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High Genetic Diversity and Adaptive Potential of Two Simian Hemorrhagic Fever Viruses in a Wild Primate Population

Adam Bailey, Michael Lauck, Andrea Weiler, Samuel Sibley, Jorge Dinis, Zachary Bergman, Chase Nelson, Michael Correll, Michael Gleicher, David Hyeroba, Alex Tumukunde, Geoffrey Weny, Colin Chapman, Jens Kuhn, Austin Hughes, Thomas Friedrich, Tony Goldberg, David O'Connor
PLoS ONE, Volume 9, Number 3 — mar 2014
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 106-107 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.

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BibTex references

  author       = "Bailey, Adam and Lauck, Michael and Weiler, Andrea and Sibley, Samuel and Dinis, Jorge and Bergman, Zachary and Nelson, Chase and Correll, Michael and Gleicher, Michael and Hyeroba, David and Tumukunde, Alex and Weny, Geoffrey and Chapman, Colin and Kuhn, Jens and Hughes, Austin and Friedrich, Thomas and Goldberg, Tony and O'Connor, David",
  title        = "High Genetic Diversity and Adaptive Potential of Two Simian Hemorrhagic Fever Viruses in a Wild Primate Population",
  journal      = "PLoS ONE",
  number       = "3",
  volume       = "9",
  month        = "mar",
  year         = "2014",
  ee           = "http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0090714",
  doi          = "10.1371/journal.pone.0090714",
  projecturl   = "http://graphics.cs.wisc.edu/Vis/LayerCake/",
  url          = "http://graphics.cs.wisc.edu/Papers/2014/BLWSDBNCGHTWCKHFGO14"

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