title: Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch.
abstract: Viruses preserved in ancient materials provide snapshots of past viral diversity and a means to trace viral evolution through time. Here, we use a metagenomics approach to identify filterable and nuclease-resistant nucleic acids preserved in 700-y-old caribou feces frozen in a permanent ice patch. We were able to recover and characterize two viruses in replicated experiments performed in two different laboratories: a small circular DNA viral genome (ancient caribou feces associated virus, or aCFV) and a partial RNA viral genome (Ancient Northwest Territories cripavirus, or aNCV). Phylogenetic analysis identifies aCFV as distantly related to the plant-infecting geminiviruses and the fungi-infecting Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 and aNCV as within the insect-infecting Cripavirus genus. We hypothesize that these viruses originate from plant material ingested by caribou or from flying insects and that their preservation can be attributed to protection within viral capsids maintained at cold temperatures. To investigate the tropism of aCFV, we used the geminiviral reverse genetic system and introduced a multimeric clone into the laboratory model plant Nicotiana benthamiana. Evidence for infectivity came from the detection of viral DNA in newly emerged leaves and the precise excision of the viral genome from the multimeric clones in inoculated leaves. Our findings indicate that viral genomes may in some circumstances be protected from degradation for centuries.
authors.affiliation: Blood Systems Research Institute, San Francisco, CA 94118; Department of Laboratory Medicine, University of California, San Francisco, CA 94118;
authors.forename: Terry Fei Fan
authors.identifier: http://orcid.org/0000-0002-4815-8697
authors.initials: TF
authors.lastname: Ng
authors.affiliation: Department of Plant Pathology, University of California, Davis, CA 95616;
authors.forename: Li-Fang
authors.initials: LF
authors.lastname: Chen
authors.affiliation: Blood Systems Research Institute, San Francisco, CA 94118; Department of Laboratory Medicine, University of California, San Francisco, CA 94118;
authors.forename: Yanchen
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Department of Ecology & Evolutionary Biology, University of California, Santa Cruz, CA 95064;
authors.forename: Beth
authors.initials: B
authors.lastname: Shapiro
authors.affiliation: Department of Ecology & Evolutionary Biology, University of California, Santa Cruz, CA 95064;
authors.forename: Mathias
authors.initials: M
authors.lastname: Stiller
authors.affiliation: Department of Ecology & Evolutionary Biology, University of California, Santa Cruz, CA 95064;
authors.forename: Peter D
authors.identifier: http://orcid.org/0000-0002-6449-0219
authors.initials: PD
authors.lastname: Heintzman
authors.affiliation: School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611; Electron Microscope Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, Cape Town, 7701, South Africa;
authors.forename: Arvind
authors.initials: A
authors.lastname: Varsani
authors.affiliation: Blood Systems Research Institute, San Francisco, CA 94118;
authors.forename: Nikola O
authors.initials: NO
authors.lastname: Kondov
authors.affiliation: Blood Systems Research Institute, San Francisco, CA 94118;
authors.forename: Walt
authors.initials: W
authors.lastname: Wong
authors.affiliation: Blood Systems Research Institute, San Francisco, CA 94118; Department of Laboratory Medicine, University of California, San Francisco, CA 94118;
authors.forename: Xutao
authors.initials: X
authors.lastname: Deng
authors.affiliation: Prince of Wales Northern Heritage Centre, Government of the Northwest Territories, Yellowknife, NT, Canada X1A2L9;
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Andrews
authors.affiliation: Department of Geography, University of Calgary, Calgary, AB, Canada T2N1N4; and.
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Moorman
authors.affiliation: Department of Physical and Environmental Sciences, University of Toronto, Scarborough, Toronto, Ontario, Canada M1C1A4.
authors.forename: Thomas
authors.initials: T
authors.lastname: Meulendyk
authors.affiliation: Prince of Wales Northern Heritage Centre, Government of the Northwest Territories, Yellowknife, NT, Canada X1A2L9;
authors.forename: Glen
authors.initials: G
authors.lastname: MacKay
authors.affiliation: Department of Plant Pathology, University of California, Davis, CA 95616;
authors.forename: Robert L
authors.initials: RL
authors.lastname: Gilbertson
authors.affiliation: Blood Systems Research Institute, San Francisco, CA 94118; Department of Laboratory Medicine, University of California, San Francisco, CA 94118; delwarte@medicine.ucsf.edu.
authors.forename: Eric
authors.initials: E
authors.lastname: Delwart
mesh_terms: D000818:Animals; D001110:Arctic Regions; D005243:Feces / Q000821:virology*; D016679:Genome, Viral; D008969:Molecular Sequence Data; D012053:Reindeer
keywords: aDNA; ancient virus; metagenomics; paleopathology; reverse genetics