusters was found for patients from Eastern Europe and Italy (88.9% and 60.4%, respectively) compared to those from Africa (20%) (p < .001). Higher proportions of clustering sequences were found in intravenous drug users with respect to heterosexuals (85.7% vs. 59.3%, p = .056) and in women with respect to men (81.4% vs. 53.2%, p < .006). Subtype A1 dated phylogeny indicated an East African origin around 1961. Phylogeographical reconstruction highlighted 3 significant groups. One involved East European and some Italian variants, the second encompassed some Italian and African strains, the latter included the majority of viruses carried by African and Italian subjects and all viral sequences from Albania and Greece. Conclusions Subtype A1 originated in Central Africa and spread among East European countries in 1982. It entered Italy through three introduction events: directly from East Africa, from Albania and Greece, and from the area encompassing Moldavia and Ukraine. As in previously documented A1 epidemics of East European countries, HIV-1 A1 subtype spread in Italy in part through intravenous drug users. However, Eastern European women contributed to the penetration of such variant, probably through sex work.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
- * E-mail:
| | - Giorgio Bozzi
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
| | - Marco Franzetti
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
| | - Francesca Binda
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
| | - Francesco R. Simonetti
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
| | - Andrea De Luca
- Division of Infectious Diseases, Siena University Hospital, Siena, Italy
| | - Valeria Micheli
- Laboratory of Microbiology, ‘L. Sacco’ Hospital, Milan, Italy
| | - Paola Meraviglia
- 2nd Division of Infectious Diseases, ‘L. Sacco’ Hospital, Milan, Italy
| | - Patrizia Bagnarelli
- Department of Biomedical Science, Section of Microbiology, Laboratory of Virology, University Politecnica delle Marche, Ancona, Italy
| | | | - Laura Monno
- Division of Infectious Disease, University of Bari, Bari, Italy
| | | | - Maurizio Zazzi
- Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
| | - Massimo Ciccozzi
- Epidemiology Unit, Department of Infectious, Parasite and Immune-Mediated Diseases, Italian Institute of Health, Rome, Italy
| | - Claudia Balotta
- Department of Biomedical and Clinical Sciences ‘L. Sacco’, Infectious Diseases and Immunopathology Section, ‘L. Sacco’ Hospital, University of Milan, Milan, Italy
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15
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Luk KC, Berg MG, Naccache SN, Kabre B, Federman S, Mbanya D, Kaptué L, Chiu CY, Brennan CA, Hackett J. Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity. PLoS One 2015; 10:e0141723. [PMID: 26599538 PMCID: PMC4658132 DOI: 10.1371/journal.pone.0141723] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/12/2015] [Indexed: 02/06/2023] Open
Abstract
Given the dynamic changes in HIV-1 complexity and diversity, next-generation sequencing (NGS) has the potential to revolutionize strategies for effective HIV global surveillance. In this study, we explore the utility of metagenomic NGS to characterize divergent strains of HIV-1 and to simultaneously screen for other co-infecting viruses. Thirty-five HIV-1-infected Cameroonian blood donor specimens with viral loads of >4.4 log10 copies/ml were selected to include a diverse representation of group M strains. Random-primed NGS libraries, prepared from plasma specimens, resulted in greater than 90% genome coverage for 88% of specimens. Correct subtype designations based on NGS were concordant with sub-region PCR data in 31 of 35 (89%) cases. Complete genomes were assembled for 25 strains, including circulating recombinant forms with relatively limited data available (7 CRF11_cpx, 2 CRF13_cpx, 1 CRF18_cpx, and 1 CRF37_cpx), as well as 9 unique recombinant forms. HPgV (formerly designated GBV-C) co-infection was detected in 9 of 35 (25%) specimens, of which eight specimens yielded complete genomes. The recovered HPgV genomes formed a diverse cluster with genotype 1 sequences previously reported from Ghana, Uganda, and Japan. The extensive genome coverage obtained by NGS improved accuracy and confidence in phylogenetic classification of the HIV-1 strains present in the study population relative to conventional sub-region PCR. In addition, these data demonstrate the potential for metagenomic analysis to be used for routine characterization of HIV-1 and identification of other viral co-infections.
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Affiliation(s)
- Ka-Cheung Luk
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America
| | - Michael G Berg
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America
| | - Samia N Naccache
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
| | - Beniwende Kabre
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
| | - Scot Federman
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
| | | | | | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America.,Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, California, United States of America
| | - Catherine A Brennan
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America
| | - John Hackett
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America
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16
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Heimer R, Levina OS, Osipenko V, Ruiz MS, Sergeyev B, Sirotkin AV, Vyshemirskaya I. Impact of incarceration experiences on reported HIV status and associated risk behaviours and disease comorbidities. Eur J Public Health 2015; 25:1089-94. [PMID: 26381650 DOI: 10.1093/eurpub/ckv157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The Russian human immunodeficiency virus (HIV) epidemic among people who inject drugs (PWID) originated in Kaliningrad, but research into risk behaviours among PWID has been lacking. The potential for heterosexual spread has not been analysed. METHODS A sample of PWID was accrued using two methods. A questionnaire was administered to assess HIV-related risk behaviours for parenteral and sexual transmission, sociodemographic factors, HIV knowledge and attitudes about sexual risks. Data were analysed focusing on the role of imprisonment, factors associated with awareness of being HIV infected and condom use. RESULTS More than a quarter of the sample reported having been diagnosed with HIV infection, with higher prevalence among women and those with a history of incarceration. More than half reported having been diagnosed with hepatitis C virus infection. Those reporting being HIV positive were less likely to distribute used syringes to other PWID and more likely to have used a condom the last time they had sex. A history of incarceration was associated with higher rates of receptive syringe sharing among those not having ever received an HIV-positive diagnosis and a lower likelihood of believing that condoms are needed when having sex with a casual partner. CONCLUSION Although extensive HIV testing has alerted many PWID to their HIV-positive status, which is associated with less distributive syringe sharing and higher likelihood of condom use, substantial risk for parenteral and especially sexual HIV transmission remains. More active prevention programs will be required to control the heterosexual spread of HIV.
