1
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Hawley DM, Pérez-Umphrey AM, Adelman JS, Fleming-Davies AE, Garrett-Larsen J, Geary SJ, Childs LM, Langwig KE. Prior exposure to pathogens augments host heterogeneity in susceptibility and has key epidemiological consequences. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.05.583455. [PMID: 38496428 PMCID: PMC10942282 DOI: 10.1101/2024.03.05.583455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Pathogen epidemics are key threats to human and wildlife health. Across systems, host protection from pathogens following initial exposure is often incomplete, resulting in recurrent epidemics through partially-immune hosts. Variation in population-level protection has important consequences for epidemic dynamics, but whether acquired protection influences host heterogeneity in susceptibility and its epidemiological consequences remains unexplored. We experimentally investigated whether prior exposure (none, low-dose, or high-dose) to a bacterial pathogen alters host heterogeneity in susceptibility among songbirds. Hosts with no prior pathogen exposure had little variation in protection, but heterogeneity in susceptibility was significantly augmented by prior pathogen exposure, with the highest variability detected in hosts given high-dose prior exposure. An epidemiological model parameterized with experimental data found that heterogeneity in susceptibility from prior exposure more than halved epidemic sizes compared with a homogeneous population with identical mean protection. However, because infection-induced mortality was also greatly reduced in hosts with prior pathogen exposure, reductions in epidemic size were smaller than expected in hosts with prior exposure. These results highlight the importance of variable protection from prior exposure and/or vaccination in driving host heterogeneity and epidemiological dynamics. Author Summary Individuals in a population can be highly variable in terms of whether or not they get sick during a pathogen outbreak. This individual variability in susceptibility has important consequences for how widely a disease can spread in a population. Therefore, it is key to understand what drives such variability in susceptibility among individuals. One possibility is that variable levels of standing immunity in a population, whether from vaccination or previous infection, lead to variability in susceptibility among individuals. We tested whether acquired immunity creates more variability in susceptibility among individuals in a host population, using a songbird disease system as a model. We found that birds that had acquired immunity to a bacterial pathogen were far more variable in their susceptibility. We also show that this population-level variability in itself can strongly suppress disease outbreaks.
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2
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Tovar M, Sanz J, Moreno Y. Model-based impact evaluation of new tuberculosis vaccines in aging populations under different modeling scenarios: the case of China. Front Public Health 2024; 12:1302688. [PMID: 38463158 PMCID: PMC10920235 DOI: 10.3389/fpubh.2024.1302688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 02/05/2024] [Indexed: 03/12/2024] Open
Abstract
Introduction The slow descent in TB burden, the COVID-19 pandemic, along with the rise of multidrug-resistant strains of Mycobacterium tuberculosis, seriously threaten TB control and the goals of the End TB strategy. To fight back, several vaccine candidates are under development, with some of them undergoing the phases 2B and 3 of the development pipeline. The impact of these vaccines on the general population needs to be addressed using disease-transmission models, and, in a country like China, which last year ranked third in number of cases worldwide, and where the population is aging at a fast pace, the impact of TB vaccination campaigns may depend heavily upon the age of targeted populations, the mechanistic descriptions of the TB vaccines and the coupling between TB dynamics and demographic evolution. Methods In this work, we studied the potential impact of a new TB vaccine in China targeting adolescents (15-19 y.o.) or older adults (60-64 y.o.), according to varying vaccine descriptions that represent reasonable mechanisms of action leading to prevention of disease, or prevention of recurrence, each of them targetting specific routes to TB disease. To measure the influence of the description of the coupling between transmission dynamics and aging in TB transmission models, we explored two different approaches to compute the evolution of the contact matrices, which relate to the spreading among different age strata. Results Our findings highlight the dependence of model-based impact estimates on vaccine profiles and the chosen modeling approach for describing the evolution of contact matrices. Our results also show, in line with previous modeling works, that older adult vaccination is a suitable option in China to reduce the incidence of TB as long as the vaccine is able to protect already exposed individuals. Discussion This study underscores the importance of considering vaccine characteristics and demographic dynamics in shaping TB control strategies. In this sense, older adult vaccination emerges as a promising avenue for mitigating TB transmission in China but also remarks the need for tailored intervention strategies aligned with demographic trends.
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Affiliation(s)
- Mario Tovar
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain
- Department of Theoretical Physics, University of Zaragoza, Zaragoza, Spain
| | - Joaquín Sanz
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain
- Department of Theoretical Physics, University of Zaragoza, Zaragoza, Spain
| | - Yamir Moreno
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain
- Department of Theoretical Physics, University of Zaragoza, Zaragoza, Spain
- CENTAI Institute, Turin, Italy
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3
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Miura F, Klinkenberg D, Wallinga J. Quantifying the Individual Variation in Susceptibility to Endemic Coronavirus and SARS-CoV-2 with Human Challenge Trials. Epidemiology 2024; 35:113-117. [PMID: 38032803 PMCID: PMC10683973 DOI: 10.1097/ede.0000000000001679] [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: 05/22/2023] [Accepted: 09/22/2023] [Indexed: 12/02/2023]
Abstract
Human challenge trials reveal how the infection risk depends on a given infectious dose. We propose a mathematical framework to analyze and interpret the outcomes of human challenge trials by incorporating the variability between individuals in susceptibility to infection. We illustrate the framework for two distinctive diseases; endemic diseases where a fraction of the study population has been exposed to the target pathogen previously and is thus immune, and novel diseases where the study population is fully susceptible. Based on available data from published trials, we estimate the immune proportion and the variation in susceptibility to endemic HCoV-229E and present plausible infection risks with SARS-CoV-2 over multiple orders of magnitude of the infectious dose. The results show that the proposed method captures heterogeneous background susceptibility in the study population, and we suggest ways to improve the design of future trials and to translate their outcomes to the general population.
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Affiliation(s)
- Fuminari Miura
- From the Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Japan
| | - Don Klinkenberg
- From the Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Jacco Wallinga
- From the Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
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4
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Anderson TL, Nande A, Merenstein C, Raynor B, Oommen A, Kelly BJ, Levy MZ, Hill AL. Quantifying individual-level heterogeneity in infectiousness and susceptibility through household studies. Epidemics 2023; 44:100710. [PMID: 37556994 PMCID: PMC10594662 DOI: 10.1016/j.epidem.2023.100710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/17/2023] [Accepted: 07/18/2023] [Indexed: 08/11/2023] Open
Abstract
The spread of SARS-CoV-2, like that of many other pathogens, is governed by heterogeneity. "Superspreading," or "over-dispersion," is an important factor in transmission, yet it is hard to quantify. Estimates from contact tracing data are prone to potential biases due to the increased likelihood of detecting large clusters of cases, and may reflect variation in contact behavior more than biological heterogeneity. In contrast, the average number of secondary infections per contact is routinely estimated from household surveys, and these studies can minimize biases by testing all members of a household. However, the models used to analyze household transmission data typically assume that infectiousness and susceptibility are the same for all individuals or vary only with predetermined traits such as age. Here we develop and apply a combined forward simulation and inference method to quantify the degree of inter-individual variation in both infectiousness and susceptibility from observations of the distribution of infections in household surveys. First, analyzing simulated data, we show our method can reliably ascertain the presence, type, and amount of these heterogeneities given data from a sufficiently large sample of households. We then analyze a collection of household studies of COVID-19 from diverse settings around the world, and find strong evidence for large heterogeneity in both the infectiousness and susceptibility of individuals. Our results also provide a framework to improve the design of studies to evaluate household interventions in the presence of realistic heterogeneity between individuals.
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Affiliation(s)
- Thayer L Anderson
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, United States of America
| | - Anjalika Nande
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, United States of America
| | - Carter Merenstein
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America
| | - Brinkley Raynor
- Department of Biostatistics, Epidemiology, & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America
| | - Anisha Oommen
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, United States of America; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, United States of America
| | - Brendan J Kelly
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America; Department of Biostatistics, Epidemiology, & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America; Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America
| | - Michael Z Levy
- Department of Biostatistics, Epidemiology, & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America
| | - Alison L Hill
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, United States of America; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, United States of America.
