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Kupperman MD, Ke R, Leitner T. SEEPS: A Simulation Tool for Understanding Impacts of Contact Tracing on Epidemiological Inference from Phylogenetic Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.30.567148. [PMID: 38076930 PMCID: PMC10705478 DOI: 10.1101/2023.11.30.567148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Motivation Robust sampling methods are foundational to inferences using phylogenies. Yet the impact of using contact tracing, a type of non-uniform sampling used in public health applications such as infectious disease outbreak investigations, is not well understood. To understand how this non-uniform sampling method influences a recovered phylogeny, a new simulation tool is needed. Results We developed a new simulation tool called SEEPS (Sequence Evolution and Epidemiological Process Simulator) that allows for the simulation of contact tracing and the resulting transmission tree, pathogen phylogeny, and corresponding virus genetic sequences. Importantly, SEEPS takes within-host evolution into account when generating pathogen phylogenies and sequences from transmission histories. Using SEEPS, we demonstrate that contact tracing can significantly impact the structure of the resulting tree, as described by popular tree statistics. We also examined real data from a 2007-2008 Swedish HIV-1 outbreak and the broader 1998-2010 European HIV-1 epidemic to highlight the differences in contact tracing and expected phylogenies. Aided by SEEPS, we show that the data collection of the Swedish outbreak was strongly influenced by contact tracing even after downsampling, while the broader European Union epidemic showed little evidence of universal contact tracing, agreeing with the known epidemiological information about sampling and spread. Overall, our results highlight the importance of including possible non-uniform sampling schemes when examining phylogenetic trees. For that, SEEPS serves as a useful tool to evaluate such impacts, thereby facilitating better phylogenetic inferences of the characteristics of a disease outbreak. Availability SEEPS is available at github.com/MolEvolEpid/SEEPS.
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Affiliation(s)
- Michael D. Kupperman
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, New Mexico, United States of America
- Department of Applied Mathematics, University of Washington, Washington, United States of America
| | - Ruian Ke
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, New Mexico, United States of America
| | - Thomas Leitner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, New Mexico, United States of America
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Weibull Wärnberg A, Brännström J, Elvstam O, Gisslén M, Månsson F, Sönnerborg A, van de Klundert MA. The molecular epidemiology of HIV-1 in Sweden 1996 to 2022, and the influence of migration from Ukraine. Euro Surveill 2023; 28:2300224. [PMID: 38037731 PMCID: PMC10690863 DOI: 10.2807/1560-7917.es.2023.28.48.2300224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/04/2023] [Indexed: 12/02/2023] Open
Abstract
BackgroundThe global distribution of HIV-1 subtypes is evolving, which is reflected in the Swedish HIV cohort. The subtype HIV-1A6, which may be prone to developing resistance to cabotegravir, is the most common subtype in Ukraine.AimWe aimed to examine trends in HIV-1 subtype distribution in Sweden, with a special focus on HIV-1A6, and to describe the virology, demography and treatment of Ukrainian people living with HIV (PLWH) who migrated to Sweden in 2022.MethodsData about PLWH in Sweden are included in a national database (InfCareHIV). We used the online tool COMET to establish HIV-1 subtypes and the Stanford database to define drug resistance mutations. We investigated the relation between virological characteristics and demographic data.ResultsThe early epidemic was predominated by HIV-1 subtype B infections in people born in Sweden. After 1990, the majority of new PLWH in Sweden were PLWH migrating to Sweden, resulting in an increasingly diverse epidemic. In 2022, HIV-1A6 had become the sixth most common subtype in Sweden and 98 of the 431 new PLWH that were registered in Sweden came from Ukraine. We detected HIV RNA in plasma of 32 Ukrainian patients (34%), of whom 17 were previously undiagnosed, 10 had interrupted therapy and five were previously diagnosed but not treated. We found HIV-1A6 in 23 of 24 sequenced patients.ConclusionThe molecular HIV epidemiology in Sweden continues to diversify and PLWH unaware of their HIV status and predominance of HIV-1A6 should be considered when arranging care directed at PLWH from Ukraine.
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Affiliation(s)
- Anna Weibull Wärnberg
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Johanna Brännström
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Södersjukhuset, Stockholm, Sweden
| | - Olof Elvstam
- Department of Translational Medicine, Clinical Infection Medicine, Lund University, Malmö
- Department of Infectious Diseases, Växjö Central Hospital, Växjö, Sweden
| | - Magnus Gisslén
- Region Västra Götaland, Department of Infectious Diseases, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Månsson
- Department of Translational Medicine, Clinical Infection Medicine, Lund University, Malmö
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Maarten Aa van de Klundert
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
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A deep learning approach to real-time HIV outbreak detection using genetic data. PLoS Comput Biol 2022; 18:e1010598. [PMID: 36240224 PMCID: PMC9604978 DOI: 10.1371/journal.pcbi.1010598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 10/26/2022] [Accepted: 09/23/2022] [Indexed: 12/15/2022] Open
Abstract
Pathogen genomic sequence data are increasingly made available for epidemiological monitoring. A main interest is to identify and assess the potential of infectious disease outbreaks. While popular methods to analyze sequence data often involve phylogenetic tree inference, they are vulnerable to errors from recombination and impose a high computational cost, making it difficult to obtain real-time results when the number of sequences is in or above the thousands. Here, we propose an alternative strategy to outbreak detection using genomic data based on deep learning methods developed for image classification. The key idea is to use a pairwise genetic distance matrix calculated from viral sequences as an image, and develop convolutional neutral network (CNN) models to classify areas of the images that show signatures of active outbreak, leading to identification of subsets of sequences taken from an active outbreak. We showed that our method is efficient in finding HIV-1 outbreaks with R0 ≥ 2.5, and overall a specificity exceeding 98% and sensitivity better than 92%. We validated our approach using data from HIV-1 CRF01 in Europe, containing both endemic sequences and a well-known dual outbreak in intravenous drug users. Our model accurately identified known outbreak sequences in the background of slower spreading HIV. Importantly, we detected both outbreaks early on, before they were over, implying that had this method been applied in real-time as data became available, one would have been able to intervene and possibly prevent the extent of these outbreaks. This approach is scalable to processing hundreds of thousands of sequences, making it useful for current and future real-time epidemiological investigations, including public health monitoring using large databases and especially for rapid outbreak identification.
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Nduva GM, Otieno F, Kimani J, McKinnon LR, Cholette F, Sandstrom P, Graham SM, Price MA, Smith AD, Bailey RC, Hassan AS, Esbjörnsson J, Sanders EJ. Phylogeographic Assessment Reveals Geographic Sources of HIV-1 Dissemination Among Men Who Have Sex With Men in Kenya. Front Microbiol 2022; 13:843330. [PMID: 35356525 PMCID: PMC8959701 DOI: 10.3389/fmicb.2022.843330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 01/19/2022] [Indexed: 12/14/2022] Open
Abstract
HIV-1 transmission dynamics involving men who have sex with men (MSM) in Africa are not well understood. We investigated the rates of HIV-1 transmission between MSM across three regions in Kenya: Coast, Nairobi, and Nyanza. We analyzed 372 HIV-1 partial pol sequences sampled during 2006-2019 from MSM in Coast (N = 178, 47.9%), Nairobi (N = 137, 36.8%), and Nyanza (N = 57, 15.3%) provinces in Kenya. Maximum-likelihood (ML) phylogenetics and Bayesian inference were used to determine HIV-1 clusters, evolutionary dynamics, and virus migration rates between geographic regions. HIV-1 sub-subtype A1 (72.0%) was most common followed by subtype D (11.0%), unique recombinant forms (8.9%), subtype C (5.9%), CRF 21A2D (0.8%), subtype G (0.8%), CRF 16A2D (0.3%), and subtype B (0.3%). Forty-six clusters (size range 2-20 sequences) were found-half (50.0%) of which had evidence of extensive HIV-1 mixing among different provinces. Data revealed an exponential increase in infections among MSM during the early-to-mid 2000s and stable or decreasing transmission dynamics in recent years (2017-2019). Phylogeographic inference showed significant (Bayes factor, BF > 3) HIV-1 dissemination from Coast to Nairobi and Nyanza provinces, and from Nairobi to Nyanza province. Strengthening HIV-1 prevention programs to MSM in geographic locations with higher HIV-1 prevalence among MSM (such as Coast and Nairobi) may reduce HIV-1 incidence among MSM in Kenya.
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Affiliation(s)
- George M. Nduva
- Department of Translational Medicine, Lund University, Lund, Sweden
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Joshua Kimani
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Lyle R. McKinnon
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Francois Cholette
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Paul Sandstrom
- National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Susan M. Graham
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - Matt A. Price
- IAVI, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Adrian D. Smith
- Nuffield Department of Medicine, The University of Oxford, Oxford, United Kingdom
| | - Robert C. Bailey
- Nyanza Reproductive Health Society, Kisumu, Kenya
- Division of Epidemiology and Biostatistics, University of Illinois Chicago, Chicago, IL, United States
| | - Amin S. Hassan
- Department of Translational Medicine, Lund University, Lund, Sweden
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, Lund, Sweden
- Nuffield Department of Medicine, The University of Oxford, Oxford, United Kingdom
| | - Eduard J. Sanders
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, The University of Oxford, Oxford, United Kingdom
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Nduva GM, Nazziwa J, Hassan AS, Sanders EJ, Esbjörnsson J. The Role of Phylogenetics in Discerning HIV-1 Mixing among Vulnerable Populations and Geographic Regions in Sub-Saharan Africa: A Systematic Review. Viruses 2021; 13:1174. [PMID: 34205246 PMCID: PMC8235305 DOI: 10.3390/v13061174] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/19/2022] Open
Abstract
To reduce global HIV-1 incidence, there is a need to understand and disentangle HIV-1 transmission dynamics and to determine the geographic areas and populations that act as hubs or drivers of HIV-1 spread. In Sub-Saharan Africa (sSA), the region with the highest HIV-1 burden, information about such transmission dynamics is sparse. Phylogenetic inference is a powerful method for the study of HIV-1 transmission networks and source attribution. In this review, we assessed available phylogenetic data on mixing between HIV-1 hotspots (geographic areas and populations with high HIV-1 incidence and prevalence) and areas or populations with lower HIV-1 burden in sSA. We searched PubMed and identified and reviewed 64 studies on HIV-1 transmission dynamics within and between risk groups and geographic locations in sSA (published 1995-2021). We describe HIV-1 transmission from both a geographic and a risk group perspective in sSA. Finally, we discuss the challenges facing phylogenetic inference in mixed epidemics in sSA and offer our perspectives and potential solutions to the identified challenges.