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Affiliation(s)
- Robert Heimer
- 1 Department of Epidemiology of Microbial Diseases and the Center for Interdisciplinary Research on AIDS, Yale University School of Public Health, New Haven, CT 06520, USA
| | | | | | - Monica S Ruiz
- 4 Department of Prevention and Community Health, Milkin Institute School of Public Health, The George Washington University, Washington, DC, USA
| | - Boris Sergeyev
- 5 Office of the Nordic Council of Ministers, Kaliningrad, RF
| | - Aleksander V Sirotkin
- 6 International Laboratory for Applied Network Research, National Research University Higher School of Economics, St. Petersburg, RF
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17
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A uniquely prevalent nonnucleoside reverse transcriptase inhibitor resistance mutation in Russian subtype A HIV-1 viruses. AIDS 2014; 28:F1-8. [PMID: 25259833 DOI: 10.1097/qad.0000000000000485] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The subtype A variant in the Former Soviet Union (A(FSU)) causes most of Russia's HIV-1 infections. However, the spectrum of drug-resistance mutations (DRMs) in antiretroviral experienced patients with this variant has not been studied. METHODS Between 2010 and 2013, genotypic resistance testing was performed on plasma samples from 366 antiretroviral-experienced patients in Siberia. RESULTS Three-hundred patients (82%) had subtype A(FSU) and 55 (15%) had CRF02_AG viruses. The pattern of DRMs was consistent with patient antiretroviral history with one exception. G190S was the most common nonnucleoside reverse transcriptase inhibitor (NNRTI) resistance mutation, occurring in 55 (33%) subtype A(FSU) viruses from 167 NNRTI-experienced patients compared with none of 37 CRF02_AG viruses from NNRTI-experienced patients (P < 0.001). The next most common subtype A(FSU) NNRTI-resistance mutation, K103N, occurred in 25 (15%) viruses. Wild-type glycine (G) at position 190 is encoded by GGC in more than 99% of published A(FSU) strains. By contrast, G190 is encoded by GGA or GGG in 97% of other subtypes and in subtype A strains outside of the FSU. Therefore, G190S results from a single G→A transition: G (GGC) → S (AGC) almost exclusively in subtype A(FSU) viruses. CONCLUSION The predisposition of subtype A(FSU) to G190S is concerning because G→A is the most common HIV-1 mutation and because G190S causes higher levels of nevirapine and efavirenz resistance than K103N. This study exemplifies the need for characterizing the genetic mechanisms of resistance in diverse populations and warrants studies to verify that NRTI/NNRTI regimens are as efficacious in treating subtype A(FSU) as viruses belonging to other subtypes.
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18
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Ruiseñor-Escudero H, Wirtz AL, Berry M, Mfochive-Njindan I, Paikan F, Yousufi HA, Yadav RS, Burnham G, Vu A. Risky behavior and correlates of HIV and Hepatitis C Virus infection among people who inject drugs in three cities in Afghanistan. Drug Alcohol Depend 2014; 143:127-33. [PMID: 25131717 DOI: 10.1016/j.drugalcdep.2014.07.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 07/12/2014] [Accepted: 07/13/2014] [Indexed: 01/07/2023]
Abstract
BACKGROUND Injecting drug use is the primary mode of HIV transmission and acquisition in Afghanistan. People who inject drugs (PWID) in the country have been characterized by high risk injecting behavior and a high burden of HCV infection. We aimed to estimate the burden of HIV, HCV, and other infectious diseases and to identify the correlates of HIV and HCV infection among PWID living in three major Afghan cities in 2009. METHODS Epidemiologic data was collected among PWID for the integrated biological and behavioral surveillance (IBBS) survey between May and August, 2009 in three Afghan cities. Data were collected using a structured questionnaire and biologic specimens to screen for HIV, HBV, HCV, syphilis, and HSV-2 using rapid testing kits. Multiple logistic regression models were constructed to identify correlates of infection. RESULTS Among 548 participants, pooled HIV prevalence was 7.1% (Mazar-i-Sharif: 1.0%, Kabul: 3.1%, Herat: 18.4%) and HCV prevalence was 40.3%. Almost all participants with HIV infection were co-infected with HCV (94.9%). Pooled prevalence estimates for other diseases included 7.1% for HBV, 5.5% for syphilis; and 9.3% for HSV-2. Living in Herat, ever in prison and time injecting were independently associated with HIV infection. Living in Kabul, Herat and time injecting were independently associated with HCV infection. CONCLUSIONS There is a high and heterogeneous burden of HIV and HCV among PWID in Afghan cities. Provision of comprehensive harm reduction services to PWID in Afghanistan is warranted to reduce exposures associated with HIV and HCV infection, especially in the city of Herat.
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Affiliation(s)
- Horacio Ruiseñor-Escudero
- Department of Psychiatry, Michigan State University, 965 E Fee Hall Suite A227, East Lansing, MI, 48824, USA; Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
| | - Andrea L Wirtz
- Department of Emergency Medicine, Johns Hopkins Medical Institution, Baltimore, MD, 21205, USA; Center for Public Health and Human Rights, Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Mark Berry
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Iliassou Mfochive-Njindan
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Feda Paikan
- National AIDS Control Program, Ministry of Public Health, Kabul, Afghanistan
| | - Hussain A Yousufi
- National AIDS Control Program, Ministry of Public Health, Kabul, Afghanistan
| | | | - Gilbert Burnham
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Alexander Vu
- Department of Emergency Medicine, Johns Hopkins Medical Institution, Baltimore, MD, 21205, USA; Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
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19
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Shcherbakova NS, Shalamova LA, Delgado E, Fernández-García A, Vega Y, Karpenko LI, Ilyichev AA, Sokolov YV, Shcherbakov DN, Pérez-Álvarez L, Thomson MM. Short communication: Molecular epidemiology, phylogeny, and phylodynamics of CRF63_02A1, a recently originated HIV-1 circulating recombinant form spreading in Siberia. AIDS Res Hum Retroviruses 2014; 30:912-9. [PMID: 25050828 DOI: 10.1089/aid.2014.0075] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The HIV-1 epidemic in Russia is dominated by the former Soviet Union subtype A (A(FSU)) variant, but other genetic forms are circulating in the country. One is the recently described CRF63_02A1, derived from recombination between a CRF02_AG variant circulating in Central Asia and A(FSU), which has spread in the Novosibirsk region, Siberia. Here we phylogenetically analyze pol and env segments from 24 HIV-1 samples from the Novosibirsk region collected in 2013, with characterization of three new near full-length genome CRF63_02A1 sequences, and estimate the time of the most recent common ancestor (tMRCA) and the demographic growth of CRF63_02A1 using a Bayesian method. The analyses revealed that CRF63_02A1 is highly predominant in the Novosibirsk region (81.2% in pol sequences) and is transmitted both among injecting drug users and by heterosexual contact. Similarity searches with database sequences combined with phylogenetic analyses show that CRF63_02A1 is circulating in East Kazakhstan and the Eastern area of Russia bordering China. The analyses of near full-length genome sequences show that its mosaic structure is more complex than reported, with 18 breakpoints. The tMRCA of CRF63_02A1 was estimated around 2006, with exponential growth in 2008-2009 and subsequent stabilization. These results provide new insights into the molecular epidemiology, phylogeny, and phylodynamics of CRF63_02A1.
