title: Clonality and intracellular polyploidy in virus evolution and pathogenesis.
abstract: In the present article we examine clonality in virus evolution. Most viruses retain an active recombination machinery as a potential means to initiate new levels of genetic exploration that go beyond those attainable solely by point mutations. However, despite abundant recombination that may be linked to molecular events essential for genome replication, herein we provide evidence that generation of recombinants with altered biological properties is not essential for the completion of the replication cycles of viruses, and that viral lineages (near-clades) can be defined. We distinguish mechanistically active but inconsequential recombination from evolutionarily relevant recombination, illustrated by episodes in the field and during experimental evolution. In the field, recombination has been at the origin of new viral pathogens, and has conferred fitness advantages to some viruses once the parental viruses have attained a sufficient degree of diversification by point mutations. In the laboratory, recombination mediated a salient genome segmentation of foot-and-mouth disease virus, an important animal pathogen whose genome in nature has always been characterized as unsegmented. We propose a model of continuous mutation and recombination, with punctuated, biologically relevant recombination events for the survival of viruses, both as disease agents and as promoters of cellular evolution. Thus, clonality is the standard evolutionary mode for viruses because recombination is largely inconsequential, since the decisive events for virus replication and survival are not dependent on the exchange of genetic material and formation of recombinant (mosaic) genomes.
authors.affiliation: Centro de Biologia Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, E-28049 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Spain; and Liver Unit, Internal Medicine, Laboratory of Malalties Hepàtiques, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain.
authors.forename: Celia
authors.initials: C
authors.lastname: Perales
authors.affiliation: Centro de Biologia Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, E-28049 Madrid, Spain;
authors.forename: Elena
authors.initials: E
authors.lastname: Moreno
authors.affiliation: Centro de Biologia Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, E-28049 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Spain; and edomingo@cbm.csic.es.
authors.forename: Esteban
authors.initials: E
authors.lastname: Domingo
mesh_terms: D000818:Animals; D005075:Biological Evolution; D002999:Clone Cells; D029544:Foot-and-Mouth Disease Virus / Q000235:genetics; D042541:Intracellular Space / Q000821:virology*; D008954:Models, Biological; D011123:Polyploidy; D011995:Recombination, Genetic / Q000235:genetics; D009626:Terminology as Topic; D014780:Viruses / Q000235:genetics*
keywords: evolutionary dynamics; genome segmentation; mutation; quasispecies; recombination