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DeGruttola V, Goyal R, Martin NK, Wang R. Network methods and design of randomized trials: Application to investigation of COVID-19 vaccination boosters. Clin Trials 2022; 19:363-374. [PMID: 35894099 DOI: 10.1177/17407745221111818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Network science methods can be useful in design, monitoring, and analysis of randomized trials for control of spread of infections. Their usefulness arises from the role of statistical network models in molecular epidemiology and in study design. Computational models, such as agent-based models that propagate disease on simulated contact networks, can be used to investigate the properties of different study designs and analysis plans. Particularly valuable is the use of these methods to assess how magnitude and detectability of intervention effects depend on both individual-level and network-level characteristics of the enrolled populations. Such investigation also provides an important approach to assessing consequences of study data being incomplete or measured with error. To address these goals, we consider two statistical network models: exponential random graph models and the more flexible congruence class models. We focus first on an historical use of these methods in design and monitoring of a cluster randomized trial in Botswana to evaluate the effect of combination HIV prevention modalities compared to standard of care on HIV incidence. We then present a framework for the design of a study of booster vaccine effects on infection with, and forward transmission of, SARS-CoV-2 variants. Motivation for the study is driven in part by guidance from the United Kingdom to base approval of booster vaccines with "strain changes" that target variants on results of neutralizing antibody tests and information about safety, but without requiring evidence of clinical efficacy. Using designs informed by our agent-based network models, we show it may be feasible to conduct a trial of novel SARS-CoV-2 vaccines in a single large campus to obtain useful information regarding vaccine efficacy against susceptibility and infectiousness. If needed, the sample size could be increased by extending the study to a small number of campuses. Novel network methods may be useful in developing pragmatic SARS-CoV-2 vaccine trials that can leverage existing infrastructure to reduce costs and hasten the development of results.
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Affiliation(s)
- Victor DeGruttola
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Division of Infectious Diseases & Global Public Health, Department of Medicine, University of California San Diego La Jolla, CA, USA
| | - Ravi Goyal
- Division of Infectious Diseases & Global Public Health, Department of Medicine, University of California San Diego La Jolla, CA, USA
| | - Natasha K Martin
- Division of Infectious Diseases & Global Public Health, Department of Medicine, University of California San Diego La Jolla, CA, USA
| | - Rui Wang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA, USA
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2
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Hemming K, Proschan MA, Stephens-Shields AJ. Thirteenth annual UPenn conference on statistical issues in clinical trials: Cluster randomized clinical trials-opportunities and challenges (morning panel session). Clin Trials 2022; 19:384-395. [PMID: 35787213 DOI: 10.1177/17407745221101267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | - Michael A Proschan
- National Institute of allergy and Infectious Disease, NIH, Bethesda, MD, USA
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3
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Magosi LE, Zhang Y, Golubchik T, DeGruttola V, Tchetgen Tchetgen E, Novitsky V, Moore J, Bachanas P, Segolodi T, Lebelonyane R, Pretorius Holme M, Moyo S, Makhema J, Lockman S, Fraser C, Essex MM, Lipsitch M. Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial - BCPP/ Ya Tsie trial. eLife 2022; 11:72657. [PMID: 35229714 PMCID: PMC8912920 DOI: 10.7554/elife.72657] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 02/08/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Mathematical models predict that community-wide access to HIV testing-and-treatment can rapidly and substantially reduce new HIV infections. Yet several large universal test-and-treat HIV prevention trials in high-prevalence epidemics demonstrated variable reduction in population-level incidence. Methods: To elucidate patterns of HIV spread in universal test-and-treat trials we quantified the contribution of geographic-location, gender, age and randomized-HIV-intervention to HIV transmissions in the 30-community Ya Tsie trial in Botswana. We sequenced HIV viral whole genomes from 5,114 trial participants among the 30 trial communities. Results: Deep-sequence phylogenetic analysis revealed that most inferred HIV transmissions within the trial occurred within the same or between neighboring communities, and between similarly-aged partners. Transmissions into intervention communities from control communities were more common than the reverse post-baseline (30% [12.2 - 56.7] versus 3% [0.1 - 27.3]) than at baseline (7% [1.5 - 25.3] versus 5% [0.9 - 22.9]) compatible with a benefit from treatment-as-prevention. Conclusion: Our findings suggest that population mobility patterns are fundamental to HIV transmission dynamics and to the impact of HIV control strategies. Funding: This study was supported by the National Institute of General Medical Sciences (U54GM088558); the Fogarty International Center (FIC) of the U.S. National Institutes of Health (D43 TW009610); and the President's Emergency Plan for AIDS Relief through the Centers for Disease Control and Prevention (CDC) (Cooperative agreements U01 GH000447 and U2G GH001911).