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Affiliation(s)
- George M. Nduva
- Department of Translational Medicine, Lund University, 205 02 Malmö, Sweden; (G.M.N.); (J.N.); (A.S.H.)
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi 80108, Kenya;
| | - Jamirah Nazziwa
- Department of Translational Medicine, Lund University, 205 02 Malmö, Sweden; (G.M.N.); (J.N.); (A.S.H.)
| | - Amin S. Hassan
- Department of Translational Medicine, Lund University, 205 02 Malmö, Sweden; (G.M.N.); (J.N.); (A.S.H.)
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi 80108, Kenya;
| | - Eduard J. Sanders
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi 80108, Kenya;
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, The University of Oxford, Oxford OX1 2JD, UK
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, 205 02 Malmö, Sweden; (G.M.N.); (J.N.); (A.S.H.)
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, The University of Oxford, Oxford OX1 2JD, UK
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Dennis AM, Hué S, Billock R, Levintow S, Sebastian J, Miller WC, Eron JJ. Human Immunodeficiency Virus Type 1 Phylodynamics to Detect and Characterize Active Transmission Clusters in North Carolina. J Infect Dis 2021; 221:1321-1330. [PMID: 31028702 DOI: 10.1093/infdis/jiz176] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 04/11/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) phylodynamics can be used to monitor epidemic trends and help target prevention through identification and characterization of transmission clusters. METHODS We analyzed HIV-1 pol sequences sampled in North Carolina from 1997 to 2014. Putative clusters were identified using maximum-likelihood trees and dated using Bayesian Markov Chain Monte Carlo inference. Active clusters were defined as clusters including internal nodes from 2009 to 2014. Effective reproductive numbers (Re) were estimated using birth-death models for large clusters that expanded ≥2-fold from 2009 to 2014. RESULTS Of 14 921 persons, 7508 (50%) sequences were identified in 2264 clusters. Only 288 (13%) clusters were active from 2009 to 2014; 37 were large (10-36 members). Compared to smaller clusters, large clusters were increasingly populated by men and younger persons; however, nearly 60% included ≥1 women. Clusters with ≥3 members demonstrated assortative mixing by sex, age, and sample region. Of 15 large clusters with ≥2-fold expansion, nearly all had Re approximately 1 by 2014. CONCLUSIONS Phylodynamics revealed transmission cluster expansion in this densely sampled region and allowed estimates of Re to monitor active clusters, showing the propensity for steady, onward propagation. Associations with clustering and cluster characteristics vary by cluster size. Harnessing sequence-derived epidemiologic parameters within routine surveillance could allow refined monitoring of local subepidemics.
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Affiliation(s)
- Ann M Dennis
- Division of Infectious Diseases, University of North Carolina at Chapel Hill
| | - Stéphane Hué
- London School of Hygiene and Tropical Medicine, United Kingdom
| | - Rachael Billock
- Department of Epidemiology, University of North Carolina at Chapel Hill
| | - Sara Levintow
- Department of Epidemiology, University of North Carolina at Chapel Hill
| | - Joseph Sebastian
- Campbell University School of Osteopathic Medicine, South Lillington, North Carolina
| | | | - Joseph J Eron
- Division of Infectious Diseases, University of North Carolina at Chapel Hill
- Department of Epidemiology, University of North Carolina at Chapel Hill
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Karlsson N, Berglund T, Ekström AM, Hammarberg A, Tammi T. Could 30 years of political controversy on needle exchange programmes in Sweden contribute to scaling-up harm reduction services in the world? NORDIC STUDIES ON ALCOHOL AND DRUGS 2020; 38:66-88. [PMID: 35309093 PMCID: PMC8899060 DOI: 10.1177/1455072520965013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 09/17/2020] [Indexed: 11/17/2022] Open
Abstract
Aims: To end the hepatitis and AIDS epidemics in the world by 2030, countries are encouraged to scale-up harm reduction services and target people who inject drugs (PWID). Blood-borne viruses (BBV) among PWID spread via unsterile injection equipment sharing and to combat this, many countries have introduced needle and syringe exchange programmes (NEP), though not without controversy. Sweden’s long, complicated harm reduction policy transition has been deviant compared to the Nordic countries. After launch in 1986, no NEP were started in Sweden for 23 years, the reasons for which are analysed in this study. Methods: Policy documents, grey literature and research mainly published in 2000–2017 were collected and analysed using a hierarchical framework, to understand how continuous build-up of evidence, decisions and key events, over time influenced NEP development. Results: Sweden’s first NEP opened in a repressive-control drug policy era with a drug-free society goal. Despite high prevalence of BBV among PWID with recurring outbreaks, growing research and key-actor support including a NEP law, no NEP were launched. Political disagreements, fluctuating actor-coalitions, questioning of research, and a municipality veto against NEP, played critical roles. With an individual-centred perspective being brought into the drug policy domain, the manifestation of a dual drug and health policy track, a revised NEP law in 2017 and removal of the veto, Sweden would see fast expansion of new NEP. Conclusions: Lessons from the Swedish case could provide valuable insight for countries about to scale-up harm reduction services including how to circumvent costly time- and resource-intensive obstacles and processes involving ideological and individual moral dimensions.
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Affiliation(s)
- Niklas Karlsson
- Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden; and Department of Public Health Analysis and Development, Public Health Agency of Sweden, Solna, Sweden
| | - Torsten Berglund
- Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden; and Department of Public Health Analysis and Development, Public Health Agency of Sweden, Solna, Sweden
| | - Anna Mia Ekström
- Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden; and Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Anders Hammarberg
- Centre for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden; and Stockholm Centre for Dependency Disorders, Stockholm Health Care Services, Stockholm County Council, Sweden
| | - Tuukka Tammi
- Finnish Institute for Health and Welfare, Finland
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Zhang Y, Leitner T, Albert J, Britton T. Inferring transmission heterogeneity using virus genealogies: Estimation and targeted prevention. PLoS Comput Biol 2020; 16:e1008122. [PMID: 32881984 PMCID: PMC7494101 DOI: 10.1371/journal.pcbi.1008122] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 09/16/2020] [Accepted: 07/02/2020] [Indexed: 12/19/2022] Open
Abstract
Spread of HIV typically involves uneven transmission patterns where some individuals spread to a large number of individuals while others to only a few or none. Such transmission heterogeneity can impact how fast and how much an epidemic spreads. Further, more efficient interventions may be achieved by taking such transmission heterogeneity into account. To address these issues, we developed two phylogenetic methods based on virus sequence data: 1) to generally detect if significant transmission heterogeneity is present, and 2) to pinpoint where in a phylogeny high-level spread is occurring. We derive inference procedures to estimate model parameters, including the amount of transmission heterogeneity, in a sampled epidemic. We show that it is possible to detect transmission heterogeneity under a wide range of simulated situations, including incomplete sampling, varying levels of heterogeneity, and including within-host genetic diversity. When evaluating real HIV-1 data from different epidemic scenarios, we found a lower level of transmission heterogeneity in slowly spreading situations and a higher level of heterogeneity in data that included a rapid outbreak, while R0 and Sackin's index (overall tree shape statistic) were similar in the two scenarios, suggesting that our new method is able to detect transmission heterogeneity in real data. We then show by simulations that targeted prevention, where we pinpoint high-level spread using a coalescence measurement, is efficient when sequence data are collected in an ongoing surveillance system. Such phylogeny-guided prevention is efficient under both single-step contact tracing as well as iterative contact tracing as compared to random intervention.
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Affiliation(s)
- Yunjun Zhang
- Department of Biostatistics, School of Public Health, Peking University, Beijing, China
- Department of Mathematics, Stockholm University, Stockholm, Sweden
- * E-mail:
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Tom Britton
- Department of Mathematics, Stockholm University, Stockholm, Sweden
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Des Jarlais DC, Sypsa V, Feelemyer J, Abagiu AO, Arendt V, Broz D, Chemtob D, Seguin-Devaux C, Duwve JM, Fitzgerald M, Goldberg DJ, Hatzakis A, Jipa RE, Katchman E, Keenan E, Khan I, Konrad S, McAuley A, Skinner S, Wiessing L. HIV outbreaks among people who inject drugs in Europe, North America, and Israel. Lancet HIV 2020; 7:e434-e442. [PMID: 32504576 PMCID: PMC10150936 DOI: 10.1016/s2352-3018(20)30082-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 01/25/2023]
Abstract
During 2011-16, HIV outbreaks occurred among people who inject drugs (PWID) in Canada (southeastern Saskatchewan), Greece (Athens), Ireland (Dublin), Israel (Tel Aviv), Luxembourg, Romania (Bucharest), Scotland (Glasgow), and USA (Scott County, Indiana). Factors common to many of these outbreaks included community economic problems, homelessness, and changes in drug injection patterns. The outbreaks differed in size (from under 100 to over 1000 newly reported HIV cases among PWID) and in the extent to which combined prevention had been implemented before, during, and after the outbreaks. Countries need to ensure high coverage of HIV prevention services and coverage higher than the current UNAIDS recommendation might be needed in areas in which short acting drugs are injected. In addition, monitoring of PWID with special attention for changing drug use patterns, risk behaviours, and susceptible subgroups (eg, PWID experiencing homelessness) needs to be in place to prevent or rapidly detect and contain new HIV outbreaks.
