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The COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spurred unprecedented and concerted worldwide research to curtail and eradicate this pathogen. SARS-CoV-2 has four structural proteins:…
We propose a mathematical model with five compartments for the SARS-CoV-2 transmission: susceptible $S$, undetected infected asymptomatic $A$, undetected infected symptomatic $I$, confirmed positive and isolated $L$, and recovered $ R$, for…
Since its emergence, SARS-CoV-2 has demonstrated a rapid and unpredictable evolutionary trajectory, characterized by the continual emergence of immune-evasive variants. This poses persistent challenges to public health and vaccine…
The growing literature on the propagation of COVID-19 relies on various dynamic SIR-type models (Susceptible-Infected-Recovered) which yield model-dependent results. For transparency and ease of comparing the results, we introduce a common…
Covid-19 infection, which spread to the whole world in December 2019 and is still active, caused more than 250 thousand deaths in the world today. Researches on this subject have been focused on analyzing the genetic structure of the virus,…
We introduce a new probabilistic model to estimate the real spread of the novel SARS-CoV-2 virus along regions or countries. Our model simulates the behavior of each individual in a population according to a probabilistic model through an…
The viral load of patients infected with SARS-CoV-2 varies on logarithmic scales and possibly with age. Controversial claims have been made in the literature regarding whether the viral load distribution actually depends on the age of the…
Significantly higher transmissibility of SARS CoV-2 (2019) compared to SARS CoV (2003) can be attributed to mutations of structural proteins (Spike S, Nucleocapsid N, Membrane M, and Envelope E) and the role played by non-structural…
Protein sequence data from nature exhibits survivorship bias: we only observe data from those organisms that survive and reproduce, while non-functional protein mutations are eliminated by natural selection. Thus, predicting whether a…
The latest severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant Omicron (B.1.1.529) has ushered panic responses around the world due to its contagious and vaccine escape mutations. The essential infectivity and antibody…
In this paper we create a compartmental, stochastic process model of SARS-CoV-2 transmission, where the process's mean and variance have distinct dynamics. The model is fit to time series data from Washington from January 2020 to March 2021…
During a virus's evolution,various regions of the genome are subjected to distinct levels of functional constraints.Combined with factors like codon bias and DNA repair efficiency,these constraints contribute to unique mutation patterns…
We consider the SEIRS epidemiology model with such features of the COVID-19 outbreak as: abundance of unidentified infected individuals, limited time of immunity and a possibility of vaccination. The control of the pandemic dynamics is…
Antigenic variation is the main immune escape mechanism for RNA viruses like influenza or SARS-CoV-2. While high mutation rates promote antigenic escape, they also induce large mutational loads and reduced fitness. It remains unclear how…
The SARS-CoV-2 pandemic has created a global race for a cure. One approach focuses on designing a novel variant of the human angiotensin-converting enzyme 2 (ACE2) that binds more tightly to the SARS-CoV-2 spike protein and diverts it from…
The outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) threatens global medical systems and economies, and rules our daily living life. Controlling the outbreak of SARS-CoV-2 has become one of the most important…
The COVID-19 pandemic has given rise to numerous articles from different scientific fields (epidemiology, virology, immunology, airflow physics...) without any effort to link these different insights. In this review, we aim to establish…
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,…
There is a growing interest in modeling and analyzing the spread of diseases like the SARS-CoV-2 infection using stochastic models. These models are typically analyzed quantitatively and are not often subject to validation using formal…
We explore the inclusion of vaccination in compartmental epidemiological models concerning the delta and omicron variants of the SARS-CoV-2 virus that caused the COVID-19 pandemic. We expand on our earlier compartmental-model work by…