title: New insights into flavivirus evolution, taxonomy and biogeographic history, extended by analysis of canonical and alternative coding sequences.
abstract: To generate the most diverse phylogenetic dataset for the flaviviruses to date, we determined the genomic sequences and phylogenetic relationships of 14 flaviviruses, of which 10 are primarily associated with Culex spp. mosquitoes. We analyze these data, in conjunction with a comprehensive collection of flavivirus genomes, to characterize flavivirus evolutionary and biogeographic history in unprecedented detail and breadth. Based on the presumed introduction of yellow fever virus into the Americas via the transatlantic slave trade, we extrapolated a timescale for a relevant subset of flaviviruses whose evolutionary history, shows that different Culex-spp. associated flaviviruses have been introduced from the Old World to the New World on at least five separate occasions, with 2 different sets of factors likely to have contributed to the dispersal of the different viruses. We also discuss the significance of programmed ribosomal frameshifting in a central region of the polyprotein open reading frame in some mosquito-associated flaviviruses.
authors.affiliation: Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 Emergence des Pathologies Virales, Marseille, France.
authors.forename: Gregory
authors.initials: G
authors.lastname: Moureau
authors.affiliation: Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom.
authors.forename: Shelley
authors.initials: S
authors.lastname: Cook
authors.affiliation: Department of Microbiology and Immunology, Rega Institute, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium.
authors.forename: Philippe
authors.initials: P
authors.lastname: Lemey
authors.affiliation: Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 Emergence des Pathologies Virales, Marseille, France.
authors.forename: Antoine
authors.initials: A
authors.lastname: Nougairede
authors.affiliation: Institute for Human Infections and Immunity and Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, United States of America.
authors.forename: Naomi L
authors.initials: NL
authors.lastname: Forrester
authors.affiliation: Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Crowmarsh, Gifford, Wallingford, Oxfordshire, OX10, United Kingdom.
authors.forename: Maxim
authors.initials: M
authors.lastname: Khasnatinov
authors.affiliation: Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 Emergence des Pathologies Virales, Marseille, France.
authors.forename: Remi N
authors.initials: RN
authors.lastname: Charrel
authors.affiliation: Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom.
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Firth
authors.affiliation: Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 Emergence des Pathologies Virales, Marseille, France.
authors.forename: Ernest A
authors.initials: EA
authors.lastname: Gould
authors.affiliation: Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 Emergence des Pathologies Virales, Marseille, France.
authors.forename: Xavier
authors.initials: X
authors.lastname: de Lamballerie
mesh_terms: D001483:Base Sequence; D019143:Evolution, Molecular; D005416:Flavivirus / Q000145:classification / Q000235:genetics* / Q000502:physiology; D018965:Frameshifting, Ribosomal; D016679:Genome, Viral; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D058974:Phylogeography