title: Single-Cell Analysis of RNA Virus Infection Identifies Multiple Genetically Diverse Viral Genomes within Single Infectious Units.
abstract: Genetic diversity enables a virus to colonize novel hosts, evade immunity, and evolve drug resistance. However, viral diversity is typically assessed at the population level. Given the existence of cell-to-cell variation, it is critical to understand viral genetic structure at the single-cell level. By combining single-cell isolation with ultra-deep sequencing, we characterized the genetic structure and diversity of a RNA virus shortly after single-cell bottlenecks. Full-length sequences from 881 viral plaques derived from 90 individual cells reveal that sequence variants pre-existing in different viral genomes can be co-transmitted within the same infectious unit to individual cells. Further, the rate of spontaneous virus mutation varies across individual cells, and early production of diversity depends on the viral yield of the very first infected cell. These results unravel genetic and structural features of a virus at the single-cell level, with implications for viral diversity and evolution.
authors.affiliation: Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, C/ Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain.
authors.forename: Marine
authors.initials: M
authors.lastname: Combe
authors.affiliation: Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, C/ Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain.
authors.forename: Raquel
authors.initials: R
authors.lastname: Garijo
authors.affiliation: Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, C/ Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain.
authors.forename: Ron
authors.initials: R
authors.lastname: Geller
authors.affiliation: Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, C/ Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain.
authors.forename: José M
authors.initials: JM
authors.lastname: Cuevas
authors.affiliation: Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, C/ Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain. Electronic address: rafael.sanjuan@uv.es.
authors.forename: Rafael
authors.initials: R
authors.lastname: Sanjuán
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D006224:Cricetinae; D004847:Epithelial Cells / Q000821:virology*; D014644:Genetic Variation; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D059010:Single-Cell Analysis / Q000379:methods*; D018116:Vesiculovirus / Q000145:classification / Q000235:genetics* / Q000254:growth & development*; D014773:Virology / Q000379:methods