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1. Correction to: CpG‑creating mutations are costly in many human viruses

Author

Samuel Melvin Goodfellow, Shannel Bermudez, Nicole Allen, Kaho H. Tisthammer, Anjani Pradhananga, Caroline Solis, Katia Koelle, Jasmeen Kaur, Jacky Lo, Kellen Hopp, Krystal Tran, Emily Fryer, Christen Kinney, Alejandro G. Lopez, Katrina A. Lythgoe, Albert Wong, Elizabeth J. Winters, Livia Tran, Hasan Sulaeman, Pleuni S. Pennings, Milo Aviles, Adrienne Le, E. Geo Pineda, Rebecca L. Melton, William Bauer, Corey Carlson, Derek Lao, Amirhossein Jaberi, Jacob Elliot, Gordon T. Luu, Rima Singh, Andrew R. Mahoney, Roland R. Regoes, Victoria R. Caudill, Natalie Fiutek, Scott William Roy, Fernando G. Lorenzo, Jennifer Kim, Ricky Thu, Rosalind M Eggo, Mordecai Hecht, E. Deshawn Hopson, Ryan Winstead, Angeline Katia Chemel, Trevor Bedford, Dwayne Evans, Jasmine Sims, Sarina Qin, Gabriela Do Nascimento, Nicole S. Rodrigues, Oana Carja, Annie Shieh, Andrea López, Brittany A. Baker, Francisca L. Catalan, Sarah Cobey, and Edgar Castellanos

Subjects
CpG site, Animal ecology, Evolutionary biology, Ecology (disciplines), Biology, Publication process, Ecology, Evolution, Behavior and Systematics
Abstract

In the original article, the co-author name "Jennifer Kim" has been inadvertently missed during the publication process. The complete author group is given in this correction.

Published
2020

2. CpG-creating Mutations are Costly in Many Human Viruses

Author

Corey Carlson, Samuel Melvin Goodfellow, Nicole Allen, Pleuni S. Pennings, Milo Aviles, Jacky Lo, Rima Singh, Andrew R. Mahoney, Shannel Bermudez, Rebecca L. Melton, Anjani Pradhananga, Annie Shieh, Mordecai Hecht, Sarah Cobey, William Bauer, Francisca L. Catalan, Kellen Hopp, Edgar Castellanos, Ryan Winstead, Hasan Sulaeman, Angeline Katia Chemel, Rosalind M Eggo, Alejandro G. Lopez, Ricky Thu, Adrienne Le, Victoria R. Caudill, Trevor Bedford, E. Geo Pineda, Livia Tran, Andrea López, Fernando G. Lorenzo, Dwayne Evans, Sarina Qin, Gabriela Do Nascimento, Amirhossein Jaberi, Nicole S. Rodrigues, Oana Carja, Katia Koelle, Brittany A. Baker, Gordon T. Luu, Elizabeth J. Winters, Krystal Tran, Christen Kinney, Natalie Fiutek, Scott William Roy, Roland R. Regoes, Katrina A. Lythgoe, Caroline Solis, Jasmeen Kaur, Emily Fryer, Albert Wong, Kaho H. Tisthammer, Derek Lao, Jacob Elliot, E. Deshawn Hopson, and Jasmine Sims

Subjects
0106 biological sciences, 0301 basic medicine, viruses, CpG sites, Mutations, Viruses, Fitness costs, Biology, medicine.disease_cause, 010603 evolutionary biology, 01 natural sciences, Genome, Virus, 03 medical and health sciences, 0302 clinical medicine, medicine, Gene, Allele frequency, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Genetics, 0303 health sciences, Mutation, Original Paper, Transition (genetics), 3. Good health, 030104 developmental biology, CpG site, Animal ecology, GenBank, 030217 neurology & neurosurgery
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., Evolutionary Ecology, 34, ISSN:0269-7653, ISSN:1573-8477

Published
2019
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