Outbreaks of coinfections: the critical role of cooperativity

Modeling epidemic dynamics plays an important role in studying how diseases spread, predicting their future course, and designing strategies to control them. In this letter, we introduce a model of SIR (susceptible-infected-removed) type which explicitly incorporates the effect of {\it cooperative coinfection}. More precisely, each individual can get infected by two different diseases, and an individual already infected with one disease has an increased probability to get infected by the other. Depending on the amount of this increase, we observe different threshold scenarios. Apart from the standard continuous phase transition for single disease outbreaks, we observe continuous transitions where both diseases must coexist, but also discontinuous transitions are observed, where a finite fraction of the population is already affected by both diseases at the threshold. All our results are obtained in a mean field model using rate equations, but we argue that they should hold also in more general frameworks.Comment: 5 pages, including 5 figure

Impact of individual nodes in Boolean network dynamics

Boolean networks serve as discrete models of regulation and signaling in biological cells. Identifying the key controllers of such processes is important for understanding the dynamical systems and planning further analysis. Here we quantify the dynamical impact of a node as the probability of damage spreading after switching the node's state. We find that the leading eigenvector of the adjacency matrix is a good predictor of dynamical impact in the case of long-term spreading. This so-called eigenvector centrality is also a good proxy measure of the influence a node's initial state has on the attractor the system eventually arrives at. Quality of prediction is further improved when eigenvector centrality is based on the weighted matrix of activities rather than the unweighted adjacency matrix. Simulations are performed with ensembles of random Boolean networks and a Boolean model of signaling in fibroblasts. The findings are supported by analytic arguments from a linear approximation of damage spreading.Comment: 6 pages, 3 figures, 3 table

Particle velocity controls phase transitions in contagion dynamics

Interactions often require the proximity between particles. The movement of particles, thus, drives the change of the neighbors which are located in their proximity, leading to a sequence of interactions. In pathogenic contagion, infections occur through proximal interactions, but at the same time the movement facilitates the co-location of different strains. We analyze how the particle velocity impacts on the phase transitions on the contagion process of both a single infection and two cooperative infections. First, we identify an optimal velocity (close to half of the interaction range normalized by the recovery time) associated with the largest epidemic threshold, such that decreasing the velocity below the optimal value leads to larger outbreaks. Second, in the cooperative case, the system displays a continuous transition for low velocities, which becomes discontinuous for velocities of the order of three times the optimal velocity. Finally, we describe these characteristic regimes and explain the mechanisms driving the dynamics.Comment: 9 pages, 5 figures, 12 supplementary figure

Extracting information from S-curves of language change

It is well accepted that adoption of innovations are described by S-curves (slow start, accelerating period, and slow end). In this paper, we analyze how much information on the dynamics of innovation spreading can be obtained from a quantitative description of S-curves. We focus on the adoption of linguistic innovations for which detailed databases of written texts from the last 200 years allow for an unprecedented statistical precision. Combining data analysis with simulations of simple models (e.g., the Bass dynamics on complex networks) we identify signatures of endogenous and exogenous factors in the S-curves of adoption. We propose a measure to quantify the strength of these factors and three different methods to estimate it from S-curves. We obtain cases in which the exogenous factors are dominant (in the adoption of German orthographic reforms and of one irregular verb) and cases in which endogenous factors are dominant (in the adoption of conventions for romanization of Russian names and in the regularization of most studied verbs). These results show that the shape of S-curve is not universal and contains information on the adoption mechanism. (published at "J. R. Soc. Interface, vol. 11, no. 101, (2014) 1044"; DOI: http://dx.doi.org/10.1098/rsif.2014.1044)Comment: 9 pages, 5 figures, Supplementary Material is available at http://dx.doi.org/10.6084/m9.figshare.122178

Risk of Coinfection Outbreaks in Temporal Networks: A Case Study of a Hospital Contact Network

We study the spreading of cooperative infections in an empirical temporal network of contacts between people, including health care workers and patients, in a hospital. The system exhibits a phase transition leading to one or several endemic branches, depending on the connectivity pattern and the temporal correlations. There are two endemic branches in the original setting and the non-cooperative case. However, the cooperative interaction between infections reinforces the upper branch, leading to a smaller epidemic threshold and a higher probability for having a big outbreak. We show the microscopic mechanisms leading to these differences, characterize three different risks, and use the influenza features as an example for this dynamics.DFG, 345463468, Interacting Dynamics on Networks, Applications to Epidemiology (idonate

Interplay between competitive and cooperative interactions in a three-player pathogen system

In ecological systems, heterogeneous interactions between pathogens take place simultaneously. This occurs, for instance, when two pathogens cooperate, while at the same time, multiple strains of these pathogens co-circulate and compete. Notable examples include the cooperation of human immunodeficiency virus with antibiotic-resistant and susceptible strains of tuberculosis or some respiratory infections with Streptococcus pneumoniae strains. Models focusing on competition or cooperation separately fail to describe how these concurrent interactions shape the epidemiology of such diseases. We studied this problem considering two cooperating pathogens, where one pathogen is further structured in two strains. The spreading follows a susceptible-infected-susceptible process and the strains differ in transmissibility and extent of cooperation with the other pathogen. We combined a mean-field stability analysis with stochastic simulations on networks considering both well-mixed and structured populations. We observed the emergence of a complex phase diagram, where the conditions for the less transmissible, but more cooperative strain to dominate are non-trivial, e.g. non-monotonic boundaries and bistability. Coupled with community structure, the presence of the cooperative pathogen enables the coexistence between strains by breaking the spatial symmetry and dynamically creating different ecological niches. These results shed light on ecological mechanisms that may impact the epidemiology of diseases of public health concern