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Affiliation(s)
- Don C Des Jarlais
- College of Global Public Health, New York University, New York, NY, USA.
| | - Vana Sypsa
- Department of Hygiene, Epidemiology and Medical Statistics, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Adrian O Abagiu
- National Institute for Infectious Diseases, Bucharest, Romania
| | - Vic Arendt
- Service National des Maladies Infectieuses, Centre Hospitalier de Luxembourg, Luxembourg, USA
| | - Dita Broz
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Daniel Chemtob
- Department of Tuberculosis and AIDS, Ministry of Health, Jerusalem, Israel; Faculty of Medicine, Hebrew University-Hadassah Medical School, Braun School of Public Health and Community Medicine, Jerusalem, Israel
| | - Carole Seguin-Devaux
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch sur Alzette, Luxembourg
| | - Joan M Duwve
- Richard M Fairbanks School of Public Health, Indianapolis, IN, USA
| | | | | | - Angelos Hatzakis
- Department of Hygiene, Epidemiology and Medical Statistics, National and Kapodistrian University of Athens, Athens, Greece; NHS National Services Scotland, Glasgow, UK
| | - Raluca E Jipa
- National Institute for Infectious Diseases, Bucharest, Romania
| | - Eugene Katchman
- Infectious Diseases Unit, Tel Aviv Sourasky Medical Centre and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Ibrahim Khan
- First Nations and Inuit Health Branch, Indigenous Services Canada, Regina, SK, Canada
| | - Stephanie Konrad
- First Nations and Inuit Health Branch, Indigenous Services Canada, Regina, SK, Canada
| | - Andrew McAuley
- NHS National Services Scotland, Glasgow, UK; School of Health and Life Sciences, Glasgow Caledonian University, Glasgow, UK
| | - Stuart Skinner
- College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Lucas Wiessing
- European Monitoring Centre for Drugs and Drug Addiction, Lisbon, Portugal
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Nduva GM, Hassan AS, Nazziwa J, Graham SM, Esbjörnsson J, Sanders EJ. HIV-1 Transmission Patterns Within and Between Risk Groups in Coastal Kenya. Sci Rep 2020; 10:6775. [PMID: 32317722 PMCID: PMC7174422 DOI: 10.1038/s41598-020-63731-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/30/2020] [Indexed: 11/09/2022] Open
Abstract
HIV-1 transmission patterns within and between populations at different risk of HIV-1 acquisition in Kenya are not well understood. We investigated HIV-1 transmission networks in men who have sex with men (MSM), injecting drug users (IDU), female sex workers (FSW) and heterosexuals (HET) in coastal Kenya. We used maximum-likelihood and Bayesian phylogenetics to analyse new (N = 163) and previously published (N = 495) HIV-1 polymerase sequences collected during 2005-2019. Of the 658 sequences, 131 (20%) were from MSM, 58 (9%) IDU, 109 (17%) FSW, and 360 (55%) HET. Overall, 206 (31%) sequences formed 61 clusters. Most clusters (85%) consisted of sequences from the same risk group, suggesting frequent within-group transmission. The remaining clusters were mixed between HET/MSM (7%), HET/FSW (5%), and MSM/FSW (3%) sequences. One large IDU-exclusive cluster was found, indicating an independent sub-epidemic among this group. Phylodynamic analysis of this cluster revealed a steady increase in HIV-1 infections among IDU since the estimated origin of the cluster in 1987. Our results suggest mixing between high-risk groups and heterosexual populations and could be relevant for the development of targeted HIV-1 prevention programmes in coastal Kenya.
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Affiliation(s)
- George M Nduva
- Lund University, Lund, Sweden
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
| | - Amin S Hassan
- Lund University, Lund, Sweden
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Susan M Graham
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- University of Washington, Seattle, WA, USA
| | - Joakim Esbjörnsson
- Lund University, Lund, Sweden.
- The University of Oxford, Oxford, United Kingdom.
| | - Eduard J Sanders
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- The University of Oxford, Oxford, United Kingdom
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11
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The Impact of Human Mobility on Regional and Global Efforts to Control HIV Transmission. Viruses 2020; 12:v12010067. [PMID: 31935811 PMCID: PMC7019949 DOI: 10.3390/v12010067] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/30/2019] [Accepted: 01/02/2020] [Indexed: 12/30/2022] Open
Abstract
HIV prevention and control methods are implemented on different scales to reduce the spread of the virus amongst populations. However, despite such efforts, HIV continues to persist in populations with a global incidence rate of 1.8 million in 2017 alone. The introduction of new infections into susceptible regional populations promotes the spread of HIV, indicating a crucial need to study the impact of migration and mobility on regional and global efforts to prevent HIV transmission. Here we reviewed studies that assess the impact of human mobility on HIV transmission and spread. We found an important role for both travel and migration in driving the spread of HIV across regional and national borders. Combined, our results indicate that even in the presence of control and preventive efforts, if migration and travel are occurring, public health efforts will need to remain persistent to ensure that new infections do not grow into outbreaks.
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Ragonnet-Cronin M, Jackson C, Bradley-Stewart A, Aitken C, McAuley A, Palmateer N, Gunson R, Goldberg D, Milosevic C, Leigh Brown AJ. Recent and Rapid Transmission of HIV Among People Who Inject Drugs in Scotland Revealed Through Phylogenetic Analysis. J Infect Dis 2019; 217:1875-1882. [PMID: 29546333 DOI: 10.1093/infdis/jiy130] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 03/08/2018] [Indexed: 11/13/2022] Open
Abstract
Background Harm reduction has dramatically reduced HIV incidence among people who inject drugs (PWID). In Glasgow, Scotland, <10 infections/year have been diagnosed among PWID since the mid-1990s. However, in 2015 a sharp rise in diagnoses was noted among PWID; many were subtype C with 2 identical drug-resistant mutations and some displayed low avidity, suggesting the infections were linked and recent. Methods We collected Scottish pol sequences and identified closely related sequences from public databases. Genetic linkage was ascertained among 228 Scottish, 1820 UK, and 524 global sequences. The outbreak cluster was extracted to estimate epidemic parameters. Results All 104 outbreak sequences originated from Scotland and contained E138A and V179E. Mean genetic distance was <1% and mean time between transmissions was 6.7 months. The average number of onward transmissions consistently exceeded 1, indicating that spread was ongoing. Conclusions In contrast to other recent HIV outbreaks among PWID, harm reduction services were not clearly reduced in Scotland. Nonetheless, the high proportion of individuals with a history of homelessness (45%) suggests that services were inadequate for those in precarious living situations. The high prevalence of hepatitis C (>90%) is indicative of sharing of injecting equipment. Monitoring the epidemic phylogenetically in real time may accelerate public health action.
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Affiliation(s)
| | | | | | | | - Andrew McAuley
- Health Protection Scotland, Glasgow.,Glasgow Caledonian University, United Kingdom
| | - Norah Palmateer
- Health Protection Scotland, Glasgow.,Glasgow Caledonian University, United Kingdom
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Grossman Z, Avidor B, Girshengoren S, Katchman E, Maldarelli F, Turner D. Transmission Dynamics of HIV Subtype A in Tel Aviv, Israel: Implications for HIV Spread and Eradication. Open Forum Infect Dis 2019; 6:5538894. [PMID: 31363777 DOI: 10.1093/ofid/ofz304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 07/03/2019] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE Subtype-A HIV was introduced into Israel in the mid-1990s, predominantly by immigrants from the former Soviet Union (FSU) infected via intravenous drug use (IVDU). HIV subsequently spread beyond the FSU-IVDU community. In 2012, a mini-HIV outbreak, associated with injection of amphetamine cathinone derivatives, started in Tel Aviv, prompting public health response. To assess current trends and the impact of the outbreak and control measures, we conducted a phyloepidemiologic analysis. METHOD Demographic and clinical records and HIV sequences were compiled from 312 subtype-A HIV-infected individuals attending the Tel-Aviv Sourasky Medical Center between 2005-2016, where >40% of all subtype-A HIV-infected individuals in Israel are undergoing care. Molecular evolutionary genetics analysis (MEGA) and ayesian evolutionary analysis sampling trees (BEAST) programs were implemented in a phylogenetic analysis of pol sequences. Reconstructed phylogenies were assessed in the context of demographic information and drug-resistance profiles. Clusters were identified as sequence populations with posterior probability ≥0.95 of having a recent common ancestor. RESULTS After 2010, the subtype-A epidemic acquired substantial phylogenetic structure, having been unrecognized in studies covering the earlier period. Nearly 50% of all sequences were present in 11 distinct clusters consisting of 4-43 individuals. Cluster composition reflected transmission across ethnic groups, with men who have sex with men (MSM) playing an increasing role. The cathinone-associated cluster was larger than previously documented, containing variants that continued to spread within and beyond the IVDU community. CONCLUSIONS Phyloepidemiologic analysis revealed diverse clusters of HIV infection with MSM having a central role in transmission across ethic groups. A mini outbreak was reduced by public health measures, but molecular evidence of ongoing transmission suggests additional measures are necessary.
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Affiliation(s)
- Zehava Grossman
- School of Public Health, Tel Aviv University, Israel.,National Cancer Institute, Frederick, Maryland
| | - Boaz Avidor
- Crusaid Kobler AIDS Center, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel.,Laboratory of Viruses and Molecular Biology, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Shirley Girshengoren
- Crusaid Kobler AIDS Center, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel.,Laboratory of Viruses and Molecular Biology, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Eugene Katchman
- Crusaid Kobler AIDS Center, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel
| | | | - Dan Turner
- Crusaid Kobler AIDS Center, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel
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Karlsson N, Santacatterina M, Käll K, Hägerstrand M, Wallin S, Berglund T, Ekström AM. Risk behaviour determinants among people who inject drugs in Stockholm, Sweden over a 10-year period, from 2002 to 2012. Harm Reduct J 2017; 14:57. [PMID: 28814336 PMCID: PMC5559856 DOI: 10.1186/s12954-017-0184-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/09/2017] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND People who inject drugs (PWID) frequently engage in injection risk behaviours exposing them to blood-borne infections. Understanding the underlying causes that drive various types and levels of risk behaviours is important to better target preventive interventions. METHODS A total of 2150 PWID in Swedish remand prisons were interviewed between 2002 and 2012. Questions on socio-demographic and drug-related variables were asked in relation to the following outcomes: Having shared injection drug solution and having lent out or having received already used drug injection equipment within a 12 month recall period. RESULTS Women shared solutions more than men (odds ratio (OR) 1.51, 95% confidence interval (CI) 1.03; 2.21). Those who had begun to inject drugs before age 17 had a higher risk (OR 1.43, 95% CI 0.99; 2.08) of having received used equipment compared to 17-19 year olds. Amphetamine-injectors shared solutions more than those injecting heroin (OR 2.43, 95% CI 1.64; 3.62). A housing contract lowered the risk of unsafe injection by 37-59% compared to being homeless. CONCLUSIONS Women, early drug debut, amphetamine users and homeless people had a significantly higher level of injection risk behaviour and need special attention and tailored prevention to successfully combat hepatitis C and HIV transmission among PWID. TRIAL REGISTRATION ClinicalTrials.gov Identifier, NCT02234167.
