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CpG-creating mutations are costly in many human viruses.

  • Caudill VR Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Qin S Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Winstead R Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Kaur J Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Tisthammer K Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Pineda EG Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Solis C Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Cobey S Department of Ecology and Evolution, University of Chicago, Chicago, IL USA.
  • Bedford T Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA.
  • Carja O Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, USA.
  • Eggo RM Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK.
  • Koelle K Department of Biology, Emory University, Atlanta, GA USA.
  • Lythgoe K Big Data Institute, University of Oxford, Oxford, UK.
  • Regoes R Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland.
  • Roy S Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Allen N Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Aviles M Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Baker BA Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Bauer W Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Bermudez S Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Carlson C Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Castellanos E Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Catalan FL Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Chemel AK Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Elliot J Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Evans D Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Fiutek N Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Fryer E Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Goodfellow SM Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Hecht M Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Hopp K Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Hopson ED Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Jaberi A Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Kinney C Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Lao D Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Le A Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Lo J Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Lopez AG Department of Biology, San Francisco State University, San Francisco, CA USA.
  • López A Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Lorenzo FG Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Luu GT Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Mahoney AR Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Melton RL Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Nascimento GD Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Pradhananga A Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Rodrigues NS Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Shieh A Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Sims J Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Singh R Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Sulaeman H Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Thu R Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Tran K Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Tran L Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Winters EJ Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Wong A Department of Biology, San Francisco State University, San Francisco, CA USA.
  • Pennings PS Department of Biology, San Francisco State University, San Francisco, CA USA.
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  • 2020-06-09
Published in:
  • Evolutionary ecology. - 2020
CpG sites
Fitness costs
Mutations
Viruses
English Mutations can occur throughout the virus genome and may be beneficial, neutral or deleterious. We are interested in mutations that yield a C next to a G, producing CpG sites. CpG sites are rare in eukaryotic and viral genomes. For the eukaryotes, it is thought that CpG sites are rare because they are prone to mutation when methylated. In viruses, we know less about why CpG sites are rare. A previous study in HIV suggested that CpG-creating transition mutations are more costly than similar non-CpG-creating mutations. To determine if this is the case in other viruses, we analyzed the allele frequencies of CpG-creating and non-CpG-creating mutations across various strains, subtypes, and genes of viruses using existing data obtained from Genbank, HIV Databases, and Virus Pathogen Resource. Our results suggest that CpG sites are indeed costly for most viruses. By understanding the cost of CpG sites, we can obtain further insights into the evolution and adaptation of viruses.
Language
  • English
Open access status
hybrid
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Persistent URL
https://sonar.ch/global/documents/3776
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