CpG-creating mutations are costly in many human viruses

Author:

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

Abstract

AbstractMutations 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.

Funder

National Science Foundation

National Institutes of Health

Genentech Foundation

Publisher

Springer Science and Business Media LLC

Subject

Ecology, Evolution, Behavior and Systematics

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3