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Affiliation(s)
- Niklas Karlsson
- Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
- Department of Monitoring and Evaluation, Public Health Agency of Sweden, 171 82 Solna, Sweden
| | - Michele Santacatterina
- Unit of Biostatistics, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kerstin Käll
- Dependency Clinic, Linköping University Hospital, Linköping, Sweden
| | | | - Susanne Wallin
- Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Torsten Berglund
- Department of Monitoring and Evaluation, Public Health Agency of Sweden, 171 82 Solna, Sweden
| | - Anna Mia Ekström
- Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
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Abstract
Understanding HIV-1 transmission dynamics is relevant to both screening and intervention strategies of HIV-1 infection. Commonly, HIV-1 transmission chains are determined based on sequence similarity assessed either directly from a sequence alignment or by inferring a phylogenetic tree. This review is aimed at both nonexperts interested in understanding and interpreting studies of HIV-1 transmission, and experts interested in finding the most appropriate cluster definition for a specific dataset and research question. We start by introducing the concepts and methodologies of how HIV-1 transmission clusters usually have been defined. We then present the results of a systematic review of 105 HIV-1 molecular epidemiology studies summarizing the most common methods and definitions in the literature. Finally, we offer our perspectives on how HIV-1 transmission clusters can be defined and provide some guidance based on examples from real life datasets.
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Giardina F, Romero-Severson EO, Albert J, Britton T, Leitner T. Inference of Transmission Network Structure from HIV Phylogenetic Trees. PLoS Comput Biol 2017; 13:e1005316. [PMID: 28085876 PMCID: PMC5279806 DOI: 10.1371/journal.pcbi.1005316] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 01/30/2017] [Accepted: 12/19/2016] [Indexed: 11/22/2022] Open
Abstract
Phylogenetic inference is an attractive means to reconstruct transmission histories and epidemics. However, there is not a perfect correspondence between transmission history and virus phylogeny. Both node height and topological differences may occur, depending on the interaction between within-host evolutionary dynamics and between-host transmission patterns. To investigate these interactions, we added a within-host evolutionary model in epidemiological simulations and examined if the resulting phylogeny could recover different types of contact networks. To further improve realism, we also introduced patient-specific differences in infectivity across disease stages, and on the epidemic level we considered incomplete sampling and the age of the epidemic. Second, we implemented an inference method based on approximate Bayesian computation (ABC) to discriminate among three well-studied network models and jointly estimate both network parameters and key epidemiological quantities such as the infection rate. Our ABC framework used both topological and distance-based tree statistics for comparison between simulated and observed trees. Overall, our simulations showed that a virus time-scaled phylogeny (genealogy) may be substantially different from the between-host transmission tree. This has important implications for the interpretation of what a phylogeny reveals about the underlying epidemic contact network. In particular, we found that while the within-host evolutionary process obscures the transmission tree, the diversification process and infectivity dynamics also add discriminatory power to differentiate between different types of contact networks. We also found that the possibility to differentiate contact networks depends on how far an epidemic has progressed, where distance-based tree statistics have more power early in an epidemic. Finally, we applied our ABC inference on two different outbreaks from the Swedish HIV-1 epidemic.
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Affiliation(s)
- Federica Giardina
- Department of Mathematics, Stockholm University, Stockholm, Sweden
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Ethan Obie Romero-Severson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Tom Britton
- Department of Mathematics, Stockholm University, Stockholm, Sweden
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
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Papachristou E, Tsagkovits A, Zavitsanou A, Hatzakis A, Paraskevis D. HCV dispersal patterns among intravenous drug users (IDUs) in Athens metropolitan area. INFECTION GENETICS AND EVOLUTION 2016; 45:415-419. [PMID: 27721034 DOI: 10.1016/j.meegid.2016.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 10/03/2016] [Accepted: 10/04/2016] [Indexed: 01/06/2023]
Abstract
BACKGROUND Most of the HCV transmission the recent years in Greece was among IDUs. Our aim was to estimate the prevalence of HCV genotypes and to investigate the patterns of HCV dispersal among IDUs in Athens using current state of the art molecular epidemiology methods. METHODS HCV sequences were determined from 238 HIV-negative IDUs collected on the basis of the "ARISTOTLE" prevention program carried out in Athens between 2012 and 2013. Phylogenetic trees were inferred on HCV sequences isolated from IDUs in Athens for the most prevalent HCV clades (subtypes 1a and 3a). Phylogenetic analysis was performed by Neighbor-Joining and Bayesian methods using GTR+G as nucleotide substitution model. HCV dispersal patterns were estimated using as references, all globally available HCV sequences for subtypes 1a and 3a. RESULTS The prevalence of HCV subtypes was: 3a (59.2%), 1a (21.9%), 4 (13.0%), 1b (5.4%) and 2 (0.5%). Phylogenetic analyses revealed that most sequences (63.5%) οf subtypes 1a and 3a fell within IDU-specific monophyletic groups. The proportion of sequences in monophyletic clades was similar for subtype 3a (62.9%) and 1a (65.3%). For the latter group, monophyletic clades were smaller in size. Multivariable logistic regression analyses showed that monophyletic clustering was marginally associated recent onset of injecting ([AOR]=1.44; 95% CI (0.97-2.13), p=0.068). CONCLUSIONS The high proportions of HCV sequences within IDU-specific monophyletic clusters suggest that transmissions occurred locally among IDUs in Greece. The numerous clusters for both 1a and 3a provide evidence that both sub-epidemics were the result of multiple introductions among the IDUs. Higher regional clustering was probably associated with a more recent onset of drug use.
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Affiliation(s)
- Eleni Papachristou
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Assimina Zavitsanou
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Angelos Hatzakis
- 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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18
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Beloukas A, Psarris A, Giannelou P, Kostaki E, Hatzakis A, Paraskevis D. Molecular epidemiology of HIV-1 infection in Europe: An overview. INFECTION GENETICS AND EVOLUTION 2016; 46:180-189. [PMID: 27321440 DOI: 10.1016/j.meegid.2016.06.033] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 12/19/2022]
Abstract
Human Immunodeficiency Virus type 1 (HIV-1) is characterised by vast genetic diversity. Globally circulating HIV-1 viruses are classified into distinct phylogenetic strains (subtypes, sub-subtypes) and several recombinant forms. Here we describe the characteristics and evolution of European HIV-1 epidemic over time through a review of published literature and updated queries of existing HIV-1 sequence databases. HIV-1 in Western and Central Europe was introduced in the early-1980s in the form of subtype B, which is still the predominant clade. However, in Eastern Europe (Former Soviet Union (FSU) countries and Russia) the predominant strain, introduced into Ukraine in the mid-1990s, is subtype A (AFSU) with transmission mostly occurring in People Who Inject Drugs (PWID). In recent years, the epidemic is evolving towards a complex tapestry with an increase in the prevalence of non-B subtypes and recombinants in Western and Central Europe. Non-B epidemics are mainly associated with immigrants, heterosexuals and females but more recently, non-B clades have also spread amongst groups where non-B strains were previously absent - non-immigrant European populations and amongst men having sex with men (MSM). In some countries, non-B clades have spread amongst the native population, for example subtype G in Portugal and subtype A in Greece, Albania and Cyprus. Romania provides a unique case where sub-subtype F1 has predominated throughout the epidemic. In contrast, HIV-1 epidemic in FSU countries remains more homogeneous with AFSU clade predominating in all countries. The differences between the evolution of the Western epidemic and the Eastern epidemic may be attributable to differences in transmission risk behaviours, lifestyle and the patterns of human mobility. The study of HIV-1 epidemic diversity provides a useful tool by which we can understand the history of the pandemic in addition to allowing us to monitor the spread and growth of the epidemic over time.
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Affiliation(s)
- Apostolos Beloukas
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece; Institute of Infection & Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Alexandros Psarris
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Polina Giannelou
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Evangelia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Angelos Hatzakis
- 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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Paraskevis D, Nikolopoulos GK, Magiorkinis G, Hodges-Mameletzis I, Hatzakis A. The application of HIV molecular epidemiology to public health. INFECTION GENETICS AND EVOLUTION 2016; 46:159-168. [PMID: 27312102 DOI: 10.1016/j.meegid.2016.06.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 02/02/2023]
Abstract
HIV is responsible for one of the largest viral pandemics in human history. Despite a concerted global response for prevention and treatment, the virus persists. Thus, urgent public health action, utilizing novel interventions, is needed to prevent future transmission events, critical to eliminating HIV. For public health planning to prove effective and successful, we need to understand the dynamics of regional epidemics and to intervene appropriately. HIV molecular epidemiology tools as implemented in phylogenetic, phylodynamic and phylogeographic analyses have proven to be powerful tools in public health planning across many studies. Numerous applications with HIV suggest that molecular methods alone or in combination with mathematical modelling can provide inferences about the transmission dynamics, critical epidemiological parameters (prevalence, incidence, effective number of infections, Re, generation times, time between infection and diagnosis), or the spatiotemporal characteristics of epidemics. Molecular tools have been used to assess the impact of an intervention and outbreak investigation which are of great public health relevance. In some settings, molecular sequence data may be more readily available than HIV surveillance data, and can therefore allow for molecular analyses to be conducted more easily. Nonetheless, classic methods have an integral role in monitoring and evaluation of public health programmes, and should supplement emerging techniques from the field of molecular epidemiology. Importantly, molecular epidemiology remains a promising approach in responding to viral diseases.
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Affiliation(s)
- D Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
| | - G K Nikolopoulos
- Hellenic Center for Diseases Control and Prevention, Maroussi, Greece
| | - G Magiorkinis
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece; Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, Oxford, United Kingdom
| | | | - A Hatzakis
- Hellenic Center for Diseases Control and Prevention, Maroussi, Greece
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20
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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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Abstract
Although the use of phylogenetic trees in epidemiological investigations has become commonplace, their epidemiological interpretation has not been systematically evaluated. Here, we use an HIV-1 within-host coalescent model to probabilistically evaluate transmission histories of two epidemiologically linked hosts. Previous critique of phylogenetic reconstruction has claimed that direction of transmission is difficult to infer, and that the existence of unsampled intermediary links or common sources can never be excluded. The phylogenetic relationship between the HIV populations of epidemiologically linked hosts can be classified into six types of trees, based on cladistic relationships and whether the reconstruction is consistent with the true transmission history or not. We show that the direction of transmission and whether unsampled intermediary links or common sources existed make very different predictions about expected phylogenetic relationships: (i) Direction of transmission can often be established when paraphyly exists, (ii) intermediary links can be excluded when multiple lineages were transmitted, and (iii) when the sampled individuals' HIV populations both are monophyletic a common source was likely the origin. Inconsistent results, suggesting the wrong transmission direction, were generally rare. In addition, the expected tree topology also depends on the number of transmitted lineages, the sample size, the time of the sample relative to transmission, and how fast the diversity increases after infection. Typically, 20 or more sequences per subject give robust results. We confirm our theoretical evaluations with analyses of real transmission histories and discuss how our findings should aid in interpreting phylogenetic results.