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Affiliation(s)
- Nadezhda S. Shcherbakova
- Department of Bioengineering, State Research Center of Virology and Biotechnology “Vector,” Koltsovo, Novosibirsk, Russia
| | - Lyudmila A. Shalamova
- Department of Zoonotic Infections and Influenza, State Research Center of Virology and Biotechnology “Vector,” Koltsovo, Novosibirsk, Russia
| | - Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Aurora Fernández-García
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Yolanda Vega
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Larissa I. Karpenko
- Laboratory of Recombinant Vaccine, State Research Center of Virology and Biotechnology “Vector,” Koltsovo, Novosibirsk, Russia
| | - Alexander A. Ilyichev
- Department of Bioengineering, State Research Center of Virology and Biotechnology “Vector,” Koltsovo, Novosibirsk, Russia
| | - Yuri V. Sokolov
- Center for Prevention and Control of AIDS and Infectious Diseases, Koltsovo, Novosibirsk, Russia
| | | | - Lucía Pérez-Álvarez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Michael M. Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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20
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Lapovok I, Kazennova E, Laga V, Vasilyev A, Utegenova A, Abishev A, Dzissyuk N, Tukeev M, Bobkova M. Short communication: molecular epidemiology of HIV type 1 infection in Kazakhstan: CRF02_AG prevalence is increasing in the southeastern provinces. AIDS Res Hum Retroviruses 2014; 30:769-74. [PMID: 24873898 DOI: 10.1089/aid.2013.0291] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To analyze HIV-1 genetic variants in Kazakhstan, HIV-1 sequences were obtained from 205 antiretroviral-treated (ART) and naive patients in 2009-2013. Samples were collected in the most populous cities and provinces of Kazakhstan. On the basis of phylogenetic analyses of partial pol sequences, subtype A variant intravenous drug user (IDU)-A (which is dominant in the former Soviet Union) was found in 60.0% of the individuals, followed by CRF02_AG (34.6%); the rest of the samples were subtype B, CRF03_AB, CRF63_02A1, and CRF07_BC. The proportion of CRF02_AG has increased significantly since 2001-2003, when it was less than 5%. The majority of the CRF02_AG cases were found in Almaty, the former capital and the most populous city in Kazakhstan. The IDU-A variant dominated in the industrial regions of northern and central Kazakhstan and some other regions. Both dominant HIV-1 genetic variants were almost equally represented in the two main transmission groups: IDUs and heterosexuals. The analysis of drug-resistant mutations found a low prevalence of drug resistance in 165 therapy-naive individuals (3.0%). Thus, in the beginning of the second decade of the 2000s, the HIV epidemic in Kazakhstan is driven by two main genetic variants: IDU-A and CRF02_AG.
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Affiliation(s)
| | | | - Vita Laga
- Ivanovsky Institute of Virology, Moscow, Russia
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Parczewski M, Urbanska A, Grzeszczuk A, Maciejewska K, Witak-Jedra M, Leszczyszyn-Pynka M. Phylogeographic analysis on the travel-related introduction of HIV-1 non-B subtypes to Northern Poland. INFECTION GENETICS AND EVOLUTION 2014; 27:121-30. [PMID: 25038296 DOI: 10.1016/j.meegid.2014.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 06/27/2014] [Accepted: 07/05/2014] [Indexed: 11/16/2022]
Abstract
Phylodynamic, sequence data based reconstructions for the surveillance of the geographic spatial spread are a powerful tool in molecular epidemiology. In this study region of origin for the set of 57 partial pol sequences derived from the patients the history of travel-related HIV transmission was analyzed using phylogeographic approach. Maximum likelihood trees based on the sets of country-annotated reference sequences were inferred for identified non-B variants. Region of sequence import was assigned using on the highest approximate likelihood ratios. Import of the A1 clades was traced to the Eastern Europe and associated with immigration from this region. Subtype C infections clustered most frequently with sequences of the South African origin while majority of subtype Ds were similar to the European clades. Subtype G sequences clustered with Portuguese lineage, CRF01_AE with Eastern or South-Eastern Asian. Eastern European, Middle African or Western African lineage was assigned for the CFR02_AG. Rare circulating recombinants originated either from Central Africa (CRF11_cpx - Democratic Republic of Congo, CRF13_cpx - Central African Republic, CRF37_cpx - Cameroon) or South America (CRF28_BF and CRF46_BF - Brazil). Import of the HIV-1 non-B variants, including recombinant forms previously rarely found in Poland and Europe is frequent among travelers. Observed founder events result in the heterosexually-driven introduction of the novel HIV-1 variants into the population.
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Affiliation(s)
- Milosz Parczewski
- Department of Infectious Diseases and Hepatology, Pomeranian Medical University, Szczecin, Poland.
| | - Anna Urbanska
- Department of Infectious Diseases and Hepatology, Pomeranian Medical University, Szczecin, Poland
| | - Anna Grzeszczuk
- Department of Infectious Diseases and Hepatology, Medical University of Bialystok, Bialystok, Poland
| | - Katarzyna Maciejewska
- Department of Infectious Diseases and Hepatology, Pomeranian Medical University, Szczecin, Poland
| | - Magdalena Witak-Jedra
- Department of Infectious Diseases and Hepatology, Pomeranian Medical University, Szczecin, Poland
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Simonetti FR, Lai A, Monno L, Binda F, Brindicci G, Punzi G, Bozzi G, Violin M, Galli M, Zazzi M, Angarano G, Balotta C. Identification of a new HIV-1 BC circulating recombinant form (CRF60_BC) in Italian young men having sex with men. INFECTION GENETICS AND EVOLUTION 2014; 23:176-81. [DOI: 10.1016/j.meegid.2014.02.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 02/14/2014] [Accepted: 02/17/2014] [Indexed: 12/20/2022]
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Andrianov AM, Kornoushenko YV, Anishchenko IV, Eremin VF, Tuzikov AV. Structural analysis of the envelope gp120 V3 loop for some HIV-1 variants circulating in the countries of Eastern Europe. J Biomol Struct Dyn 2013; 31:665-83. [DOI: 10.1080/07391102.2012.706455] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Booth RE. 'Krokodil' and other home-produced drugs for injection: a perspective from Ukraine. THE INTERNATIONAL JOURNAL OF DRUG POLICY 2013; 24:277-8. [PMID: 23764188 DOI: 10.1016/j.drugpo.2013.05.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 05/14/2013] [Indexed: 11/19/2022]
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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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Parczewski M, Leszczyszyn-Pynka M, Bander D, Urbanska A, Boroń-Kaczmarska A. HIV-1 subtype D infections among Caucasians from Northwestern Poland--phylogenetic and clinical analysis. PLoS One 2012; 7:e31674. [PMID: 22359615 PMCID: PMC3280981 DOI: 10.1371/journal.pone.0031674] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 01/11/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND HIV-1 subtype D infections, which are associated with a faster rate of progression and lymphocyte CD4 decline, cognitive deficit and higher mortality, have rarely been found in native Europeans. In Northwestern Poland, however, infections with this subtype had been identified. This study aimed to analyze the sequence and clinical data for patients with subtype D using molecular phylogeography and identify transmission clusters and ancestry, as well as drug resistance, baseline HIV tropism and antiretroviral treatment efficacy. METHODS Phylogenetic analyses of local HIV-1 subtype D sequences were performed, with time to the most recent common ancestor inferred using bayesian modeling. Sequence and drug resistance data were linked with the clinical and epidemiological information. RESULTS Subtype D was found in 24 non-immigrant Caucasian, heterosexually infected patients (75% of females, median age at diagnosis of 49.5 years; IQR: 29-56 years). Partial pol sequences clustered monophyletically with the clades of Ugandan origin and no evidence of transmission from other European countries was found. Time to the most common recent ancestor was 1989.24 (95% HPD: 1968.83-1994.46). Baseline drug resistance to nucleoside reverse transcriptase inhibitors was observed in 54.5% of cases (mutations: M41L, K103N, T215S/D) with evidence of clustering, no baseline integrase or protease resistance and infrequent non-R5 tropism (13.6%). Virologic failure was observed in 60% of cases and was associated with poor adherence (p<0.001) and subsequent development of drug resistance (p = 0.008, OR: 20 (95%CI: 1.7-290). CONCLUSIONS Local subtype D represented an independently transmitted network with probably single index case, high frequency of primary drug resistance and evidence of transmission clusters.
