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1.
J Theor Biol ; 539: 111059, 2022 04 21.
Artigo em Inglês | MEDLINE | ID: mdl-35181285

RESUMO

Trade is a complex, multi-faceted process that can contribute to the spread and persistence of disease. We here develop novel mechanistic models of supply. Our model is framed within a livestock trading system, where farms form and end trade partnerships with rates dependent on current demand, with these trade partnerships facilitating trade between partners. With these time-varying, stock dependent partnership and trade dynamics, our trading model goes beyond current state of the art modelling approaches. By studying instantaneous shocks to farm-level supply and demand we show that behavioural responses of farms lead to trading systems that are highly resistant to shocks with only temporary disturbances to trade observed. Individual adaptation in response to permanent alterations to trading propensities, such that animal flows are maintained, illustrates the ability for farms to find new avenues of trade, minimising disruptions imposed by such alterations to trade that common modelling approaches cannot adequately capture. In the context of endemic disease control, we show that these adaptations hinder the potential beneficial reductions in prevalence such changes to trading propensities have previously been shown to confer. Assessing the impact of a common disease control measure, post-movement batch testing, highlights the ability for our model to measure the stress on multiple components of trade imposed by such control measures and also highlights the temporary and, in some cases, the permanent disturbances to trade that post-movement testing has on the trading system.


Assuntos
Gado , Animais
2.
PLoS Comput Biol ; 17(12): e1009652, 2021 12.
Artigo em Inglês | MEDLINE | ID: mdl-34851954

RESUMO

Variants of the susceptible-infected-removed (SIR) model of Kermack & McKendrick (1927) enjoy wide application in epidemiology, offering simple yet powerful inferential and predictive tools in the study of diverse infectious diseases across human, animal and plant populations. Direct transmission models (DTM) are a subset of these that treat the processes of disease transmission as comprising a series of discrete instantaneous events. Infections transmitted indirectly by persistent environmental pathogens, however, are examples where a DTM description might fail and are perhaps better described by models that comprise explicit environmental transmission routes, so-called environmental transmission models (ETM). In this paper we discuss the stochastic susceptible-exposed-infected-removed (SEIR) DTM and susceptible-exposed-infected-removed-pathogen (SEIR-P) ETM and we show that the former is the timescale separation limit of the latter, with ETM host-disease dynamics increasingly resembling those of a DTM when the pathogen's characteristic timescale is shortened, relative to that of the host population. Using graphical posterior predictive checks (GPPC), we investigate the validity of the SEIR model when fitted to simulated SEIR-P host infection and removal times. Such analyses demonstrate how, in many cases, the SEIR model is robust to departure from direct transmission. Finally, we present a case study of white spot disease (WSD) in penaeid shrimp with rates of environmental transmission and pathogen decay (SEIR-P model parameters) estimated using published results of experiments. Using SEIR and SEIR-P simulations of a hypothetical WSD outbreak management scenario, we demonstrate how relative shortening of the pathogen timescale comes about in practice. With atttempts to remove diseased shrimp from the population every 24h, we see SEIR and SEIR-P model outputs closely conincide. However, when removals are 6-hourly, the two models' mean outputs diverge, with distinct predictions of outbreak size and duration.


Assuntos
Doenças Transmissíveis/transmissão , Surtos de Doenças , Doenças Endêmicas , Epidemias , Animais , Teorema de Bayes , Doenças Transmissíveis/fisiopatologia , Biologia Computacional/métodos , Simulação por Computador , Meio Ambiente , Modelos Epidemiológicos , Humanos , Modelos Biológicos , Modelos Teóricos , Método de Monte Carlo , Probabilidade , Processos Estocásticos
3.
Ecol Appl ; 32(8): e2696, 2022 12.
Artigo em Inglês | MEDLINE | ID: mdl-35735258