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Affiliation(s)
- Lerato E Magosi
- Department of Epidemiology, Harvard University, Boston, United States
| | - Yinfeng Zhang
- Division of Molecular and Genomic Pathology, University of Pittsburgh Medical Center, Pittsburgh, United States
| | - Tanya Golubchik
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Victor DeGruttola
- Department of Biostatistics, Harvard T H Chan School of Public Health, Boston, United States
| | | | - Vladimir Novitsky
- Department of Immunology and Infectious Disease, Harvard T H Chan School of Public Health, Boston, United States
| | - Janet Moore
- Division of Global HIV/AIDS and TB, Centers for Disease Control and Prevention, Atlanta, United States
| | - Pam Bachanas
- Division of Global HIV/AIDS and TB, Centers for Disease Control and Prevention, Atlanta, United States
| | - Tebogo Segolodi
- HIV Prevention Research Unit, Centers for Disease Control and Prevention, Gaborone, Botswana
| | | | - Molly Pretorius Holme
- epartment of Immunology and Infectious Disease, Harvard T H Chan School of Public Health, Boston, United States
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Joseph Makhema
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Shahin Lockman
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, United States
| | - Christophe Fraser
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Myron Max Essex
- Department of Immunology and Infectious Disease, Harvard T H Chan School of Public Health, Boston, United States
| | - Marc Lipsitch
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, United States
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4
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Zheng M, Yu M, Cheng S, Zhou N, Ning T, Li L, Zhao F, Zhao X, Zhu J, Jiang G. Characteristics of HIV-1 molecular transmission networks and drug resistance among men who have sex with men in Tianjin, China (2014-2018). Virol J 2020; 17:169. [PMID: 33143744 PMCID: PMC7640427 DOI: 10.1186/s12985-020-01441-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/27/2020] [Indexed: 11/25/2022] Open
Abstract
Background In Tianjin, China, there is a relatively high prevalence of HIV in men who have sex with men (MSM). The number of HIV cases in Tianjin is also increasing. We investigated the HIV molecular transmission network, genetic tropisms, and drug resistance mutations in Tianjin.
Methods Blood samples were collected from 510 newly diagnosed antiretroviral therapy (ART)-naïve HIV-1-infected subjects among MSM in Tianjin. Partial pol and env genes were sequenced and used for phylogenetic, genetic tropism, and genotypic drug resistance analyses. Molecular clusters were identified with 1.5% genetic distance and 90% bootstrap support. Results Among the 436 HIV-1 pol sequences obtained from the study participants, various genotypes were identified, including CRF01_AE (56.9%), CRF07_BC (27.8%), B (7.3%), CRF55_01B (4.1%), unique recombinant forms (URFs) (3.7%), and CRF59_01B (0.2%). A higher prevalence of X4 viruses was observed in individuals infected with CRF55_01B (56.3%) and CRF01_AE (46.2%) than with other subtypes. Of all 110 sequences in the 36 clusters, 62 (56.4%) were observed in 23 CRF01_AE clusters and 18 (16.4%) in four CRF07_BC clusters. Eight sequences clustered with at least one other shared the same drug resistance mutation (DRM). In different cluster sizes, the distributions of individuals by age, presence of sexually transmitted disease, and presence of DRMs, were significantly different. Conclusion We revealed the characteristics of HIV molecular transmission, tropism, and DRMs of ART-naïve HIV-infected individuals among the MSM population in Tianjin. Identifying infected persons at risk of transmission is necessary for proposing counseling and treating these patients to reduce the risk of HIV transmission.
