Human mobility networks and persistence of rapidly mutating pathogens

Rapidly mutating pathogens may be able to persist in the population and reach an endemic equilibrium by escaping hosts' acquired immunity. For such diseases, multiple biological, environmental and population-level mechanisms determine the dynamics of the outbreak, including pathogen's epidemiological traits (e.g. transmissibility, infectious period and duration of immunity), seasonality, interaction with other circulating strains and hosts' mixing and spatial fragmentation. Here, we study a susceptible-infected-recovered-susceptible model on a metapopulation where individuals are distributed in subpopulations connected via a network of mobility flows. Through extensive numerical simulations, we explore the phase space of pathogen's persistence and map the dynamical regimes of the pathogen following emergence. Our results show that spatial fragmentation and mobility play a key role in the persistence of the disease whose maximum is reached at intermediate mobility values. We describe the occurrence of different phenomena including local extinction and emergence of epidemic waves, and assess the conditions for large scale spreading. Findings are highlighted in reference to previous works and to real scenarios. Our work uncovers the crucial role of hosts' mobility on the ecological dynamics of rapidly mutating pathogens, opening the path for further studies on disease ecology in the presence of a complex and heterogeneous environment.Comment: 29 pages, 7 figures. Submitted for publicatio

A generalized-growth model to characterize the early ascending phase of infectious disease outbreaks

A better characterization of the early growth dynamics of an epidemic is needed to dissect the important drivers of disease transmission. We introduce a 2-parameter generalized-growth model to characterize the ascending phase of an outbreak and capture epidemic profiles ranging from sub-exponential to exponential growth. We test the model against empirical outbreak data representing a variety of viral pathogens and provide simulations highlighting the importance of sub-exponential growth for forecasting purposes. We applied the generalized-growth model to 20 infectious disease outbreaks representing a range of transmission routes. We uncovered epidemic profiles ranging from very slow growth (p=0.14 for the Ebola outbreak in Bomi, Liberia (2014)) to near exponential (p>0.9 for the smallpox outbreak in Khulna (1972), and the 1918 pandemic influenza in San Francisco). The foot-and-mouth disease outbreak in Uruguay displayed a profile of slower growth while the growth pattern of the HIV/AIDS epidemic in Japan was approximately linear. The West African Ebola epidemic provided a unique opportunity to explore how growth profiles vary by geography; analysis of the largest district-level outbreaks revealed substantial growth variations (mean p=0.59, range: 0.14-0.97). Our findings reveal significant variation in epidemic growth patterns across different infectious disease outbreaks and highlights that sub-exponential growth is a common phenomenon. Sub-exponential growth profiles may result from heterogeneity in contact structures or risk groups, reactive behavior changes, or the early onset of interventions strategies, and consideration of "deceleration parameters" may be useful to refine existing mathematical transmission models and improve disease forecasts.Comment: 31 pages, 9 Figures, 1 Supp. Figure, 1 Table, final accepted version (in press), Epidemics - The Journal on Infectious Disease Dynamics, 201

Dynamics of multi-stage infections on networks

This paper investigates the dynamics of infectious diseases with a nonexponentially distributed infectious period. This is achieved by considering a multistage infection model on networks. Using pairwise approximation with a standard closure, a number of important characteristics of disease dynamics are derived analytically, including the final size of an epidemic and a threshold for epidemic outbreaks, and it is shown how these quantities depend on disease characteristics, as well as the number of disease stages. Stochastic simulations of dynamics on networks are performed and compared to output of pairwise models for several realistic examples of infectious diseases to illustrate the role played by the number of stages in the disease dynamics. These results show that a higher number of disease stages results in faster epidemic outbreaks with a higher peak prevalence and a larger final size of the epidemic. The agreement between the pairwise and simulation models is excellent in the cases we consider

Natural, persistent oscillations in a spatial multi-strain disease system with application to dengue.

This is a freely-available open access publication. Please cite the published version which is available via the DOI link in this record.Many infectious diseases are not maintained in a state of equilibrium but exhibit significant fluctuations in prevalence over time. For pathogens that consist of multiple antigenic types or strains, such as influenza, malaria or dengue, these fluctuations often take on the form of regular or irregular epidemic outbreaks in addition to oscillatory prevalence levels of the constituent strains. To explain the observed temporal dynamics and structuring in pathogen populations, epidemiological multi-strain models have commonly evoked strong immune interactions between strains as the predominant driver. Here, with specific reference to dengue, we show how spatially explicit, multi-strain systems can exhibit all of the described epidemiological dynamics even in the absence of immune competition. Instead, amplification of natural stochastic differences in disease transmission, can give rise to persistent oscillations comprising semi-regular epidemic outbreaks and sequential dominance of dengue's four serotypes. Not only can this mechanism explain observed differences in serotype and disease distributions between neighbouring geographical areas, it also has important implications for inferring the nature and epidemiological consequences of immune mediated competition in multi-strain pathogen systems.Fundacao para a Ciencia e TecnologiaSiemens PortugalRoyal Societ

Targeting vaccination against novel infections : risk, age and spatial structure for pandemic influenza in Great Britain

