Related papers: What Omicron Does, and How It Does It
Proteins can exhibit dynamic structural flexibility as they carry out their functions, especially in binding regions that interact with other molecules. For the key SARS-CoV-2 spike protein that facilitates COVID-19 infection, studies have…
Epidemic models study the spread of an undesired agent through a population, be it infectious diseases through a country, misinformation in online social media, or pests infesting a region. In combating these epidemics, we rely neither on…
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…
We study the role of recombination, as practiced by genetically-competent bacteria, in speeding up Darwinian evolution. This is done by adding a new process to a previously-studied Markov model of evolution on a smooth fitness landscape;…
During chronic infection, HIV-1 engages in a rapid coevolutionary arms race with the host's adaptive immune system. While it is clear that HIV exerts strong selection on the adaptive immune system, the characteristics of the somatic…
Genomic surveillance of infectious diseases allows monitoring circulating and emerging variants and quantifying their epidemic potential. However, due to the high costs associated with genomic sequencing, only a limited number of samples…
Spike proteins, 1200 amino acids, are divided into two nearly equal parts, S1 and S2. We review here phase transition theory, implemented quantitatively by thermodynamic scaling. The theory explains the evolution of Coronavirus extremely…
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…
Intragenomic recombination (crossover) is a very important evolutionary mechanism. The crossover events are not evenly distributed along the natural chromosomes. Monte Carlo simulations revealed that frequency of recombinations decides…
New COVID-19 epidemic strains like Delta and Omicron with increased transmissibility and pathogenicity emerge and spread across the whole world rapidly while causing high mortality during the pandemic period. Early prediction of possible…
With the present highly infectious dominant SARS-CoV-2 strain of B1.1.529 or Omicron spreading around the globe, there is concern that the COVID-19 pandemic will not end soon and that it will be a race against time until a more contagious…
This chapter gives a synopsis of recent approaches to model and analyse the evolution of microbial populations under selection. The first part reviews two population genetic models of Lenski's long-term evolution experiment with Escherichia…
Social contagion is a ubiquitous and fundamental process that drives individual and social changes. Although social contagion arises as a result of cognitive processes and biases, the integration of cognitive mechanisms with the theory of…
Multipartite viruses replicate through a puzzling evolutionary strategy. Their genome is segmented into two or more parts, and encapsidated in separate particles that appear to propagate independently. Completing the replication cycle,…
Cooperation is a widespread natural phenomenon yet current evolutionary thinking is dominated by the paradigm of selfish competition. Recent advanced in many fronts of Biology and Non-linear Physics are helping to bring cooperation to its…
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…
One strategy for winning a coevolutionary struggle is to evolve rapidly. Most of the literature on host-pathogen coevolution focuses on this phenomenon, and looks for consequent evidence of coevolutionary arms races. An alternative…
Antibiotic resistance is a growing public health problem. To gain a fundamental understanding of resistance evolution, a combination of systematic experimental and theoretical approaches is required. Evolution experiments combined with…
Since the first case of COVID-19 disease in Wuhan in December 2019, there is a worldwide struggle to reduce the transmission of acute respiratory syndrome coronavirus SARS-CoV-2. Many countries worldwide decided to impose local lockdowns in…
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…