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Affiliation(s)
- Minna Zheng
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Maohe Yu
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Shaohui Cheng
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Ning Zhou
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Tielin Ning
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Long Li
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Fangning Zhao
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Xuan Zhao
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Jingjin Zhu
- Department for AIDS/STD Control and Prevention, Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China
| | - Guohong Jiang
- Tianjin Centers for Disease Control and Prevention, No.6 Huayue Road, Hedong District, Tianjin, 300011, China.
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Kiwuwa-Muyingo S, Nazziwa J, Ssemwanga D, Ilmonen P, Njai H, Ndembi N, Parry C, Kitandwe PK, Gershim A, Mpendo J, Neilsen L, Seeley J, Seppälä H, Lyagoba F, Kamali A, Kaleebu P. HIV-1 transmission networks in high risk fishing communities on the shores of Lake Victoria in Uganda: A phylogenetic and epidemiological approach. PLoS One 2017; 12:e0185818. [PMID: 29023474 PMCID: PMC5638258 DOI: 10.1371/journal.pone.0185818] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 09/20/2017] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Fishing communities around Lake Victoria in sub-Saharan Africa have been characterised as a population at high risk of HIV-infection. METHODS Using data from a cohort of HIV-positive individuals aged 13-49 years, enrolled from 5 fishing communities on Lake Victoria between 2009-2011, we sought to identify factors contributing to the epidemic and to understand the underlying structure of HIV transmission networks. Clinical and socio-demographic data were combined with HIV-1 phylogenetic analyses. HIV-1 gag-p24 and env-gp-41 sub-genomic fragments were amplified and sequenced from 283 HIV-1-infected participants. Phylogenetic clusters with ≥2 highly related sequences were defined as transmission clusters. Logistic regression models were used to determine factors associated with clustering. RESULTS Altogether, 24% (n = 67/283) of HIV positive individuals with sequences fell within 34 phylogenetically distinct clusters in at least one gene region (either gag or env). Of these, 83% occurred either within households or within community; 8/34 (24%) occurred within household partnerships, and 20/34 (59%) within community. 7/12 couples (58%) within households clustered together. Individuals in clusters with potential recent transmission (11/34) were more likely to be younger 71% (15/21) versus 46% (21/46) in un-clustered individuals and had recently become resident in the community 67% (14/21) vs 48% (22/46). Four of 11 (36%) potential transmission clusters included incident-incident transmissions. Independently, clustering was less likely in HIV subtype D (adjusted Odds Ratio, aOR = 0.51 [95% CI 0.26-1.00]) than A and more likely in those living with an HIV-infected individual in the household (aOR = 6.30 [95% CI 3.40-11.68]). CONCLUSIONS A large proportion of HIV sexual transmissions occur within house-holds and within communities even in this key mobile population. The findings suggest localized HIV transmissions and hence a potential benefit for the test and treat approach even at a community level, coupled with intensified HIV counselling to identify early infections.