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5
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Tovar M, Moreno Y, Sanz J. Addressing mechanism bias in model-based impact forecasts of new tuberculosis vaccines. Nat Commun 2023; 14:5312. [PMID: 37658078 PMCID: PMC10474143 DOI: 10.1038/s41467-023-40976-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 08/15/2023] [Indexed: 09/03/2023] Open
Abstract
In tuberculosis (TB) vaccine development, multiple factors hinder the design and interpretation of the clinical trials used to estimate vaccine efficacy. The complex transmission chain of TB includes multiple routes to disease, making it hard to link the vaccine efficacy observed in a trial to specific protective mechanisms. Here, we present a Bayesian framework to evaluate the compatibility of different vaccine descriptions with clinical trial outcomes, unlocking impact forecasting from vaccines whose specific mechanisms of action are unknown. Applying our method to the analysis of the M72/AS01E vaccine trial -conducted on IGRA+ individuals- as a case study, we found that most plausible models for this vaccine needed to include protection against, at least, two over the three possible routes to active TB classically considered in the literature: namely, primary TB, latent TB reactivation and TB upon re-infection. Gathering new data regarding the impact of TB vaccines in various epidemiological settings would be instrumental to improve our model estimates of the underlying mechanisms.
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Affiliation(s)
- M Tovar
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, 50009, Spain
- Department of Theoretical Physics, University of Zaragoza, Zaragoza, 50009, Spain
| | - Y Moreno
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, 50009, Spain
- Department of Theoretical Physics, University of Zaragoza, Zaragoza, 50009, Spain
- Centai Institute S.p.A, 10138, Torino, Italy
| | - J Sanz
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, 50009, Spain.
- Department of Theoretical Physics, University of Zaragoza, Zaragoza, 50009, Spain.
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6
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Anderson TL, Nande A, Merenstein C, Raynor B, Oommen A, Kelly BJ, Levy MZ, Hill AL. Quantifying individual-level heterogeneity in infectiousness and susceptibility through household studies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.12.02.22281853. [PMID: 36523404 PMCID: PMC9753792 DOI: 10.1101/2022.12.02.22281853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The spread of SARS-CoV-2, like that of many other pathogens, is governed by heterogeneity. "Superspreading," or "over-dispersion," is an important factor in transmission, yet it is hard to quantify. Estimates from contact tracing data are prone to potential biases due to the increased likelihood of detecting large clusters of cases, and may reflect variation in contact behavior more than biological heterogeneity. In contrast, the average number of secondary infections per contact is routinely estimated from household surveys, and these studies can minimize biases by testing all members of a household. However, the models used to analyze household transmission data typically assume that infectiousness and susceptibility are the same for all individuals or vary only with predetermined traits such as age. Here we develop and apply a combined forward simulation and inference method to quantify the degree of inter-individual variation in both infectiousness and susceptibility from observations of the distribution of infections in household surveys. First, analyzing simulated data, we show our method can reliably ascertain the presence, type, and amount of these heterogeneities with data from a sufficiently large sample of households. We then analyze a collection of household studies of COVID-19 from diverse settings around the world, and find strong evidence for large heterogeneity in both the infectiousness and susceptibility of individuals. Our results also provide a framework to improve the design of studies to evaluate household interventions in the presence of realistic heterogeneity between individuals.
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Affiliation(s)
- Thayer L Anderson
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218
| | - Anjalika Nande
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218
| | - Carter Merenstein
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Brinkley Raynor
- Department of Biostatistics, Epidemiology, & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Anisha Oommen
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Brendan J Kelly
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Michael Z Levy
- Department of Biostatistics, Epidemiology, & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Alison L Hill
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218
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7
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Domenech de Cellès M, Wong A, Andrea Barrero Guevara L, Rohani P. Immunological heterogeneity informs estimation of the durability of vaccine protection. J R Soc Interface 2022; 19:20220070. [PMID: 35611620 PMCID: PMC9131131 DOI: 10.1098/rsif.2022.0070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/26/2022] [Indexed: 11/30/2022] Open
Abstract
Deciphering the properties of vaccines against an emerging pathogen is essential for optimizing immunization strategies. Early after vaccine roll-out, however, uncertainties about vaccine immunity raise the question of how much time is needed to estimate these properties, particularly the durability of vaccine protection. Here we designed a simulation study, based on a generic transmission model of vaccination, to simulate the impact of a breadth of vaccines with different mean (range: 10 months-2 years) and variability (coefficient of variation range: 50-100%) of the duration of protection. Focusing on the dynamics of SARS-CoV-2 in the year after start of mass immunization in Germany as a case study, we then assessed how confidently the duration of protection could be estimated under a range of epidemiological scenarios. We found that lower mean and higher heterogeneity facilitated estimation of the duration of vaccine protection. Across the vaccines tested, rapid waning and high heterogeneity permitted complete identification of the duration of protection; by contrast, slow waning and low heterogeneity allowed only estimation of the fraction of vaccinees with rapid loss of immunity. These findings suggest that limited epidemiological data can inform the duration of vaccine immunity. More generally, they highlight the need to carefully consider immunological heterogeneity when designing transmission models to evaluate vaccines.
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Affiliation(s)
| | - Anabelle Wong
- Infectious Disease Epidemiology group, Max Planck Institute for Infection Biology, 10117 Berlin, Germany
- Institute of Public Health, Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Laura Andrea Barrero Guevara
- Infectious Disease Epidemiology group, Max Planck Institute for Infection Biology, 10117 Berlin, Germany
- Institute of Public Health, Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Pejman Rohani
- Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
- Center for Influenza Disease & Emergence Research (CIDER), University of Georgia, Athens, GA 30602, USA
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8
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Gilbertson MLJ, Onorato D, Cunningham M, VandeWoude S, Craft ME. Paradoxes and synergies: Optimizing management of a deadly virus in an endangered carnivore. J Appl Ecol 2022; 59:1548-1558. [DOI: 10.1111/1365-2664.14165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Dave Onorato
- Fish and Wildlife Research Institute Florida Fish and Wildlife Conservation Commission Naples FL USA
| | - Mark Cunningham
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission Gainesville FL USA
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology Colorado State University Fort Collins CO USA
| | - Meggan E. Craft
- Department of Veterinary Population Medicine University of Minnesota St Paul MN USA
- Department of Ecology, Evolution and Behavior University of Minnesota St Paul MN USA
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9
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Gomes MGM, Ferreira MU, Corder RM, King JG, Souto-Maior C, Penha-Gonçalves C, Gonçalves G, Chikina M, Pegden W, Aguas R. Individual variation in susceptibility or exposure to SARS-CoV-2 lowers the herd immunity threshold. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2020.04.27.20081893. [PMID: 32511451 PMCID: PMC7239079 DOI: 10.1101/2020.04.27.20081893] [Citation(s) in RCA: 128] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Individual variation in susceptibility and exposure is subject to selection by natural infection, accelerating the acquisition of immunity, and reducing herd immunity thresholds and epidemic final sizes. This is a manifestation of a wider population phenomenon known as "frailty variation". Despite theoretical understanding, public health policies continue to be guided by mathematical models that leave out considerable variation and as a result inflate projected disease burdens and overestimate the impact of interventions. Here we focus on trajectories of the coronavirus disease (COVID-19) pandemic in England and Scotland until November 2021. We fit models to series of daily deaths and infer relevant epidemiological parameters, including coefficients of variation and effects of non-pharmaceutical interventions which we find in agreement with independent empirical estimates based on contact surveys. Our estimates are robust to whether the analysed data series encompass one or two pandemic waves and enable projections compatible with subsequent dynamics. We conclude that vaccination programmes may have contributed modestly to the acquisition of herd immunity in populations with high levels of pre-existing naturally acquired immunity, while being critical to protect vulnerable individuals from severe outcomes as the virus becomes endemic.
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Affiliation(s)
- M Gabriela M Gomes
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK
- Centro de Matemática e Aplicações, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Marcelo U Ferreira
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, Nova University of Lisbon, Lisbon, Portugal
| | - Rodrigo M Corder
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Jessica G King
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Caetano Souto-Maior
- Laboratory of Systems Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Guilherme Gonçalves
- Unidade Multidisciplinar de Investigação Biomédica, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Maria Chikina
- Department of Computational and Systems Biology, University of Pittsburgh, Pittburgh, PA, USA
| | - Wesley Pegden
- Department of Mathematical Sciences, Carnegie Mellon University, , Pittburgh" , PA, USA
| | - Ricardo Aguas
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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10
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Lipsitch M, Krammer F, Regev-Yochay G, Lustig Y, Balicer RD. SARS-CoV-2 breakthrough infections in vaccinated individuals: measurement, causes and impact. Nat Rev Immunol 2022; 22:57-65. [PMID: 34876702 PMCID: PMC8649989 DOI: 10.1038/s41577-021-00662-4] [Citation(s) in RCA: 182] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2021] [Indexed: 02/04/2023]
Abstract
Breakthrough infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in fully vaccinated individuals are receiving intense scrutiny because of their importance in determining how long restrictions to control virus transmission will need to remain in place in highly vaccinated populations as well as in determining the need for additional vaccine doses or changes to the vaccine formulations and/or dosing intervals. Measurement of breakthrough infections is challenging outside of randomized, placebo-controlled, double-blind field trials. However, laboratory and observational studies are necessary to understand the impact of waning immunity, viral variants and other determinants of changing vaccine effectiveness against various levels of coronavirus disease 2019 (COVID-19) severity. Here, we describe the approaches being used to measure vaccine effectiveness and provide a synthesis of the burgeoning literature on the determinants of vaccine effectiveness and breakthrough rates. We argue that, rather than trying to tease apart the contributions of factors such as age, viral variants and time since vaccination, the rates of breakthrough infection are best seen as a consequence of the level of immunity at any moment in an individual, the variant to which that individual is exposed and the severity of disease being considered. We also address key open questions concerning the transition to endemicity, the potential need for altered vaccine formulations to track viral variants, the need to identify immune correlates of protection, and the public health challenges of using various tools to counter breakthrough infections, including boosters in an era of global vaccine shortages.
