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Handel A, Martinez L, Sekandi JN, Bellan SE, Zhu L, Chen C, Liu Q, Donkor S, Sutherland J, Hill PC, Gilman RH, Grandjean L, Whalen CC. Evidence for supercoughers in an analysis of six tuberculosis cohorts from China, Peru, The Gambia and Uganda. Int J Tuberc Lung Dis 2020; 23:1286-1292. [PMID: 31931913 DOI: 10.5588/ijtld.18.0819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND: It is very difficult to observe tuberculosis (TB) transmission chains and thus, identify superspreaders. We investigate cough duration as a proxy measure of transmission to assess the presence of potential TB superspreaders.DESIGN: We analyzed six studies from China, Peru, The Gambia and Uganda, and determined the distribution of cough duration and compared it with several theoretical distributions. To determine factors associated with cough duration, we used linear regression and boosted regression trees to examine the predictive power of patient, clinical and environmental characteristics.RESULTS: We found within-study heterogeneity in cough duration and strong similarities across studies. Approximately 20% of patients contributed 50% of total cough days, and around 50% of patients contributed 80% of total cough days. The cough duration distribution suggested an initially increasing, and subsequently, decreasing hazard of diagnosis. While some of the exposure variables showed statistically significant associations with cough duration, none of them had a strong effect. Multivariate analyses of different model types did not produce a model that had good predictive power.CONCLUSION: We found consistent evidence for the presence of supercoughers, but no characteristics predictive of such individuals.
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Affiliation(s)
- A Handel
- Department of Epidemiology and Biostatistics, and Health Informatics Institute and Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - L Martinez
- Department of Epidemiology and Biostatistics, and Health Informatics Institute and Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - J N Sekandi
- Department of Epidemiology and Biostatistics, and Health Informatics Institute and Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - S E Bellan
- Department of Epidemiology and Biostatistics, and Health Informatics Institute and Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - L Zhu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, People's Republic of China
| | - C Chen
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, People's Republic of China
| | - Q Liu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, People's Republic of China
| | - S Donkor
- Vaccines and Immunity, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - J Sutherland
- Vaccines and Immunity, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - P C Hill
- Centre for International Health, School of Medicine, University of Otago, Dunedin, New Zealand
| | - R H Gilman
- Universidad Peruana Cayetano Heredia, Lima, Peru, Johns Hopkins Bloomberg School of Public Health, Department of International Health, Baltimore, MD, USA
| | - L Grandjean
- Universidad Peruana Cayetano Heredia, Lima, Peru, Wellcome Centre for Clinical Tropical Medicine, Imperial College London, London, Institute of Child Health, University College London, London, UK
| | - C C Whalen
- Department of Epidemiology and Biostatistics, and Health Informatics Institute and Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
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Bellan SE, Eggo RM, Gsell PS, Kucharski AJ, Dean NE, Donohue R, Zook M, Edmunds WJ, Odhiambo F, Longini IM, Brisson M, Mahon BE, Henao-Restrepo AM. An online decision tree for vaccine efficacy trial design during infectious disease epidemics: The InterVax-Tool. Vaccine 2019; 37:4376-4381. [PMID: 31242963 PMCID: PMC6620503 DOI: 10.1016/j.vaccine.2019.06.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 05/30/2019] [Accepted: 06/10/2019] [Indexed: 12/31/2022]
Abstract
Phase 3 vaccine efficacy trial design during outbreaks and emergencies is challenging. InterVax-Tool (vaxeval.com) is a structured decision-support tool for trial design. Optimal design must include epidemiological, statistical, ethical, and logistical difficulties. Navigating these issues in real-time requires tools to assist in decision-making. Dynamic guidance, note taking, and tailored choices are key to good user engagement.
