RT Journal Article
SR Electronic
T1 CpG-creating Mutations are Costly in Many Human Viruses
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 702175
DO 10.1101/702175
A1 Victoria R. Caudill
A1 Sarina Qin
A1 Ryan Winstead
A1 Jasmeen Kaur
A1 Kaho Tisthammer
A1 E. Geo Pineda
A1 Oana Carja
A1 Rosalind M Eggo
A1 Katia Koelle
A1 Katrina Lythgoe
A1 Scott Roy
A1 Nicole Allen
A1 Milo Aviles
A1 Brittany A. Baker
A1 William Bauer
A1 Shannel Bermudez
A1 Corey Carlson
A1 Francisca L. Catalan
A1 Angeline Katia Chemel
A1 Dwayne Evans
A1 Natalie Fiutek
A1 Emily Fryer
A1 Samuel Melvin Goodfellow
A1 Mordecai Hecht
A1 Kellen Hopp
A1 E. Deshawn Hopson, Jr
A1 Amirhossein Jaberi
A1 Christen Kinney
A1 Derek Lao
A1 Adrienne Le
A1 Jacky Lo
A1 Alejandro G. Lopez
A1 Andrea López
A1 Fernando G Lorenzo
A1 Gordon T Luu
A1 Andrew R Mahoney
A1 Rebecca L. Melton
A1 Gabriela Do Nascimento
A1 Anjani Pradhananga
A1 Nicole S. Rodrigues
A1 Annie Shieh
A1 Jasmine Sims
A1 Rima Singh
A1 Hasan Sulaeman
A1 Ricky Thu
A1 Krystal Tran
A1 Livia Tran
A1 Elizabeth J. Winters
A1 Albert Wong
A1 Pleuni S. Pennings
YR 2019
UL http://biorxiv.org/content/early/2019/07/25/702175.abstract
AB Mutations can occur throughout the virus genome and may be beneficial 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 that 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 costly for most viruses. By understanding the cost of CpG sites, we can obtain further insights into the evolution and adaptation of viruses.