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Affiliation(s)
- Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology and Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gili Regev-Yochay
- Infection Prevention & Control Unit, Sheba Medical Center, Ramat-Gan, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yaniv Lustig
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer, Israel
| | - Ran D Balicer
- Clalit Research Institute, Innovation Division, Clalit Health Services, Tel Aviv, Israel
- The School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
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11
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Wargo AR, Kurath G, Scott RJ, Kerr B. Virus shedding kinetics and unconventional virulence tradeoffs. PLoS Pathog 2021; 17:e1009528. [PMID: 33970967 PMCID: PMC8109835 DOI: 10.1371/journal.ppat.1009528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/03/2021] [Indexed: 11/19/2022] Open
Abstract
Tradeoff theory, which postulates that virulence provides both transmission costs and benefits for pathogens, has become widely adopted by the scientific community. Although theoretical literature exploring virulence-tradeoffs is vast, empirical studies validating various assumptions still remain sparse. In particular, truncation of transmission duration as a cost of virulence has been difficult to quantify with robust controlled in vivo studies. We sought to fill this knowledge gap by investigating how transmission rate and duration were associated with virulence for infectious hematopoietic necrosis virus (IHNV) in rainbow trout (Oncorhynchus mykiss). Using host mortality to quantify virulence and viral shedding to quantify transmission, we found that IHNV did not conform to classical tradeoff theory. More virulent genotypes of the virus were found to have longer transmission durations due to lower recovery rates of infected hosts, but the relationship was not saturating as assumed by tradeoff theory. Furthermore, the impact of host mortality on limiting transmission duration was minimal and greatly outweighed by recovery. Transmission rate differences between high and low virulence genotypes were also small and inconsistent. Ultimately, more virulent genotypes were found to have the overall fitness advantage, and there was no apparent constraint on the evolution of increased virulence for IHNV. However, using a mathematical model parameterized with experimental data, it was found that host culling resurrected the virulence tradeoff and provided low virulence genotypes with the advantage. Human-induced or natural culling, as well as host population fragmentation, may be some of the mechanisms by which virulence diversity is maintained in nature. This work highlights the importance of considering non-classical virulence tradeoffs.
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Affiliation(s)
- Andrew R. Wargo
- Virginia Institute of Marine Science, William & Mary, Gloucester Point, Virginia, United States of America
| | - Gael Kurath
- U.S. Geological Survey, Western Fisheries Research Center, Seattle, Washington, United States of America
| | - Robert J. Scott
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Benjamin Kerr
- Department of Biology, University of Washington, Seattle, Washington, United States of America
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12
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Souto-Maior C, King JG, Sartori LM, Maciel-de-Freitas R, Gomes MGM. Reply to: "Enhancement of Aedes aegypti susceptibility to dengue by Wolbachia is not supported". Nat Commun 2020; 11:6113. [PMID: 33257667 PMCID: PMC7705658 DOI: 10.1038/s41467-020-19831-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 10/29/2020] [Indexed: 11/09/2022] Open
Affiliation(s)
- Caetano Souto-Maior
- Laboratory of Systems Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jessica G King
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Larissa M Sartori
- Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, Brazil
| | - Rafael Maciel-de-Freitas
- Laboratório de Transmissores de Hematozoários, IOC, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - M Gabriela M Gomes
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK.
- Centro de Matemática da Universidade do Porto, Porto, Portugal.
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13
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Jones DR, Rutan BJ, Wargo AR. Impact of Vaccination and Pathogen Exposure Dosage on Shedding Kinetics of Infectious Hematopoietic Necrosis Virus (IHNV) in Rainbow Trout. JOURNAL OF AQUATIC ANIMAL HEALTH 2020; 32:95-108. [PMID: 32443164 PMCID: PMC7540492 DOI: 10.1002/aah.10108] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 04/03/2020] [Accepted: 04/27/2020] [Indexed: 06/11/2023]
Abstract
Vaccine efficacy in preventing clinical disease has been well characterized. However, vaccine impacts on transmission under diverse field conditions, such as variable pathogen exposure dosages, are not fully understood. We evaluated the impacts of vaccination on disease-induced host mortality and shedding of infectious hematopoietic necrosis virus (IHNV) in Rainbow Trout Oncorhynchus mykiss. Fish, in up to three different genetic lines, were exposed to different dosages of IHNV to simulate field variability. Mortality and viral shedding of each individual fish were quantified over the course of infection. As the exposure dosage increased, mortality, number of fish shedding virus, daily virus quantity shed, and total amount of virus shed also increased. Vaccination significantly reduced mortality but had a much smaller impact on shedding, such that vaccinated fish still shed significant amounts of virus, particularly at higher viral exposure dosages. These studies demonstrate that the consideration of pathogen exposure dosage and transmission are critical for robust inference of vaccine efficacy.
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Affiliation(s)
- Darbi R. Jones
- Virginia Institute of Marine ScienceWilliam & MaryPost Office Box 1346, 1370 Greate RoadGloucester PointVirginia23062USA
| | - Barbara J. Rutan
- Virginia Institute of Marine ScienceWilliam & MaryPost Office Box 1346, 1370 Greate RoadGloucester PointVirginia23062USA
| | - Andrew R. Wargo
- Virginia Institute of Marine ScienceWilliam & MaryPost Office Box 1346, 1370 Greate RoadGloucester PointVirginia23062USA
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14
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Bailey RI, Cheng HH, Chase-Topping M, Mays JK, Anacleto O, Dunn JR, Doeschl-Wilson A. Pathogen transmission from vaccinated hosts can cause dose-dependent reduction in virulence. PLoS Biol 2020; 18:e3000619. [PMID: 32134914 PMCID: PMC7058279 DOI: 10.1371/journal.pbio.3000619] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/30/2020] [Indexed: 02/07/2023] Open
Abstract
Many livestock and human vaccines are leaky because they block symptoms but do not prevent infection or onward transmission. This leakiness is concerning because it increases vaccination coverage required to prevent disease spread and can promote evolution of increased pathogen virulence. Despite leakiness, vaccination may reduce pathogen load, affecting disease transmission dynamics. However, the impacts on post-transmission disease development and infectiousness in contact individuals are unknown. Here, we use transmission experiments involving Marek disease virus (MDV) in chickens to show that vaccination with a leaky vaccine substantially reduces viral load in both vaccinated individuals and unvaccinated contact individuals they infect. Consequently, contact birds are less likely to develop disease symptoms or die, show less severe symptoms, and shed less infectious virus themselves, when infected by vaccinated birds. These results highlight that even partial vaccination with a leaky vaccine can have unforeseen positive consequences in controlling the spread and symptoms of disease.
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Affiliation(s)
- Richard I. Bailey
- Division of Genetics and Genomics, The Roslin Institute, Easter Bush, Midlothian, United Kingdom
| | - Hans H. Cheng
- USDA, Agricultural Research Service, US National Poultry Research Center, Avian Disease and Oncology Laboratory, East Lansing, Michigan, United States of America
| | - Margo Chase-Topping
- Division of Genetics and Genomics, The Roslin Institute, Easter Bush, Midlothian, United Kingdom
- Usher Institute of Population Health Sciences & Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Jody K. Mays
- USDA, Agricultural Research Service, US National Poultry Research Center, Avian Disease and Oncology Laboratory, East Lansing, Michigan, United States of America
| | - Osvaldo Anacleto
- Division of Genetics and Genomics, The Roslin Institute, Easter Bush, Midlothian, United Kingdom
| | - John R. Dunn
- USDA, Agricultural Research Service, US National Poultry Research Center, Avian Disease and Oncology Laboratory, East Lansing, Michigan, United States of America
| | - Andrea Doeschl-Wilson
- Division of Genetics and Genomics, The Roslin Institute, Easter Bush, Midlothian, United Kingdom
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15
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Meehan MT, Cope RC, McBryde ES. On the probability of strain invasion in endemic settings: Accounting for individual heterogeneity and control in multi-strain dynamics. J Theor Biol 2019; 487:110109. [PMID: 31816294 PMCID: PMC7094110 DOI: 10.1016/j.jtbi.2019.110109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 11/28/2019] [Accepted: 12/05/2019] [Indexed: 01/21/2023]
Abstract
Endemic infection can insulate host populations from invasion by mutant variants. The timing of control implementation strongly influences its efficacy. Controls that exacerbate host heterogeneity outperform those that curtail it. Differential control can facilitate strain invasion and eventual replacement.