Background Licensed vaccines are urgently needed for emerging infectious diseases, but the nature of these epidemics causes challenges for the design of phase III trials to evaluate vaccine efficacy. Designing and executing rigorous, fast, and ethical, vaccine efficacy trials is difficult, and the decisions and limitations in the design of these trials encompass epidemiological, logistical, regulatory, statistical, and ethical dimensions. Results Trial design decisions are complex and interrelated, but current guidance documents do not lend themselves to efficient decision-making. We created InterVax-Tool (http://vaxeval.com), an online, interactive decision-support tool, to help diverse stakeholders navigate the decisions in the design of phase III vaccine trials. InterVax-Tool offers high-level visual and interactive assistance through a set of four decision trees, guiding users through selection of the: (1) Primary Endpoint, (2) Target Population, (3) Randomization Scheme, and, (4) Comparator. We provide guidance on how key considerations – grouped as Epidemiological, Vaccine-related, Infrastructural, or Sociocultural – inform each decision in the trial design process. Conclusions InterVax-Tool facilitates structured, transparent, and collaborative discussion of trial design, while recording the decision-making process. Users can save and share their decisions, which is useful both for comparing proposed trial designs, and for justifying particular design choices. Here, we describe the goals and features of InterVax-Tool as well as its application to the design of a Zika vaccine efficacy trial.
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Affiliation(s)
- Steven E Bellan
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, GA, USA; Center for Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA.
| | - Rosalind M Eggo
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK.
| | | | - Adam J Kucharski
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Natalie E Dean
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Richard Donohue
- Department of Geography, University of Kentucky, Lexington, KY, USA
| | - Matt Zook
- Department of Geography, University of Kentucky, Lexington, KY, USA
| | - W John Edmunds
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Frank Odhiambo
- Kenya Medical Research Institute, Centre for Global Health Research, Kisumu, Kenya
| | - Ira M Longini
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Marc Brisson
- Centre de recherche du CHU de Québec, Québec, Canada; Département de médecine sociale et préventive, Université Laval, Québec, Canada; Department of Infectious Disease Epidemiology, Imperial College, London, UK
| | - Barbara E Mahon
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Fox SJ, Bellan SE, Perkins TA, Johansson MA, Meyers LA. Downgrading disease transmission risk estimates using terminal importations. PLoS Negl Trop Dis 2019; 13:e0007395. [PMID: 31199809 PMCID: PMC6594658 DOI: 10.1371/journal.pntd.0007395] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 06/26/2019] [Accepted: 04/16/2019] [Indexed: 12/19/2022] Open
Abstract
As emerging and re-emerging infectious arboviruses like dengue, chikungunya, and Zika threaten new populations worldwide, officials scramble to assess local severity and transmissibility, with little to no epidemiological history to draw upon. Indirect estimates of risk from vector habitat suitability maps are prone to great uncertainty, while direct estimates from epidemiological data are only possible after cases accumulate and, given environmental constraints on arbovirus transmission, cannot be widely generalized beyond the focal region. Combining these complementary methods, we use disease importation and transmission data to improve the accuracy and precision of a priori ecological risk estimates. We demonstrate this approach by estimating the spatiotemporal risks of Zika virus transmission throughout Texas, a high-risk region in the southern United States. Our estimates are, on average, 80% lower than published ecological estimates-with only six of 254 Texas counties deemed capable of sustaining a Zika epidemic-and they are consistent with the number of autochthonous cases detected in 2017. Importantly our method provides a framework for model comparison, as our mechanistic understanding of arbovirus transmission continues to improve. Real-time updating of prior risk estimates as importations and outbreaks arise can thereby provide critical, early insight into local transmission risks as emerging arboviruses expand their global reach.
