An ecological and digital epidemiology analysis on the role of human behavior on the 2014 Chikungunya outbreak in Martinique

Understanding the spatio-temporal dynamics of endemic infections is of critical importance for a deeper understanding of pathogen transmission, and for the design of more efficient public health strategies. However, very few studies in this domain have focused on emerging infections, generating a gap of knowledge that hampers epidemiological response planning. Here, we analyze the case of a Chikungunya outbreak that occurred in Martinique in 2014. Using time series estimates from a network of sentinel practitioners covering the entire island, we first analyze the spatio-temporal dynamics and show that the largest city has served as the epicenter of this epidemic. We further show that the epidemic spread from there through two different propagation waves moving northwards and southwards, probably by individuals moving along the road network. We then develop a mathematical model to explore the drivers of the temporal dynamics of this mosquito-borne virus. Finally, we show that human behavior, inferred by a textual analysis of messages published on the social network Twitter, is required to explain the epidemiological dynamics over time. Overall, our results suggest that human behavior has been a key component of the outbreak propagation, and we argue that such results can lead to more efficient public health strategies specifically targeting the propagation process.

Dynamics and control of diseases in networks with community structure

Marcel Salathé

The dynamics of infectious diseases spread via direct person-to-person transmission (such as influenza, smallpox, HIV/AIDS, etc.) depends on the underlying host contact network. Human contact networks exhibit strong community structure. Understanding how such community structure affects epidemics may provide insights for preventing the spread of disease between communities by changing the structure of the contact network through pharmaceutical or non-pharmaceutical interventions. We use empirical and simulated networks to investigate the spread of disease in networks with community structure. We find that community structure has a major impact on disease dynamics, and we show that in networks with strong community structure, immunization interventions targeted at individuals bridging communities are more effective than those simply targeting highly connected individuals. Because the structure of relevant contact networks is generally not known, and vaccine supply is often limited, there is great need for efficient vaccination algorithms that do not require full knowledge of the network. We developed an algorithm that acts only on locally available network information and is able to quickly identify targets for successful immunization intervention. The algorithm generally outperforms existing algorithms when vaccine supply is limited, particularly in networks with strong community structure. Understanding the spread of infectious diseases and designing optimal control strategies is a major goal of public health. Social networks show marked patterns of community structure, and our results, based on empirical and simulated data, demonstrate that community structure strongly affects disease dynamics. These results have implications for the design of control strategies.

Public Library of Science2010

Infectious Disease Containment Based on a Wireless Sensor System

Marcel Salathé, Xiao Sun

Infectious diseases pose a serious threat to public health due to its high infectivity and potentially high mortality. One of the most effective ways to protect people from being infected by these diseases is through vaccination. However, due to various resource constraints, vaccinating all the people in a community is not practical. Therefore, targeted vaccination, which vaccinates a small group of people, is an alternative approach to contain infectious diseases. Since many infectious diseases spread among people by droplet transmission within a certain range, we deploy a wireless sensor system in a high school to collect contacts happened within the disease transmission distance. Based on the collected traces, a graph is constructed to model the disease propagation, and a new metric (called connectivity centrality) is presented to find the important nodes in the constructed graph for disease containment. Connectivity centrality considers both a node's local and global effect to measure its importance in disease propagation. Centrality based algorithms are presented and further enhanced by exploiting the information of the known infected nodes, which can be detected during targeted vaccination. Simulation results show that our algorithms can effectively contain infectious diseases and outperform other schemes under various conditions.

Ieee-Inst Electrical Electronics Engineers Inc2016

Modeling infectious disease dynamics towards informed public health interventions, with applications on COVID-19 and cholera

Joseph Chadi Benoit Lemaitre

Emerging and existing infectious diseases pose a constant threat to individuals and communities across the world. In many cases, the burden of these diseases is preventable through public health interventions. However, taking the right decisions and designing effective policies is an intricate task: epidemics are complex phenomena resulting from the interaction between the environment, pathogens, individuals, and societies. Modeling offers a principled way to reason about infectious disease dynamics from scarce and biased information and to guide decision-makers towards effective policies. This thesis tackles selected topics in cholera and COVID-19 modeling towards informed public-health decisions. These two contrasting diseases were associated by a twist of fate, but also through the lens of a common modeling approach: compartmental, SIR-based, models are conditioned on the available evidence using computer-age statistical inference frameworks. A set of five models is developed, each tackling a different facet of the spread and control of these two infectious diseases. Each model aims at answering questions related to either the understanding of the mechanisms behind disease transmission, the projection of the future dynamics under different scenarios, or the assessment of the effectiveness of past interventions. Moreover, a novel application of epidemiological models to the formal design of control policies is proposed. Optimal control provides a rigorous framework to identify the most effective control measures under a set of operational constraints, providing a benchmark on what it is possible to achieve with the available resources.The results presented in this thesis range from scientific insight on the relationship between cholera and rainfall in Juba, South Sudan to the COVID Scenario Pipeline which produces reports used to inform the response to the COVID-19 pandemic of different governmental entities. Furthermore, the effectiveness of the non-pharmaceutical interventions against COVID-19 in Switzerland is evaluated; and so is the probability of eliminating cholera from Haiti under different scenarios of mass vaccination campaigns. Finally, the development of an optimal control framework towards the effective spatial allocation of vaccines against SARS-CoV-2 in Italy closes this conversation of models.The present thesis demonstrates how infectious disease modeling enables informed decision-making by projecting the uncertainties under the light of the available evidence. It also highlights the effort needed to tailor the models and inference methods to the specificities of the transmission setting and the research question considered. From insights on transmission pathways to weekly reports aimed at decision-makers, it explores different applications of infectious disease modeling. Methods developed along the way enrich the toolbox available to modelers, to guide policy decisions further towards a reduction of the burden of infectious diseases on communities.

EPFL2021

Modeling infectious disease dynamics towards informed public health interventions, with applications on COVID-19 and cholera

Joseph Chadi Benoit Lemaitre

EPFL2021