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Affiliation(s)
- Sylvia Kiwuwa-Muyingo
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Jamirah Nazziwa
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Deogratius Ssemwanga
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Pauliina Ilmonen
- Aalto University, School of Science, Department of Mathematics and Systems Analysis, Espoo, Finland
| | - Harr Njai
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Nicaise Ndembi
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Chris Parry
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | | | - Asiki Gershim
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | | | - Leslie Neilsen
- International AIDS Vaccine Initiative, New York, United States of America
| | - Janet Seeley
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Heikki Seppälä
- Aalto University, School of Science, Department of Mathematics and Systems Analysis, Espoo, Finland
| | - Fred Lyagoba
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Anatoli Kamali
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
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6
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Ratmann O, Hodcroft EB, Pickles M, Cori A, Hall M, Lycett S, Colijn C, Dearlove B, Didelot X, Frost S, Hossain ASMM, Joy JB, Kendall M, Kühnert D, Leventhal GE, Liang R, Plazzotta G, Poon AFY, Rasmussen DA, Stadler T, Volz E, Weis C, Leigh Brown AJ, Fraser C. Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison. Mol Biol Evol 2016; 34:185-203. [PMID: 28053012 PMCID: PMC5854118 DOI: 10.1093/molbev/msw217] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Viral phylogenetic methods contribute to understanding how HIV spreads in populations, and thereby help guide the design of prevention interventions. So far, most analyses have been applied to well-sampled concentrated HIV-1 epidemics in wealthy countries. To direct the use of phylogenetic tools to where the impact of HIV-1 is greatest, the Phylogenetics And Networks for Generalized HIV Epidemics in Africa (PANGEA-HIV) consortium generates full-genome viral sequences from across sub-Saharan Africa. Analyzing these data presents new challenges, since epidemics are principally driven by heterosexual transmission and a smaller fraction of cases is sampled. Here, we show that viral phylogenetic tools can be adapted and used to estimate epidemiological quantities of central importance to HIV-1 prevention in sub-Saharan Africa. We used a community-wide methods comparison exercise on simulated data, where participants were blinded to the true dynamics they were inferring. Two distinct simulations captured generalized HIV-1 epidemics, before and after a large community-level intervention that reduced infection levels. Five research groups participated. Structured coalescent modeling approaches were most successful: phylogenetic estimates of HIV-1 incidence, incidence reductions, and the proportion of transmissions from individuals in their first 3 months of infection correlated with the true values (Pearson correlation > 90%), with small bias. However, on some simulations, true values were markedly outside reported confidence or credibility intervals. The blinded comparison revealed current limits and strengths in using HIV phylogenetics in challenging settings, provided benchmarks for future methods' development, and supports using the latest generation of phylogenetic tools to advance HIV surveillance and prevention.
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Affiliation(s)
- Oliver Ratmann
- Department of Infectious Disease Epidemiology, MRC Centre for Outbreak Analyses and Modelling, School of Public Health, Imperial College London, London, United Kingdom
| | - Emma B Hodcroft
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Michael Pickles
- Department of Infectious Disease Epidemiology, MRC Centre for Outbreak Analyses and Modelling, School of Public Health, Imperial College London, London, United Kingdom
| | - Anne Cori
- Department of Infectious Disease Epidemiology, MRC Centre for Outbreak Analyses and Modelling, School of Public Health, Imperial College London, London, United Kingdom
| | - Matthew Hall
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.,Nuffield Department of Medicine, Li Ka Shing Centre for Health Information and Discovery, Oxford Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Samantha Lycett
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.,The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Caroline Colijn
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Bethany Dearlove
- Department of Veterinary Medicine, Cambridge Veterinary School, Cambridge, United Kingdom
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, MRC Centre for Outbreak Analyses and Modelling, School of Public Health, Imperial College London, London, United Kingdom
| | - Simon Frost
- Department of Veterinary Medicine, Cambridge Veterinary School, Cambridge, United Kingdom
| | | | - Jeffrey B Joy
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Michelle Kendall
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Denise Kühnert
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.,Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Gabriel E Leventhal
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.,Department of Civil and Environmental Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA
| | - Richard Liang
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Giacomo Plazzotta
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Art F Y Poon
- Department of Pathology & Laboratory Medicine, Western University, Ontario, Canada
| | - David A Rasmussen
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Erik Volz
- Department of Infectious Disease Epidemiology, MRC Centre for Outbreak Analyses and Modelling, School of Public Health, Imperial College London, London, United Kingdom
| | - Caroline Weis
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Andrew J Leigh Brown
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Christophe Fraser
- Department of Infectious Disease Epidemiology, MRC Centre for Outbreak Analyses and Modelling, School of Public Health, Imperial College London, London, United Kingdom.,Nuffield Department of Medicine, Li Ka Shing Centre for Health Information and Discovery, Oxford Big Data Institute, University of Oxford, Oxford, United Kingdom
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7
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Ratmann O, van Sighem A, Bezemer D, Gavryushkina A, Jurriaans S, Wensing A, de Wolf F, Reiss P, Fraser C. Sources of HIV infection among men having sex with men and implications for prevention. Sci Transl Med 2016; 8:320ra2. [PMID: 26738795 DOI: 10.1126/scitranslmed.aad1863] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
New HIV diagnoses among men having sex with men (MSM) have not decreased appreciably in most countries, even though care and prevention services have been scaled up substantially in the past 20 years. To maximize the impact of prevention strategies, it is crucial to quantify the sources of transmission at the population level. We used viral sequence and clinical patient data from one of Europe's nationwide cohort studies to estimate probable sources of transmission for 617 recently infected MSM. Seventy-one percent of transmissions were from undiagnosed men, 6% from men who had initiated antiretroviral therapy (ART), 1% from men with no contact to care for at least 18 months, and 43% from those in their first year of infection. The lack of substantial reductions in incidence among Dutch MSM is not a result of ineffective ART provision or inadequate retention in care. In counterfactual modeling scenarios, 19% of these past cases could have been averted with current annual testing coverage and immediate ART to those testing positive. Sixty-six percent of these cases could have been averted with available antiretrovirals (immediate ART provided to all MSM testing positive, and preexposure antiretroviral prophylaxis taken by half of all who test negative for HIV), but only if half of all men at risk of transmission had tested annually. With increasing sequence coverage, molecular epidemiological analyses can be a key tool to direct HIV prevention strategies to the predominant sources of infection, and help send HIV epidemics among MSM into a decisive decline.
