title: Ebola virus genome plasticity as a marker of its passaging history: a comparison of in vitro passaging to non-human primate infection.
abstract: To identify polymorphic sites that could be used as biomarkers of Ebola virus passage history, we repeatedly amplified Ebola virus (Kikwit variant) in vitro and in vivo and performed deep sequencing analysis of the complete genomes of the viral subpopulations. We then determined the sites undergoing selection during passage in Vero E6 cells. Four locations within the Ebola virus Kikwit genome were identified that together segregate cell culture-passaged virus and virus obtained from infected non-human primates. Three of the identified sites are located within the glycoprotein gene (GP) sequence: the poly-U (RNA editing) site at position 6925, as well as positions 6677, and 6179. One site was found in the VP24 gene at position 10833. In all cases, in vitro and in vivo, both populations (majority and minority variants) were maintained in the viral swarm, with rapid selections occurring after a few passages or infections. This analysis approach will be useful to differentiate whether filovirus stocks with unknown history have been passaged in cell culture and may support filovirus stock standardization for medical countermeasure development.
authors.affiliation: Genomics Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, United States of America.
authors.forename: Jeffrey R
authors.initials: JR
authors.lastname: Kugelman
authors.forename: Michael S
authors.initials: MS
authors.lastname: Lee
authors.forename: Cynthia A
authors.initials: CA
authors.lastname: Rossi
authors.forename: Sarah E
authors.initials: SE
authors.lastname: McCarthy
authors.forename: Sheli R
authors.initials: SR
authors.lastname: Radoshitzky
authors.forename: John M
authors.initials: JM
authors.lastname: Dye
authors.forename: Lisa E
authors.initials: LE
authors.lastname: Hensley
authors.forename: Anna
authors.initials: A
authors.lastname: Honko
authors.forename: Jens H
authors.initials: JH
authors.lastname: Kuhn
authors.forename: Peter B
authors.initials: PB
authors.lastname: Jahrling
authors.forename: Travis K
authors.initials: TK
authors.lastname: Warren
authors.forename: Chris A
authors.initials: CA
authors.lastname: Whitehouse
authors.forename: Sina
authors.initials: S
authors.lastname: Bavari
authors.forename: Gustavo
authors.initials: G
authors.lastname: Palacios
mesh_terms: D000818:Animals; D018929:Cell Culture Techniques; D016000:Cluster Analysis; D029043:Ebolavirus / Q000235:genetics*; D005819:Genetic Markers; D016679:Genome, Viral; D006023:Glycoproteins / Q000235:genetics; D019142:Hemorrhagic Fever, Ebola / Q000235:genetics / Q000821:virology; D009154:Mutation; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide; D011323:Primates / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D014709:Vero Cells; D014764:Viral Proteins / Q000235:genetics
chemical_list: D005819:Genetic Markers; D006023:Glycoproteins; D012367:RNA, Viral; D014764:Viral Proteins