Pathogen evolution is an imminent threat to global health that has warranted, and duly received, considerable attention within the medical, microbiological and modelling communities. Outbreaks of new pathogens are often ignited by the emergence and transmission of mutant variants descended from wild-type strains circulating in the community. In this work we investigate the stochastic dynamics of the emergence of a novel disease strain, introduced into a population in which it must compete with an existing endemic strain. In analogy with past work on single-strain epidemic outbreaks, we apply a branching process approximation to calculate the probability that the new strain becomes established. As expected, a critical determinant of the survival prospects of any invading strain is the magnitude of its reproduction number relative to that of the background endemic strain. Whilst in most circumstances this ratio must exceed unity in order for invasion to be viable, we show that differential control scenarios can lead to less-fit novel strains invading populations hosting a fitter endemic one. This analysis and the accompanying findings will inform our understanding of the mechanisms that have led to past instances of successful strain invasion, and provide valuable lessons for thwarting future drug-resistant strain incursions.
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Affiliation(s)
- Michael T Meehan
- James Cook University, Australian Institute of Tropical Health and Medicine, Townsville, Australia.
| | - Robert C Cope
- The University of Adelaide, School of Mathematical Sciences, Adelaide, Australia
| | - Emma S McBryde
- James Cook University, Australian Institute of Tropical Health and Medicine, Townsville, Australia
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16
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Miller IF, Metcalf CJ. Vaccine-driven virulence evolution: consequences of unbalanced reductions in mortality and transmission and implications for pertussis vaccines. J R Soc Interface 2019; 16:20190642. [PMID: 31822219 PMCID: PMC6936036 DOI: 10.1098/rsif.2019.0642] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/19/2019] [Indexed: 11/12/2022] Open
Abstract
Many vaccines have heterogeneous effects across individuals. Additionally, some vaccines do not prevent infection, but reduce disease-associated mortality and transmission. Both of these factors will alter selection pressures on pathogens and thus shape the evolution of pathogen virulence. We use a mathematical modelling framework to show that (i) the balance of how vaccines reduce transmission versus mortality and (ii) individual variability in protection conferred both shape the evolution of pathogen virulence. Epidemiological (burden of disease) and evolutionary (pathogen virulence) outcomes are both worse when vaccines confer smaller reductions in transmission than in mortality. Furthermore, outcomes are modulated by variability in vaccine effects, with increased variability limiting the extent of virulence evolution but in some cases preventing eradication. These findings are pertinent to current concerns about the global resurgence of pertussis and the efficacy of pertussis vaccines, as the two classes of these vaccines may reduce disease symptoms without preventing infection and differ in their ability to reduce transmission. Furthermore, these findings point to the importance of generating precise predictions for virulence evolution in Bordetella pertussis (and other similar pathogens) by incorporating empirical characterizations of vaccine effects into models capturing the epidemiological details of this system.
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Affiliation(s)
- Ian F. Miller
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - C. Jessica Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Woodrow Wilson School of Public Affairs, Princeton University, Princeton, NJ, USA
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17
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Lewnard JA, Lopman BA, Parashar UD, Bennett A, Bar-Zeev N, Cunliffe NA, Samuel P, Guerrero ML, Ruiz-Palacios G, Kang G, Pitzer VE. Heterogeneous susceptibility to rotavirus infection and gastroenteritis in two birth cohort studies: Parameter estimation and epidemiological implications. PLoS Comput Biol 2019; 15:e1007014. [PMID: 31348775 PMCID: PMC6690553 DOI: 10.1371/journal.pcbi.1007014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 08/12/2019] [Accepted: 04/09/2019] [Indexed: 11/19/2022] Open
Abstract
Cohort studies, randomized trials, and post-licensure studies have reported reduced natural and vaccine-derived protection against rotavirus gastroenteritis (RVGE) in low- and middle-income countries. While susceptibility of children to rotavirus is known to vary within and between settings, implications for estimation of immune protection are not well understood. We sought to re-estimate naturally-acquired protection against rotavirus infection and RVGE, and to understand how differences in susceptibility among children impacted estimates. We re-analyzed data from studies conducted in Mexico City, Mexico and Vellore, India. Cumulatively, 573 rotavirus-unvaccinated children experienced 1418 rotavirus infections and 371 episodes of RVGE over 17,636 child-months. We developed a model that characterized susceptibility to rotavirus infection and RVGE among children, accounting for aspects of the natural history of rotavirus and differences in transmission rates between settings. We tested whether model-generated susceptibility measurements were associated with demographic and anthropometric factors, and with the severity of RVGE symptoms. We identified greater variation in susceptibility to rotavirus infection and RVGE in Vellore than in Mexico City. In both cohorts, susceptibility to rotavirus infection and RVGE were associated with male sex, lower birth weight, lower maternal education, and having fewer siblings; within Vellore, susceptibility was also associated with lower socioeconomic status. Children who were more susceptible to rotavirus also experienced higher rates of rotavirus-negative diarrhea, and higher risk of moderate-to-severe symptoms when experiencing RVGE. Simulations suggested that discrepant estimates of naturally-acquired immunity against RVGE can be attributed, in part, to between-setting differences in susceptibility of children, but result primarily from the interaction of transmission rates with age-dependent risk for infections to cause RVGE. We found that more children in Vellore than in Mexico City belong to a high-risk group for rotavirus infection and RVGE, and demonstrate that unmeasured individual- and age-dependent susceptibility may influence estimates of naturally-acquired immune protection against RVGE. Differences in susceptibility can help explain why some individuals, and not others, acquire infection and exhibit symptoms when exposed to infectious disease agents. However, it is difficult to distinguish between differences in susceptibility versus exposure in epidemiological studies. We developed a modeling approach to distinguish transmission intensity and susceptibility in data from cohort studies of rotavirus infection among children in Mexico City, Mexico, and Vellore, India, and evaluated how these factors may have contributed to differences in estimates of naturally-acquired immune protection between the studies. Given the same exposure, more children were at high risk of acquiring rotavirus infection, and of experiencing gastroenteritis when infected, in Vellore than in Mexico City. The probability of belonging to this high-risk stratum was associated with well-known individual factors such as lower socioeconomic status, lower birth weight, and incidence of diarrhea due to other causes. We also found the risk for rotavirus infections to cause symptoms declined with age, independent of acquired immunity. These findings can, in part, account for estimates of lower protective efficacy of acquired immunity against rotavirus gastroenteritis in high-incidence settings, mirroring estimates of reduced effectiveness of live oral rotavirus vaccines in low- and middle-income countries.
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Affiliation(s)
- Joseph A. Lewnard
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, California, United States of America
- * E-mail:
| | - Benjamin A. Lopman
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Umesh D. Parashar
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Aisleen Bennett
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
- Center for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool, University of Liverpool, Liverpool, United Kingdom
| | - Naor Bar-Zeev
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
- Center for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool, University of Liverpool, Liverpool, United Kingdom
- International Vaccine Access Center, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Nigel A. Cunliffe
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
- Center for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool, University of Liverpool, Liverpool, United Kingdom
| | - Prasanna Samuel
- Department of Gastrointestinal Sciences, Christian Medical College, Vellore, Tamil Nadu, India
| | - M. Lourdes Guerrero
- Instituto Nacional de Ciences Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | | | - Gagandeep Kang
- Department of Gastrointestinal Sciences, Christian Medical College, Vellore, Tamil Nadu, India
| | - Virginia E. Pitzer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
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18
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Langwig KE, Gomes MGM, Clark MD, Kwitny M, Yamada S, Wargo AR, Lipsitch M. Limited available evidence supports theoretical predictions of reduced vaccine efficacy at higher exposure dose. Sci Rep 2019; 9:3203. [PMID: 30824732 PMCID: PMC6397254 DOI: 10.1038/s41598-019-39698-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 01/30/2019] [Indexed: 12/18/2022] Open
Abstract
Understanding the causes of vaccine failure is important for predicting disease dynamics in vaccinated populations and planning disease interventions. Pathogen exposure dose and heterogeneity in host susceptibility have both been implicated as important factors that may reduce overall vaccine efficacy and cause vaccine failure. Here, we explore the effect of pathogen dose and heterogeneity in host susceptibility in reducing efficacy of vaccines. Using simulation-based methods, we find that increases in pathogen exposure dose decrease vaccine efficacy, but this effect is modified by heterogeneity in host susceptibility. In populations where the mode of vaccine action is highly polarized, vaccine efficacy decreases more slowly with exposure dose than in populations with less variable protection. We compared these theoretical results to empirical estimates from a systematic literature review of vaccines tested over multiple exposure doses. We found that few studies (nine of 5,389) tested vaccine protection against infection over multiple pathogen challenge doses, with seven studies demonstrating a decrease in vaccine efficacy with increasing exposure dose. Our research demonstrates that pathogen dose has potential to be an important determinant of vaccine failure, although the limited empirical data highlight a need for additional studies to test theoretical predictions on the plausibility of reduced host susceptibility and high pathogen dose as mechanisms responsible for reduced vaccine efficacy in high transmission settings.