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Esbjörnsson J, Mild M, Audelin A, Fonager J, Skar H, Bruun Jørgensen L, Liitsola K, Björkman P, Bratt G, Gisslén M, Sönnerborg A, Nielsen C, Medstrand P, Albert J. HIV-1 transmission between MSM and heterosexuals, and increasing proportions of circulating recombinant forms in the Nordic Countries. Virus Evol 2016; 2:vew010. [PMID: 27774303 PMCID: PMC4989887 DOI: 10.1093/ve/vew010] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Increased knowledge about HIV-1 transmission dynamics in different transmission groups and geographical regions is fundamental for assessing and designing prevention efforts against HIV-1 spread. Since the first reported cases of HIV infection during the early 1980s, the HIV-1 epidemic in the Nordic countries has been dominated by HIV-1 subtype B and MSM transmission. HIV-1 pol sequences and clinical data of 51 per cent of all newly diagnosed HIV-1 infections in Sweden, Denmark, and Finland in the period 2000-2012 (N = 3,802) were analysed together with a large reference sequence dataset (N = 4,537) by trend analysis and phylogenetics. Analysis of the eight dominating subtypes and CRFs in the Nordic countries (A, B, C, D, G, CRF01_AE, CRF02_AG, and CRF06_cpx) showed that the subtype B proportion decreased while the CRF proportion increased over the study period. A majority (57 per cent) of the Nordic sequences formed transmission clusters, with evidence of mixing both geographically and between transmission groups. Detailed analyses showed multiple occasions of transmissions from MSM to heterosexuals and that active transmission clusters more often involved single than multiple Nordic countries. The strongest geographical link was between Denmark and Sweden. Finally, Denmark had a larger proportion of heterosexual domestic spread of HIV-1 subtype B (75 per cent) compared with Sweden (49 per cent) and Finland (57 per cent). We describe different HIV-1 transmission patterns between countries and transmission groups in a large geographical region. Our results may have implications for public health interventions in targeting HIV-1 transmission networks and identifying where to introduce such interventions.
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Affiliation(s)
- Joakim Esbjörnsson
- Department of Microbiology Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- REGA Institute, Katholieke Universiteit, Leuven, Belgium
| | - Mattias Mild
- Department of Microbiology, Public Health Agency of Sweden, Stockholm, Sweden
| | - Anne Audelin
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Helena Skar
- Department of Science and Technology, Linköping University, Campus Norrköping, Norrköping, Sweden
| | - Louise Bruun Jørgensen
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Kirsi Liitsola
- Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki, Finland
| | - Per Björkman
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Göran Bratt
- Department of Clinical Science and Education, Venhälsan, Stockholm South General Hospital, Stockholm, Sweden
| | - Magnus Gisslén
- Department of Infectious Diseases, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Anders Sönnerborg
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
- Division of Clinical Microbiology, Karolinska Institute, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Claus Nielsen
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - SPREAD/ESAR Programme
- Department of Microbiology Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- REGA Institute, Katholieke Universiteit, Leuven, Belgium
- Department of Microbiology, Public Health Agency of Sweden, Stockholm, Sweden
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
- Department of Science and Technology, Linköping University, Campus Norrköping, Norrköping, Sweden
- Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki, Finland
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
- Department of Clinical Science and Education, Venhälsan, Stockholm South General Hospital, Stockholm, Sweden
- Department of Infectious Diseases, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
- Division of Clinical Microbiology, Karolinska Institute, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Patrik Medstrand
- Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Jan Albert
- Department of Microbiology Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
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Delgado E, Cuevas MT, Domínguez F, Vega Y, Cabello M, Fernández-García A, Pérez-Losada M, Castro MÁ, Montero V, Sánchez M, Mariño A, Álvarez H, Ordóñez P, Ocampo A, Miralles C, Pérez-Castro S, López-Álvarez MJ, Rodríguez R, Trigo M, Diz-Arén J, Hinojosa C, Bachiller P, Hernáez-Crespo S, Cisterna R, Garduño E, Pérez-Álvarez L, Thomson MM. Phylogeny and Phylogeography of a Recent HIV-1 Subtype F Outbreak among Men Who Have Sex with Men in Spain Deriving from a Cluster with a Wide Geographic Circulation in Western Europe. PLoS One 2015; 10:e0143325. [PMID: 26599410 PMCID: PMC4658047 DOI: 10.1371/journal.pone.0143325] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 11/03/2015] [Indexed: 11/18/2022] Open
Abstract
We recently reported the rapid expansion of an HIV-1 subtype F cluster among men who have sex with men (MSM) in the region of Galicia, Northwest Spain. Here we update this outbreak, analyze near full-length genomes, determine phylogenetic relationships, and estimate its origin. For this study, we used sequences of HIV-1 protease-reverse transcriptase and env V3 region, and for 17 samples, near full-length genome sequences were obtained. Phylogenetic analyses were performed via maximum likelihood. Locations and times of most recent common ancestors were estimated using Bayesian inference. Among samples analyzed by us, 100 HIV-1 F1 subsubtype infections of monophyletic origin were diagnosed in Spain, including 88 in Galicia and 12 in four other regions. Most viruses (n = 90) grouped in a subcluster (Galician subcluster), while 7 from Valladolid (Central Spain) grouped in another subcluster. At least 94 individuals were sexually-infected males and at least 71 were MSM. Seventeen near full-length genomes were uniformly of F1 subsubtype. Through similarity searches and phylogenetic analyses, we identified 18 viruses from four other Western European countries [Switzerland (n = 8), Belgium (n = 5), France (n = 3), and United Kingdom (n = 2)] and one from Brazil, from samples collected in 2005–2011, which branched within the subtype F cluster, outside of both Spanish subclusters, most of them corresponding to recently infected individuals. The most probable geographic origin and age of the Galician subcluster was Ferrol, Northwest Galicia, around 2007, while the Western European cluster probably emerged in Switzerland around 2002. In conclusion, a recently expanded HIV-1 subtype F cluster, the largest non-subtype B cluster reported in Western Europe, continues to spread among MSM in Spain; this cluster is part of a larger cluster with a wide geographic circulation in diverse Western European countries.
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Affiliation(s)
- Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - María Teresa Cuevas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Francisco Domínguez
- 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
| | - Marina Cabello
- 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
| | - Marcos Pérez-Losada
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-InBIO), Vairão, Portugal
| | - María Ángeles Castro
- Department of Internal Medicine, Complejo Hospitalario Universitario de A Coruña, A Coruña, Spain
| | - Vanessa Montero
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Mónica Sánchez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Ana Mariño
- Infectious Diseases Unit, Department of Internal Medicine, Complejo Hospitalario Universitario Arquitecto Marcide, Ferrol, A Coruña, Spain
| | - Hortensia Álvarez
- Infectious Diseases Unit, Department of Internal Medicine, Complejo Hospitalario Universitario Arquitecto Marcide, Ferrol, A Coruña, Spain
| | - Patricia Ordóñez
- Department of Microbiology, Complejo Hospitalario Universitario Arquitecto Marcide, Ferrol, A Coruña, Spain
| | - Antonio Ocampo
- Department of Internal Medicine, Complejo Hospitalario Universitario de Vigo, Vigo, Pontevedra, Spain
| | - Celia Miralles
- Department of Internal Medicine, Complejo Hospitalario Universitario de Vigo, Vigo, Pontevedra, Spain
| | - Sonia Pérez-Castro
- Department of Microbiology, Complejo Hospitalario Universitario de Vigo, Vigo, Pontevedra, Spain
| | | | - Raúl Rodríguez
- Department of Internal Medicine, Complejo Hospitalario Universitario de Ourense, Ourense, Spain
| | - Matilde Trigo
- Department of Microbiology, Complejo Hospitalario Provincial de Pontevedra, Pontevedra, Spain
| | - Julio Diz-Arén
- Department of Internal Medicine, Complejo Hospitalario Provincial de Pontevedra, Pontevedra, Spain
| | - Carmen Hinojosa
- Department of Internal Medicine, Hospital Clínico Universitario de Valladolid, Valladolid, Spain
| | - Pablo Bachiller
- Department of Internal Medicine, Hospital Universitario Río Hortega, Valladolid, Spain
| | - Silvia Hernáez-Crespo
- Department of Clinical Microbiology and Infection Control, Hospital Universitario de Basurto, Bilbao, Vizcaya, Spain
| | - Ramón Cisterna
- Department of Clinical Microbiology and Infection Control, Hospital Universitario de Basurto, Bilbao, Vizcaya, Spain
| | - Eugenio Garduño
- Department of Microbiology, Hospital Infanta Cristina, Badajoz, 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
- * E-mail:
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Paraskevis D, Paraschiv S, Sypsa V, Nikolopoulos G, Tsiara C, Magiorkinis G, Psichogiou M, Flampouris A, Mardarescu M, Niculescu I, Batan I, Malliori M, Otelea D, Hatzakis A. Enhanced HIV-1 surveillance using molecular epidemiology to study and monitor HIV-1 outbreaks among intravenous drug users (IDUs) in Athens and Bucharest. INFECTION GENETICS AND EVOLUTION 2015; 35:109-21. [PMID: 26247720 DOI: 10.1016/j.meegid.2015.08.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 07/28/2015] [Accepted: 08/03/2015] [Indexed: 11/30/2022]
Abstract
BACKGROUND A significant increase in HIV-1 diagnoses was reported among Injecting Drug Users (IDUs) in the Athens (17-fold) and Bucharest (9-fold) metropolitan areas starting 2011. METHODS Molecular analyses were conducted on HIV-1 sequences from IDUs comprising 51% and 20% of the diagnosed cases among IDUs during 2011-2013 for Greece and Romania, respectively. Phylodynamic analyses were performed using the newly developed birth-death serial skyline model which allows estimating of important epidemiological parameters, as implemented in BEAST programme. RESULTS Most infections (>90%) occurred within four and three IDU local transmission networks in Athens and Bucharest, respectively. For all Romanian clusters, the viral strains originated from local circulating strains, whereas in Athens, the local strains seeded only two of the four sub-outbreaks. Birth-death skyline plots suggest a more explosive nature for sub-outbreaks in Bucharest than in Athens. In Athens, two sub-outbreaks had been controlled (Re<1.0) by 2013 and two appeared to be endemic (Re∼1). In Bucharest one outbreak continued to expand (Re>1.0) and two had been controlled (Re<1.0). The lead times were shorter for the outbreak in Athens than in Bucharest. CONCLUSIONS Enhanced molecular surveillance proved useful to gain information about the origin, causal pathways, dispersal patterns and transmission dynamics of the outbreaks that can be useful in a public health setting.
