Related papers: Concepts and methods for predicting viral evolutio…
During the COVID-19 pandemic, a major driver of new surges has been the emergence of new variants. When a new variant emerges in one or more countries, other nations monitor its spread in preparation for its potential arrival. The impact of…
Identifying viral pathogens and characterizing their transmission is essential to developing effective public health measures in response to a pandemic. Phylogenetics, though currently the most popular tool used to characterize the likely…
A physics-informed neural network (PINN) embedded with the susceptible-infected-removed (SIR) model is devised to understand the temporal evolution dynamics of infectious diseases. Firstly, the effectiveness of this approach is demonstrated…
At the end of 2020, policy responses to the SARS-CoV-2 outbreak have been shaken by the emergence of virus variants. The emergence of these more contagious, more severe, or even vaccine-resistant strains have challenged worldwide policy…
Infectious disease dynamics operate across multiple biological scales, with within-host viral dynamics being a key driver of between-host transmission. However, while models that explicitly link these scales exist, none have been developed…
Reputed intractable, the question of the origin of viruses has long been neglected. In the modern literature 'Virus evolution' has come to refer to study more akin to population genetics, such as the world-wide scrutiny on new polymorphisms…
The discovery of SARS-CoV-2, the responsible virus for the Covid-19 epidemic, has sparked a global health concern with many countries affected. Developing models that can interpret the epidemic and give common trend parameters are useful…
Population heterogeneity is a key factor in epidemic dynamics, influencing both transmission and final epidemic size. While heterogeneity is often modelled through age structure, spatial location, or contact patterns, differences in host…
Much traditional statistical modelling assumes that the outcome variables of interest are independent of each other when conditioned on the explanatory variables. This assumption is strongly violated in the case of infectious diseases,…
Historically, infectious diseases caused considerable damage to human societies, and they continue to do so today. To help reduce their impact, mathematical models of disease transmission have been studied to help understand disease…
Numerous studies have attempted to model the effect of mass media on the transmission of diseases such as influenza, however quantitative data on media engagement has until recently been difficult to obtain. With the recent explosion of…
We provide a predictive analysis of the spread of COVID-19, also known as SARS-CoV-2, using the dataset made publicly available online by the Johns Hopkins University. Our main objective is to provide predictions of the number of infected…
The increase in the connectivity between hosts in recent times has facilitated the emergence of more aggressive mutant viral strains, making their containment and eradication significantly more challenging compared to the original variants.…
Timely and accurate forecasts of seasonal influenza would assist public health decision-makers in planning intervention strategies, efficiently allocating resources, and possibly saving lives. For these reasons, influenza forecasts are…
We define a new parameter to quantify the antigenic distance between two H3N2 influenza strains: we use this parameter to measure antigenic distance between circulating H3N2 strains and the closest vaccine component of the influenza…
Genomic surveillance of SARS-CoV-2 has been instrumental in tracking the spread and evolution of the virus during the pandemic. The availability of SARS-CoV-2 molecular sequences isolated from infected individuals, coupled with phylodynamic…
Many biological networks have to filter out useful information from a vast excess of spurious interactions. We use computational evolution to predict design features of networks processing ligand categorization. The important problem of…
Chronic infections of the human immunodeficiency virus (HIV) create a very complex co-evolutionary process, where the virus tries to escape the continuously adapting host immune system. Quantitative details of this process are largely…
Recently, an elegant approach in phylogenetics was introduced by Billera-Holmes-Vogtmann that allows a systematic comparison of different evolutionary histories using the metric geometry of tree spaces. In many problem settings one…
Throughout human history, epidemics have been a constant presence. Understanding their dynamics is essential to predict scenarios and make substantiated decisions. Mathematical models are powerful tools to describe an epidemic behavior.…