Related papers: Concepts and methods for predicting viral evolutio…
We introduce a minimal multiscale framework that links within-host virus dynamics to population-level SIRS epidemiology through explicit, bidirectional coupling. At the microscopic layer, a two variant quasispecies (master and mutant…
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…
The spread of infectious disease and the evolution of antigenically distinct strains are often modeled separately, despite strong feedbacks mediated by host immune memory and heterogeneous contacts. To tackle this challenging problem, we…
Infectious zoonotic disease emergence, through spillover events, is of global concern and has the potential to cause significant harm to society, as recently demonstrated by COVID-19. More than 70% of the 400 infectious diseases that…
A principal component analysis of a multiple sequence alignement of hemagglutinin sequences of subtype H1 has been performed, the sequences being encoded using the amino-acid property that maximizes the weight of the major component. In the…
Common respiratory viruses cause seasonal epidemics in sequential patterns. The underlying mechanisms for this pattern have been debated for some time. For influenza, contenders include temperature, humidity, and vitamin D levels. While…
Transmission models for infectious diseases are typically formulated in terms of dynamics between individuals or groups with processes such as disease progression or recovery for each individual captured phenomenologically, without…
Effective property prediction methods can help accelerate the search for COVID-19 antivirals either through accurate in-silico screens or by effectively guiding on-going at-scale experimental efforts. However, existing prediction tools have…
This paper develops mathematical tools to estimate seasonal changes in measles transmission rates and corresponding variation in population susceptibility. The tools are designed to leverage times series of cases in the absence of…
SARS-CoV-2 usually evolves at a relatively constant rate over time. Occasionally, however, lineages arise with higher-than-expected numbers of mutations given the date of sampling. Such lineages can arise for a variety of reasons, including…
After more than 6 million deaths worldwide, the ongoing vaccination to conquer the COVID-19 disease is now competing with the emergence of increasingly contagious mutations, repeatedly supplanting earlier strains. Following the near-absence…
The accurate estimation of time-varying transmission rates is fundamental for understanding infectious disease dynamics and implementing effective public health interventions. To this end, we propose an improved inverse method for…
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…
This article reviews quantitative methods to estimate the basic reproduction number of pandemic influenza, a key threshold quantity to help determine the intensity of interventions required to control the disease. Although it is difficult…
This paper seeks to study the evolution of the COVID-19 pandemic based on daily published data from Worldometer website, using a time-dependent SIR model. Our findings indicate that this model fits well such data, for different chosen…
The understanding of the mechanisms of SARS-CoV-2 evolution and transmission is one of the greatest challenges of our time. By integrating artificial intelligence (AI), viral genomes isolated from patients, tens of thousands of mutational…
Until now, design of the annual influenza vaccine has relied on phylogenetic or whole-sequence comparisons of the viral coat proteins hemagglutinin and neuraminidase, with vaccine effectiveness assumed to correlate monotonically to the…
Population-wide vaccination is critical for containing the SARS-CoV-2 (Covid-19) pandemic when combined with restrictive and prevention measures. In this study, we introduce SAIVR, a mathematical model able to forecast the Covid-19 epidemic…
While machine learning is rapidly being developed and deployed in health settings such as influenza prediction, there are critical challenges in using data from one environment in another due to variability in features; even within disease…
With the unprecedented global vaccination campaign against SARS-CoV-2 attention has now turned to the potential impact of this large-scale intervention on the evolution of the virus. In this perspective we summarize what is currently known…