RESUMO

Control of crop pests by shifting host plant availability and natural enemy activity at landscape scales has great potential to enhance the sustainability of agriculture. However, mainstreaming natural pest control requires improved understanding of how its benefits can be realized across a variety of agroecological contexts. Empirical studies suggest significant but highly variable responses of natural pest control to land-use change. Current ecological models are either too specific to provide insight across agroecosystems or too generic to guide management with actionable predictions. We suggest obtaining the full benefit of available empirical, theoretical, and methodological knowledge by combining trait-mediated understanding from correlative studies with the explicit representation of causal relationships achieved by mechanistic modeling. To link these frameworks, we adapt the concept of archetypes, or context-specific generalizations, from sustainability science. Similar responses of natural pest control to land-use gradients across cases that share key attributes, such as functional traits of focal organisms, indicate general processes that drive system behavior in a context-sensitive manner. Based on such observations of natural pest control, a systematic definition of archetypes can provide the basis for mechanistic models of intermediate generality that cover all major agroecosystems worldwide. Example applications demonstrate the potential for upscaling understanding and improving predictions of natural pest control, based on knowledge transfer and scientific synthesis. A broader application of this mechanistic archetype approach promises to enhance ecology's contribution to natural resource management across diverse regions and social-ecological contexts.


Assuntos
Ecossistema , Controle Biológico de Vetores , Controle de Pragas , Agricultura , Produtos Agrícolas , Recursos Naturais
4.
Genet Sel Evol ; 54(1): 59, 2022 Sep 05.
Artigo em Inglês | MEDLINE | ID: mdl-36064318

RESUMO

BACKGROUND: The spread of infectious diseases in populations is controlled by the susceptibility (propensity to acquire infection), infectivity (propensity to transmit infection), and recoverability (propensity to recover/die) of individuals. Estimating genetic risk factors for these three underlying host epidemiological traits can help reduce disease spread through genetic control strategies. Previous studies have identified important 'disease resistance single nucleotide polymorphisms (SNPs)', but how these affect the underlying traits is an unresolved question. Recent advances in computational statistics make it now possible to estimate the effects of SNPs on host traits from epidemic data (e.g. infection and/or recovery times of individuals or diagnostic test results). However, little is known about how to effectively design disease transmission experiments or field studies to maximise the precision with which these effects can be estimated. RESULTS: In this paper, we develop and validate analytical expressions for the precision of the estimates of SNP effects on the three above host traits for a disease transmission experiment with one or more non-interacting contact groups. Maximising these expressions leads to three distinct 'experimental' designs, each specifying a different set of ideal SNP genotype compositions across groups: (a) appropriate for a single contact-group, (b) a multi-group design termed "pure", and (c) a multi-group design termed "mixed", where 'pure' and 'mixed' refer to groupings that consist of individuals with uniformly the same or different SNP genotypes, respectively. Precision estimates for susceptibility and recoverability were found to be less sensitive to the experimental design than estimates for infectivity. Whereas the analytical expressions suggest that the multi-group pure and mixed designs estimate SNP effects with similar precision, the mixed design is preferred because it uses information from naturally-occurring rather than artificial infections. The same design principles apply to estimates of the epidemiological impact of other categorical fixed effects, such as breed, line, family, sex, or vaccination status. Estimation of SNP effect precisions from a given experimental setup is implemented in an online software tool SIRE-PC. CONCLUSIONS: Methodology was developed to aid the design of disease transmission experiments for estimating the effect of individual SNPs and other categorical variables that underlie host susceptibility, infectivity and recoverability. Designs that maximize the precision of estimates were derived.


