title: High genetic diversity and adaptive potential of two simian hemorrhagic fever viruses in a wild primate population.
abstract: Key biological properties such as high genetic diversity and high evolutionary rate enhance the potential of certain RNA viruses to adapt and emerge. Identifying viruses with these properties in their natural hosts could dramatically improve disease forecasting and surveillance. Recently, we discovered two novel members of the viral family Arteriviridae: simian hemorrhagic fever virus (SHFV)-krc1 and SHFV-krc2, infecting a single wild red colobus (Procolobus rufomitratus tephrosceles) in Kibale National Park, Uganda. Nearly nothing is known about the biological properties of SHFVs in nature, although the SHFV type strain, SHFV-LVR, has caused devastating outbreaks of viral hemorrhagic fever in captive macaques. Here we detected SHFV-krc1 and SHFV-krc2 in 40% and 47% of 60 wild red colobus tested, respectively. We found viral loads in excess of 10(6)-10(7) RNA copies per milliliter of blood plasma for each of these viruses. SHFV-krc1 and SHFV-krc2 also showed high genetic diversity at both the inter- and intra-host levels. Analyses of synonymous and non-synonymous nucleotide diversity across viral genomes revealed patterns suggestive of positive selection in SHFV open reading frames (ORF) 5 (SHFV-krc2 only) and 7 (SHFV-krc1 and SHFV-krc2). Thus, these viruses share several important properties with some of the most rapidly evolving, emergent RNA viruses.
authors.affiliation: Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America; Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America.
authors.forename: Adam L
authors.initials: AL
authors.lastname: Bailey
authors.affiliation: Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America; Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America.
authors.forename: Michael
authors.initials: M
authors.lastname: Lauck
authors.affiliation: Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America; Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
authors.forename: Andrea
authors.initials: A
authors.lastname: Weiler
authors.affiliation: Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America; Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
authors.forename: Samuel D
authors.initials: SD
authors.lastname: Sibley
authors.affiliation: Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
authors.forename: Jorge M
authors.initials: JM
authors.lastname: Dinis
authors.affiliation: Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America; Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
authors.forename: Zachary
authors.initials: Z
authors.lastname: Bergman
authors.affiliation: Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America.
authors.forename: Chase W
authors.initials: CW
authors.lastname: Nelson
authors.affiliation: Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
authors.forename: Michael
authors.initials: M
authors.lastname: Correll
authors.affiliation: Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
authors.forename: Michael
authors.initials: M
authors.lastname: Gleicher
authors.affiliation: Makerere University, Kampala, Uganda.
authors.forename: David
authors.initials: D
authors.lastname: Hyeroba
authors.affiliation: Makerere University, Kampala, Uganda.
authors.forename: Alex
authors.initials: A
authors.lastname: Tumukunde
authors.affiliation: Makerere University, Kampala, Uganda.
authors.forename: Geoffrey
authors.initials: G
authors.lastname: Weny
authors.affiliation: Makerere University, Kampala, Uganda; Department of Anthropology and School of Environment, McGill University, Montreal, Quebec, Canada.
authors.forename: Colin
authors.initials: C
authors.lastname: Chapman
authors.affiliation: Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, United States of America.
authors.forename: Jens H
authors.initials: JH
authors.lastname: Kuhn
authors.affiliation: Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America.
authors.forename: Austin L
authors.initials: AL
authors.lastname: Hughes
authors.affiliation: Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America; Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Friedrich
authors.affiliation: Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America; Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
authors.forename: Tony L
authors.initials: TL
authors.lastname: Goldberg
authors.affiliation: Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America; Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America.
authors.forename: David H
authors.initials: DH
authors.lastname: O'Connor
mesh_terms: D000818:Animals; D000835:Animals, Wild / Q000821:virology*; D018018:Arterivirus / Q000235:genetics*; D018174:Arterivirus Infections / Q000662:veterinary* / Q000821:virology; D001483:Base Sequence; D014644:Genetic Variation; D016679:Genome, Viral / Q000235:genetics; D054884:Host-Pathogen Interactions / Q000235:genetics; D011323:Primates / Q000235:genetics / Q000821:virology*; D019562:Viral Load / Q000235:genetics