Publications related to Rapid Intrahost Evolution of Human Cytomegalovirus Is Shaped by Demography and Positive Selection

Related publications (30)

Genome-wide allele-specific expression in multi-tissue samples from healthy male baboons reveals the transcriptional complexity of mammals

Allele-specific expression (ASE) is pivotal in understanding the genetic underpinnings of phenotypic variation within species, differences in disease susceptibility, and responses to environmental factors. We processed 11 different tissue types collected f ...

2025

Reproductive isolation arises during laboratory adaptation to a novel hot environment

Ana Marija Jaksic

Background: Reproductive isolation can result from adaptive processes (e.g., ecological speciation and mutation-order speciation) or stochastic processes such as "system drift" model. Ecological speciation predicts barriers to gene flow between populations ...

BMC2024

Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics

Tamar Kohn, Xavier Fernandez Cassi

Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preampli ...

2024

Variational quantum time evolution without the quantum geometric tensor

Giuseppe Carleo, Jannes Willy E. Nys, Riccardo Rossi, Julien Sebastian Gacon

Realand imaginary -time quantum state evolutions are crucial in physics and chemistry for exploring quantum dynamics, preparing ground states, and computing thermodynamic observables. On near -term devices, variational quantum time evolution is a promising ...

Amer Physical Soc2024

Euclid preparation XXXVII. Galaxy colour selections with Euclid and ground photometry for cluster weak-lensing analyses

Maurizio Martinelli, Frédéric Courbin, Georges Meylan, Gianluca Castignani, Matthias Wiesmann

Aims. We derived galaxy colour selections from Euclid and ground-based photometry, aiming to accurately define background galaxy samples in cluster weak-lensing analyses. These selections have been implemented in the Euclid data analysis pipelines for gala ...

Edp Sciences S A2024

Stability of a liquid layer draining around a horizontal cylinder: Interplay of capillary and gravity forces

François Gallaire, Shahab Eghbali, Simeon Vladimirov Djambov

We study the drainage of a viscous liquid film coating the outside of a solid horizontal cylinder, where gravity acts vertically. We focus on the limit of large Ohnesorge numbers Oh, where inertia is negligible compared to viscous effects. We first study t ...

Amer Physical Soc2024

Peptide-based virucidal drugs

Francesca Olgiati

Before the COVID-19 pandemic, viruses were not a major priority for the scientific community. Today, many events have changed the world and the importance of studying viruses, vaccines, and antiviral drugs is fully appreciated. The development of effective ...

EPFL2024

At what spatial scale does natural selection operate? Using multiscale frameworks to calibrate the effects of environmental factors across landscape continuums

Annie Sandrine Guillaume

Patterns in nature arise from processes interacting across a continuum of spatial scales, where new relationships emerge at each level of investigation. These patterns are nested features encompassing fine-scale local patterns, such as topography and geolo ...

EPFL2024

Stability of influenza A virus in droplets and aerosols is heightened by the presence of commensal respiratory bacteria

Athanasios Nenes, Tamar Kohn, Kalliopi Violaki, Ghislain Gilles Jean-Michel Motos, Aline Laetitia Schaub, Shannon Christa David, Walter Hugentobler, Htet Kyi Wynn, Céline Terrettaz, Laura José Costa Henriques

Aerosol transmission remains a major challenge for control of respiratory viruses, particularly those causing recurrent epidemics, like influenza A virus (IAV). These viruses are rarely expelled alone, but instead are embedded in a consortium of microorgan ...

American Society for Microbiology2024

Waterborne Virus Transport and Risk Assessment in Lake Geneva Under Climate Change

Tamar Kohn, Chaojie Li

Climate changes influence lake hydrodynamics and radiation levels and thus may affect the fate and transport of waterborne pathogens in lakes. This study examines the impact of climate change on the fate, transport, and associated risks of four waterborne ...

2024

Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing

Dariia Gudkova, Bart Deplancke, Daniel Migliozzi, Riccardo Dainese, Hüseyin Baris Atakan, Daniel Alpern, Mustafa Demir

High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatm ...

Springer2024

Impact of population size on early adaptation in rugged fitness landscapes

Anne-Florence Raphaëlle Bitbol, Richard Marie Servajean

Owing to stochastic fluctuations arising from finite population size, known as genetic drift, the ability of a population to explore a rugged fitness landscape depends on its size. In the weak mutation regime, while the mean steady-state fitness increases ...

ROYAL SOC2023

Viral Genetic Determinants of Prolonged Respiratory Syncytial Virus Infection Among Infants in a Healthy Term Birth Cohort

Jacques Fellay, Thomas Junier, Zhi Ming Xu, Dylan Lawless

Background. Respiratory syncytial virus (RSV) is associated with acute respiratory infection. We sought to identify RSV variants associated with prolonged infection. ...

OXFORD UNIV PRESS INC2023

PSGL-1 is an evolutionarily conserved antiviral restriction factor

Ying Liu

The arms race between viruses and their hosts shaped the evolutionary history and the genome composition of both parties. Restriction factors are the first-line antiviral effectors encoded by the host genomes and are often conserved through evolution to pr ...

AMER SOC MICROBIOLOGY2023

Frequent asymmetric migrations suppress natural selection in spatially structured populations

Anne-Florence Raphaëlle Bitbol, Alia Abbara

Natural microbial populations often have complex spatial structures. This can impact their evolution, in particular the ability of mutants to take over. While mutant fixation probabilities are known to be unaffected by sufficiently symmetric structures, ev ...

Oxford Univ Press2023

Identifying genetic and dietary modulators of metabolic disorders using systems genetics

Xiaoxu Li

Long-term consumption of lipid-rich foods can contribute to common metabolic diseases and systemic low-grade inflammation. However, dietary responses and the development of non-communicable diseases are shaped by genetic factors and gene-by-environment int ...

EPFL2023

Ligand concentration determines antiviral efficacy of silica multivalent nanoparticles

Francesco Stellacci, Paulo Henrique Jacob Silva, Quy Ong Khac, Heyun Wang, Xufeng Xu, Rémi Andréa La Polla

We have learned from the recent COVID-19 pandemic that the emergence of a new virus can quickly become a global health burden and kill millions of lives. Antiviral drugs are essential in our fight against viral diseases, but most of them are virus-specific ...

Academic Press Inc Elsevier Science2023

Reanalysis of mtDNA mutations of human primordial germ cells (PGCs) reveals NUMT contamination and suggests that selection in PGCs may be positive

Konstantin Popadin

The resilience of the mitochondrial genome (mtDNA) to a high mutational pressure depends, in part, on negative purifying selection in the germline. A paradigm in the field has been that such selection, at least in part, takes place in primordial germ cells ...

Elsevier Sci Ltd2023

Information Theory in Transmembrane Transport

Solange Marie Flatt

The past decades have seen the advent of information theory in various fields, from quantum physics to cosmology. At an intermediary scale between atomic and cosmological scales are biological systems and in particular the cell, as a constitutive element o ...

EPFL2023

Systematic benchmarking of single-cell ATAC-sequencing protocols

Bart Deplancke, Jörn Pezoldt, Camille Lucie Germaine Lambert

Benchmarking of scATAC-seq protocols demonstrates the effects of data quality on downstream analyses. ...

NATURE PORTFOLIO2023