Assuntos
Modelos Genéticos , Projetos de Pesquisa , Cruzamento , Genótipo , Humanos , Polimorfismo de Nucleotídeo Único
5.
Philos Trans A Math Phys Eng Sci ; 380(2233): 20210298, 2022 Oct 03.
Artigo em Inglês | MEDLINE | ID: mdl-35965466

RESUMO

Well parameterized epidemiological models including accurate representation of contacts are fundamental to controlling epidemics. However, age-stratified contacts are typically estimated from pre-pandemic/peace-time surveys, even though interventions and public response likely alter contacts. Here, we fit age-stratified models, including re-estimation of relative contact rates between age classes, to public data describing the 2020-2021 COVID-19 outbreak in England. This data includes age-stratified population size, cases, deaths, hospital admissions and results from the Coronavirus Infection Survey (almost 9000 observations in all). Fitting stochastic compartmental models to such detailed data is extremely challenging, especially considering the large number of model parameters being estimated (over 150). An efficient new inference algorithm ABC-MBP combining existing approximate Bayesian computation (ABC) methodology with model-based proposals (MBPs) is applied. Modified contact rates are inferred alongside time-varying reproduction numbers that quantify changes in overall transmission due to pandemic response, and age-stratified proportions of asymptomatic cases, hospitalization rates and deaths. These inferences are robust to a range of assumptions including the values of parameters that cannot be estimated from available data. ABC-MBP is shown to enable reliable joint analysis of complex epidemiological data yielding consistent parametrization of dynamic transmission models that can inform data-driven public health policy and interventions. This article is part of the theme issue 'Technical challenges of modelling real-life epidemics and examples of overcoming these'.


Assuntos
COVID-19 , Algoritmos , Teorema de Bayes , COVID-19/epidemiologia , Surtos de Doenças , Humanos , Pandemias
6.
Philos Trans A Math Phys Eng Sci ; 380(2233): 20210300, 2022 Oct 03.
Artigo em Inglês | MEDLINE | ID: mdl-35965468

RESUMO

Modern epidemiological analyses to understand and combat the spread of disease depend critically on access to, and use of, data. Rapidly evolving data, such as data streams changing during a disease outbreak, are particularly challenging. Data management is further complicated by data being imprecisely identified when used. Public trust in policy decisions resulting from such analyses is easily damaged and is often low, with cynicism arising where claims of 'following the science' are made without accompanying evidence. Tracing the provenance of such decisions back through open software to primary data would clarify this evidence, enhancing the transparency of the decision-making process. Here, we demonstrate a Findable, Accessible, Interoperable and Reusable (FAIR) data pipeline. Although developed during the COVID-19 pandemic, it allows easy annotation of any data as they are consumed by analyses, or conversely traces the provenance of scientific outputs back through the analytical or modelling source code to primary data. Such a tool provides a mechanism for the public, and fellow scientists, to better assess scientific evidence by inspecting its provenance, while allowing scientists to support policymakers in openly justifying their decisions. We believe that such tools should be promoted for use across all areas of policy-facing research. This article is part of the theme issue 'Technical challenges of modelling real-life epidemics and examples of overcoming these'.


Assuntos
COVID-19 , Gerenciamento de Dados , Humanos , Pandemias , Software , Fluxo de Trabalho
7.
PLoS Comput Biol ; 16(12): e1008447, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-33347459

RESUMO

Individuals differ widely in their contribution to the spread of infection within and across populations. Three key epidemiological host traits affect infectious disease spread: susceptibility (propensity to acquire infection), infectivity (propensity to transmit infection to others) and recoverability (propensity to recover quickly). Interventions aiming to reduce disease spread may target improvement in any one of these traits, but the necessary statistical methods for obtaining risk estimates are lacking. In this paper we introduce a novel software tool called SIRE (standing for "Susceptibility, Infectivity and Recoverability Estimation"), which allows for the first time simultaneous estimation of the genetic effect of a single nucleotide polymorphism (SNP), as well as non-genetic influences on these three unobservable host traits. SIRE implements a flexible Bayesian algorithm which accommodates a wide range of disease surveillance data comprising any combination of recorded individual infection and/or recovery times, or disease diagnostic test results. Different genetic and non-genetic regulations and data scenarios (representing realistic recording schemes) were simulated to validate SIRE and to assess their impact on the precision, accuracy and bias of parameter estimates. This analysis revealed that with few exceptions, SIRE provides unbiased, accurate parameter estimates associated with all three host traits. For most scenarios, SNP effects associated with recoverability can be estimated with highest precision, followed by susceptibility. For infectivity, many epidemics with few individuals give substantially more statistical power to identify SNP effects than the reverse. Importantly, precise estimates of SNP and other effects could be obtained even in the case of incomplete, censored and relatively infrequent measurements of individuals' infection or survival status, albeit requiring more individuals to yield equivalent precision. SIRE represents a new tool for analysing a wide range of experimental and field disease data with the aim of discovering and validating SNPs and other factors controlling infectious disease transmission.