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Affiliation(s)
- Miłosz Parczewski
- Department of Infectious Diseases and Hepatology, Pomeranian Medical University, Szczecin, Poland.
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Eremin VF, Gasich EL, Sasinovich SV. A new unique recombinant HIV type 1 isolated from a child born to an HIV-infected mother. AIDS Res Hum Retroviruses 2011; 27:1323-6. [PMID: 21534848 DOI: 10.1089/aid.2011.0112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The new HIV-1 recombinant, with a B(gag) A(pol)A(env) structure, is described. This recombinant virus differs from the classical "Kaliningrad" (AF193276.1) virus with an A(gag) B(pol)B(env) structure. The number of new HIV cases in Belarus has been increasing in the past few years. Within the 12 months of 2010, 1069 new cases of HIV infection were registered. Molecular epidemiological investigations have shown that though HIV-1 subtype A (84.5%) still dominates in HIV/AIDS patients, the quantity of CRFs has also increased to 7.1%. Although cases with the CRF03_AB virus were previously described in patients from Belarus, CRF06_cpx and CRF02_AG are described in Belarus for the first time.
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Affiliation(s)
- Vladimir F. Eremin
- Department of Clinical Virology, Republican Research Practical Center for Epidemiology and Microbiology, Minsk, Belarus
| | - Elena L. Gasich
- Department of Clinical Virology, Republican Research Practical Center for Epidemiology and Microbiology, Minsk, Belarus
| | - Sviataslau V. Sasinovich
- Department of Clinical Virology, Republican Research Practical Center for Epidemiology and Microbiology, Minsk, Belarus
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Skar H, Hedskog C, Albert J. HIV-1 evolution in relation to molecular epidemiology and antiretroviral resistance. Ann N Y Acad Sci 2011; 1230:108-18. [PMID: 21824168 DOI: 10.1111/j.1749-6632.2011.06128.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
HIV/AIDS has become one of the most important infectious diseases with a cumulative number of almost 60 million infections worldwide. The prevalence and epidemiological patterns are unevenly distributed across the globe and also within countries. HIV is one of the fastest evolving organisms known. Several genetically distinct subtypes are present and new circulating recombinant forms are continuously emerging. This review discusses HIV-1 evolution in relation to molecular epidemiology and antiretroviral resistance. Factors and concepts that influence global spread and within-patient evolution of HIV-1 are discussed as well as future perspectives on the use of phylodynamics in HIV epidemiology.
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Affiliation(s)
- Helena Skar
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden.
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Kousiappa I, Achilleos C, Hezka J, Lazarou Y, Othonos K, Demetriades I, Kostrikis LG. Molecular characterization of HIV type 1 strains from newly diagnosed patients in Cyprus (2007-2009) recovers multiple clades including unique recombinant strains and lack of transmitted drug resistance. AIDS Res Hum Retroviruses 2011; 27:1183-99. [PMID: 21453134 DOI: 10.1089/aid.2011.0060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
HIV-1 evolution generates substantial genetic diversity among isolates, the majority of which are represented in areas where multiple strains cocirculate. A heterogeneous genetic HIV-1 pool has been found in Cyprus, directing us to determine the dynamics of the local HIV-1 infection by characterizing strains isolated from 74 subjects during 2007-2009, representing 88% of the known-living HIV-1-infected population, of whom 53 are newly diagnosed therapy-naive patients and 21 are chronic patients, according to the European HIV Resistance guidelines. Near full-length genome sequences were amplified by RT-nested PCR using diluted RNA from all HIV-1 seropositives and sequenced using a newly designed assay. Resistant mutations were not found among the population of the newly diagnosed therapy-naive patients either to protease, reverse transcriptase, or integrase inhibitors. Phylogenetic analyses indicated subtype B as the main subtype (48.6%), followed by subtype A (18.9%), subtype C (10.8%), CRF02_AG (8.1%), CRF11_cpx (2.7%), and (sub)subtype F1 and CRF37_cpx (1.4% each). Six HIV-1 isolates (8.1%) were not classified in any pure (sub)subtype or circulating recombinant form (CRF). Complete phylogenetic and bootscanning analyses revealed that each isolate had a new, unique recombinant pattern and is distinct from all other CRFs or unique recombinant forms (URFs) reported so far. Two of the six isolates have the same mosaic pattern. Analogous to results of the earlier epidemiological studies, this study expands on the HIV-1 sequence database and reveals the high degree of diversity of HIV-1 infection in Cyprus.
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Affiliation(s)
- Ioanna Kousiappa
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Charis Achilleos
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Johana Hezka
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Yiota Lazarou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Katerina Othonos
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
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Circulation of multiple patterns of unique recombinant forms B/CRF02_AG in France: precursor signs of the emergence of an upcoming CRF B/02. AIDS 2011; 25:1371-7. [PMID: 21522007 DOI: 10.1097/qad.0b013e328347c060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND HIV-1 group M is characterized by substantial genetic diversity, and includes nine subtypes, more than 45 circulating recombinant forms (CRFs), and numerous unique recombinant forms (URFs). In France, the epidemic is characterized by predominance of subtype B strains, increasing prevalence of non-B subtypes (CRF02_AG being the most prevalent) and increasing at-risk behaviour in the MSM population. The high prevalence and co-circulation of B and CRF02_AG strains in this population raise the possibility that recombinant forms might emerge and spread. METHODS Samples from seven patients (five being MSM) were selected on the basis of subtyping discordances in different regions. The pattern of each near full-length genome of the viruses was characterized. The relationships between the newly and previously described B/CRF02_AG URFs were analysed using phylogenetic networks. Single genome amplification was used to search for the parental strains and confirmation of the breakpoints. RESULTS Seven unique recombination patterns were identified, breakpoints being found throughout the genomes, with hotspots in pol and accessory genes. No link was observed with the previous forms, but the CRF02 regions of two new viruses indicated that they are phylogenetically associated, suggesting a common ancestral strain. No evidence of circulating parental strains was found. CONCLUSION This description of seven URFs involving subtype B and CRF02_AG highlights the growing complexity of HIV molecular epidemiology in France. These multiple patterns, found mostly in MSM, and the hypothesis of a better fitness of some recombinant strains, argue for a context that could lead to the genesis of CRFB/02_AG strains in France.
