1
|
Caudill VR, Qin S, Winstead R, Kaur J, Tisthammer K, Pineda EG, Solis C, Cobey S, Bedford T, Carja O, Eggo RM, Koelle K, Lythgoe K, Regoes R, Roy S, Allen N, Aviles M, Baker BA, Bauer W, Bermudez S, Carlson C, Castellanos E, Catalan FL, Chemel AK, Elliot J, Evans D, Fiutek N, Fryer E, Goodfellow SM, Hecht M, Hopp K, Hopson ED, Jaberi A, Kinney C, Lao D, Le A, Lo J, Lopez AG, López A, Lorenzo FG, Luu GT, Mahoney AR, Melton RL, Nascimento GD, Pradhananga A, Rodrigues NS, Shieh A, Sims J, Singh R, Sulaeman H, Thu R, Tran K, Tran L, Winters EJ, Wong A, Pennings PS. CpG-creating mutations are costly in many human viruses. Evol Ecol 2020; 34:339-359. [PMID: 32508375 PMCID: PMC7245597 DOI: 10.1007/s10682-020-10039-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 03/11/2020] [Indexed: 01/26/2023]
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.
Collapse
Affiliation(s)
- Victoria R. Caudill
- Department of Biology, San Francisco State University, San Francisco, CA USA
- Department of Biology, University of Oregon, Eugene, OR USA
| | - Sarina Qin
- Department of Biology, San Francisco State University, San Francisco, CA USA
- Quantitative Systems Biology, Univeristy of California, Merced, CA USA
| | - Ryan Winstead
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Jasmeen Kaur
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Kaho Tisthammer
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - E. Geo Pineda
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Caroline Solis
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Oana Carja
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, USA
| | - Rosalind M. Eggo
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, GA USA
| | | | - Roland Regoes
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Scott Roy
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Nicole Allen
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Milo Aviles
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Brittany A. Baker
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - William Bauer
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Shannel Bermudez
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Corey Carlson
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Edgar Castellanos
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Francisca L. Catalan
- Department of Biology, San Francisco State University, San Francisco, CA USA
- Department of Neurological Surgery, University of California, San Francisco, CA USA
| | | | - Jacob Elliot
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Dwayne Evans
- Department of Biology, San Francisco State University, San Francisco, CA USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Natalie Fiutek
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Emily Fryer
- Department of Biology, San Francisco State University, San Francisco, CA USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA USA
| | - Samuel Melvin Goodfellow
- Department of Biology, San Francisco State University, San Francisco, CA USA
- Health Sciences Center, University of New Mexico, Albuquerque, NM USA
| | - Mordecai Hecht
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Kellen Hopp
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - E. Deshawn Hopson
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Amirhossein Jaberi
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Christen Kinney
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Derek Lao
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Adrienne Le
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Jacky Lo
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Alejandro G. Lopez
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Andrea López
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Fernando G. Lorenzo
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Gordon T. Luu
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Andrew R. Mahoney
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Rebecca L. Melton
- Department of Biology, San Francisco State University, San Francisco, CA USA
- UCSD Biomed Sciences PhD Program, University of California, San Diego, CA USA
| | | | - Anjani Pradhananga
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Nicole S. Rodrigues
- Department of Biology, San Francisco State University, San Francisco, CA USA
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis, CA USA
| | - Annie Shieh
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Jasmine Sims
- Department of Biology, San Francisco State University, San Francisco, CA USA
- UCSF Tetrad Graduate Program, University of California, San Francisco, CA USA
| | - Rima Singh
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Hasan Sulaeman
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Ricky Thu
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Krystal Tran
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Livia Tran
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | | | - Albert Wong
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Pleuni S. Pennings
- Department of Biology, San Francisco State University, San Francisco, CA USA
| |
Collapse
|