Assuntos
Doenças Transmissíveis/genética , Doenças Transmissíveis/transmissão , Epidemias , Algoritmos , Teorema de Bayes , Doenças Transmissíveis/epidemiologia , Humanos , Modelos Estatísticos , Polimorfismo de Nucleotídeo Único
8.
J Anim Ecol ; 89(5): 1216-1229, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32096554

RESUMO

Aphid populations frequently include phenotypes that are resistant to parasitism by hymenopterous parasitoid wasps, which is often attributed to the presence of 'protective' facultative endosymbionts residing in aphid tissues, particularly Hamiltonella defensa. In field conditions, under parasitoid pressure, the observed coexistence of aphids with and without protective symbionts cannot be explained by their difference in fitness alone. Using the cereal aphid Rhopalosiphum padi as a model, we propose an alternative mechanism whereby parasitoids are more efficient at finding common phenotypes of aphid and experience a fitness cost when switching to the less common phenotype. We construct a model based on delay differential equations and parameterize and validate the model with values within the ranges obtained from experimental studies. We then use it to explore the possible effects on system dynamics under conditions of environmental stress, using our existing data on the effects of drought stress in crops as an example. We show the 'switching penalty' incurred by parasitoids leads to stable coexistence of aphids with and without H. defensa and provides a potential mechanism for maintaining phenotypic diversity among host organisms. We show that drought-induced reduction in aphid development time has little impact. However, greater reduction in fecundity on droughted plants of symbiont-protected aphids can cause insect population cycles when the system would be stable in the absence of drought stress. The stabilizing effect of the increased efficiency in dealing with more commonly encountered host phenotypes is applicable to a broad range of consumer-resource systems and could explain stable coexistence in competitive environments. The loss of stable coexistence when drought has different effects on the competing aphid phenotypes highlights the importance of scenario testing when considering biocontrol for pest management.


Assuntos
Afídeos , Vespas , Animais , Enterobacteriaceae , Fenótipo , Estresse Fisiológico , Simbiose
9.
PLoS Comput Biol ; 12(7): e1004901, 2016 07.
Artigo em Inglês | MEDLINE | ID: mdl-27384712

RESUMO

Infectious disease surveillance is key to limiting the consequences from infectious pathogens and maintaining animal and public health. Following the detection of a disease outbreak, a response in proportion to the severity of the outbreak is required. It is thus critical to obtain accurate information concerning the origin of the outbreak and its forward trajectory. However, there is often a lack of situational awareness that may lead to over- or under-reaction. There is a widening range of tests available for detecting pathogens, with typically different temporal characteristics, e.g. in terms of when peak test response occurs relative to time of exposure. We have developed a statistical framework that combines response level data from multiple diagnostic tests and is able to 'hindcast' (infer the historical trend of) an infectious disease epidemic. Assuming diagnostic test data from a cross-sectional sample of individuals infected with a pathogen during an outbreak, we use a Bayesian Markov Chain Monte Carlo (MCMC) approach to estimate time of exposure, and the overall epidemic trend in the population prior to the time of sampling. We evaluate the performance of this statistical framework on simulated data from epidemic trend curves and show that we can recover the parameter values of those trends. We also apply the framework to epidemic trend curves taken from two historical outbreaks: a bluetongue outbreak in cattle, and a whooping cough outbreak in humans. Together, these results show that hindcasting can estimate the time since infection for individuals and provide accurate estimates of epidemic trends, and can be used to distinguish whether an outbreak is increasing or past its peak. We conclude that if temporal characteristics of diagnostics are known, it is possible to recover epidemic trends of both human and animal pathogens from cross-sectional data collected at a single point in time.


