title: Recombination in viruses: mechanisms, methods of study, and evolutionary consequences.
abstract: Recombination is a pervasive process generating diversity in most viruses. It joins variants that arise independently within the same molecule, creating new opportunities for viruses to overcome selective pressures and to adapt to new environments and hosts. Consequently, the analysis of viral recombination attracts the interest of clinicians, epidemiologists, molecular biologists and evolutionary biologists. In this review we present an overview of three major areas related to viral recombination: (i) the molecular mechanisms that underlie recombination in model viruses, including DNA-viruses (Herpesvirus) and RNA-viruses (Human Influenza Virus and Human Immunodeficiency Virus), (ii) the analytical procedures to detect recombination in viral sequences and to determine the recombination breakpoints, along with the conceptual and methodological tools currently used and a brief overview of the impact of new sequencing technologies on the detection of recombination, and (iii) the major areas in the evolutionary analysis of viral populations on which recombination has an impact. These include the evaluation of selective pressures acting on viral populations, the application of evolutionary reconstructions in the characterization of centralized genes for vaccine design, and the evaluation of linkage disequilibrium and population structure.
authors.affiliation: CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Portugal; Computational Biology Institute, George Washington University, Ashburn, VA 20147, USA.
authors.forename: Marcos
authors.initials: M
authors.lastname: Pérez-Losada
authors.affiliation: Centre for Molecular Biology "Severo Ochoa", Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.
authors.forename: Miguel
authors.initials: M
authors.lastname: Arenas
authors.affiliation: Servicio de Microbiología, Hospital Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; CIBER en Epidemiología y Salud Pública, Spain.
authors.forename: Juan Carlos
authors.initials: JC
authors.lastname: Galán
authors.affiliation: CIBER en Epidemiología y Salud Pública, Spain; Unidad Mixta Infección y Salud Pública, FISABIO-Universitat de València, Valencia, Spain.
authors.forename: Ferran
authors.initials: F
authors.lastname: Palero
authors.affiliation: CIBER en Epidemiología y Salud Pública, Spain; Unidad Mixta Infección y Salud Pública, FISABIO-Universitat de València, Valencia, Spain. Electronic address: fernando.gonzalez@uv.es.
authors.forename: Fernando
authors.initials: F
authors.lastname: González-Candelas
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D006801:Humans; D015810:Linkage Disequilibrium; D009154:Mutation; D016865:Reassortant Viruses; D011995:Recombination, Genetic / Q000235:genetics*; D014777:Virus Diseases / Q000821:virology; D014780:Viruses / Q000235:genetics*
keywords: Linkage disequilibrium; Mutation rate; Population structure; Reassortment; Recombination; Recombination rate