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Affiliation(s)
- Oliver Ratmann
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W21PG, UK.
| | - Ard van Sighem
- Stichting HIV Monitoring, 1105 BD Amsterdam, the Netherlands
| | - Daniela Bezemer
- Stichting HIV Monitoring, 1105 BD Amsterdam, the Netherlands
| | | | - Suzanne Jurriaans
- Department of Medical Microbiology, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Annemarie Wensing
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Frank de Wolf
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W21PG, UK
| | - Peter Reiss
- Stichting HIV Monitoring, 1105 BD Amsterdam, the Netherlands. Department of Global Health, Academic Medical Center, 1105 BM Amsterdam, the Netherlands
| | - Christophe Fraser
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W21PG, UK
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8
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Abstract
Effective HIV prevention requires knowledge of the structure and dynamics of the social networks across which infections are transmitted. These networks most commonly comprise chains of sexual relationships, but in some populations, sharing of contaminated needles is also an important, or even the main mechanism that connects people in the network. Whereas network data have long been collected during survey interviews, new data sources have become increasingly common in recent years, because of advances in molecular biology and the use of partner notification services in HIV prevention and treatment programmes. We review current and emerging methods for collecting HIV-related network data, as well as modelling frameworks commonly used to infer network parameters and map potential HIV transmission pathways within the network. We discuss the relative strengths and weaknesses of existing methods and models, and we propose a research agenda for advancing network analysis in HIV epidemiology. We make the case for a combination approach that integrates multiple data sources into a coherent statistical framework.
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9
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Liu SH, Erion G, Novitsky V, De Gruttola V. Viral Genetic Linkage Analysis in the Presence of Missing Data. PLoS One 2015; 10:e0135469. [PMID: 26301919 DOI: 10.1371/journal.pone.0135469] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 07/23/2015] [Indexed: 02/07/2023] Open
Abstract
Analyses of viral genetic linkage can provide insight into HIV transmission dynamics and the impact of prevention interventions. For example, such analyses have the potential to determine whether recently-infected individuals have acquired viruses circulating within or outside a given community. In addition, they have the potential to identify characteristics of chronically infected individuals that make their viruses likely to cluster with others circulating within a community. Such clustering can be related to the potential of such individuals to contribute to the spread of the virus, either directly through transmission to their partners or indirectly through further spread of HIV from those partners. Assessment of the extent to which individual (incident or prevalent) viruses are clustered within a community will be biased if only a subset of subjects are observed, especially if that subset is not representative of the entire HIV infected population. To address this concern, we develop a multiple imputation framework in which missing sequences are imputed based on a model for the diversification of viral genomes. The imputation method decreases the bias in clustering that arises from informative missingness. Data from a household survey conducted in a village in Botswana are used to illustrate these methods. We demonstrate that the multiple imputation approach reduces bias in the overall proportion of clustering due to the presence of missing observations.
