6 papers
Bacteriophage Q: Six Decades at the Frontier of Molecular and Viral Evolution
Ester Lázaro, Susanna Manrubia
Bacteriophage Q, first isolated in 1961, has served for more than six decades as a model system for molecular and viral evolution. The development of cell-free replication syste…
Shared quasispecies architecture in experimental and natural RNA virus populations
Samuel Martínez-Alcalá, Iker Atienza-Diez, Pilar Somovilla +5
RNA viruses form genetically diverse populations structured as mutant spectra, or quasispecies, whose internal organization influences their evolutionary and adaptive dynamics. Whi…
A generative model for bipartite gene-sharing networks
Jaime Iranzo, Pedro Jódar, Eugene V. Koonin +2
Gene-sharing networks provide a powerful framework to study the evolution of viruses and mobile genetic elements. These bipartite networks, which link genes to the genomes that con…
The challenge of scale in molecular adaptation: Local searches in astronomical genotype networks
Susanna Manrubia, Luis F. Seoane, José A. Cuesta
The exploration of vast genotype spaces poses fundamental challenges for evolving populations. As the number of genotypes encoding viable phenotypes grows exponentially with genome…
Optimal COVID-19 vaccine prioritization by age depends critically on inter-group contacts and vaccination rates
Iker Atienza-Diez, Gabriel Rodriguez-Maroto, Saúl Ares +1
The limited availability of COVID-19 vaccines has prompted extensive research on optimal vaccination strategies. Previous studies have considered various non-pharmaceutical interve…
Hierarchical genotype networks and incipient ecological speciation in Q phage quasispecies
Luis F Seoane, Henry Secaira-Morocho, Ester Lázaro +1
Understanding how viral mutant spectra organize and explore genotype space is essential for unraveling the mechanisms driving evolution at the finest scale. Here we use deep-sequen…