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Affiliation(s)
- Spencer J. Fox
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Steven E. Bellan
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, Georgia, United States of America
- Center for Ecology of Infectious Diseases, University of Georgia, Athens, Gerogia, United States of America
| | - T. Alex Perkins
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Michael A. Johansson
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
- Center for Communicable Disease Dynamics, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Lauren Ancel Meyers
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
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Abstract
Zika virus (ZIKV) infection during pregnancy is associated with microcephaly and other birth defects, collectively termed Congenital Zika Syndrome (CZS). During the epidemic in 2015-16, ZIKV spread through the Americas and quickly joined the list of other known teratogenic pathogens, TORCH. Multiple ZIKV vaccines have been developed for protection of pregnant women and women of childbearing age. However, ZIKV infection incidence has since waned substantially, and adverse birth outcomes are rare outcomes of infection. Studying a vaccine's protective efficacy against CZS in a large phase III clinical trial may be infeasible in such times of low incidence. Should trials be initiated, researchers may resort to alternative clinical endpoints. In this study, we simulate a variety of vaccine clinical trial scenarios to evaluate the feasibility of the CZS endpoint in vaccine studies and compare CZS to other potential outcomes: ZIKV infection detected through weekly, biweekly, or monthly testing and laboratory-confirmed, symptomatic Zika Virus Disease. We compare the sample size required for 80% statistical power to detect vaccine efficacy and trial duration for each scenario. Our results show the feasibility of CZS clinical endpoints depends on the timing of simulated clinical trials in the course of a seasonal epidemic, due to CZS risk varying with trimester of infection. This result highlights additional considerations needed when designing vaccine efficacy trials of protection against teratogenic pathogens.
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Affiliation(s)
- Rachel A Mercaldo
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, GA, USA.
| | - Steven E Bellan
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, GA, USA; Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA; South African Center for Epidemiological Modelling and Analysis, University of Stellenbosch, Stellenbosch, South Africa
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Kahn R, Hitchings M, Wang R, Bellan SE, Lipsitch M. Analyzing Vaccine Trials in Epidemics With Mild and Asymptomatic Infection. Am J Epidemiol 2019; 188:467-474. [PMID: 30329134 PMCID: PMC6357804 DOI: 10.1093/aje/kwy239] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 10/11/2018] [Indexed: 12/22/2022] Open
Abstract
Vaccine efficacy against susceptibility to infection (VES), regardless of symptoms, is an important endpoint of vaccine trials for pathogens with a high proportion of asymptomatic infection, because such infections may contribute to onward transmission and long-term sequelae, such as congenital Zika syndrome. However, estimating VES is resource-intensive. We aimed to identify approaches for accurately estimating VES when limited information is available and resources are constrained. We modeled an individually randomized vaccine trial by generating a network of individuals and simulating an epidemic. The disease natural history followed a “susceptible-exposed-infectious/symptomatic (or infectious/asymptomatic)-recovered” model. We then used 7 approaches to estimate VES, and we also estimated vaccine efficacy against progression to symptoms (VEP). A corrected relative risk and an interval-censored Cox model accurately estimate VES and only require serological testing of participants once, while a Cox model using only symptomatic infections returns biased estimates. Only acquiring serological endpoints in a 10% sample and imputing the remaining infection statuses yields unbiased VES estimates across values of the basic reproduction number (R0) and accurate estimates of VEP for higher R0 values. Identifying resource-preserving methods for accurately estimating VES and VEP is important in designing trials for diseases with a high proportion of asymptomatic infection.
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Affiliation(s)
- Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Matt Hitchings
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Rui Wang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, Massachusetts
| | - Steven E Bellan
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, Georgia
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, Georgia
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
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Hitchings MDT, Lipsitch M, Wang R, Bellan SE. Competing Effects of Indirect Protection and Clustering on the Power of Cluster-Randomized Controlled Vaccine Trials. Am J Epidemiol 2018. [PMID: 29522080 DOI: 10.1093/aje/kwy047] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Power considerations for trials evaluating vaccines against infectious diseases are complicated by indirect protective effects of vaccination. While cluster-randomized controlled trials (cRCTs) are less statistically efficient than individually randomized controlled trials (iRCTs), a cRCT's ability to measure direct and indirect vaccine effects may mitigate the loss of efficiency due to clustering. Within cRCTs, the number and size of clusters affects 3 determinants of power: the effect size being measured, disease incidence, and intracluster correlation. We simulated trials conducted in a collection of small communities to assess how indirect protection and clustering affected the power of cRCTs and iRCTs during an emerging epidemic. Across diverse parameters, we found that within the same trial population, cRCTs were never more powerful than iRCTs, although the difference can be small. We also identified 2 effects that attenuated the loss of cRCT power traditionally associated with increased cluster size. First, if enrollment of fewer, larger clusters was performed to achieve higher vaccine coverage within vaccinated communities, this increased the effect to be measured and, consequently, power. Second, the greater rate of imported transmission in larger communities may increase the attack rate and similarly mitigate loss of power relative to a trial in many, smaller communities.