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Affiliation(s)
- Shelley H Liu
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Gabriel Erion
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, United States of America
| | - Vladimir Novitsky
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Victor De Gruttola
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
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10
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Long-Range HIV Genotyping Using Viral RNA and Proviral DNA for Analysis of HIV Drug Resistance and HIV Clustering. J Clin Microbiol 2015; 53:2581-92. [PMID: 26041893 DOI: 10.1128/jcm.00756-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/26/2015] [Indexed: 12/15/2022] Open
Abstract
The goal of the study was to improve the methodology of HIV genotyping for analysis of HIV drug resistance and HIV clustering. Using the protocol of Gall et al. (A. Gall, B. Ferns, C. Morris, S. Watson, M. Cotten, M. Robinson, N. Berry, D. Pillay, and P. Kellam, J Clin Microbiol 50:3838-3844, 2012, doi:10.1128/JCM.01516-12), we developed a robust methodology for amplification of two large fragments of viral genome covering about 80% of the unique HIV-1 genome sequence. Importantly, this method can be applied to both viral RNA and proviral DNA amplification templates, allowing genotyping in HIV-infected subjects with suppressed viral loads (e.g., subjects on antiretroviral therapy [ART]). The two amplicons cover critical regions across the HIV-1 genome (including pol and env), allowing analysis of mutations associated with resistance to protease inhibitors, reverse transcriptase inhibitors (nucleoside reverse transcriptase inhibitors [NRTIs] and nonnucleoside reverse transcriptase inhibitors [NNRTIs]), integrase strand transfer inhibitors, and virus entry inhibitors. The two amplicons generated span 7,124 bp, providing substantial sequence length and numbers of informative sites for comprehensive phylogenic analysis and greater refinement of viral linkage analyses in HIV prevention studies. The long-range HIV genotyping from proviral DNA was successful in about 90% of 212 targeted blood specimens collected in a cohort where the majority of patients had suppressed viral loads, including 65% of patients with undetectable levels of HIV-1 RNA loads. The generated amplicons could be sequenced by different methods, such as population Sanger sequencing, single-genome sequencing, or next-generation ultradeep sequencing. The developed method is cost-effective-the cost of the long-range HIV genotyping is under $140 per subject (by Sanger sequencing)-and has the potential to enable the scale up of public health HIV prevention interventions.
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11
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Novitsky V, Moyo S, Lei Q, DeGruttola V, Essex M. Importance of Viral Sequence Length and Number of Variable and Informative Sites in Analysis of HIV Clustering. AIDS Res Hum Retroviruses 2015; 31:531-42. [PMID: 25560745 DOI: 10.1089/aid.2014.0211] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
To improve the methodology of HIV cluster analysis, we addressed how analysis of HIV clustering is associated with parameters that can affect the outcome of viral clustering. The extent of HIV clustering and tree certainty was compared between 401 HIV-1C near full-length genome sequences and subgenomic regions retrieved from the LANL HIV Database. Sliding window analysis was based on 99 windows of 1,000 bp and 45 windows of 2,000 bp. Potential associations between the extent of HIV clustering and sequence length and the number of variable and informative sites were evaluated. The near full-length genome HIV sequences showed the highest extent of HIV clustering and the highest tree certainty. At the bootstrap threshold of 0.80 in maximum likelihood (ML) analysis, 58.9% of near full-length HIV-1C sequences but only 15.5% of partial pol sequences (ViroSeq) were found in clusters. Among HIV-1 structural genes, pol showed the highest extent of clustering (38.9% at a bootstrap threshold of 0.80), although it was significantly lower than in the near full-length genome sequences. The extent of HIV clustering was significantly higher for sliding windows of 2,000 bp than 1,000 bp. We found a strong association between the sequence length and proportion of HIV sequences in clusters, and a moderate association between the number of variable and informative sites and the proportion of HIV sequences in clusters. In HIV cluster analysis, the extent of detectable HIV clustering is directly associated with the length of viral sequences used, as well as the number of variable and informative sites. Near full-length genome sequences could provide the most informative HIV cluster analysis. Selected subgenomic regions with a high extent of HIV clustering and high tree certainty could also be considered as a second choice.