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Sarkar R, Pal R, Bal B, Mullick R, Sengupta S, Sarkar K, Chakrabarti S. Genetic Characterization of HIV-1 Strains Among the Injecting Drug Users in Nagaland, India. Open Virol J 2011; 5:96-102. [PMID: 21792382 PMCID: PMC3141332 DOI: 10.2174/1874357901105010096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 04/19/2011] [Accepted: 04/20/2011] [Indexed: 11/23/2022] Open
Abstract
Global HIV-1 surveillance has led to the detection of its new recombinant forms. This study was carried out for the first time to elucidate the genetic characterization and evolutionary relationship of HIV-1 strains among injecting drug users of Nagaland, northeastern India. A total of 156 injecting drug users participated in this study voluntarily. Among them 18 were seropositive for HIV-1 (11.5%).The Heteroduplex Mobility Assay (HMA) of HIV-1 based on p24-p7 region of gag gene and C2-V3 region of env gene revealed 11 samples to be subtype C (gag/env), 1 sample as subtype B (gag/env) and 6 samples to be recombinants between subtype C and B. Also, the sequencing and phylogenetic analysis of gag (p24-p7) and env (C2-V3) genes from eighteen samples of Nagaland IDUs with different global HIV-1 strains showed the presence of Indian, African, Thai and their recombinant forms. However, more recombinant strains based on different genomic regions of HIV-1 were detected using Multiregional Hybridization Assay (MHA) where 8 out of 18 samples were found to be recombinants between subtype C and B. Thus, multiregional hybridization assay along with heteroduplex mobility assay can serve as an efficient tool in the characterization of recombination pattern among the newly emerging HIV-1 recombinants.
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Affiliation(s)
| | | | | | | | | | | | - Sekhar Chakrabarti
- HIV/AIDS Laboratory, Division of Virology & Epidemiology, National Institute of Cholera & Enteric Diseases, Kolkata 700010, India
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Extensive HLA-driven viral diversity following a narrow-source HIV-1 outbreak in rural China. Blood 2011; 118:98-106. [PMID: 21562042 DOI: 10.1182/blood-2010-06-291963] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Obstacles to developing an HIV-1 vaccine include extensive viral diversity and lack of correlates of protective immunity. High mutation rates allow HIV-1 to adapt rapidly to selective forces such as antiretroviral therapy and immune pressure, including HIV-1-specific CTLs that select viral variants which escape T-cell recognition. Multiple factors contribute to HIV-1 diversity, making it difficult to disentangle the contribution of CTL selection without using complex analytical approaches. We describe an HIV-1 outbreak in 231 former plasma donors in China, where a narrow-source virus that had contaminated the donation system was apparently transmitted to many persons contemporaneously. The genetic divergence now evident in these subjects should uniquely reveal how much viral diversity at the population level is solely attributable to host factors. We found significant correlations between pair-wise divergence of viral sequences and HLA class I genotypes across epitope-length windows in HIV-1 Gag, reverse transcriptase, integrase, and Nef, corresponding to sites of 140 HLA class I allele-associated viral polymorphisms. Of all polymorphic sites across these 4 proteins, 24%-56% were sites of HLA-associated selection. These data confirm that CTL pressure has a major effect on inter-host HIV-1 viral diversity and probably represents a key element of viral control.
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Brenner BG, Lowe M, Moisi D, Hardy I, Gagnon S, Charest H, Baril JG, Wainberg MA, Roger M. Subtype diversity associated with the development of HIV-1 resistance to integrase inhibitors. J Med Virol 2011; 83:751-9. [PMID: 21360548 DOI: 10.1002/jmv.22047] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2011] [Indexed: 11/08/2022]
Abstract
We used genotypic and phylogenetic analysis to determine integrase diversity among subtypes, and studied natural polymorphisms and mutations implicated in resistance to integrase inhibitors (INI) in treatment-naïve persons (n = 220) and -experienced individuals (n = 24). Phylogenetics revealed 7 and 10% inter-subtype diversity in the integrase and reverse transcriptase (RT)/protease regions, respectively. Integrase sequencing identified a novel A/B recombinant in which all viruses in a male-sex-male (MSM) transmission cluster (n = 12) appeared to possess subtype B in integrase and subtype A in the remainder of the pol region. Natural variations and signature polymorphisms were observed at codon positions 140, 148, 151, 157, and 160 among HIV subtypes. These variations predicted higher genetic barriers to G140S and G140C in subtypes C, CRF02_AG, and A/CRF01_AE, as well as higher genetic barriers toward acquisition of V151I in subtypes CRF02_AG and A/CRF01_AE. The E157Q and E160Q mutational motif was observed in 35% of INI-naïve patients harboring subtype C infections, indicating intra-subtype variations. Thirteen patients failed raltegravir (RAL)-containing regimens within 8 ± 1 months, in association with the major Q148K/R/H and G140A/S (n = 8/24) or N155H (n = 5/24) mutational pathways. Of note, the remaining patients on RAL regimens for 14 ± 3 months harbored no or only minor integrase mutations/polymorphisms (T66I, T97A, H114P, S119P, A124S, G163R, I203M, R263K). These results demonstrate the importance of understanding subtype variability in the development of resistance to INIs.
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Affiliation(s)
- Bluma G Brenner
- McGill AIDS Centre, Lady Davis Research Institute, Jewish General Hospital, Montreal, Canada
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Booth RE, Lehman WEK, Latkin CA, Dvoryak S, Brewster JT, Royer MS, Sinitsyna L. Individual and network interventions with injection drug users in 5 Ukraine cities. Am J Public Health 2011; 101:336-43. [PMID: 20395584 PMCID: PMC3020184 DOI: 10.2105/ajph.2009.172304] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2009] [Indexed: 11/04/2022]
Abstract
OBJECTIVES We evaluated the effects of an individual intervention versus a network intervention on HIV-related injection and sexual risk behaviors among street-recruited opiate injection drug users in 5 Ukraine cities. METHODS Between 2004 and 2006, 722 opiate injection drug users were recruited to participate in interventions that were either individually based or based on a social network model in which peer educators intervened with their network members. Audio computer-assisted self-interview techniques were used to interview participants at baseline and follow-up. RESULTS Multiple logistic analyses controlling for baseline injection and sexual risks revealed that both peer educators and network members in the network intervention reduced injection-related risk behaviors significantly more than did those in the individually based intervention and that peer educators increased condom use significantly more than did those in the individual intervention. Individual intervention participants, however, showed significantly greater improvements than did network members with respect to reductions in sexual risk behaviors. CONCLUSIONS Social network interventions may be more effective than individually based interventions in changing injection risk behaviors among both peer educators and network members. The effectiveness of network interventions in changing sexual risk behaviors is less clear, probably owing to network composition and inhibitions regarding discussing sexual risk behaviors.