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Affiliation(s)
- Matt D T Hitchings
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Rui Wang
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Steven E Bellan
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, Georgia
- Center for the Ecology of Infectious Disease, University of Georgia, Athens, Georgia
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Bellan SE, Champredon D, Dushoff J, Meyers LA. Couple serostatus patterns in sub-Saharan Africa illuminate the relative roles of transmission rates and sexual network characteristics in HIV epidemiology. Sci Rep 2018; 8:6675. [PMID: 29703941 PMCID: PMC5923291 DOI: 10.1038/s41598-018-24249-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 03/19/2018] [Indexed: 11/21/2022] Open
Abstract
HIV prevalence has surpassed 30% in some African countries while peaking at less than 1% in others. The extent to which this variation is driven by biological factors influencing the HIV transmission rate or by variation in sexual network characteristics remains widely debated. Here, we leverage couple serostatus patterns to address this question. HIV prevalence is strongly correlated with couple serostatus patterns across the continent; in particular, high prevalence countries tend to have a lower ratio of serodiscordancy to concordant positivity. To investigate the drivers of this continental pattern, we fit an HIV transmission model to Demographic and Health Survey data from 45,041 cohabiting couples in 25 countries. In doing so, we estimated country-specific HIV transmission rates and sexual network characteristics reflective of pre-couple and extra-couple sexual contact patterns. We found that variation in the transmission rate could parsimoniously explain between-country variation in both couple serostatus patterns and prevalence. In contrast, between-country variation in pre-couple or extra-couple sexual contact rates could not explain the observed patterns. Sensitivity analyses suggest that future work should examine the robustness of this result to between-country variation in how heterogeneous infection risk is within a country, or to assortativity, i.e. the extent to which individuals at higher risk are likely to partner with each other.
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Affiliation(s)
- Steven E Bellan
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, Georgia, United States of America.
- Center for Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America.
| | - David Champredon
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Jonathan Dushoff
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Lauren Ancel Meyers
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
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Shen M, Xiao Y, Rong L, Meyers LA, Bellan SE. The cost-effectiveness of oral HIV pre-exposure prophylaxis and early antiretroviral therapy in the presence of drug resistance among men who have sex with men in San Francisco. BMC Med 2018; 16:58. [PMID: 29688862 PMCID: PMC5914040 DOI: 10.1186/s12916-018-1047-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 03/28/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Poor adherence to either antiretroviral treatment (ART) or pre-exposure prophylaxis (PrEP) can promote drug resistance, though this risk is thought to be considerably higher for ART. In the population of men who have sex with men (MSM) in San Francisco, PrEP coverage reached 9.6% in 2014 and has continued to rise. Given the risk of drug resistance and high cost of second-line drugs, the costs and benefits of initiating ART earlier while expanding PrEP coverage remain unclear. METHODS We develop an infection-age-structured mathematical model and fit this model to the annual incidence of AIDS cases and deaths directly, and to resistance and demographic data indirectly. We investigate the impact of six various intervention scenarios (low, medium, or high PrEP coverage, with or without earlier ART) over the next 20 years. RESULTS Low (medium, high) PrEP coverage with earlier ART could prevent 22% (42%, 57%) of a projected 44,508 total new infections and 8% (26%, 41%) of a projected 18,426 new drug-resistant infections, and result in a gain of 43,649 (74,048, 103,270) QALYs over 20 years compared to the status quo, at a cost of $4745 ($78,811, $115,320) per QALY gained, respectively. CONCLUSIONS High PrEP coverage with earlier ART is expected to provide the greatest benefit but also entail the highest costs among the strategies considered. This strategy is cost-effective for the San Francisco MSM population, even considering the acquisition and transmission of ART-mediated drug resistance. However, without a substantial increase to San Francisco's annual HIV budget, the most advisable strategy may be initiating ART earlier, while maintaining current strategies of PrEP enrollment.