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Affiliation(s)
- Dimitrios Paraskevis
- National Retrovirus Reference Center, Medical School, University of Athens, Athens, Greece.
| | - Simona Paraschiv
- Molecular Diagnostics Laboratory, National Institute for Infectious Diseases, Bucharest, Romania
| | - Vana Sypsa
- National Retrovirus Reference Center, Medical School, University of Athens, Athens, Greece
| | | | - Chryssa Tsiara
- Hellenic Center for Diseases Control and Prevention, Athens, Greece
| | - Gkikas Magiorkinis
- Department of Zoology, University of Oxford, UK; Virus Reference Department, Colindale, Public Health England, UK
| | | | - Andreas Flampouris
- National Retrovirus Reference Center, Medical School, University of Athens, Athens, Greece
| | - Mariana Mardarescu
- Molecular Diagnostics Laboratory, National Institute for Infectious Diseases, Bucharest, Romania
| | - Iulia Niculescu
- Molecular Diagnostics Laboratory, National Institute for Infectious Diseases, Bucharest, Romania
| | - Ionelia Batan
- Molecular Diagnostics Laboratory, National Institute for Infectious Diseases, Bucharest, Romania
| | - Meni Malliori
- Medical School, University of Athens, Athens, Greece
| | - Dan Otelea
- Molecular Diagnostics Laboratory, National Institute for Infectious Diseases, Bucharest, Romania
| | - Angelos Hatzakis
- National Retrovirus Reference Center, Medical School, University of Athens, Athens, Greece
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Romero-Severson EO, Lee Petrie C, Ionides E, Albert J, Leitner T. Trends of HIV-1 incidence with credible intervals in Sweden 2002-09 reconstructed using a dynamic model of within-patient IgG growth. Int J Epidemiol 2015; 44:998-1006. [PMID: 26163684 DOI: 10.1093/ije/dyv034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2015] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND HIV-1 is a lifelong disease, often without serious symptoms for years after infection, and thus many infected persons go undetected for a long time. This makes it difficult to track incidence, and thus epidemics may go through dramatic changes largely unnoticed, only to be detected years later. Because direct measurement of incidence is expensive and difficult, several biomarker-based tests and algorithms have been developed to distinguish between recent and long-term infections. However, current methods have been criticized and demands for novel methods have been raised. METHODS We developed and applied a biomarker-based incidence model, joining a time-continuous model of immunoglobulin G (IgG) growth (measured by the IgG-capture BED-enzyme immunoassay) with statistical corrections for both sample size and unobserved diagnoses. Our method uses measurements of IgG concentration in newly diagnosed people to calculate the posterior distribution of infection times. Time from infection to diagnosis is modelled for all individuals in a given period and is used to calculate a sample weight to correct for undiagnosed individuals. We then used a bootstrapping method to reconstruct point estimates and credible intervals of the incidence of HIV-1 in Sweden based on a sample of newly diagnosed people. RESULTS We found evidence for: (i) a slowly but steadily increasing trend in both the incidence and incidence rate in Sweden; and (ii) an increasing but well-controlled epidemic in gay men in Stockholm. Sensitivity analyses showed that our method was robust to realistic levels (up to 15%) of BED misclassification of non-recently infected persons as early infections. CONCLUSIONS We developed a novel incidence estimator based on previously published theoretical work that has the potential to provide rapid, up-to-date estimates of HIV-1 incidence in populations where BED test data are available.
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Affiliation(s)
| | - Cody Lee Petrie
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Edward Ionides
- Department of Statistics, University of Michigan, Ann Arbor, MI, USA and
| | - Jan Albert
- Departments of Microbiology, Karolinska Institute and Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
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Angelis K, Albert J, Mamais I, Magiorkinis G, Hatzakis A, Hamouda O, Struck D, Vercauteren J, Wensing AMJ, Alexiev I, Åsjö B, Balotta C, Camacho RJ, Coughlan S, Griskevicius A, Grossman Z, Horban A, Kostrikis LG, Lepej S, Liitsola K, Linka M, Nielsen C, Otelea D, Paredes R, Poljak M, Puchhammer-Stöckl E, Schmit JC, Sönnerborg A, Staneková D, Stanojevic M, Boucher CAB, Kaplan L, Vandamme AM, Paraskevis D. Global Dispersal Pattern of HIV Type 1 Subtype CRF01_AE: A Genetic Trace of Human Mobility Related to Heterosexual Sexual Activities Centralized in Southeast Asia. J Infect Dis 2014; 211:1735-44. [PMID: 25512631 DOI: 10.1093/infdis/jiu666] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 11/24/2014] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) subtype CRF01_AE originated in Africa and then passed to Thailand, where it established a major epidemic. Despite the global presence of CRF01_AE, little is known about its subsequent dispersal pattern. METHODS We assembled a global data set of 2736 CRF01_AE sequences by pooling sequences from public databases and patient-cohort studies. We estimated viral dispersal patterns, using statistical phylogeographic analysis run over bootstrap trees estimated by the maximum likelihood method. RESULTS We show that Thailand has been the source of viral dispersal to most areas worldwide, including 17 of 20 sampled countries in Europe. Japan, Singapore, Vietnam, and other Asian countries have played a secondary role in the viral dissemination. In contrast, China and Taiwan have mainly imported strains from neighboring Asian countries, North America, and Africa without any significant viral exportation. DISCUSSION The central role of Thailand in the global spread of CRF01_AE can be probably explained by the popularity of Thailand as a vacation destination characterized by sex tourism and by Thai emigration to the Western world. Our study highlights the unique case of CRF01_AE, the only globally distributed non-B clade whose global dispersal did not originate in Africa.
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Affiliation(s)
- Konstantinos Angelis
- Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, University of Athens, Greece
| | - Jan Albert
- Department of Microbiology, Tumor, and Cell Biology Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Ioannis Mamais
- Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, University of Athens, Greece
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, University of Athens, Greece Department of Zoology, University of Oxford, United Kingdom
| | - Angelos Hatzakis
- Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, University of Athens, Greece
| | | | | | - Jurgen Vercauteren
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Belgium
| | | | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | | | - Ricardo J Camacho
- Centro de Malária e OutrasDoenças Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Portugal
| | | | | | | | | | | | - Snjezana Lepej
- Department of Molecular Diagnostics and Flow Cytometry, University Hospital for Infectious Diseases Dr F. Mihaljevic, Zagreb, Croatia
| | - Kirsi Liitsola
- National Institute of Health and Welfare, Helsinki, Finland
| | - Marek Linka
- National Reference Laboratory of AIDS, National Institute of Health, Prague, Czech Republic
| | | | - Dan Otelea
- National Institute for Infectious Diseases Prof Dr Matei Bals, Bucharest, Romania
| | | | - Mario Poljak
- Faculty of Medicine, Slovenian HIV/AIDS Reference Center, University of Ljubljana, Slovenia
| | | | | | - Anders Sönnerborg
- Division of Infectious Diseases Division of Clinical Virology, Karolinska Institute Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | | | | | | | - Lauren Kaplan
- Alcohol Research Group, University California, Berkeley
| | - Anne-Mieke Vandamme
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Belgium Centro de Malária e OutrasDoenças Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Portugal
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, University of Athens, Greece
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Widgren K, Skar H, Berglund T, Kling AM, Tegnell A, Albert J. Delayed HIV diagnosis common in Sweden, 2003-2010. ACTA ACUST UNITED AC 2014; 46:862-7. [PMID: 25290584 PMCID: PMC4266095 DOI: 10.3109/00365548.2014.953575] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Background Early diagnosis of HIV is important for the prognosis of individual patients, because antiretroviral treatment can be started at the appropriate time, and for public health, because transmission can be prevented. Methods Data were collected from 767 HIV patients who were diagnosed in Sweden during 2003–2010 and were infected in Sweden or born in Sweden and infected abroad. A recent infection testing algorithm (RITA) was applied to BED-EIA test results (OD-n < 0.8), CD4 counts (≥ 200 cells/μl), and clinical information. A recent infection classification was used as indicator for early diagnosis. Time trends in early diagnosis were investigated to detect population changes in HIV testing behavior. Patients with early diagnosis were compared to patients with delayed diagnosis with respect to age, gender, transmission route, and country of infection (Sweden or abroad). Results Early diagnosis was observed in 271 patients (35%). There was no statistically significant time trend in the yearly percentage of patients with early diagnosis in the entire study group (p = 0.836) or in subgroups. Early diagnosis was significantly more common in men who have sex men (MSM) (45%) than in heterosexuals (21%) and injecting drug users (27%) (p < 0.001 and p = 0.001, respectively) in both univariate and multivariable analyses. The only other factor that remained associated with early diagnosis in multivariable analysis was young age group. Conclusion Approximately one-third of the study patients were diagnosed early with no significant change over time. Delayed HIV diagnosis is a considerable problem in Sweden, which does not appear to diminish.
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Affiliation(s)
- Katarina Widgren
- From the 1 Department for Monitoring and Evaluation, Public Health Agency of Sweden , Solna , Sweden *
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Romero-Severson E, Skar H, Bulla I, Albert J, Leitner T. Timing and order of transmission events is not directly reflected in a pathogen phylogeny. Mol Biol Evol 2014; 31:2472-82. [PMID: 24874208 DOI: 10.1093/molbev/msu179] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Pathogen phylogenies are often used to infer spread among hosts. There is, however, not an exact match between the pathogen phylogeny and the host transmission history. Here, we examine in detail the limitations of this relationship. First, all splits in a pathogen phylogeny of more than 1 host occur within hosts, not at the moment of transmission, predating the transmission events as described by the pretransmission interval. Second, the order in which nodes in a phylogeny occur may be reflective of the within-host dynamics rather than epidemiologic relationships. To investigate these phenomena, motivated by within-host diversity patterns, we developed a two-phase coalescent model that includes a transmission bottleneck followed by linear outgrowth to a maximum population size followed by either stabilization or decline of the population. The model predicts that the pretransmission interval shrinks compared with predictions based on constant population size or a simple transmission bottleneck. Because lineages coalesce faster in a small population, the probability of a pathogen phylogeny to resemble the transmission history depends on when after infection a donor transmits to a new host. We also show that the probability of inferring the incorrect order of multiple transmissions from the same host is high. Finally, we compare time of HIV-1 infection informed by genetic distances in phylogenies to independent biomarker data, and show that, indeed, the pretransmission interval biases phylogeny-based estimates of when transmissions occurred. We describe situations where caution is needed not to misinterpret which parts of a phylogeny that may indicate outbreaks and tight transmission clusters.