Assuntos
Biologia Computacional/métodos , Epidemias/estatística & dados numéricos , Modelos Estatísticos , Vigilância da População/métodos , Algoritmos , Animais , Bluetongue , Bovinos , Doenças dos Bovinos , Estudos Transversais , Epidemias/prevenção & controle , Humanos , Coqueluche
10.
PLoS Comput Biol ; 11(11): e1004633, 2015 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-26599399

RESUMO

Genetic sequence data on pathogens have great potential to inform inference of their transmission dynamics ultimately leading to better disease control. Where genetic change and disease transmission occur on comparable timescales additional information can be inferred via the joint analysis of such genetic sequence data and epidemiological observations based on clinical symptoms and diagnostic tests. Although recently introduced approaches represent substantial progress, for computational reasons they approximate genuine joint inference of disease dynamics and genetic change in the pathogen population, capturing partially the joint epidemiological-evolutionary dynamics. Improved methods are needed to fully integrate such genetic data with epidemiological observations, for achieving a more robust inference of the transmission tree and other key epidemiological parameters such as latent periods. Here, building on current literature, a novel Bayesian framework is proposed that infers simultaneously and explicitly the transmission tree and unobserved transmitted pathogen sequences. Our framework facilitates the use of realistic likelihood functions and enables systematic and genuine joint inference of the epidemiological-evolutionary process from partially observed outbreaks. Using simulated data it is shown that this approach is able to infer accurately joint epidemiological-evolutionary dynamics, even when pathogen sequences and epidemiological data are incomplete, and when sequences are available for only a fraction of exposures. These results also characterise and quantify the value of incomplete and partial sequence data, which has important implications for sampling design, and demonstrate the abilities of the introduced method to identify multiple clusters within an outbreak. The framework is used to analyse an outbreak of foot-and-mouth disease in the UK, enhancing current understanding of its transmission dynamics and evolutionary process.


Assuntos
Teorema de Bayes , Biologia Computacional/métodos , Modelos Biológicos , Epidemiologia Molecular/métodos , Algoritmos , Animais , Simulação por Computador , Bases de Dados Factuais , Febre Aftosa/epidemiologia
11.
J Theor Biol ; 342: 62-9, 2014 Feb 07.
Artigo em Inglês | MEDLINE | ID: mdl-24211524

RESUMO

Microbial diversity in the human colon is very high with apparently large functional redundancy such that within each bacterial functional group there are many coexisting strains. Modelling this mathematically is problematic since strains within a functional group are often competing for the same limited number of resources and therefore competitive exclusion theory predicts a loss of diversity over time. Here we investigate, through computer simulation, a fluctuation dependent mechanism for the promotion of diversity. A variable pH environment caused by acidic by-products of bacterial growth on a fluctuating substrate coupled with small differences in acid tolerance between strains promotes diversity under both equilibrium and far-from-equilibrium conditions. Under equilibrium conditions pH fluctuations and relative nonlinearity in pH limitation among strains combine to prevent complete competitive exclusion. Under far-from-equilibrium conditions, loss of diversity through extinctions is made more difficult because pH cycling leads to fluctuations in the competitive ranking of strains, thereby helping to equalise fitness. We assume a trade-off between acid tolerance and maximum growth rate so that our microbial system consists of strains ranging from specialists to generalists. By altering the magnitude of the effect of the system on its pH environment (e.g. the buffering capacity of the colon) and the pattern of incoming resource we explore the conditions that promote diversity.