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Affiliation(s)
- Mingwang Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, People's Republic of China.,School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China.,Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Yanni Xiao
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China.
| | - Libin Rong
- Department of Mathematics, University of Florida, Gainesville, FL, 32611, USA
| | - Lauren Ancel Meyers
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA.,The Santa Fe Institute, Santa Fe, NM, 87501, USA
| | - Steven E Bellan
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, GA, 30602, USA.,Center for Ecology of Infectious Diseases, University of Georgia, Athens, GA, 30602, USA
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Halloran ME, Auranen K, Baird S, Basta NE, Bellan SE, Brookmeyer R, Cooper BS, DeGruttola V, Hughes JP, Lessler J, Lofgren ET, Longini IM, Onnela JP, Özler B, Seage GR, Smith TA, Vespignani A, Vynnycky E, Lipsitch M. Simulations for designing and interpreting intervention trials in infectious diseases. BMC Med 2017; 15:223. [PMID: 29287587 PMCID: PMC5747936 DOI: 10.1186/s12916-017-0985-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/05/2017] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Interventions in infectious diseases can have both direct effects on individuals who receive the intervention as well as indirect effects in the population. In addition, intervention combinations can have complex interactions at the population level, which are often difficult to adequately assess with standard study designs and analytical methods. DISCUSSION Herein, we urge the adoption of a new paradigm for the design and interpretation of intervention trials in infectious diseases, particularly with regard to emerging infectious diseases, one that more accurately reflects the dynamics of the transmission process. In an increasingly complex world, simulations can explicitly represent transmission dynamics, which are critical for proper trial design and interpretation. Certain ethical aspects of a trial can also be quantified using simulations. Further, after a trial has been conducted, simulations can be used to explore the possible explanations for the observed effects. CONCLUSION Much is to be gained through a multidisciplinary approach that builds collaborations among experts in infectious disease dynamics, epidemiology, statistical science, economics, simulation methods, and the conduct of clinical trials.
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Affiliation(s)
- M Elizabeth Halloran
- Vaccine and Infectious Disease Division, Fred Hutchinson Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA.
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA.
| | - Kari Auranen
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
| | - Sarah Baird
- Department of Global Health, Milken Institute School of Public Health, The George Washington University, Washington DC, USA
| | - Nicole E Basta
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Steven E Bellan
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, GA, USA
| | - Ron Brookmeyer
- Department of Biostatistics, The Fielding School of Public Health, UCLA, Los Angeles, CA, USA
| | - Ben S Cooper
- Mahidol Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Victor DeGruttola
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - James P Hughes
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Eric T Lofgren
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
| | - Ira M Longini
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Jukka-Pekka Onnela
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Berk Özler
- Development Research Group, The World Bank, Washington DC, USA
| | - George R Seage
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Thomas A Smith
- Department of Epidemiology and Public Health, Swiss Tropical & Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Emilia Vynnycky
- Modelling and Economics Unit, Public Health England, Colindale, UK
- TB Modelling Group, Centre for Mathematical Modelling of Infectious Diseases, TB Centre and Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Marc Lipsitch
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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Shen M, Xiao Y, Rong L, Meyers LA, Bellan SE. Early antiretroviral therapy and potent second-line drugs could decrease HIV incidence of drug resistance. Proc Biol Sci 2017; 284:20170525. [PMID: 28659449 PMCID: PMC5489726 DOI: 10.1098/rspb.2017.0525] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/26/2017] [Indexed: 11/12/2022] Open
Abstract
Early initiation of antiretroviral therapy (ART) reduces the risk of drug-sensitive HIV transmission but may increase the transmission of drug-resistant HIV. We used a mathematical model to estimate the long-term population-level benefits of ART and determine the scenarios under which earlier ART (treatment at 1 year post-infection, on average) could decrease simultaneously both total and drug-resistant HIV incidence (new infections). We constructed an infection-age-structured mathematical model that tracked the transmission rates over the course of infection and modelled the patients' life expectancy as a function of ART initiation timing. We fitted this model to the annual AIDS incidence and death data directly, and to resistance data and demographic data indirectly among men who have sex with men (MSM) in San Francisco. Using counterfactual scenarios, we assessed the impact on total and drug-resistant HIV incidence of ART initiation timing, frequency of acquired drug resistance, and second-line drug effectiveness (defined as the combination of resistance monitoring, biomedical drug efficacy and adherence). Earlier ART initiation could decrease the number of both total and drug-resistant HIV incidence when second-line drug effectiveness is sufficiently high (greater than 80%), but increase the proportion of new infections that are drug resistant. Thus, resistance may paradoxically appear to be increasing while actually decreasing.