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Affiliation(s)
- Ethan Romero-Severson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM
| | - Helena Skar
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM
| | - Ingo Bulla
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, SwedenDepartment of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM
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29
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Bezemer D, Faria NR, Hassan A, Hamers RL, Mutua G, Anzala O, Mandaliya K, Cane P, Berkley JA, Rinke de Wit TF, Wallis C, Graham SM, Price MA, Coutinho RA, Sanders EJ. HIV Type 1 transmission networks among men having sex with men and heterosexuals in Kenya. AIDS Res Hum Retroviruses 2014; 30:118-26. [PMID: 23947948 DOI: 10.1089/aid.2013.0171] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We performed a molecular phylogenetic study on HIV-1 polymerase sequences of men who have sex with men (MSM) and heterosexual patient samples in Kenya to characterize any observed HIV-1 transmission networks. HIV-1 polymerase sequences were obtained from samples in Nairobi and coastal Kenya from 84 MSM, 226 other men, and 364 women from 2005 to 2010. Using Bayesian phylogenetics, we tested whether sequences clustered by sexual orientation and geographic location. In addition, we used trait diffusion analyses to identify significant epidemiological links and to quantify the number of transmissions between risk groups. Finally, we compared 84 MSM sequences with all HIV-1 sequences available online at GenBank. Significant clustering of sequences from MSM at both coastal Kenya and Nairobi was found, with evidence of HIV-1 transmission between both locations. Although a transmission pair between a coastal MSM and woman was confirmed, no significant HIV-1 transmission was evident between MSM and the comparison population for the predominant subtype A (60%). However, a weak but significant link was evident when studying all subtypes together. GenBank comparison did not reveal other important transmission links. Our data suggest infrequent intermingling of MSM and heterosexual HIV-1 epidemics in Kenya.
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Affiliation(s)
| | - Nuno Rodrigues Faria
- Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Amin Hassan
- Kenya Medical Research Institute, Centre for Geographic Medicine Research–Coast, Kilifi, Kenya
| | - Raph L. Hamers
- PharmAccess Foundation, Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | - Gaudensia Mutua
- Kenya AIDS Vaccine Initiative, University of Nairobi, Nairobi, Kenya
| | - Omu Anzala
- Kenya AIDS Vaccine Initiative, University of Nairobi, Nairobi, Kenya
| | | | | | - James A. Berkley
- Kenya Medical Research Institute, Centre for Geographic Medicine Research–Coast, Kilifi, Kenya
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Tobias F. Rinke de Wit
- PharmAccess Foundation, Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | | | - Susan M. Graham
- Kenya Medical Research Institute, Centre for Geographic Medicine Research–Coast, Kilifi, Kenya
- University of Washington, Seattle, Washington
| | - Matthew A. Price
- International AIDS Vaccine Initiative, New York, New York
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, California
| | - Roel A. Coutinho
- Centre for Infectious Disease Control, RIVM, Utrecht, The Netherlands
- Julius Center for Health Science and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Eduard J. Sanders
- Kenya Medical Research Institute, Centre for Geographic Medicine Research–Coast, Kilifi, Kenya
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
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Novitsky V, Bussmann H, Logan A, Moyo S, van Widenfelt E, Okui L, Mmalane M, Baca J, Buck L, Phillips E, Tim D, McLane MF, Lei Q, Wang R, Makhema J, Lockman S, DeGruttola V, Essex M. Phylogenetic relatedness of circulating HIV-1C variants in Mochudi, Botswana. PLoS One 2013; 8:e80589. [PMID: 24349005 PMCID: PMC3859477 DOI: 10.1371/journal.pone.0080589] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/04/2013] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Determining patterns of HIV transmission is increasingly important for the most efficient use of modern prevention interventions. HIV phylogeny can provide a better understanding of the mechanisms underlying HIV transmission networks in communities. METHODS To reconstruct the structure and dynamics of a local HIV/AIDS epidemic, the phylogenetic relatedness of HIV-1 subtype C env sequences obtained from 785 HIV-infected community residents in the northeastern sector of Mochudi, Botswana, during 2010-2013 was estimated. The genotyping coverage was estimated at 44%. Clusters were defined based on relatedness of HIV-1C env sequences and bootstrap support of splits. RESULTS The overall proportion of clustered HIV-1C env sequences was 19.1% (95% CI 17.5% to 20.8%). The proportion of clustered sequences from Mochudi was significantly higher than the proportion of non-Mochudi sequences that clustered, 27.0% vs. 14.7% (p = 5.8E-12; Fisher exact test). The majority of clustered Mochudi sequences (90.1%; 95% CI 85.1% to 93.6%) were found in the Mochudi-unique clusters. None of the sequences from Mochudi clustered with any of the 1,244 non-Botswana HIV-1C sequences. At least 83 distinct HIV-1C variants, or chains of HIV transmission, in Mochudi were enumerated, and their sequence signatures were reconstructed. Seven of 20 genotyped seroconverters were found in 7 distinct clusters. CONCLUSIONS The study provides essential characteristics of the HIV transmission network in a community in Botswana, suggests the importance of high sampling coverage, and highlights the need for broad HIV genotyping to determine the spread of community-unique and community-mixed viral variants circulating in local epidemics. The proposed methodology of cluster analysis enumerates circulating HIV variants and can work well for surveillance of HIV transmission networks. HIV genotyping at the community level can help to optimize and balance HIV prevention strategies in trials and combined intervention packages.
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Affiliation(s)
- Vladimir Novitsky
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | | | - Andrew Logan
- Botswana–Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Sikhulile Moyo
- Botswana–Harvard AIDS Institute Partnership, Gaborone, Botswana
| | | | - Lillian Okui
- Botswana–Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Mompati Mmalane
- Botswana–Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Jeannie Baca
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Lauren Buck
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Eleanor Phillips
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - David Tim
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Mary Fran McLane
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Quanhong Lei
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Rui Wang
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Joseph Makhema
- Botswana–Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Shahin Lockman
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Victor DeGruttola
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - M. Essex
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
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Pagán I, Holguín A. Reconstructing the timing and dispersion routes of HIV-1 subtype B epidemics in the Caribbean and Central America: a phylogenetic story. PLoS One 2013; 8:e69218. [PMID: 23874917 PMCID: PMC3706403 DOI: 10.1371/journal.pone.0069218] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 06/05/2013] [Indexed: 01/05/2023] Open
Abstract
The Caribbean and Central America are among the regions with highest HIV-1B prevalence worldwide. Despite of this high virus burden, little is known about the timing and the migration patterns of HIV-1B in these regions. Migration is one of the major processes shaping the genetic structure of virus populations. Thus, reconstruction of epidemiological network may contribute to understand HIV-1B evolution and reduce virus prevalence. We have investigated the spatio-temporal dynamics of the HIV-1B epidemic in The Caribbean and Central America using 1,610 HIV-1B partial pol sequences from 13 Caribbean and 5 Central American countries. Timing of HIV-1B introduction and virus evolutionary rates, as well as the spatial genetic structure of the HIV-1B populations and the virus migration patterns were inferred. Results revealed that in The Caribbean and Central America most of the HIV-1B variability was generated since the 80 s. At odds with previous data suggesting that Haiti was the origin of the epidemic in The Caribbean, our reconstruction indicated that the virus could have been disseminated from Puerto Rico and Antigua. These two countries connected two distinguishable migration areas corresponding to the (mainly Spanish-colonized) Easter and (mainly British-colonized) Western islands, which indicates that virus migration patterns are determined by geographical barriers and by the movement of human populations among culturally related countries. Similar factors shaped the migration of HIV-1B in Central America. The HIV-1B population was significantly structured according to the country of origin, and the genetic diversity in each country was associated with the virus prevalence in both regions, which suggests that virus populations evolve mainly through genetic drift. Thus, our work contributes to the understanding of HIV-1B evolution and dispersion pattern in the Americas, and its relationship with the geography of the area and the movements of human populations.
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Affiliation(s)
- Israel Pagán
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, Madrid, Spain.
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Skar H, Albert J, Leitner T. Towards estimation of HIV-1 date of infection: a time-continuous IgG-model shows that seroconversion does not occur at the midpoint between negative and positive tests. PLoS One 2013; 8:e60906. [PMID: 23613753 PMCID: PMC3628711 DOI: 10.1371/journal.pone.0060906] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 03/05/2013] [Indexed: 11/18/2022] Open
Abstract
Estimating date of infection for HIV-1-infected patients is vital for disease tracking and informed public health decisions, but is difficult to obtain because most patients have an established infection of unknown duration at diagnosis. Previous studies have used HIV-1-specific immunoglobulin G (IgG) levels as measured by the IgG capture BED enzyme immunoassay (BED assay) to indicate if a patient was infected recently, but a time-continuous model has not been available. Therefore, we developed a logistic model of IgG production over time. We used previously published metadata from 792 patients for whom the HIV-1-specific IgG levels had been longitudinally measured using the BED assay. To account for patient variability, we used mixed effects modeling to estimate general population parameters. The typical patient IgG production rate was estimated at r = 6.72[approximate 95% CI 6.17,7.33]×10−3 OD-n units day−1, and the carrying capacity at K = 1.84[1.75,1.95] OD-n units, predicting how recently patients seroconverted in the interval ∧t = (31,711) days. Final model selection and validation was performed on new BED data from a population of 819 Swedish HIV-1 patients diagnosed in 2002–2010. On an appropriate subset of 350 patients, the best model parameterization had an accuracy of 94% finding a realistic seroconversion date. We found that seroconversion on average is at the midpoint between last negative and first positive HIV-1 test for patients diagnosed in prospective/cohort studies such as those included in the training dataset. In contrast, seroconversion is strongly skewed towards the first positive sample for patients identified by regular public health diagnostic testing as illustrated in the validation dataset. Our model opens the door to more accurate estimates of date of infection for HIV-1 patients, which may facilitate a better understanding of HIV-1 epidemiology on a population level and individualized prevention, such as guidance during contact tracing.
