Related papers: Concepts and methods for predicting viral evolutio…
Influenza has been circulating in the human population and has caused three pandemics in the last century (1918 H1N1, 1957 H2N2, 1968 H3N2). The 2009 A(H1N1) was classified by the World Health Organization (WHO) as the fourth pandemic.…
In this work, we aim to formalize a novel scientific machine learning framework to reconstruct the hidden dynamics of the transmission rate, whose inaccurate extrapolation can significantly impair the quality of the epidemic forecasts, by…
Motivated by our intention to use SIR-type epidemiological models in the context of dynamic networks as provided by large-scale highly interacting inhomogeneous human crowds, we investigate in this framework possibilities to reduce the…
We propose an approach based on a combination of physical, chemical, and mathematical methods to identify and characterize virulent influenza A viruses (IAVs) through the analysis of the hemagglutinin protein. These methods include the…
We perform an analytical sensitivity analysis for a model of a continuous-time branching process evolving on a fixed network. This allows us to determine the relative importance of the model parameters to the growth of the population on the…
Airborne infection risk analysis is usually performed for enclosed spaces where susceptible individuals are exposed to infectious airborne respiratory droplets by inhalation. It is usually based on exponential, dose-response models of which…
Intent of this research is to explore how mathematical models, specifically Susceptible-Infected-Removed (SIR) model, can be utilized to forecast peak outbreak timeline of COVID-19 epidemic amongst a population of interest starting from the…
The surprisingly mercurial Covid-19 pandemic has highlighted the need to not only accelerate research on infectious disease, but to also study them using novel techniques and perspectives. A major contributor to the difficulty of containing…
The rapid outbreak of bird flu challenges the outcome of effective vaccine for the upcoming years. The recent research established different norms to eliminate flu pandemics. This can be made possible with skilled experimental analyses and…
This study releases an adaptable framework that can provide insights to policymakers to predict the complex recurring waves of the pandemic in the medium postemergence of the virus spread, a phase marked by rapidly changing factors like…
We present a study of the worldwide spread of a pandemic influenza and its possible containment at a global level taking into account all available information on air travel. We studied a metapopulation stochastic epidemic model on a global…
The reconstruction of phylogenetic trees based on viral genetic sequence data sequentially sampled from an epidemic provides estimates of the past transmission dynamics, by fitting epidemiological models to these trees. To our knowledge,…
Human immunodeficiency virus (HIV) evolves with extraordinary rapidity. However, its evolution is constrained by interactions between mutations in its fitness landscape. Here we show that an Ising model describing these interactions,…
Each year, seasonal influenza epidemics cause hundreds of thousands of deaths worldwide and put high loads on health care systems. A main concern for resource planning is the risk of exceptionally severe epidemics. Taking advantage of…
The importance of understanding SARS-CoV-2 evolution cannot be overemphasized. Recent studies confirm that natural selection is the dominating mechanism of SARS-CoV-2 evolution, which favors mutations that strengthen viral infectivity. We…
Life forms exhibit such a degree of exquisite organization that it seems impossible that they could have developed out of a process of trial and error, as intimated by the theory of Darwinian evolution. In this general public paper I…
Mutational escape from vaccine induced immune responses has thwarted the development of a successful vaccine against AIDS, whose causative agent is HIV, a highly mutable virus. Knowing the virus' fitness as a function of its proteomic…
The mechanism of SARS-CoV-2 evolution and transmission is elusive and its understanding, a prerequisite to forecast emerging variants, is of paramount importance. SARS-CoV-2 evolution is driven by the mechanisms at molecular and organism…
Epidemiological data on seasonal influenza show that the growth rate of the number of infected individuals can increase passing from one exponential growth rate to another one with a larger exponent. Such behavior is not described by…
Infectious disease outbreaks recapitulate biology: they emerge from the multi-level interaction of hosts, pathogens, and their shared environment. As a result, predicting when, where, and how far diseases will spread requires a complex…