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Affiliation(s)
- Mingwang Shen
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yanni Xiao
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Libin Rong
- Department of Mathematics and Statistics, Oakland University, Rochester, MI 48309, USA
- Department of Mathematics, University of Florida, Gainesville, FL 32611, USA
| | - Lauren Ancel Meyers
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
- The Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Steven E Bellan
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, GA 30602, USA
- Center for Ecology of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
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Castro LA, Fox SJ, Chen X, Liu K, Bellan SE, Dimitrov NB, Galvani AP, Meyers LA. Assessing real-time Zika risk in the United States. BMC Infect Dis 2017; 17:284. [PMID: 28468671 PMCID: PMC5415743 DOI: 10.1186/s12879-017-2394-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/11/2017] [Indexed: 05/29/2023] Open
Abstract
Background Confirmed local transmission of Zika Virus (ZIKV) in Texas and Florida have heightened the need for early and accurate indicators of self-sustaining transmission in high risk areas across the southern United States. Given ZIKV’s low reporting rates and the geographic variability in suitable conditions, a cluster of reported cases may reflect diverse scenarios, ranging from independent introductions to a self-sustaining local epidemic. Methods We present a quantitative framework for real-time ZIKV risk assessment that captures uncertainty in case reporting, importations, and vector-human transmission dynamics. Results We assessed county-level risk throughout Texas, as of summer 2016, and found that importation risk was concentrated in large metropolitan regions, while sustained ZIKV transmission risk is concentrated in the southeastern counties including the Houston metropolitan region and the Texas-Mexico border (where the sole autochthonous cases have occurred in 2016). We found that counties most likely to detect cases are not necessarily the most likely to experience epidemics, and used our framework to identify triggers to signal the start of an epidemic based on a policymakers propensity for risk. Conclusions This framework can inform the strategic timing and spatial allocation of public health resources to combat ZIKV throughout the US, and highlights the need to develop methods to obtain reliable estimates of key epidemiological parameters. Electronic supplementary material The online version of this article (doi:10.1186/s12879-017-2394-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lauren A Castro
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Spencer J Fox
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA.