Assuntos
Bactérias/metabolismo , Biodiversidade , Retroalimentação Fisiológica , Trato Gastrointestinal/microbiologia , Bactérias/crescimento & desenvolvimento , Humanos , Concentração de Íons de Hidrogênio , Fenótipo
12.
BMC Vet Res ; 8: 92, 2012 Jun 27.
Artigo em Inglês | MEDLINE | ID: mdl-22738118

RESUMO

BACKGROUND: The persistence of bovine TB (bTB) in various countries throughout the world is enhanced by the existence of wildlife hosts for the infection. In Britain and Ireland, the principal wildlife host for bTB is the badger (Meles meles). The objective of our study was to examine the dynamics of bTB in badgers in relation to both badger-derived infection from within the population and externally-derived, trickle-type, infection, such as could occur from other species or environmental sources, using a spatial stochastic simulation model. RESULTS: The presence of external sources of infection can increase mean prevalence and reduce the threshold group size for disease persistence. Above the threshold equilibrium group size of 6-8 individuals predicted by the model for bTB persistence in badgers based on internal infection alone, external sources of infection have relatively little impact on the persistence or level of disease. However, within a critical range of group sizes just below this threshold level, external infection becomes much more important in determining disease dynamics. Within this critical range, external infection increases the ratio of intra- to inter-group infections due to the greater probability of external infections entering fully-susceptible groups. The effect is to enable bTB persistence and increase bTB prevalence in badger populations which would not be able to maintain bTB based on internal infection alone. CONCLUSIONS: External sources of bTB infection can contribute to the persistence of bTB in badger populations. In high-density badger populations, internal badger-derived infections occur at a sufficient rate that the additional effect of external sources in exacerbating disease is minimal. However, in lower-density populations, external sources of infection are much more important in enhancing bTB prevalence and persistence. In such circumstances, it is particularly important that control strategies to reduce bTB in badgers include efforts to minimise such external sources of infection.


Assuntos
Reservatórios de Doenças/veterinária , Mustelidae/microbiologia , Tuberculose Bovina/epidemiologia , Animais , Bovinos , Simulação por Computador , Modelos Biológicos , Modelos Estatísticos , Mustelidae/fisiologia , Dinâmica Populacional , Prevalência
13.
BMC Vet Res ; 8: 159, 2012 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-22963482

RESUMO

BACKGROUND: A common approach to the application of epidemiological models is to determine a single (point estimate) parameterisation using the information available in the literature. However, in many cases there is considerable uncertainty about parameter values, reflecting both the incomplete nature of current knowledge and natural variation, for example between farms. Furthermore model outcomes may be highly sensitive to different parameter values. Paratuberculosis is an infection for which many of the key parameter values are poorly understood and highly variable, and for such infections there is a need to develop and apply statistical techniques which make maximal use of available data. RESULTS: A technique based on Latin hypercube sampling combined with a novel reweighting method was developed which enables parameter uncertainty and variability to be incorporated into a model-based framework for estimation of prevalence. The method was evaluated by applying it to a simulation of paratuberculosis in dairy herds which combines a continuous time stochastic algorithm with model features such as within herd variability in disease development and shedding, which have not been previously explored in paratuberculosis models. Generated sample parameter combinations were assigned a weight, determined by quantifying the model's resultant ability to reproduce prevalence data. Once these weights are generated the model can be used to evaluate other scenarios such as control options. To illustrate the utility of this approach these reweighted model outputs were used to compare standard test and cull control strategies both individually and in combination with simple husbandry practices that aim to reduce infection rates. CONCLUSIONS: The technique developed has been shown to be applicable to a complex model incorporating realistic control options. For models where parameters are not well known or subject to significant variability, the reweighting scheme allowed estimated distributions of parameter values to be combined with additional sources of information, such as that available from prevalence distributions, resulting in outputs which implicitly handle variation and uncertainty. This methodology allows for more robust predictions from modelling approaches by allowing for parameter uncertainty and combining different sources of information, and is thus expected to be useful in application to a large number of disease systems.


