title: Germline viral "fossils" guide in silico reconstruction of a mid-Cenozoic era marsupial adeno-associated virus.
abstract: Germline endogenous viral elements (EVEs) genetically preserve viral nucleotide sequences useful to the study of viral evolution, gene mutation, and the phylogenetic relationships among host organisms. Here, we describe a lineage-specific, adeno-associated virus (AAV)-derived endogenous viral element (mAAV-EVE1) found within the germline of numerous closely related marsupial species. Molecular screening of a marsupial DNA panel indicated that mAAV-EVE1 occurs specifically within the marsupial suborder Macropodiformes (present-day kangaroos, wallabies, and related macropodoids), to the exclusion of other Diprotodontian lineages. Orthologous mAAV-EVE1 locus sequences from sixteen macropodoid species, representing a speciation history spanning an estimated 30 million years, facilitated compilation of an inferred ancestral sequence that recapitulates the genome of an ancient marsupial AAV that circulated among Australian metatherian fauna sometime during the late Eocene to early Oligocene. In silico gene reconstruction and molecular modelling indicate remarkable conservation of viral structure over a geologic timescale. Characterisation of AAV-EVE loci among disparate species affords insight into AAV evolution and, in the case of macropodoid species, may offer an additional genetic basis for assignment of phylogenetic relationships among the Macropodoidea. From an applied perspective, the identified AAV "fossils" provide novel capsid sequences for use in translational research and clinical applications.
authors.affiliation: Laboratory of Molecular Virology and Gene Therapy, National Heart, Lung and Blood Institute, Bethesda, Maryland, United States of America.
authors.forename: Richard H
authors.initials: RH
authors.lastname: Smith
authors.affiliation: Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales, Australia.
authors.forename: Claus V
authors.initials: CV
authors.lastname: Hallwirth
authors.affiliation: Department of Biochemistry and Genetics, La Trobe University, Bundoora, Victoria, Australia.
authors.forename: Michael
authors.initials: M
authors.lastname: Westerman
authors.affiliation: Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales, Australia.
authors.forename: Nicola A
authors.initials: NA
authors.lastname: Hetherington
authors.affiliation: The McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America.
authors.forename: Yu-Shan
authors.initials: YS
authors.lastname: Tseng
authors.affiliation: Laboratory of Molecular Virology and Gene Therapy, National Heart, Lung and Blood Institute, Bethesda, Maryland, United States of America.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Cecchini
authors.affiliation: Laboratory of Molecular Virology and Gene Therapy, National Heart, Lung and Blood Institute, Bethesda, Maryland, United States of America.
authors.forename: Tamas
authors.initials: T
authors.lastname: Virag
authors.affiliation: Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales, Australia.
authors.forename: Mona-Larissa
authors.initials: ML
authors.lastname: Ziegler
authors.affiliation: Evolutionary Genomics Research Group, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America.
authors.forename: Igor B
authors.initials: IB
authors.lastname: Rogozin
authors.affiliation: Evolutionary Genomics Research Group, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America.
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Koonin
authors.affiliation: The McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America.
authors.forename: Mavis
authors.initials: M
authors.lastname: Agbandje-McKenna
authors.affiliation: Laboratory of Molecular Virology and Gene Therapy, National Heart, Lung and Blood Institute, Bethesda, Maryland, United States of America.
authors.forename: Robert M
authors.initials: RM
authors.lastname: Kotin
authors.affiliation: Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales, Australia.|The University of Sydney, Discipline of Paediatrics and Child Health, Westmead, New South Wales, Australia.
authors.forename: Ian E
authors.initials: IE
authors.lastname: Alexander
mesh_terms: D000818:Animals; D019295:Computational Biology; D000229:Dependovirus / Q000145:classification* / Q000235:genetics*; D019143:Evolution, Molecular; D005580:Fossils; D005854:Germ Cells / Q000821:virology*; D008394:Marsupialia / Q000821:virology*