| | - Xi Chen
- Graduate Program in Operations Research and Industrial Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Kai Liu
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Steven E Bellan
- Center for Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA.,Department of Epidemiology and Biostatistics, University of Georgia, Athens, Athens, GA, USA
| | - Nedialko B Dimitrov
- Graduate Program in Operations Research and Industrial Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Alison P Galvani
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, New Haven, CT, USA.,Department of Ecology and Evolution, Yale University, New Haven, CT, USA
| | - Lauren Ancel Meyers
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA.,The Santa Fe Institute, Santa Fe, NM, USA
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Means AR, Risher KA, Ujeneza EL, Maposa I, Nondi J, Bellan SE. Correction: Impact of Age and Sex on CD4+ Cell Count Trajectories following Treatment Initiation: An Analysis of the Tanzanian HIV Treatment Database. PLoS One 2017; 12:e0170155. [PMID: 28060915 PMCID: PMC5218484 DOI: 10.1371/journal.pone.0170155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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13
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Sempa JB, Dushoff J, Daniels MJ, Castelnuovo B, Kiragga AN, Nieuwoudt M, Bellan SE. Reevaluating Cumulative HIV-1 Viral Load as a Prognostic Predictor: Predicting Opportunistic Infection Incidence and Mortality in a Ugandan Cohort. Am J Epidemiol 2016; 184:67-77. [PMID: 27188943 DOI: 10.1093/aje/kwv303] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 10/29/2015] [Indexed: 11/12/2022] Open
Abstract
Recent studies have evaluated cumulative human immunodeficiency virus type 1 (HIV-1) viral load (cVL) for predicting disease outcomes, with discrepant results. We reviewed the disparate methodological approaches taken and evaluated the prognostic utility of cVL in a resource-limited setting. Using data on the Infectious Diseases Institute (Makerere University, Kampala, Uganda) cohort, who initiated antiretroviral therapy in 2004-2005 and were followed up for 9 years, we calculated patients' time-updated cVL by summing the area under their viral load curves on either a linear scale (cVL1) or a logarithmic scale (cVL2). Using Cox proportional hazards models, we evaluated both metrics as predictors of incident opportunistic infections and mortality. Among 489 patients analyzed, neither cVL measure was a statistically significant predictor of opportunistic infection risk. In contrast, cVL2 (but not cVL1) was a statistically significant predictor of mortality, with each log10 increase corresponding to a 1.63-fold (95% confidence interval: 1.02, 2.60) elevation in mortality risk when cVL2 was accumulated from baseline. However, whether cVL is predictive or not hinges on difficult choices surrounding the cVL metric and statistical model employed. Previous studies may have suffered from confounding bias due to their focus on cVL1, which strongly correlates with other variables. Further methodological development is needed to illuminate whether the inconsistent predictive utility of cVL arises from causal relationships or from statistical artifacts.
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Bellan SE, Pulliam JRC, Pearson CAB, Champredon D, Fox SJ, Skrip L, Galvani AP, Gambhir M, Lopman BA, Porco TC, Meyers LA, Dushoff J. Statistical power and validity of Ebola vaccine trials in Sierra Leone: a simulation study of trial design and analysis. Lancet Infect Dis 2015; 15:703-10. [PMID: 25886798 DOI: 10.1016/s1473-3099(15)70139-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Safe and effective vaccines could help to end the ongoing Ebola virus disease epidemic in parts of west Africa, and mitigate future outbreaks of the virus. We assess the statistical validity and power of randomised controlled trial (RCT) and stepped-wedge cluster trial (SWCT) designs in Sierra Leone, where the incidence of Ebola virus disease is spatiotemporally heterogeneous, and is decreasing rapidly. METHODS We projected district-level Ebola virus disease incidence for the next 6 months, using a stochastic model fitted to data from Sierra Leone. We then simulated RCT and SWCT designs in trial populations comprising geographically distinct clusters at high risk, taking into account realistic logistical constraints, and both individual-level and cluster-level variations in risk. We assessed false-positive rates and power for parametric and non-parametric analyses of simulated trial data, across a range of vaccine efficacies and trial start dates. FINDINGS For an SWCT, regional variation in Ebola virus disease incidence trends produced increased false-positive rates (up to 0·15 at α=0·05) under standard statistical models, but not when analysed by a permutation test, whereas analyses of RCTs remained statistically valid under all models. With the assumption of a 6-month trial starting on Feb 18, 2015, we estimate the power to detect a 90% effective vaccine to be between 49% and 89% for an RCT, and between 6% and 26% for an SWCT, depending on the Ebola virus disease incidence within the trial population. We estimate that a 1-month delay in trial initiation will reduce the power of the RCT by 20% and that of the SWCT by 49%. INTERPRETATION Spatiotemporal variation in infection risk undermines the statistical power of the SWCT. This variation also undercuts the SWCT's expected ethical advantages over the RCT, because an RCT, but not an SWCT, can prioritise vaccination of high-risk clusters. FUNDING US National Institutes of Health, US National Science Foundation, and Canadian Institutes of Health Research.