Assuntos
Doenças dos Bovinos/prevenção & controle , Modelos Biológicos , Paratuberculose/prevenção & controle , Incerteza , Animais , Bélgica/epidemiologia , Bovinos , Doenças dos Bovinos/epidemiologia , Indústria de Laticínios , Fezes/microbiologia , Feminino , Paratuberculose/epidemiologia , Fatores de Risco
14.
J R Soc Interface ; 19(188): 20220013, 2022 03.
Artigo em Inglês | MEDLINE | ID: mdl-35259955

RESUMO

Pathogens such as African swine fever virus (ASFV) are an increasing threat to global livestock production with implications for economic well-being and food security. Quantification of epidemiological parameters, such as transmission rates and latent and infectious periods, is critical to inform efficient disease control. Parameter estimation for livestock disease systems is often reliant upon transmission experiments, which provide valuable insights in the epidemiology of disease but which may also be unrepresentative of at-risk populations and incur economic and animal welfare costs. Routinely collected mortality data are a potential source of readily available and representative information regarding disease transmission early in outbreaks. We develop methodology to conduct exact Bayesian parameter inference from mortality data using reversible jump Markov chain Monte Carlo incorporating multiple routes of transmission (e.g. within-farm secondary and background transmission from external sources). We use this methodology to infer epidemiological parameters for ASFV using data from outbreaks on nine farms in the Russian Federation. This approach improves inference on transmission rates in comparison with previous methods based on approximate Bayesian computation, allows better estimation of time of introduction and could readily be applied to other outbreaks or pathogens.


Assuntos
Vírus da Febre Suína Africana , Febre Suína Africana , Doenças dos Suínos , Febre Suína Africana/epidemiologia , Animais , Teorema de Bayes , Surtos de Doenças/veterinária , Suínos , Doenças dos Suínos/epidemiologia
15.
Epidemics ; 40: 100612, 2022 09.
Artigo em Inglês | MEDLINE | ID: mdl-35930904

RESUMO

The use of data has been essential throughout the unfolding COVID-19 pandemic. We have needed it to populate our models, inform our understanding, and shape our responses to the disease. However, data has not always been easy to find and access, it has varied in quality and coverage, been difficult to reuse or repurpose. This paper reviews these and other challenges and recommends steps to develop a data ecosystem better able to deal with future pandemics by better supporting preparedness, prevention, detection and response.


Assuntos
COVID-19 , Pandemias , COVID-19/epidemiologia , Ecossistema , Previsões , Humanos , Pandemias/prevenção & controle
16.
Epidemics ; 39: 100588, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-35679714

RESUMO

New disease challenges, societal demands and better or novel types of data, drive innovations in the structure, formulation and analysis of epidemic models. Innovations in modelling can lead to new insights into epidemic processes and better use of available data, yielding improved disease control and stimulating collection of better data and new data types. Here we identify key challenges for the structure, formulation, analysis and use of mathematical models of pathogen transmission relevant to current and future pandemics.


Assuntos
Modelos Teóricos , Pandemias , Pandemias/prevenção & controle
17.
Epidemics ; 38: 100547, 2022 03.
Artigo em Inglês | MEDLINE | ID: mdl-35180542

RESUMO

The estimation of parameters and model structure for informing infectious disease response has become a focal point of the recent pandemic. However, it has also highlighted a plethora of challenges remaining in the fast and robust extraction of information using data and models to help inform policy. In this paper, we identify and discuss four broad challenges in the estimation paradigm relating to infectious disease modelling, namely the Uncertainty Quantification framework, data challenges in estimation, model-based inference and prediction, and expert judgement. We also postulate priorities in estimation methodology to facilitate preparation for future pandemics.