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Affiliation(s)
- Helena Skar
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail:
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Smoleń-Dzirba J, Rosińska M, Kruszyński P, Bratosiewicz-Wąsik J, Janiec J, Beniowski M, Bociąga-Jasik M, Jabłonowska E, Szetela B, Porter K, Wąsik TJ. Molecular epidemiology of recent HIV-1 infections in southern Poland. J Med Virol 2013; 84:1857-68. [PMID: 23080488 DOI: 10.1002/jmv.23395] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The genetic diversity of human immunodeficiency virus type 1 (HIV-1) offers an opportunity to track the development of the epidemic across different populations. Viral pol gene fragments from 55 individuals of Polish origin with recent HIV-1 infection identified in 2008-2010 in four Polish cities were analyzed. Viral sequences were compared with sequences from 100 individuals (reference group) infected before 2004. Viral spread among groups with different HIV transmission categories was compared using a phylogenetic approach. The majority of sequences from individuals with recent infection were subtype B (93%) within which four transmission clusters (18% of samples) were detected. Samples from men infected through sex between men and from persons infected through injecting drugs were broadly separated (P < 0.0001), while samples from individuals infected by heterosexual contacts were dispersed uniformly within phylogenetic tree (P = 0.244) inferred from viral sequences derived from individuals infected recently and the reference group. The percentage of samples from persons infected by heterosexual contacts which clustered with samples from men infected through sex between men was not significantly higher for those with recent infection (47%), compared to the reference group (36%). In conclusion, men infected by sex between men and individuals infected through injecting drugs appear to form separate HIV transmission networks in Poland. The recent spread of HIV-1 among persons infected with subtype B by heterosexual contacts appears to be linked to both these groups.
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Affiliation(s)
- Joanna Smoleń-Dzirba
- Department and Institute of Microbiology and Virology, The School of Pharmacy and Division of Laboratory Medicine, Medical University of Silesia, Katowice, Poland
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Yebra G, Holguín Á, Pillay D, Hué S. Phylogenetic and demographic characterization of HIV-1 transmission in Madrid, Spain. INFECTION GENETICS AND EVOLUTION 2013; 14:232-9. [DOI: 10.1016/j.meegid.2012.12.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 12/10/2012] [Accepted: 12/12/2012] [Indexed: 11/26/2022]
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Balode D, Skar H, Mild M, Kolupajeva T, Ferdats A, Rozentale B, Leitner T, Albert J. Phylogenetic analysis of the Latvian HIV-1 epidemic. AIDS Res Hum Retroviruses 2012; 28:928-32. [PMID: 22049908 DOI: 10.1089/aid.2011.0310] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
Abstract
The Latvian HIV-1 outbreak among intravenous drug users (IDUs) in 1997-1998 involved subtype A1. To obtain a more complete picture of the Latvian HIV-1 epidemic, 315 HIV-1-infected patients diagnosed in 1990-2005 representing different transmission groups and geographic regions were phylogenetically characterized using env V3 and gag p17 sequences. Subtypes A1 and B infections were found in 76% and 22% of the patients, respectively. The subtype A1 sequences formed one large cluster, which also included sequences from other parts of the former Soviet Union (FSU), whereas most subtype B sequences formed three distinct clusters. We estimated that subtype A1 was introduced from FSU around 1997 and initially spread explosively among IDUs in Riga. A recent increase of heterosexually infected persons did not form a separate subepidemic, but had multiple interactions with the IDU epidemic. Subtype B was introduced before the collapse of the Soviet Union and primarily has spread among men who have sex with men.
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Affiliation(s)
- Dace Balode
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Helena Skar
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Theoretical Biology and Biophysics, MS K710, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Mattias Mild
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | | | - Andris Ferdats
- HIV/AIDS Program Unit of the Infectology Centre of Latvia, Riga, Latvia
| | | | - Thomas Leitner
- Theoretical Biology and Biophysics, MS K710, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Solna, Stockholm, Sweden
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Continuous spread of HIV-1 subtypes D and CRF01_AE in France from 2003 to 2009. J Clin Microbiol 2012; 50:2484-8. [PMID: 22553246 DOI: 10.1128/jcm.00319-12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Among 61 and 35 patients who were infected in France by viruses of the rare clades D and CRF01_AE, respectively, approximately half of them originated from areas where HIV-1 is endemic, but the data showed that both clades have spread in the French indigenous population, particularly in men having sex with men (MSM).
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Agent-based and phylogenetic analyses reveal how HIV-1 moves between risk groups: injecting drug users sustain the heterosexual epidemic in Latvia. Epidemics 2012; 4:104-16. [PMID: 22664069 DOI: 10.1016/j.epidem.2012.04.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 03/21/2012] [Accepted: 04/25/2012] [Indexed: 12/17/2022] Open
Abstract
Injecting drug users (IDUs) are a driving force for the spread of HIV-1 in Latvia and other Baltic States, accounting for a majority of cases. However, in recent years, heterosexual cases have increased disproportionately. It is unclear how the changes in incidence patterns in Latvia can be explained, and how important IDUs are for the heterosexual sub-epidemic. We introduce a novel epidemic model and use phylogenetic analyses in parallel to examine the spread of HIV-1 in Latvia between 1987 and 2010. Using a hybrid framework with a mean-field description for the susceptible population and an agent-based model for the infecteds, we track infected individuals and follow transmission histories dynamically formed during the simulation. The agent-based simulations and the phylogenetic analysis show that more than half of the heterosexual transmissions in Latvia were caused by IDU, which sustain the heterosexual epidemic. Indeed, we find that heterosexual clusters are characterized by short transmission chains with up to 63% of the chains dying out after the first introduction. In the simulations, the distribution of transmission chain sizes follows a power law distribution, which is confirmed by the phylogenetic data. Our models indicate that frequent introductions reduced the extinction probability of an autonomously spreading heterosexual HIV-1 epidemic, which now has the potential to dominate the spread of the overall epidemic in the future. Furthermore, our model shows that social heterogeneity of the susceptible population can explain the shift in HIV-1 incidence in Latvia over the course of the epidemic. Thus, the decrease in IDU incidence may be due to local heterogeneities in transmission, rather than the implementation of control measures. Increases in susceptibles, through social or geographic movement of IDU, could lead to a boost in HIV-1 infections in this risk group. Targeting individuals that bridge social groups would help prevent further spread of the epidemic.
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Karlsson A, Björkman P, Bratt G, Ekvall H, Gisslén M, Sönnerborg A, Mild M, Albert J. Low prevalence of transmitted drug resistance in patients newly diagnosed with HIV-1 infection in Sweden 2003-2010. PLoS One 2012; 7:e33484. [PMID: 22448246 PMCID: PMC3308981 DOI: 10.1371/journal.pone.0033484] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 02/15/2012] [Indexed: 11/19/2022] Open
Abstract
Transmitted drug resistance (TDR) is a clinical and epidemiological problem because it may contribute to failure of antiretroviral treatment. The prevalence of TDR varies geographically, and its prevalence in Sweden during the last decade has not been reported. Plasma samples from 1,463 patients newly diagnosed with HIV-1 infection between 2003 and 2010, representing 44% of all patients diagnosed in Sweden during this period, were analyzed using the WHO 2009 list of mutations for surveillance of TDR. Maximum likelihood phylogenetic analyses were used to determine genetic subtype and to investigate the relatedness of the sequences. Eighty-two patients showed evidence of TDR, representing a prevalence of 5.6% (95% CI: 4.5%–6.9%) without any significant time trends or differences between patients infected in Sweden or abroad. Multivariable logistic regression showed that TDR was positively associated with men who have sex with men (MSM) and subtype B infection and negatively associated with CD4 cell counts. Among patients with TDR, 54 (68%) had single resistance mutations, whereas five patients had multi-drug resistant HIV-1. Phylogenetic analyses identified nine significantly supported clusters involving 29 of the patients with TDR, including 23 of 42 (55%) of the patients with TDR acquired in Sweden. One cluster contained 18 viruses with a M41L resistance mutation, which had spread among MSM in Stockholm over a period of at least 16 years (1994–2010). Another cluster, which contained the five multidrug resistant viruses, also involved MSM from Stockholm. The prevalence of TDR in Sweden 2003–2010 was lower than in many other European countries. TDR was concentrated among MSM, where clustering of TDR strains was observed, which highlights the need for continued and improved measures for targeted interventions.
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Affiliation(s)
- Annika Karlsson
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Per Björkman
- Department of Clinical Sciences, Malmö Infectious Disease Research Unit, Malmö University Hospital, Lund University, Lund, Sweden
| | - Göran Bratt
- Venhälsan, Stockholm South General Hospital, Stockholm, Sweden
| | - Håkan Ekvall
- Department of Infectious Diseases, Sundsvall Hospital, Sundsvall, Sweden
| | - Magnus Gisslén
- Department of Infectious Diseases, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Anders Sönnerborg
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Mattias Mild
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Swedish Institute for Communicable Diseases, Stockholm, Sweden
| | - Jan Albert
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- * E-mail:
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Castro-Nallar E, Pérez-Losada M, Burton GF, Crandall KA. The evolution of HIV: inferences using phylogenetics. Mol Phylogenet Evol 2012; 62:777-92. [PMID: 22138161 PMCID: PMC3258026 DOI: 10.1016/j.ympev.2011.11.019] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 11/17/2011] [Accepted: 11/21/2011] [Indexed: 12/02/2022]
Abstract
Molecular phylogenetics has revolutionized the study of not only evolution but also disparate fields such as genomics, bioinformatics, epidemiology, ecology, microbiology, molecular biology and biochemistry. Particularly significant are its achievements in population genetics as a result of the development of coalescent theory, which have contributed to more accurate model-based parameter estimation and explicit hypothesis testing. The study of the evolution of many microorganisms, and HIV in particular, have benefited from these new methodologies. HIV is well suited for such sophisticated population analyses because of its large population sizes, short generation times, high substitution rates and relatively small genomes. All these factors make HIV an ideal and fascinating model to study molecular evolution in real time. Here we review the significant advances made in HIV evolution through the application of phylogenetic approaches. We first examine the relative roles of mutation and recombination on the molecular evolution of HIV and its adaptive response to drug therapy and tissue allocation. We then review some of the fundamental questions in HIV evolution in relation to its origin and diversification and describe some of the insights gained using phylogenies. Finally, we show how phylogenetic analysis has advanced our knowledge of HIV dynamics (i.e., phylodynamics).
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Affiliation(s)
- Eduardo Castro-Nallar
- Department of Biology, 401 Widtsoe Building, Brigham Young University, Provo, UT 84602-5181, USA.
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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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