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Affiliation(s)
- Robert E Booth
- Division of Substance Dependence, Department of Psychiatry, School of Medicine, University of Colorado Denver, 1741 Vine St, Denver, CO 80206, USA.
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Avi R, Huik K, Pauskar M, Ustina V, Karki T, Krispin T, Ainsalu K, Paap P, Schmidt J, Nikitina N, Lutsar I. Emerging transmitted drug resistance in treatment-naïve human immunodeficiency virus-1 CRF06_cpx-infected patients in Estonia. ACTA ACUST UNITED AC 2010; 43:122-8. [DOI: 10.3109/00365548.2010.526956] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Habekova M, Takacova M, Lysy J, Mokras M, Camacho R, Truska P, Stanekova D. Genetic subtypes of HIV type 1 circulating in Slovakia. AIDS Res Hum Retroviruses 2010; 26:1103-7. [PMID: 20849303 DOI: 10.1089/aid.2009.0220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Slovakia belongs to the group of European countries with a low prevalence of HIV infection. The major proportion of HIV-positive cases in Slovakia is still represented by MSM, followed by heterosexuals infected through unprotected sexual intercourse. This study was conducted to update the description of HIV subtypes circulating in Slovakia. HIV-1 partial pol gene sequences from 143 individuals were prospectively collected from 2004 to 2008 and analyzed. Phylogenetic analysis based on HIV-1 partial pol gene sequences revealed the highest prevalence of HIV-1 B subtype (93.0 %), predominantly associated with the MSM group. Ten (7.0%) individuals were infected with HIV-1 non-B subtypes. The pure subtypes were more frequent (7; 4.9%) than CRFs (3; 2.1%) and their occurrence was as follows: subtype C (3; 2, 1%), subtype A (2; 1.4%), subtype F (2; 1.4%), CRF_01AE (1; 0.7%), CRF_02AG (1; 0.7%), and CRF08_BC (1; 0.7%). Data show slightly increasing HIV-1 subtype diversity, with HIV-1 subtype B still having the highest prevalence in the Slovak-infected population.
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Affiliation(s)
- M. Habekova
- Slovak Medical University, NRC for HIV/AIDS Prevention, Bratislava, Slovakia
| | - M. Takacova
- Slovak Medical University, NRC for HIV/AIDS Prevention, Bratislava, Slovakia
| | - J. Lysy
- Slovak Medical University, NRC for HIV/AIDS Prevention, Bratislava, Slovakia
| | - M. Mokras
- Medical faculty of Commenius University, Derer Hospital, Bratislava, Slovakia
| | - R. Camacho
- Laboratório de Biologia Molecular, Centro Hospitalar de Lisboa Ocidental, Lisboa, Portugal
| | - P. Truska
- Institute of Public Health of the Capital of Slovakia, Bratislava, Slovakia
| | - D. Stanekova
- Slovak Medical University, NRC for HIV/AIDS Prevention, Bratislava, Slovakia
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Vinogradova A, Gafurova E, Muñoz-Nieto M, Rakhmanova A, Osmanov S, Thomson MM. Short communication: Molecular epidemiology of HIV type 1 in the Republic of Dagestan, Russian Federation: virtually uniform circulation of subtype A, former Soviet Union variant, with predominance of the V77I(PR) subvariant. AIDS Res Hum Retroviruses 2010; 26:395-400. [PMID: 20377421 DOI: 10.1089/aid.2009.0205] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We examine the distribution of viral genetic forms and the presence of antiretroviral drug resistance mutations in HIV-1 infections in the Republic of Dagestan, in the North Caucasus area of Russia, where a recent large increase in HIV-1 infections has been documented. Samples were collected from 41 HIV-1-infected individuals from Dagestan, most of them from the cities of Derbent (n = 21) and Mahachkala (n = 18). Thirty six were injecting drug users and five were infected by heterosexual contact. None was on antiretroviral drug treatment. HIV-1 protease and a segment of reverse transcriptase were amplified by RT-PCR from plasma RNA and sequenced, and phylogenetic trees were constructed via maximum likelihood. Forty (97.6%) of 41 samples were of subtype A, former Soviet Union variant (A(FSU)), of which 27 (67.5%) clustered with the subvariant containing the V77I substitution in protease (V77I(PR)). Within this cluster, 13 viruses formed a local subcluster, 10 of which were from Derbent. Four viruses clustered with the A(SP2) subcluster, recently identified in St. Petersburg, two with a virus from Georgia and one with a virus from Azerbaijan. No mutations associated with antiretroviral drug resistance were detected. The results, therefore, show the relationship of the HIV-1 epidemic in Dagestan with that of other areas of Russia and of neighboring countries, and reveal the spread of the A(FSU) V77I(PR) variant in the North Caucasus area.
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Affiliation(s)
| | | | - Mercedes Muñoz-Nieto
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Aza Rakhmanova
- Department of Infectious Diseases, Botkin's Infectious Diseases Hospital, St. Petersburg, Russia
| | | | - Michael M. Thomson
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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Machado LF, Ishak MO, Vallinoto AC, Lemos JAR, Azevedo VN, Moreira MR, Souza MI, Fernandes LM, Souza LL, Ishak R. Molecular epidemiology of HIV type 1 in northern Brazil: identification of subtypes C and D and the introduction of CRF02_AG in the Amazon region of Brazil. AIDS Res Hum Retroviruses 2009; 25:961-6. [PMID: 19795985 DOI: 10.1089/aid.2009.0027] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The molecular epidemiology of HIV-1 strains circulating in Belem-PA and Macapa-AP, in the Northern region of Brazil, is described using sequences of the C2V3 segment of the env and the pro gene of HIV-1 from patients of the Reference Unit for Special Infectious and Parasitary Diseases (URE-DIPE) in Belem-PA and the Central Laboratory (LACEN) in Macapa-AP. Subtype B was the most frequently found in relation to pro (88.3%) in Belem and in Macapa (97.1%) and env (88.3% in Belem and 100% in Macapa). Subtype F was also described in Belem (9.3% pro and 8.3% env) and Macapa (2.8% pro). Subtype D was described for the first time in the Northern region of the country as well as the recent entry of CRF02_AG. Furthermore, several possible recombinant forms among the various subtypes were found in both cities. The results support the hypothesis that HIV-1 infection is associated with the epidemic of the virus in the Southeast region of the country and that the city of Belem is the most important route for HIV-1 entry in the Northern region of Brazil.