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Affiliation(s)
- Kate E Langwig
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA. .,Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
| | - M Gabriela M Gomes
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Mercedes D Clark
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Molly Kwitny
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Steffany Yamada
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Andrew R Wargo
- Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, VA, 23062, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
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19
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Abstract
In a Policy Forum, Marc Lipsitch and colleagues discuss trial design issues in infectious disease outbreaks.
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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, United States of America
| | - Annette Rid
- Department of Global Health & Social Medicine, King’s College London, London, United Kingdom
| | - Peter G. Smith
- MRC Tropical Epidemiology Group, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Nir Eyal
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
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20
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Variation in Wolbachia effects on Aedes mosquitoes as a determinant of invasiveness and vectorial capacity. Nat Commun 2018; 9:1483. [PMID: 29662096 PMCID: PMC5902584 DOI: 10.1038/s41467-018-03981-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 03/27/2018] [Indexed: 12/26/2022] Open
Abstract
Wolbachia has been introduced into Aedes aegypti mosquitoes to control the spread of arboviruses, such as dengue, chikungunya and Zika. Studies showed that certain Wolbachia strains (such as wMel) reduce replication of dengue viruses in the laboratory, prompting the release of mosquitoes carrying the bacterium into the field, where vectorial capacity can be realistically assessed in relation to native non-carriers. Here we apply a new analysis to two published datasets, and show that wMel increases the mean and the variance in Ae. aegypti susceptibility to dengue infection when introgressed into Brazil and Vietnam genetic backgrounds. In the absence of other processes, higher mean susceptibility should lead to enhanced viral transmission. The increase in variance, however, widens the basis for selection imposed by unexplored natural forces, retaining the potential for reducing transmission overall. Wolbachia infection in mosquitoes reduces dengue virus spread under specific lab conditions, prompting its use in disease control. Here, King et al. show that Wolbachia increases mean and variance in mosquito susceptibility and explain how this affects Wolbachia invasion and dengue transmission.
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21
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Souto-Maior C, Sylvestre G, Braga Stehling Dias F, Gomes MGM, Maciel-de-Freitas R. Model-based inference from multiple dose, time course data reveals Wolbachia effects on infection profiles of type 1 dengue virus in Aedes aegypti. PLoS Negl Trop Dis 2018; 12:e0006339. [PMID: 29558464 PMCID: PMC5877886 DOI: 10.1371/journal.pntd.0006339] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/30/2018] [Accepted: 02/23/2018] [Indexed: 11/29/2022] Open
Abstract
Infection is a complex and dynamic process involving a population of invading microbes, the host and its responses, aimed at controlling the situation. Depending on the purpose and level of organization, infection at the organism level can be described by a process as simple as a coin toss, or as complex as a multi-factorial dynamic model; the former, for instance, may be adequate as a component of a population model, while the latter is necessary for a thorough description of the process beginning with a challenge with an infectious inoculum up to establishment or elimination of the pathogen. Experimental readouts in the laboratory are often static, snapshots of the process, assayed under some convenient experimental condition, and therefore cannot comprehensively describe the system. Different from the discrete treatment of infection in population models, or the descriptive summarized accounts of typical lab experiments, in this manuscript, infection is treated as a dynamic process dependent on the initial conditions of the infectious challenge, viral growth, and the host response along time. Here, experimental data is generated for multiple doses of type 1 dengue virus, and pathogen levels are recorded at different points in time for two populations of mosquitoes: either carrying endosymbiont bacteria Wolbachia or not. A dynamic microbe/host-response mathematical model is used to describe pathogen growth in the face of a host response like the immune system, and to infer model parameters for the two populations of insects, revealing a slight—but potentially important—protection conferred by the symbiont. Infection is usually assayed as a static observation of a pathogen within a host; it is, nevertheless, a dynamic process that cannot be described from a single time point and arbitrary conditions. Results based on the usual methods are a snapshot of a convenient laboratory condition; a more comprehensive data set is required to describe the entire process of infection from inoculation of the host with a microorganism to establishment of a systemic infection, or elimination of the threat by the host. We design an experiment that takes into account increasing pathogen challenges to a mosquito host and viral levels along time; we use a dynamic mathematical model to analyze the resulting data set. The entire framework is used to compare susceptibility to dengue virus of Aedes aegypti mosquitoes either carrying the Wolbachia symbiont or not. Instead of a simple pairwise comparison, we are able to compare infection profiles and parameters associated to host immune processes in this insect-symbiont-virus system.
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Affiliation(s)
| | - Gabriel Sylvestre
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | | | - M. Gabriela M. Gomes
- CIBIO-InBIo, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Porto, Portugal
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Rafael Maciel-de-Freitas
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM)/CNPq, Rio de Janeiro, Brazil
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22
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Lipsitch M, Li LM, Patterson S, Trammel J, Juergens C, Gruber WC, Scott DA, Dagan R. Serotype-specific immune responses to pneumococcal conjugate vaccine among children are significantly correlated by individual: Analysis of randomized controlled trial data. Vaccine 2017; 36:473-478. [PMID: 29248266 DOI: 10.1016/j.vaccine.2017.12.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 10/25/2017] [Accepted: 12/06/2017] [Indexed: 10/18/2022]
Abstract
BACKGROUND The magnitude of an individual's serotype-specific immunoglobulin G (IgG) response to a pneumococcal conjugate vaccine (PCV) has been associated with the vaccine's protective efficacy against carriage of pneumococci of that serotype, though the relationship with other serotypes needs to be understood. METHODS Using immunogenicity data collected during a trial comparing the 7-valent (PCV7) and 13-valent (PCV13) vaccines, we measured associations between serotype-specific IgG levels, and used multiple regressions to identify demographic predictors of response. RESULTS Vaccine-induced IgG levels were moderately positively correlated with one another, with pairwise correlation coefficients of 0.40-0.70. Principal component analysis of vaccine-serotype responses yielded one principal component indicating general immune responsiveness, and a second principal component mainly describing responses to serotype 14, which was the least correlated with the other responses. Overall, demographic variables explained only 17.0 and 20.4% of the geometric mean PCV7 and PCV13 responses, respectively. In both groups, older age at the first vaccine dose and shorter time from vaccination to antibody measurement were independently associated with stronger geometric mean responses. DISCUSSION Improved understanding of the nature and causes of variation in immune response may aid in optimizing vaccination schedules and identifying robust correlates of protection.
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Affiliation(s)
- Marc Lipsitch
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
| | - Lucy M Li
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Scott Patterson
- Sanofi Pasteur, 1 Discovery Drive, Swiftwater, PA 18370, USA
| | - James Trammel
- inVentiv Health Clinical, 504 Carnegie Center, Princeton, NJ 08540, USA
| | - Christine Juergens
- Pfizer Vaccine Clinical Research and Development, Pfizer Pharma GmbH, Linkstrasse 10, 10785 Berlin, Germany
| | - William C Gruber
- Pfizer Vaccine Clinical Research and Development, Pfizer Inc., 401 N Middletown Road, Pearl River, NY 10965, USA
| | - Daniel A Scott
- Pfizer Vaccine Clinical Research and Development, Pfizer Inc., 401 N Middletown Road, Pearl River, NY 10965, USA
| | - Ron Dagan
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 85025, Israel
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23
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Leon AE, Hawley DM. Host Responses to Pathogen Priming in a Natural Songbird Host. ECOHEALTH 2017; 14:793-804. [PMID: 28766063 PMCID: PMC5726927 DOI: 10.1007/s10393-017-1261-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 06/14/2017] [Accepted: 06/14/2017] [Indexed: 06/07/2023]
Abstract
Hosts in free-living populations can experience substantial variation in the frequency and dose of pathogen exposure, which can alter disease progression and protection from future exposures. In the house finch-Mycoplasma gallisepticum (MG) system, the pathogen is primarily transmitted via bird feeders, and some birds may be exposed to frequent low doses of MG while foraging. Here we experimentally determined how low dose, repeated exposures of house finches to MG influence host responses and protection from secondary high-dose challenge. MG-naive house finches were given priming exposures that varied in dose and total number. After quantifying host responses to priming exposures, all birds were given a secondary high-dose challenge to assess immunological protection. Dose, but not the number of exposures, significantly predicted both infection and disease severity following priming exposure. Furthermore, individuals given higher priming doses showed stronger protection upon secondary, high-dose challenge. However, even single low-dose exposures to MG, a proxy for what some birds likely experience in the wild while feeding, provided significant protection against a high-dose challenge. Our results suggest that bird feeders, which serve as sources of infection in the wild, may in some cases act as "immunizers," with important consequences for disease dynamics.
