Related papers: Predicting sub-population specific viral evolution
The seasonal human influenza virus undergoes rapid evolution, leading to significant changes in circulating viral strains from year to year. These changes are typically driven by adaptive mutations, particularly in the antigenic epitopes,…
Although traditional models of epidemic spreading focus on the number of infected, susceptible and recovered individuals, a lot of attention has been devoted to integrate epidemic models with population genetics. Here we develop an…
When modelling HIV epidemics, it is important to incorporate set-point viral load and its heritability. As set-point viral load distributions can differ significantly amongst epidemics, it is imperative to account for the observed local…
Viral infections are causing significant morbidity and mortality worldwide. Understanding the interaction patterns between a particular virus and human proteins plays a crucial role in unveiling the underlying mechanism of viral infection…
Applying a ML approach to the temporal variability of the Spike protein sequence enables us to identify, classify and track emerging virus variants. Our analysis is unbiased, in the sense that it does not require any prior knowledge of the…
Viral zoonoses have emerged as the key drivers of recent pandemics. Human infection by zoonotic viruses are either spillover events -- isolated infections that fail to cause a widespread contagion -- or species jumps, where successful…
As pathogens spread in a population of hosts, immunity is built up and the pool of susceptible individuals is depleted. This generates selective pressure, to which many human RNA viruses, such as influenza virus or SARS-CoV-2, respond with…
Viruses constantly undergo mutations with genomic changes. The propagation of variants of viruses is an interesting problem. We perform numerical simulations of the microscopic epidemic model based on network theory for the spread of…
The transmission rate of many acute infectious diseases varies significantly in time, but the underlying mechanisms are usually uncertain. They may include seasonal changes in the environment, contact rate, immune system response, etc. The…
The viral load is known to be a chief predictor of the risk of transmission of infectious diseases. In this work, we investigate the role of the individuals' viral load in the disease transmission by proposing a new…
Genetic variations in the COVID-19 virus are one of the main causes of the COVID-19 pandemic outbreak in 2020 and 2021. In this article, we aim to introduce a new type of model, a system coupled with ordinary differential equations (ODEs),…
We derive an analytic expression for site-specific stationary distributions of amino acids from the Structurally Constrained Neutral (SCN) model of protein evolution with conservation of folding stability. The stationary distributions that…
Throughout the course of an epidemic, the rate at which disease spreads varies with behavioral changes, the emergence of new disease variants, and the introduction of mitigation policies. Estimating such changes in transmission rates can…
Models are often employed to integrate knowledge about epidemics across scales and simulate disease dynamics. While these approaches have played a central role in studying the mechanics underlying epidemics, we lack ways to reliably predict…
We study viral transmission in crowds via the short-ranged airborne pathway using a purely model-based approach. Our goal is two-pronged. Firstly, we illustrate with a concrete and pedagogical case study how to estimate the risks of new…
Predicting counterfactual distributions in complex dynamical systems is essential for scientific modeling and decision-making in domains such as public health and medicine. However, existing methods often rely on point estimates or purely…
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…
Proteins are responsible for the most diverse set of functions in biology. The ability to extract information from protein sequences and to predict the effects of mutations is extremely valuable in many domains of biology and medicine.…
We present a general framework for adaptive allocation of viral tests in social contact networks. We pose and solve several complementary problems. First, we consider the design of a social sensing system whose objective is the early…
Computational models for the simulation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic evolution would be extremely useful to support authorities in designing healthcare policies and lockdown measures to…