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Author Notes:

Correspondence: Sarah Cobey, cobey@uchicago.edu

We thank Adi Stern and the Stern lab for discussion We thank the Student Enrichment Office for supporting student research at SF State Biology.

Disclosures: The authors declare no conflicts of interest.

Subjects:

Research Funding:

Pleuni Pennings, Victoria Caudill, Sarina Qin, Ryan Winstead, Jasmeen Kaur, Esteban Geo Pineda, Emily Fryer, Caroline Solis, Kaho Tisthammer and Anjani Pradhananga were supported by NSF Grant # 1655212 to Pleuni S. Pennings.

Sarah Cobey and Pleuni Pennings were supported by a Grant from the National Evolutionary Synthesis Center (NESCent), NSF # EF-0905606.

Angeline K. Chemel, E. Deshawn Hopson, Nicole S. Rodriques and Caroline Solis were supported by the NIH MARC Grant (T34-GM008574).

Dwayne Evans was supported by the NIH MA/MS-PhD Bridge Grant (R25-GM048972).

Dwayne Evans, Alejandro G. Lopez, A.R. Mahoney, Rebecca L. Melton Nathan O’Neill and Ryan Winstead were supported by the NIH RISE Grant (R25-GM059298) Angeline K. Chemel, Kellen Hopp and Jasmine Sims were supported by the NSF STC CCC Grant (DBI 1548297).

Dwayne Evans and Alejandro G. Lopez were supported by a Genentech Foundation MS Dissertation Scholarship. Caroline Solis was supported by a Genentech Foundation fellowship.

Keywords:

  • Science & Technology
  • Life Sciences & Biomedicine
  • Ecology
  • Evolutionary Biology
  • Genetics & Heredity
  • Environmental Sciences & Ecology
  • Mutations
  • Viruses
  • Fitness costs
  • CpG sites
  • Consequences
  • Transmission

CpG-creating mutations are costly in many human viruses

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Journal Title:

Evolutionary Ecology

Volume:

Volume 34, Number 3

Publisher:

, Pages 339-359

Type of Work:

Article | Final Publisher PDF

Abstract:

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.

Copyright information:

© The Author(s) 2020.

This is an Open Access work distributed under the terms of the Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/).
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