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Affiliation(s)
- Ariel E Leon
- Department of Biological Sciences, Virginia Tech, 2119 Derring Hall (0406), Blacksburg, VA, 24061, USA.
| | - Dana M Hawley
- Department of Biological Sciences, Virginia Tech, 2119 Derring Hall (0406), Blacksburg, VA, 24061, USA
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24
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Abstract
Heterogeneity in host susceptibility is a key determinant of infectious disease dynamics but is rarely accounted for in assessment of disease control measures. Understanding how susceptibility is distributed in populations, and how control measures change this distribution, is integral to predicting the course of epidemics with and without interventions. Using multiple experimental and modeling approaches, we show that rainbow trout have relatively homogeneous susceptibility to infection with infectious hematopoietic necrosis virus and that vaccination increases heterogeneity in susceptibility in a nearly all-or-nothing fashion. In a simple transmission model with an R0 of 2, the highly heterogeneous vaccine protection would cause a 35 percentage-point reduction in outbreak size over an intervention inducing homogenous protection at the same mean level. More broadly, these findings provide validation of methodology that can help to reduce biases in predictions of vaccine impact in natural settings and provide insight into how vaccination shapes population susceptibility. Differences among individuals influence transmission and spread of infectious diseases as well as the effectiveness of control measures. Control measures, such as vaccines, may provide leaky protection, protecting all hosts to an identical degree, or all-or-nothing protection, protecting some hosts completely while leaving others completely unprotected. This distinction can have a dramatic influence on disease dynamics, yet this distribution of protection is frequently unaccounted for in epidemiological models and estimates of vaccine efficacy. Here, we apply new methodology to experimentally examine host heterogeneity in susceptibility and mode of vaccine action as distinct components influencing disease outcome. Through multiple experiments and new modeling approaches, we show that the distribution of vaccine effects can be robustly estimated. These results offer new experimental and inferential methodology that can improve predictions of vaccine effectiveness and have broad applicability to human, wildlife, and ecosystem health.
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25
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Bompard A, Da DF, Yerbanga RS, Biswas S, Kapulu M, Bousema T, Lefèvre T, Cohuet A, Churcher TS. Evaluation of two lead malaria transmission blocking vaccine candidate antibodies in natural parasite-vector combinations. Sci Rep 2017; 7:6766. [PMID: 28754921 PMCID: PMC5533793 DOI: 10.1038/s41598-017-06130-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/08/2017] [Indexed: 12/25/2022] Open
Abstract
Transmission blocking vaccines (TBV) which aim to control malaria by inhibiting human-to-mosquito transmission show considerable promise though their utility against naturally circulating parasites remains unknown. The efficacy of two lead candidates targeting Pfs25 and Pfs230 antigens to prevent onwards transmission of naturally occurring parasites to a local mosquito strain is assessed using direct membrane feeding assays and murine antibodies in Burkina Faso. The transmission blocking activity of both candidates depends on the level of parasite exposure (as assessed by the mean number of oocysts in control mosquitoes) and antibody titers. A mathematical framework is devised to allow the efficacy of different candidates to be directly compared and determine the minimal antibody titers required to halt transmission in different settings. The increased efficacy with diminishing parasite exposure indicates that the efficacy of vaccines targeting either Pfs25 or Pfs230 may increase as malaria transmission declines. This has important implications for late-stage candidate selection and assessing how they can support the drive for malaria elimination.
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Affiliation(s)
- Anais Bompard
- MRC Centre for Outbreak Analysis and Modelling, Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, W2 1PG, United Kingdom.
| | - Dari F Da
- Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso.,Unité MIVEGEC, IRD 224-CNRS 5290-Université Montpellier, Montpellier, France
| | | | - Sumi Biswas
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Melissa Kapulu
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Teun Bousema
- Department of Medical Microbiology, Nijmegen, The Netherlands
| | - Thierry Lefèvre
- Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso.,Unité MIVEGEC, IRD 224-CNRS 5290-Université Montpellier, Montpellier, France.,Laboratoire mixte international sur les vecteurs (LAMIVECT), Bobo Dioulasso, Burkina Faso
| | - Anna Cohuet
- Unité MIVEGEC, IRD 224-CNRS 5290-Université Montpellier, Montpellier, France
| | - Thomas S Churcher
- MRC Centre for Outbreak Analysis and Modelling, Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, W2 1PG, United Kingdom
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26
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Magpantay FMG. Vaccine impact in homogeneous and age-structured models. J Math Biol 2017; 75:1591-1617. [PMID: 28417166 DOI: 10.1007/s00285-017-1126-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 01/23/2017] [Indexed: 10/19/2022]
Abstract
A general model of an imperfect vaccine for a childhood disease is presented and the effects of different types of vaccine failure on transmission were investigated using models that consider both homogeneous and age-specific mixing. The models are extensions of the standard SEIR equations with an additional vaccinated component that allows for five different vaccine parameters: three types of vaccine failure in decreasing susceptibility to infection via failure in degree ("leakiness"), take ("all-or-nothingness") and duration (waning of vaccine-derived immunity); one parameter reflecting the relative reduction in infectiousness of vaccinated individuals who get infected; and one parameter that reflects the relative reduction in reporting probability of vaccinated individuals due to a possible reduction in severity of symptoms. Only the first four parameters affect disease transmission (as measured by the basic reproduction number). The reduction in transmission due to vaccination is different for age-structured models than for homogeneous models. Notably, if the vaccine exhibits waning protection this could be larger for an age-structured model with high contact rates between young children who are still protected by the vaccine and lower contact rates between adults for whom protection might have already waned. Analytic expressions for age-specific "vaccine impacts" were also derived. The overall vaccine impact is bounded between the age-specific impact for the oldest age class and that of the youngest age class.
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Affiliation(s)
- F M G Magpantay
- Department of Mathematics, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.
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27
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Brunner JL, Beaty L, Guitard A, Russell D. Heterogeneities in the infection process drive ranavirus transmission. Ecology 2017; 98:576-582. [PMID: 27859036 DOI: 10.1002/ecy.1644] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/16/2016] [Accepted: 10/24/2016] [Indexed: 12/14/2022]
Abstract
Transmission is central to our understanding and efforts to control the spread of infectious diseases. Because transmission generally requires close contact, host movements and behaviors can shape transmission dynamics: random and complete mixing leads to the classic density-dependent model, but if hosts primarily interact locally (e.g., aggregate) or within groups, transmission may saturate. Manipulating host behavior may thus change both the rate and functional form of transmission. We used the ranavirus-wood frog (Lithobates sylvaticus) tadpole system to test whether transmission rates reflect contacts, and whether the functional form of transmission can be influenced by the distribution of food in mesocosms (widely dispersed, promoting random movement and mixing vs. a central pile, promoting aggregations). Contact rates increased with density, as expected, but transmission rapidly saturated. Observed rates of transmission were not explained by observed contact rates or the density-dependent model, but instead transmission in both treatments followed models allowing for heterogeneities in the transmission process. We argue that contacts were not generally limiting, but instead that our results are better explained by heterogeneities in host susceptibility. Moreover, manipulating host behavior to manage the spread of infectious disease may prove difficult to implement.