The emergence of a novel strain of H1N1 influenza virus in Mexico in 2009, and its subsequent worldwide spread, has focused attention to the question of optimal deployment of mass vaccination campaigns. Here, we use three relatively simple models to address three issues of primary concern in the targeting of any vaccine. The advantages of such simple models are that the underlying assumptions and effects of individual parameters are relatively clear, and the impact of uncertainty in the parametrization can be readily assessed in the early stages of an outbreak. In particular, we examine whether targeting risk-groups, age-groups or spatial regions could be optimal in terms of reducing the predicted number of cases or severe effects; and how these targeted strategies vary as the epidemic progresses. We examine the conditions under which it is optimal to initially target vaccination towards those individuals within the population who are most at risk of severe effects of infection. Using age-structured mixing matrices, we show that targeting vaccination towards the more epidemiologically important age groups (5-14 year olds and then 15-24 year olds) leads to the greatest reduction in the epidemic growth and hence reduces the total number of cases. Finally, we consider how spatially targeting the vaccine towards regions of country worst affected could provide an advantage. We discuss how all three of these priorities change as both the speed at which vaccination can be deployed and the start of the vaccination programme is varied

Spectral unmixing approach in hyperspectral remote sensing: a tool for oil palm mapping

Las plantaciones de palma de aceite típicamente abarcan grandes áreas, por esto, la teledetección remota se ha convertido en una herramienta útil para el monitoreo avanzado de este cultivo. Este trabajo revisa y evalúa dos enfoques para analizar las plantaciones de palma de aceite a partir de datos de teledetección remota hiperespectral: desmezclado espectral lineal y variabilidad espectral. Además, se propone un marco computacional basado en el desmezclado espectral para la estimación de las fracciones de abundancias de cultivos de palma de aceite. Este enfoque también considera la variabilidad espectral de las firmas en las imágenes hiperespectrales. El marco computacional propuesto modifica el modelo de mezcla lineal mediante la introducción de un vector de pesos, de manera que se puedan identificar las bandas espectrales que menos contribuyen a la estimación de fracciones de abundancias erróneas. Este enfoque aprovecha la detección de los árboles de palma de aceite, ya que permite diferenciarlos de otros materiales en términos de fracciones de abundancia. Los resultados experimentales obtenidos a partir de datos de teledetección remota hiperespectral en el rango de 410-990 nm, muestran mejoras de un 8.18 % en la métrica de Precisión del Usuario (Uacc) en la identificación de palmas de aceite por el marco propuesto con respecto a los métodos tradicionales de desmezclado espectral; el método propuesto logró un 95 % de Uacc. Esto confirma las capacidades del marco computacional formulado y facilita la gestión y el monitoreo de grandes áreas de plantaciones de palma de aceite.Oil palm plantations typically span large areas; therefore, remote sensing has become a useful tool for advanced oil palm monitoring. This work reviews and evaluates two approaches to analyze oil palm plantations based on hyperspectral remote sensing data: linear spectral unmixing and spectral variability. Moreover, a computational framework based on spectral unmixing for the estimation of fractional abundances of oil palm plantations is proposed in this study. Such approach also considers the spectral variability of hyperspectral image signatures. More specifically, the proposed computational framework modifies the linear mixing model by introducing a weighting vector, so that the spectral bands that contribute the least to the estimation of erroneous fractional abundances can be identified. This approach improves palm detection as it allows to differentiate them from other materials in terms of fractional abundances. Experimental results obtained from hyperspectral remote sensing data in the range 410-990 nm show improvements of 8.18 % in User Accuracy (Uacc) in the identification of oil palms by the proposed framework with respect to traditional unmixing methods. Thus, the proposed method achieved a 95% Uacc. This confirms the capabilities of the proposed computational framework and facilitates the management and monitoring of large areas of oil palm plantations

Virus-virus interactions impact the population dynamics of influenza and the common cold

The human respiratory tract hosts a diverse community of cocirculating viruses that are responsible for acute respiratory infections. This shared niche provides the opportunity for virus–virus interactions which have the potential to affect individual infection risks and in turn influence dynamics of infection at population scales. However, quantitative evidence for interactions has lacked suitable data and appropriate analytical tools. Here, we expose and quantify interactions among respiratory viruses using bespoke analyses of infection time series at the population scale and coinfections at the individual host scale. We analyzed diagnostic data from 44,230 cases of respiratory illness that were tested for 11 taxonomically broad groups of respiratory viruses over 9 y. Key to our analyses was accounting for alternative drivers of correlated infection frequency, such as age and seasonal dependencies in infection risk, allowing us to obtain strong support for the existence of negative interactions between influenza and noninfluenza viruses and positive interactions among noninfluenza viruses. In mathematical simulations that mimic 2-pathogen dynamics, we show that transient immune-mediated interference can cause a relatively ubiquitous common cold-like virus to diminish during peak activity of a seasonal virus, supporting the potential role of innate immunity in driving the asynchronous circulation of influenza A and rhinovirus. These findings have important implications for understanding the linked epidemiological dynamics of viral respiratory infections, an important step towards improved accuracy of disease forecasting models and evaluation of disease control interventions