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Affiliation(s)
- Vlad Novitsky
- Harvard School of Public Health AIDS Initiative, Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts
| | | | - Quanhong Lei
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
| | - Victor DeGruttola
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
| | - M. Essex
- Harvard School of Public Health AIDS Initiative, Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts
- Botswana Harvard AIDS Institute, Gaborone, Botswana
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Novitsky V, Moyo S, Lei Q, DeGruttola V, Essex M. Impact of sampling density on the extent of HIV clustering. AIDS Res Hum Retroviruses 2014; 30:1226-35. [PMID: 25275430 PMCID: PMC4250956 DOI: 10.1089/aid.2014.0173] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Identifying and monitoring HIV clusters could be useful in tracking the leading edge of HIV transmission in epidemics. Currently, greater specificity in the definition of HIV clusters is needed to reduce confusion in the interpretation of HIV clustering results. We address sampling density as one of the key aspects of HIV cluster analysis. The proportion of viral sequences in clusters was estimated at sampling densities from 1.0% to 70%. A set of 1,248 HIV-1C env gp120 V1C5 sequences from a single community in Botswana was utilized in simulation studies. Matching numbers of HIV-1C V1C5 sequences from the LANL HIV Database were used as comparators. HIV clusters were identified by phylogenetic inference under bootstrapped maximum likelihood and pairwise distance cut-offs. Sampling density below 10% was associated with stochastic HIV clustering with broad confidence intervals. HIV clustering increased linearly at sampling density >10%, and was accompanied by narrowing confidence intervals. Patterns of HIV clustering were similar at bootstrap thresholds 0.7 to 1.0, but the extent of HIV clustering decreased with higher bootstrap thresholds. The origin of sampling (local concentrated vs. scattered global) had a substantial impact on HIV clustering at sampling densities ≥10%. Pairwise distances at 10% were estimated as a threshold for cluster analysis of HIV-1 V1C5 sequences. The node bootstrap support distribution provided additional evidence for 10% sampling density as the threshold for HIV cluster analysis. The detectability of HIV clusters is substantially affected by sampling density. A minimal genotyping density of 10% and sampling density of 50-70% are suggested for HIV-1 V1C5 cluster analysis.
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Affiliation(s)
- Vlad Novitsky
- Harvard School of Public Health AIDS Initiative, Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts
| | | | - Quanhong Lei
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
| | - Victor DeGruttola
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
| | - Myron Essex
- Harvard School of Public Health AIDS Initiative, Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts
- Botswana Harvard AIDS Institute, Gaborone, Botswana
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Dennis AM, Herbeck JT, Brown AL, Kellam P, de Oliveira T, Pillay D, Fraser C, Cohen MS. Phylogenetic studies of transmission dynamics in generalized HIV epidemics: an essential tool where the burden is greatest? J Acquir Immune Defic Syndr 2014; 67:181-95. [PMID: 24977473 PMCID: PMC4304655 DOI: 10.1097/qai.0000000000000271] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Efficient and effective HIV prevention measures for generalized epidemics in sub-Saharan Africa have not yet been validated at the population level. Design and impact evaluation of such measures requires fine-scale understanding of local HIV transmission dynamics. The novel tools of HIV phylogenetics and molecular epidemiology may elucidate these transmission dynamics. Such methods have been incorporated into studies of concentrated HIV epidemics to identify proximate and determinant traits associated with ongoing transmission. However, applying similar phylogenetic analyses to generalized epidemics, including the design and evaluation of prevention trials, presents additional challenges. Here we review the scope of these methods and present examples of their use in concentrated epidemics in the context of prevention. Next, we describe the current uses for phylogenetics in generalized epidemics and discuss their promise for elucidating transmission patterns and informing prevention trials. Finally, we review logistic and technical challenges inherent to large-scale molecular epidemiological studies of generalized epidemics and suggest potential solutions.
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Affiliation(s)
- Ann M. Dennis
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Andrew Leigh Brown
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Cambridge, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Tulio de Oliveira
- Wellcome Trust-Africa Centre for Health and Population Studies, University of Kwazula-Natal, ZA
| | - Deenan Pillay
- Division of Infection and Immunity, University College London, London, UK
| | - Christophe Fraser
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Myron S. Cohen
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC
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