title: Multiple layers of chimerism in a single-stranded DNA virus discovered by deep sequencing.
abstract: Viruses with single-stranded (ss) DNA genomes infect hosts in all three domains of life and include many medically, ecologically, and economically important pathogens. Recently, a new group of ssDNA viruses with chimeric genomes has been discovered through viral metagenomics. These chimeric viruses combine capsid protein genes and replicative protein genes that, respectively, appear to have been inherited from viruses with positive-strand RNA genomes, such as tombusviruses, and ssDNA genomes, such as circoviruses, nanoviruses or geminiviruses. Here, we describe the genome sequence of a new representative of this virus group and reveal an additional layer of chimerism among ssDNA viruses. We show that not only do these viruses encompass genes for capsid proteins and replicative proteins that have distinct evolutionary histories, but also the replicative genes themselves are chimeras of functional domains inherited from viruses of different families. Our results underscore the importance of horizontal gene transfer in the evolution of ssDNA viruses and the role of genetic recombination in the emergence of novel virus groups.
authors.affiliation: Department of Microbiology, Institut Pasteur, Paris, France krupovic@pasteur.fr.
authors.forename: Mart
authors.initials: M
authors.lastname: Krupovic
authors.affiliation: Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD.
authors.forename: Ning
authors.initials: N
authors.lastname: Zhi
authors.affiliation: Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD.
authors.forename: Jungang
authors.initials: J
authors.lastname: Li
authors.affiliation: Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD.
authors.forename: Gangqing
authors.initials: G
authors.lastname: Hu
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD.
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Koonin
authors.affiliation: Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD.
authors.forename: Susan
authors.initials: S
authors.lastname: Wong
authors.affiliation: Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD.
authors.forename: Sofiya
authors.initials: S
authors.lastname: Shevchenko
authors.affiliation: Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD.
authors.forename: Keji
authors.initials: K
authors.lastname: Zhao
authors.affiliation: Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD.
authors.forename: Neal S
authors.initials: NS
authors.lastname: Young
mesh_terms: D004267:DNA Viruses / Q000235:genetics*; D004277:DNA, Single-Stranded / Q000737:chemistry; D004279:DNA, Viral / Q000737:chemistry; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D012328:RNA Viruses / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004277:DNA, Single-Stranded; D004279:DNA, Viral
keywords: genetic recombination; metagenomics; origin of viruses; ssDNA viruses; virus evolution
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