Related papers: Epistatic models predict mutable sites in SARS-CoV…

COVID-19 vaccines are highly efficacious at preventing symptomatic infection, severe disease, and death. Most of the evidence that COVID-19 vaccines also reduce transmission of SARS-CoV-2 is based on retrospective, observational studies.…

Most of the ongoing projects aimed at the development of specific therapies and vaccines against COVID-19 use the SARS-CoV-2 spike (S) protein as the main target [1-3]. The binding of the spike protein with the ACE2 receptor (ACE2) of the…

Mutating variants of COVID-19 have been reported across many US states since 2021. In the fight against COVID-19, it has become imperative to study the heterogeneity in the time-varying transmission rates for each variant in the presence of…

SARS-CoV-2 lineages are defined according to placement in a phylogenetic tree, but approximated by a list of mutations based on sequences collected from clinical sampling. Wastewater lineage abundance is generally found under the assumption…

In this work, we derive a system of Boltzmann-type equations to describe the spread of SARS-CoV-2 virus at the microscopic scale, that is by modeling the human-to-human mechanisms of transmission. To this end, we consider two populations,…

Prominently accountable for the upsurge of COVID-19 cases as the world attempts to recover from the previous two waves, Omicron has further threatened the conventional therapeutic approaches. Omicron is the fifth variant of concern (VOC),…

Interactions between SARS-CoV-2 and the immune system during infection are complex. However, understanding the within-host SARS-CoV-2 dynamics is of enormous importance, especially when it comes to assessing treatment options. Mathematical…

Governments and public health authorities use seroprevalence studies to guide responses to the COVID-19 pandemic. Seroprevalence surveys estimate the proportion of individuals who have detectable SARS-CoV-2 antibodies. However, serologic…

Predicting the binding of viral peptides to the major histocompatibility complex with machine learning can potentially extend the computational immunology toolkit for vaccine development, and serve as a key component in the fight against a…

COVID-19 is an infection caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome coronavirus 2), which has caused a global outbreak. Current research efforts are focused on the understanding of the molecular mechanisms involved in…

We compute the allele frequencies of the alpha (B.1.1.7), beta (B.1.351) and delta (B.167.2) variants of SARS-CoV-2 from almost two million genome sequences on the GISAID repository. We find that the frequencies of a majority of the…

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…

We propose a simple dynamic model for estimating the relative contagiousness of two virus variants. Maximum likelihood estimation and inference is conveniently invariant to variation in the total number of cases over the sample period and…

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…

We introduce a data-driven epistatic model of protein evolution, capable of generating evolutionary trajectories spanning very different time scales reaching from individual mutations to diverged homologs. Our in silico evolution…

The rapid spreading of SARS-CoV-2 and its dramatic consequences, are forcing policymakers to take strict measures in order to keep the population safe. At the same time, societal and economical interactions are to be safeguarded. A wide…

In this work we propose the design principles of a stochastic graph-based model for the simulation of SARS-CoV-2 transmission. The proposed approach incorporates three sub-models, namely, the spatial model, the mobility model, and the…

Network theory-based approaches provide valuable insights into the variations in global structural connectivity between differing dynamical states of proteins. Our objective is to review network-based analyses to elucidate such variations,…

The question of how SARS-CoV-2 is transmitted remains surprisingly controversial today, especially with reference to airborne transmission. In fact, despite a large body of scientific evidence, health and regulatory authorities still…

The accurate prediction of B-cell epitopes is critical for guiding vaccine development against infectious diseases, including SARS and COVID-19. This study explores the use of a deep neural network (DNN) model to predict B-cell epitopes for…