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Affiliation(s)
- Jesse L Brunner
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164, USA.,Department of Environmental and Forest Biology, SUNY College of Environmental Science and Forestry, Syracuse, New York, 13210, USA
| | - Lynne Beaty
- Department of Environmental and Forest Biology, SUNY College of Environmental Science and Forestry, Syracuse, New York, 13210, USA.,Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, 74078, USA
| | - Alexandra Guitard
- Department of Environmental and Forest Biology, SUNY College of Environmental Science and Forestry, Syracuse, New York, 13210, USA
| | - Deanna Russell
- Department of Environmental and Forest Biology, SUNY College of Environmental Science and Forestry, Syracuse, New York, 13210, USA
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28
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Churcher TS, Sinden RE, Edwards NJ, Poulton ID, Rampling TW, Brock PM, Griffin JT, Upton LM, Zakutansky SE, Sala KA, Angrisano F, Hill AVS, Blagborough AM. Probability of Transmission of Malaria from Mosquito to Human Is Regulated by Mosquito Parasite Density in Naïve and Vaccinated Hosts. PLoS Pathog 2017; 13:e1006108. [PMID: 28081253 PMCID: PMC5230737 DOI: 10.1371/journal.ppat.1006108] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 12/02/2016] [Indexed: 11/19/2022] Open
Abstract
Over a century since Ronald Ross discovered that malaria is caused by the bite of an infectious mosquito it is still unclear how the number of parasites injected influences disease transmission. Currently it is assumed that all mosquitoes with salivary gland sporozoites are equally infectious irrespective of the number of parasites they harbour, though this has never been rigorously tested. Here we analyse >1000 experimental infections of humans and mice and demonstrate a dose-dependency for probability of infection and the length of the host pre-patent period. Mosquitoes with a higher numbers of sporozoites in their salivary glands following blood-feeding are more likely to have caused infection (and have done so quicker) than mosquitoes with fewer parasites. A similar dose response for the probability of infection was seen for humans given a pre-erythrocytic vaccine candidate targeting circumsporozoite protein (CSP), and in mice with and without transfusion of anti-CSP antibodies. These interventions prevented infection more efficiently from bites made by mosquitoes with fewer parasites. The importance of parasite number has widespread implications across malariology, ranging from our basic understanding of the parasite, how vaccines are evaluated and the way in which transmission should be measured in the field. It also provides direct evidence for why the only registered malaria vaccine RTS,S was partially effective in recent clinical trials. Malaria is transmitted to humans by the bite of an infectious mosquito though it is unclear whether a mosquito with a high number of parasites is more infectious than one with only a few. Here we show that the greater the number of parasites within the salivary gland of the mosquito following blood-feeding the more likely it is to have transmitted the disease. A clear dose-response is seen with highly infected mosquitoes being more likely to have caused infection (and to have done so quicker) than lightly infected mosquitoes. This suggesting that mosquito-based methods for measuring transmission in the field need to be refined as they currently only consider whether a mosquito is infected or not (and not how heavily infected the mosquito is). Novel transmission reducing drugs and vaccines are tested by experimentally infecting people using infectious mosquitoes. This work indicates that it is important to further standardise infectious dose in malaria experimental infections to enable the efficacy of new interventions to be accurately compared. The work also provides direct evidence to suggest that the world’s first licenced malaria vaccine may be partially effective because it fails to provide protection against highly infected mosquitoes.
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Affiliation(s)
- Thomas S. Churcher
- MRC Centre for Outbreak Analysis and Modelling, Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- * E-mail:
| | - Robert E. Sinden
- Department of Life Sciences, Imperial College London, South Kensington, London, United Kingdom
- The Jenner Institute, University of Oxford, Roosevelt Drive, Oxford, United Kingdom
| | - Nick J. Edwards
- The Jenner Institute, University of Oxford, Roosevelt Drive, Oxford, United Kingdom
| | - Ian D. Poulton
- The Jenner Institute, University of Oxford, Roosevelt Drive, Oxford, United Kingdom
| | - Thomas W. Rampling
- The Jenner Institute, University of Oxford, Roosevelt Drive, Oxford, United Kingdom
| | - Patrick M. Brock
- MRC Centre for Outbreak Analysis and Modelling, Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Jamie T. Griffin
- MRC Centre for Outbreak Analysis and Modelling, Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Leanna M. Upton
- Department of Life Sciences, Imperial College London, South Kensington, London, United Kingdom
| | - Sara E. Zakutansky
- Department of Life Sciences, Imperial College London, South Kensington, London, United Kingdom
| | - Katarzyna A. Sala
- Department of Life Sciences, Imperial College London, South Kensington, London, United Kingdom
| | - Fiona Angrisano
- Department of Life Sciences, Imperial College London, South Kensington, London, United Kingdom
| | - Adrian V. S. Hill
- The Jenner Institute, University of Oxford, Roosevelt Drive, Oxford, United Kingdom
| | - Andrew M. Blagborough
- Department of Life Sciences, Imperial College London, South Kensington, London, United Kingdom
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29
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Gomes MGM, Gordon SB, Lalloo DG. Clinical trials: The mathematics of falling vaccine efficacy with rising disease incidence. Vaccine 2016; 34:3007-3009. [PMID: 27177948 PMCID: PMC5087849 DOI: 10.1016/j.vaccine.2016.04.065] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 04/15/2016] [Accepted: 04/20/2016] [Indexed: 11/23/2022]
Affiliation(s)
- M Gabriela M Gomes
- Liverpool School of Tropical Medicine, United Kingdom; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Portugal; Instituto de Matemática e Estatística, Universidade de São Paulo, Brazil.
| | - Stephen B Gordon
- Liverpool School of Tropical Medicine, United Kingdom; Malawi Liverpool Wellcome Trust Programme of Clinical Tropical Research, Blantyre, Malawi
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30
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Wilber MQ, Langwig KE, Kilpatrick AM, McCallum HI, Briggs CJ. Integral Projection Models for host-parasite systems with an application to amphibian chytrid fungus. Methods Ecol Evol 2016; 7:1182-1194. [PMID: 28239442 DOI: 10.1111/2041-210x.12561] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Host parasite models are typically constructed under either a microparasite or macroparasite paradigm. However, this has long been recognized as a false dichotomy because many infectious disease agents, including most fungal pathogens, have attributes of both microparasites and macroparasites.We illustrate how Integral Projection Models (IPM)s provide a novel, elegant modeling framework to represent both types of pathogens. We build a simple host-parasite IPM that tracks both the number of susceptible and infected hosts and the distribution of parasite burdens in infected hosts.The vital rate functions necessary to build IPMs for disease dynamics share many commonalities with classic micro and macroparasite models and we discuss how these functions can be parameterized to build a host-parasite IPM. We illustrate the utility of this IPM approach by modeling the temperature-dependent epizootic dynamics of amphibian chytrid fungus in Mountain yellow-legged frogs (Rana muscosa).The host-parasite IPM can be applied to other diseases such as facial tumor disease in Tasmanian devils and white-nose syndrome in bats. Moreover, the host-parasite IPM can be easily extended to capture more complex disease dynamics and provides an exciting new frontier in modeling wildlife disease.
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Affiliation(s)
- Mark Q Wilber
- Ecology, Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, 93117
| | - Kate E Langwig
- Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, 95064
| | - A Marm Kilpatrick
- Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, 95064
| | - Hamish I McCallum
- Griffith School of Environment, Griffith University, Nathan QLD 4111, Australia
| | - Cheryl J Briggs
- Ecology, Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, 93117
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31
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Expanding vaccine efficacy estimation with dynamic models fitted to cross-sectional prevalence data post-licensure. Epidemics 2016; 14:71-82. [DOI: 10.1016/j.epidem.2015.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 11/02/2015] [Accepted: 11/25/2015] [Indexed: 01/02/2023] Open
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32
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Gomes MGM, Gjini E, Lopes JS, Souto-Maior C, Rebelo C. A theoretical framework to identify invariant thresholds in infectious disease epidemiology. J Theor Biol 2016; 395:97-102. [PMID: 26869215 DOI: 10.1016/j.jtbi.2016.01.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 01/17/2016] [Accepted: 01/20/2016] [Indexed: 10/22/2022]
Abstract
Setting global strategies and targets for disease prevention and control often involves mathematical models. Model structure is typically subject to intense scrutiny, such as confrontation with empirical data and alternative formulations, while a less frequently challenged aspect is the widely adopted reduction of parameters to their average values. Focusing on endemic diseases, we use a general transmission model to explain how mean field approximations decrease the estimated R0 from prevalence data, while threshold phenomena - such as the epidemic and reinfection thresholds - remain invariant. This results in an underestimation of the effort required to control disease, which may be particularly severe when the approximation inappropriately places transmission estimates below important thresholds. These concepts are widely applicable across endemic pathogen systems.