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Affiliation(s)
- Luiz F.A. Machado
- Virus Laboratory, Institute of Biological Sciences, Universidade Federal do Para, Para, Brazil
| | - Marluísa O.G. Ishak
- Virus Laboratory, Institute of Biological Sciences, Universidade Federal do Para, Para, Brazil
| | - Antonio C.R. Vallinoto
- Virus Laboratory, Institute of Biological Sciences, Universidade Federal do Para, Para, Brazil
| | - José Alexandre R. Lemos
- Virus Laboratory, Institute of Biological Sciences, Universidade Federal do Para, Para, Brazil
- Laboratory of Molecular Biology, State Blood Bank, Para, Brazil
| | - Vania N. Azevedo
- Virus Laboratory, Institute of Biological Sciences, Universidade Federal do Para, Para, Brazil
| | | | - Maria I.M. Souza
- Virus Laboratory, Institute of Biological Sciences, Universidade Federal do Para, Para, Brazil
| | - Luciana M. Fernandes
- Virus Laboratory, Institute of Biological Sciences, Universidade Federal do Para, Para, Brazil
| | - Lia L.B. Souza
- Reference Unit for Special Infectious and Parasitary Diseases, Brazil
| | - Ricardo Ishak
- Virus Laboratory, Institute of Biological Sciences, Universidade Federal do Para, Para, Brazil
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Molecular epidemiology of HIV-1 in St Petersburg, Russia: predominance of subtype A, former Soviet Union variant, and identification of intrasubtype subclusters. J Acquir Immune Defic Syndr 2009; 51:332-9. [PMID: 19363451 DOI: 10.1097/qai.0b013e31819c1757] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES To examine HIV-1 genetic diversity in St. Petersburg. METHODS Partial HIV-1 pol sequences from 102 plasma samples collected in 2006 were analyzed with a Bayesian phylogeny inference method. RESULTS Subtype A, former Soviet Union (FSU) variant (AFSU), was the predominant clade (89.3%); other clades were subtypes B (9.7%) and F1 (1%). AFSU was predominant both among injecting drug users (98.2%) and heterosexually infected individuals (91.4%), whereas subtype B was more prevalent among homosexual men (75%). Within the AFSU variant, most sequences (93.5%) branched within 1 of 4 strongly supported subclusters. The largest comprised 63% AFSU viruses and was uncommon outside St Petersburg. A second subcluster (17.4% AFSU viruses) corresponds to the variant with the V77I substitution in protease, which is widely circulating in different FSU countries. Two minor subclusters comprised 8.7% and 6.5% AFSU viruses, respectively. There was no correlation between risk exposure and AFSU subclusters. Six of 8 subtype B sequences, 4 of them from homosexual men, grouped in a monophyletic subcluster. CONCLUSIONS The results of this study show a great predominance of AFSU viruses in St Petersburg and point to a few phylogenetically identifiable introductions as the origin of most current HIV-1 AFSU infections in the city.
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Lehrach WP, Husmeier D. Segmenting bacterial and viral DNA sequence alignments with a trans-dimensional phylogenetic factorial hidden Markov model. J R Stat Soc Ser C Appl Stat 2009. [DOI: 10.1111/j.1467-9876.2008.00648.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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41
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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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Lemey P, Lott M, Martin DP, Moulton V. Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning. BMC Bioinformatics 2009; 10:126. [PMID: 19397803 PMCID: PMC2684544 DOI: 10.1186/1471-2105-10-126] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Accepted: 04/27/2009] [Indexed: 12/02/2022] Open
Abstract
Background Recombination has a profound impact on the evolution of viruses, but characterizing recombination patterns in molecular sequences remains a challenging endeavor. Despite its importance in molecular evolutionary studies, identifying the sequences that exhibit such patterns has received comparatively less attention in the recombination detection framework. Here, we extend a quartet-mapping based recombination detection method to enable identification of recombinant sequences without prior specifications of either query and reference sequences. Through simulations we evaluate different recombinant identification statistics and significance tests. We compare the quartet approach with triplet-based methods that employ additional heuristic tests to identify parental and recombinant sequences. Results Analysis of phylogenetic simulations reveal that identifying the descendents of relatively old recombination events is a challenging task for all methods available, and that quartet scanning performs relatively well compared to the triplet based methods. The use of quartet scanning is further demonstrated by analyzing both well-established and putative HIV-1 recombinant strains. In agreement with recent findings, we provide evidence that the presumed circulating recombinant CRF02_AG is a 'pure' lineage, whereas the presumed parental lineage subtype G has a recombinant origin. We also demonstrate HIV-1 intrasubtype recombination, confirm the hybrid origin of SIV in chimpanzees and further disentangle the recombinant history of SIV lineages in a primate immunodeficiency virus data set. Conclusion Quartet scanning makes a valuable addition to triplet-based methods for identifying recombinant sequences without prior specifications of either query and reference sequences. The new method is available in the VisRD v.3.0 package .
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Affiliation(s)
- Philippe Lemey
- Rega Institute, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium.
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Ding N, Guo D, Zhang C. Reidentification of the recombination map of CRF03_AB: evidence for a new additional mosaic a subtype segment. AIDS Res Hum Retroviruses 2008; 24:1337-9. [PMID: 18844466 DOI: 10.1089/aid.2008.0112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Na Ding
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Dongmei Guo
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Chiyu Zhang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China
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Stimulant injectors in Ukraine: the next wave of the epidemic? AIDS Behav 2008; 12:652-61. [PMID: 18264752 DOI: 10.1007/s10461-008-9359-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2007] [Accepted: 01/22/2008] [Indexed: 10/22/2022]
Abstract
This study was designed to assess differences in drug and sex-related risk behaviors between injectors of opiates only, opiate/sedative mix only and stimulants only. Participants were current out-of-treatment injection drug users (IDUs), unaware of their HIV status, recruited through street outreach in Kiev, Odessa and Makeevka/Donetsk, Ukraine. Overall, 22% tested positive for HIV, including 39% among opiate/sedative injectors, 19% among opiate injectors and 17% among stimulant injectors. Despite these differences, stimulant injectors were at higher risk than other IDUs in sharing a used needle/syringe, always injecting with others, injecting a drug solution drawn from a common container, having an IDU sex partner, not using condoms during vaginal or anal sex and on composite measures of injection and sex risks. After controlling for age differences, stimulant injectors remained at higher risk in their needle and sex risk behaviors. Without intervention, it is likely that HIV will increase among stimulant injectors.
