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Antigenic escape constitutes the main mechanism allowing rapidly evolving viruses to achieve endemicity. Beyond granting immune escape, empirical evidence also suggests that mutations of viruses might increase their inter-host…

COVID-19 is an emerging respiratory infectious disease caused by the coronavirus SARS-CoV-2. It was first reported on in early December 2019 in Wuhan, China and within three month spread as a pandemic around the whole globe. Here, we study…

COVID-19 has affected the world tremendously. It is critical that biological experiments and clinical designs are informed by computational approaches for time- and cost-effective solutions. Comparative analyses particularly can play a key…

A key scientific challenge during the outbreak of novel infectious diseases is to predict how the course of the epidemic changes under different countermeasures that limit interaction in the population. Most epidemiological models do not…

At the end of 2020, policy responses to the SARS-CoV-2 outbreak have been shaken by the emergence of virus variants, impacting public health and policy measures worldwide. The emergence of these strains suspected to be more contagious, more…

RNA virus (e.g., SARS-CoV-2) evolves in a complex manner. Studying RNA virus evolution is vital for understanding molecular evolution and medicine development. Scientists lack, however, general frameworks to characterize the dynamics of RNA…

It is well recognised that animal and plant pathogens form complex ecological communities of interacting organisms within their hosts. Although community ecology approaches have been applied to determine pathogen interactions at the…

Despite the availability of effective vaccines, the persistence of SARS-CoV-2 suggests that co-circulation with other pathogens and resulting multi-epidemics may become increasingly frequent. To better forecast and control the risk of such…

Understanding dynamics of an outbreak like that of COVID-19 is important in designing effective control measures. This study aims to develop an agent based model that compares changes in infection progression by manipulating different…

We consider the dynamics of a virus spreading through a population that produces a mutant strain with the ability to infect individuals that were infected with the established strain. Temporary cross-immunity is included using a time delay,…

Compartmental epidemiological models categorize individuals based on their disease status, such as the SEIRD model (Susceptible-Exposed-Infected-Recovered-Dead). These models determine the parameters that influence the magnitude of an…

Specific elements of viral genomes regulate interactions within host cells. Here, we calculated the secondary structure content of >2500 coronaviruses and computed >100000 human protein interactions with severe acute respiratory syndrome…

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…

The coronavirus pandemic has rapidly evolved into an unprecedented crisis. The susceptible-infectious-removed (SIR) model and its variants have been used for modeling the pandemic. However, time-independent parameters in the classical…

The genetic evolution of SARS-CoV-2 has caused recurring epidemic waves, understanding its global dispersal patterns is critical for effective surveillance. We developed the Site-based mutation dynamics - Equal Power Sampling (S-EPS)…

Facing a global challenge with over 6.9 million fatalities, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of CoViD-19, demands novel and comprehensive approaches to understand its complex dynamics. This…

The outbreak of COVID-19 caused by SARS-CoV-2 has rapidly spread worldwide and has caused over 1,400,000 infections and 80,000 deaths. There are currently no drugs or vaccines with proven efficacy for its prevention and little knowledge was…

We analyse the data for the global corona virus (COVID-19) outbreak using the results of a previously studied Susceptible-Infected-Removed (SIR) model of epidemic spreading on Euclidean networks. We also directly study the correlation of…

Coronavirus, or COVID-19, is a hazardous disease that has endangered the health of many people around the world by directly affecting the lungs. COVID-19 is a medium-sized, coated virus with a single-stranded RNA, and also has one of the…

Motivated by epidemics such as COVID-19, we study the spread of a contagious disease when behavior responds to the disease's prevalence. We extend the SIR epidemiological model to include endogenous meeting rates. Individuals benefit from…