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Affiliation(s)
- M Gabriela M Gomes
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Portugal; Instituto de Matemática e Estatística, Universidade de São Paulo, Brazil; Liverpool School of Tropical Medicine, United Kingdom.
| | - Erida Gjini
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Joao S Lopes
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Carlota Rebelo
- Departamento de Matemática e Centro de Matemática, Aplicações Fundamentais e Investigação Operacional, Universidade de Lisboa, Portugal
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33
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McKenney DG, Kurath G, Wargo AR. Characterization of infectious dose and lethal dose of two strains of infectious hematopoietic necrosis virus (IHNV). Virus Res 2016; 214:80-9. [PMID: 26752429 DOI: 10.1016/j.virusres.2015.12.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 12/22/2015] [Accepted: 12/22/2015] [Indexed: 11/24/2022]
Abstract
The ability to infect a host is a key trait of a virus, and differences in infectivity could put one virus at an evolutionary advantage over another. In this study we have quantified the infectivity of two strains of infectious hematopoietic necrosis virus (IHNV) that are known to differ in fitness and virulence. By exposing juvenile rainbow trout (Oncorhynchus mykiss) hosts to a wide range of virus doses, we were able to calculate the infectious dose in terms of ID50 values for the two genotypes. Lethal dose experiments were also conducted to confirm the virulence difference between the two virus genotypes, using a range of virus doses and holding fish either in isolation or in batch so as to calculate LD50 values. We found that infectivity is positively correlated with virulence, with the more virulent genotype having higher infectivity. Additionally, infectivity increases more steeply over a short range of doses compared to virulence, which has a shallower increase. We also examined the data using models of virion interaction and found no evidence to suggest that virions have either an antagonistic or a synergistic effect on each other, supporting the independent action hypothesis in the process of IHNV infection of rainbow trout.
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Affiliation(s)
- Douglas G McKenney
- US Geological Survey, Western Fisheries Research Center, 6505 NE 65th St., Seattle, WA 98115, United States.
| | - Gael Kurath
- US Geological Survey, Western Fisheries Research Center, 6505 NE 65th St., Seattle, WA 98115, United States.
| | - Andrew R Wargo
- Virginia Institute of Marine Science, 1375 Greate Rd., Gloucester Point, VA 23062, United States.
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34
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Meeyai A, Praditsitthikorn N, Kotirum S, Kulpeng W, Putthasri W, Cooper BS, Teerawattananon Y. Seasonal influenza vaccination for children in Thailand: a cost-effectiveness analysis. PLoS Med 2015; 12:e1001829; discussion e1001829. [PMID: 26011712 PMCID: PMC4444096 DOI: 10.1371/journal.pmed.1001829] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 04/13/2015] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Seasonal influenza is a major cause of mortality worldwide. Routine immunization of children has the potential to reduce this mortality through both direct and indirect protection, but has not been adopted by any low- or middle-income countries. We developed a framework to evaluate the cost-effectiveness of influenza vaccination policies in developing countries and used it to consider annual vaccination of school- and preschool-aged children with either trivalent inactivated influenza vaccine (TIV) or trivalent live-attenuated influenza vaccine (LAIV) in Thailand. We also compared these approaches with a policy of expanding TIV coverage in the elderly. METHODS AND FINDINGS We developed an age-structured model to evaluate the cost-effectiveness of eight vaccination policies parameterized using country-level data from Thailand. For policies using LAIV, we considered five different age groups of children to vaccinate. We adopted a Bayesian evidence-synthesis framework, expressing uncertainty in parameters through probability distributions derived by fitting the model to prospectively collected laboratory-confirmed influenza data from 2005-2009, by meta-analysis of clinical trial data, and by using prior probability distributions derived from literature review and elicitation of expert opinion. We performed sensitivity analyses using alternative assumptions about prior immunity, contact patterns between age groups, the proportion of infections that are symptomatic, cost per unit vaccine, and vaccine effectiveness. Vaccination of children with LAIV was found to be highly cost-effective, with incremental cost-effectiveness ratios between about 2,000 and 5,000 international dollars per disability-adjusted life year averted, and was consistently preferred to TIV-based policies. These findings were robust to extensive sensitivity analyses. The optimal age group to vaccinate with LAIV, however, was sensitive both to the willingness to pay for health benefits and to assumptions about contact patterns between age groups. CONCLUSIONS Vaccinating school-aged children with LAIV is likely to be cost-effective in Thailand in the short term, though the long-term consequences of such a policy cannot be reliably predicted given current knowledge of influenza epidemiology and immunology. Our work provides a coherent framework that can be used for similar analyses in other low- and middle-income countries.
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Affiliation(s)
- Aronrag Meeyai
- Health Intervention and Technology Assessment Program, Nonthaburi, Thailand
- Department of Epidemiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Naiyana Praditsitthikorn
- Health Intervention and Technology Assessment Program, Nonthaburi, Thailand
- Bureau of AIDS, TB, and STI, Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Surachai Kotirum
- Health Intervention and Technology Assessment Program, Nonthaburi, Thailand
| | - Wantanee Kulpeng
- Health Intervention and Technology Assessment Program, Nonthaburi, Thailand
| | - Weerasak Putthasri
- International Health Policy Program, Ministry of Public Health, Nonthaburi, Thailand
| | - Ben S. Cooper
- Mahidol Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- * E-mail:
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35
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On the correlation between variance in individual susceptibilities and infection prevalence in populations. J Math Biol 2015; 71:1643-61. [PMID: 25796496 DOI: 10.1007/s00285-015-0870-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 02/28/2015] [Indexed: 10/23/2022]
Abstract
The hypothesis that infection prevalence in a population correlates negatively with variance in the susceptibility of its individuals has support from experimental, field, and theoretical studies. However, its generality has never been formally demonstrated. Here we formulate an endemic SIS model with individual susceptibility distributed according to a discrete or continuous probability function to assess the generality of such hypothesis. We introduce an ordering among susceptibility distributions with the same mean, analogous to that considered in Katriel (J Math Biol 65:237-262, 2012) to order the attack rates in an epidemic SIR model with heterogeneity. It turns out that if one distribution dominates another in this order then it has greater variance and corresponds to a lower infection prevalence for R0 varying in a suitable maximal interval of the form ]1, R0*]. We show that in both the discrete and continuous frameworks R0* can be finite, so that the expected correlation among variance and prevalence does not always hold. For discrete distributions this fact is demonstrated analytically, and the proof introduces a constructive procedure to find ordered pairs for which R0* is arbitrarily close to 1. For continuous distributions our conclusion is based on numerical studies with the beta distribution. Finally, we present explicit partial orderings among discrete susceptibility distributions and among symmetric beta distributions which guarantee that R0* = +∞.
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36
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Unveiling time in dose-response models to infer host susceptibility to pathogens. PLoS Comput Biol 2014; 10:e1003773. [PMID: 25121762 PMCID: PMC4133050 DOI: 10.1371/journal.pcbi.1003773] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 06/27/2014] [Indexed: 01/03/2023] Open
Abstract
The biological effects of interventions to control infectious diseases typically depend on the intensity of pathogen challenge. As much as the levels of natural pathogen circulation vary over time and geographical location, the development of invariant efficacy measures is of major importance, even if only indirectly inferrable. Here a method is introduced to assess host susceptibility to pathogens, and applied to a detailed dataset generated by challenging groups of insect hosts (Drosophila melanogaster) with a range of pathogen (Drosophila C Virus) doses and recording survival over time. The experiment was replicated for flies carrying the Wolbachia symbiont, which is known to reduce host susceptibility to viral infections. The entire dataset is fitted by a novel quantitative framework that significantly extends classical methods for microbial risk assessment and provides accurate distributions of symbiont-induced protection. More generally, our data-driven modeling procedure provides novel insights for study design and analyses to assess interventions. While control options for plant, animal, and human pathogens are emerging rapidly, reliable assessment of the effect of interventions in biological systems presents many challenges. A major question is how to connect laboratory experiments and measurements with the relevant process in natural settings, where hosts are subject to pathogen exposures that vary in time and geographical location. With this aim, measures of protection that are invariant under varying exposure intensity need to be developed and integrated with mathematical models. In this article, we introduce a method to assess host susceptibility to pathogens, and apply it to survival of Drosophila melanogaster challenged with different doses of Drosophila C virus. By replicating the procedure in groups of flies that carry the symbiont Wolbachia, we are able to estimate how the viral protection induced by this intracellular bacterium is distributed in the host population. Our results disentangle host infection status from observed mortality, accounting naturally for time since exposure. The multiple-dose design proposed challenges traditional study designs to assess interventions.
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37
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Hickson R, Roberts M. How population heterogeneity in susceptibility and infectivity influences epidemic dynamics. J Theor Biol 2014; 350:70-80. [DOI: 10.1016/j.jtbi.2014.01.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 11/22/2013] [Accepted: 01/08/2014] [Indexed: 12/22/2022]
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