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45
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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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46
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Global molecular epidemiology of HIV: understanding the genesis of AIDS pandemic. ADVANCES IN PHARMACOLOGY 2008; 56:1-25. [PMID: 18086407 DOI: 10.1016/s1054-3589(07)56001-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
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Eyer-Silva WA, Morgado MG. Autochthonous horizontal transmission of a CRF02_AG strain revealed by a human immunodeficiency virus type 1 diversity survey in a small city in inner state of Rio de Janeiro, Southeast Brazil. Mem Inst Oswaldo Cruz 2007; 102:809-15. [PMID: 17992366 DOI: 10.1590/s0074-02762007005000112] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2007] [Accepted: 09/25/2007] [Indexed: 11/22/2022] Open
Abstract
As part of an ongoing study on the features of AIDS spread towards small cities and rural areas, we present a molecular survey of human immunodeficiency virus type 1 (HIV-1) polymerase sequences recovered between 2004 and 2006 from 71 patients receiving care in the city of Saquarema, inner state of Rio de Janeiro. Phylogenetic reconstructions found the two prevalent lineages in the state (subtypes B [59 strains, 83.1%], F1 [6 strains; 8.4%], and BF1 recombinants [four strains; 5.6%]), as well as two (2.8%) CRF02_AG strains, which seems to be an emerging lineage in the capital. These CRF02_AG sequences were recovered from a married heterosexual couple who never traveled abroad, thus providing the first molecular evidence of autochthonous horizontal transmission of this lineage of major global importance. Also, three phylogenetic clusters of strains recovered from a total of 18.3% of the cohort were uncovered. Their close genetic relatedness suggests they were recovered from patients who probably took part in the same chain of viral spread. In conjunction with our previous surveys from inner Rio de Janeiro, these results suggest that although small cities harbor unique molecular features of HIV-1 infection, they also clearly reflect and may rapidly absorb the diversity recorded in large urban centers.
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Affiliation(s)
- Walter A Eyer-Silva
- Laboratório de Aids & Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, 21045-900, Brazil.
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Gifford RJ, de Oliveira T, Rambaut A, Pybus OG, Dunn D, Vandamme AM, Kellam P, Pillay D. Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1. J Virol 2007; 81:13050-6. [PMID: 17898057 PMCID: PMC2169105 DOI: 10.1128/jvi.00889-07] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2007] [Accepted: 09/17/2007] [Indexed: 11/20/2022] Open
Abstract
With ongoing generation of viral genetic diversity and increasing levels of migration, the global human immunodeficiency virus type 1 (HIV-1) epidemic is becoming increasingly heterogeneous. In this study, we investigate the epidemiological characteristics of 5,675 HIV-1 pol gene sequences sampled from distinct infections in the United Kingdom. These sequences were phylogenetically analyzed in conjunction with 976 complete-genome and 3,201 pol gene reference sequences sampled globally and representing the broad range of HIV-1 genetic diversity, allowing us to estimate the probable geographic origins of the various strains present in the United Kingdom. A statistical analysis of phylogenetic clustering in this data set identified several independent transmission chains within the United Kingdom involving recently introduced strains and indicated that strains more commonly associated with infections acquired heterosexually in East Africa are spreading among men who have sex with men. Coalescent approaches were also used and indicated that the transmission chains that we identify originated in the late 1980s to early 1990s. Similar changes in the epidemiological structuring of HIV epidemics are likely to be taking in place in other industrialized nations with large immigrant populations. The framework implemented here takes advantage of the vast amount of routinely generated HIV-1 sequence data and can provide epidemiological insights not readily obtainable through standard surveillance methods.
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Affiliation(s)
- Robert J Gifford
- Department of Infection, University College London, London, United Kingdom.
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Rachlis B, Brouwer KC, Mills EJ, Hayes M, Kerr T, Hogg RS. Migration and transmission of blood-borne infections among injection drug users: understanding the epidemiologic bridge. Drug Alcohol Depend 2007; 90:107-19. [PMID: 17485179 DOI: 10.1016/j.drugalcdep.2007.03.014] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Revised: 03/29/2007] [Accepted: 03/29/2007] [Indexed: 12/01/2022]
Abstract
Migration is one of many social factors contributing to the spread of HIV and other blood-borne or sexually transmitted infections (STI). Bringing together large numbers of people from diverse settings, the process of migration moves infected individuals to diverse geographic locations. Injection drug users (IDU) are a relatively mobile group, often moving between cities, smaller communities, and across international borders for reasons of work, security, or access to narcotics. This mobility indicates the potential for IDU who engage in risky behavior outside their home areas to transmit HIV infection to other IDU, their sex partners, and others in the population. The objectives of this review are to examine: (1) the influence of drug trafficking and the spread of drug use on the diffusion of HIV, (2) the influence of migration on drug use and HIV-related risk behaviors among migrants, and (3) the mobility patterns of IDU and its role in the spread of HIV. We also discuss the potential policy implications of addressing prevention and care issues in mobile drug using populations.
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Affiliation(s)
- Beth Rachlis
- BC Centre for Excellence in HIV/AIDS, St. Paul's Hospital, Vancouver, British Columbia, Canada.
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Powell RLR, Zhao J, Konings FAJ, Tang S, Nanfack A, Burda S, Urbanski MM, Saa DR, Hewlett I, Nyambi PN. Identification of a novel circulating recombinant form (CRF) 36_cpx in Cameroon that combines two CRFs (01_AE and 02_AG) with ancestral lineages of subtypes A and G. AIDS Res Hum Retroviruses 2007; 23:1008-19. [PMID: 17725418 DOI: 10.1089/aid.2006.0289] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
An array of CRFs have been identified in Cameroon, the most notable being CRF02_AG. HIV-1 in the East Province of Cameroon is particularly diverse: in a recent study, we found a high proportion of unique recombinant forms (URFs). Herein we describe the analysis of the full-length sequences of two of these URFs, which, after preliminary analysis of gag, pol, and env fragments, appeared to be a novel CRF. This novel strain, CRF36_cpx, contains fragments that can be assigned to the CRF01_AE, CRF02_AG, and subtype A and G radiations. Forty percent of the genome can be classified as CRF02_AG, including regions in gag, pol, env, and the accessory genes. Twenty-seven percent is CRF01_AE, comprising the majority of gag, the beginning of env, and the end of env into the 3' LTR. Twenty percent of the genome can be assigned to subtype A, with segments in pol and env. The remaining 13% of the sequence is classifiable as subtype G, in pol and vpu. The subtype A and G lineages formed by the CRF36_cpx sequences are unique and appear ancestral in nature. CRF36_cpx is both the first to combine more than one CRF and the first to include fragments of CRF02_AG. The ancestral sequences present in CRF36_cpx represent a link to extinct strains, and, potentially, insight into the evolution of HIV-1.
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Affiliation(s)
- Rebecca L R Powell
- Department of Microbiology, New York University School of Medicine, New York, New York 10010, USA
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