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Affiliation(s)
- Steven E Bellan
- Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, USA.
| | - Juliet R C Pulliam
- Department of Biology, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Carl A B Pearson
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - David Champredon
- School of Computational Science and Engineering, McMaster University, Hamilton, ON, Canada
| | - Spencer J Fox
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Laura Skrip
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Alison P Galvani
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, Yale University, New Haven, CT, USA; Department of Ecology and Evolution, Yale University, New Haven, CT, USA
| | - Manoj Gambhir
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Australia; Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA; IHRC Inc, Atlanta, GA, USA
| | - Ben A Lopman
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA; Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Travis C Porco
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA; Department of Ophthalmology, University of California, San Francisco, CA, USA; Department of Epidemiology & Biostatistics, University of California, San Francisco, CA, USA
| | - Lauren Ancel Meyers
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA; The Santa Fe Institute, Santa Fe, NM, USA
| | - Jonathan Dushoff
- Department of Biology, McMaster University, Hamilton, ON, Canada
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Cizauskas CA, Bellan SE, Turner WC, Vance RE, Getz WM. Frequent and seasonally variable sublethal anthrax infections are accompanied by short-lived immunity in an endemic system. J Anim Ecol 2014; 83:1078-90. [PMID: 24499424 DOI: 10.1111/1365-2656.12207] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 01/25/2014] [Indexed: 01/07/2023]
Abstract
Few studies have examined host-pathogen interactions in wildlife from an immunological perspective, particularly in the context of seasonal and longitudinal dynamics. In addition, though most ecological immunology studies employ serological antibody assays, endpoint titre determination is usually based on subjective criteria and needs to be made more objective. Despite the fact that anthrax is an ancient and emerging zoonotic infectious disease found world-wide, its natural ecology is not well understood. In particular, little is known about the adaptive immune responses of wild herbivore hosts against Bacillus anthracis. Working in the natural anthrax system of Etosha National Park, Namibia, we collected 154 serum samples from plains zebra (Equus quagga), 21 from springbok (Antidorcas marsupialis) and 45 from African elephants (Loxodonta africana) over 2-3 years, resampling individuals when possible for seasonal and longitudinal comparisons. We used enzyme-linked immunosorbent assays to measure anti-anthrax antibody titres and developed three increasingly conservative models to determine endpoint titres with more rigourous, objective mensuration. Between 52 and 87% of zebra, 0-15% of springbok and 3-52% of elephants had measurable anti-anthrax antibody titres, depending on the model used. While the ability of elephants and springbok to mount anti-anthrax adaptive immune responses is still equivocal, our results indicate that zebra in ENP often survive sublethal anthrax infections, encounter most B. anthracis in the wet season and can partially booster their immunity to B. anthracis. Thus, rather than being solely a lethal disease, anthrax often occurs as a sublethal infection in some susceptible hosts. Though we found that adaptive immunity to anthrax wanes rapidly, subsequent and frequent sublethal B. anthracis infections cause maturation of anti-anthrax immunity. By triggering host immune responses, these common sublethal infections may act as immunomodulators and affect population dynamics through indirect immunological and co-infection effects. In addition, with our three endpoint titre models, we introduce more mensuration rigour into serological antibody assays, even under the often-restrictive conditions that come with adapting laboratory immunology methods to wild systems. With these methods, we identified significantly more zebras responding immunologically to anthrax than have previous studies using less comprehensive titre analyses.
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Affiliation(s)
- Carrie A Cizauskas
- Department of Environmental Science, Policy & Management, University of California, Berkeley, Berkeley, CA, USA.,Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Steven E Bellan
- Department of Environmental Science, Policy & Management, University of California, Berkeley, Berkeley, CA, USA.,Center for Computational Biology and Informatics, University of Texas at Austin, Austin, TX, USA
| | - Wendy C Turner
- Department of Environmental Science, Policy & Management, University of California, Berkeley, Berkeley, CA, USA.,Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Russell E Vance
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Wayne M Getz
- Department of Environmental Science, Policy & Management, University of California, Berkeley, Berkeley, CA, USA.,School of Mathematical Sciences, University of KwaZulu-Natal, Durban, South Africa
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