Assuntos
Pandemias , Previsões , Incerteza
18.
R Soc Open Sci ; 8(3): 201715, 2021 Mar 03.
Artigo em Inglês | MEDLINE | ID: mdl-33959334

RESUMO

We develop and apply analytically tractable generative models of livestock movements at national scale. These go beyond current models through mechanistic modelling of heterogeneous trade partnership network dynamics and the trade events that occur on them. Linking resulting animal movements to disease transmission between farms yields analytical expressions for the basic reproduction number R 0. We show how these novel modelling tools enable systems approaches to disease control, using R 0 to explore impacts of changes in trading practices on between-farm prevalence levels. Using the Scottish cattle trade network as a case study, we show our approach captures critical complexities of real-world trade networks at the national scale for a broad range of endemic diseases. Changes in trading patterns that minimize disruption to business by maintaining in-flow of animals for each individual farm reduce R 0, with the largest reductions for diseases that are most challenging to eradicate. Incentivizing high-risk farms to adopt such changes exploits 'scale-free' properties of the system and is likely to be particularly effective in reducing national livestock disease burden and incursion risk. Encouragingly, gains made by such targeted modification of trade practices scale much more favourably than comparably targeted improvements to more commonly adopted farm-level biosecurity.

19.
Proc Natl Acad Sci U S A ; 104(51): 20392-7, 2007 Dec 18.
Artigo em Inglês | MEDLINE | ID: mdl-18077378

RESUMO

One of the principal challenges in epidemiological modeling is to parameterize models with realistic estimates for transmission rates in order to analyze strategies for control and to predict disease outcomes. Using a combination of replicated experiments, Bayesian statistical inference, and stochastic modeling, we introduce and illustrate a strategy to estimate transmission parameters for the spread of infection through a two-phase mosaic, comprising favorable and unfavorable hosts. We focus on epidemics with local dispersal and formulate a spatially explicit, stochastic set of transition probabilities using a percolation paradigm for a susceptible-infected (S-I) epidemiological model. The S-I percolation model is further generalized to allow for multiple sources of infection including external inoculum and host-to-host infection. We fit the model using Bayesian inference and Markov chain Monte Carlo simulation to successive snapshots of damping-off disease spreading through replicated plant populations that differ in relative proportions of favorable and unfavorable hosts and with time-varying rates of transmission. Epidemiologically plausible parametric forms for these transmission rates are compared by using the deviance information criterion. Our results show that there are four transmission rates for a two-phase system, corresponding to each combination of infected donor and susceptible recipient. Knowing the number and magnitudes of the transmission rates allows the dominant pathways for transmission in a heterogeneous population to be identified. Finally, we show how failure to allow for multiple transmission rates can overestimate or underestimate the rate of spread of epidemics in heterogeneous environments, which could lead to marked failure or inefficiency of control strategies.


Assuntos
Doenças Transmissíveis/transmissão , Surtos de Doenças/estatística & dados numéricos , Modelos Estatísticos , População , Humanos , Cadeias de Markov , Método de Monte Carlo
20.
Trends Microbiol ; 16(9): 420-7, 2008 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-18706814

RESUMO

Bovine tuberculosis (bTB; Mycobacterium bovis) is a bacterial infection of cattle that also affects certain wildlife species. Culling badgers (Meles meles), the principal wildlife host, results in perturbation of the badger population and an increased level of disease in cattle. Therefore, the priority for future management must be to minimize the risk of disease transmission by finding new ways to reduce the contact rate among the host community. At the farm level, targeting those individuals that represent an elevated risk of transmission might prove to be effective. At the landscape level, risk mapping can provide the basis for targeted surveillance of the host community. Here, we review the current evidence for bTB persistence in Britain and make recommendations for future management and research.


Assuntos
Animais Domésticos/microbiologia , Animais Selvagens/microbiologia , Tuberculose Bovina/epidemiologia , Tuberculose Bovina/transmissão , Animais , Bovinos , Feminino , Masculino , Fatores de Risco , Tuberculose Bovina/economia , Tuberculose Bovina/microbiologia , Reino Unido/epidemiologia
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