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
Department of Biology, San Francisco State University, San Francisco, CA USA.
Department of Biology, University of Oregon, Eugene, OR USA.
Evol Ecol. 2020;34(3):339-359. doi: 10.1007/s10682-020-10039-z. Epub 2020 Apr 24.
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.
突变可发生在病毒基因组的任何位置，可能是有益的、中性的或有害的。我们感兴趣的是那些在G旁边产生C从而形成CpG位点的突变。CpG位点在真核生物和病毒基因组中很少见。对于真核生物来说，人们认为CpG位点稀少是因为它们在甲基化时容易发生突变。在病毒中，我们对CpG位点稀少的原因了解较少。先前一项关于HIV的研究表明，产生CpG的转换突变比类似的不产生CpG的突变代价更高。为了确定在其他病毒中是否也是如此，我们利用从Genbank、HIV数据库和病毒病原体资源获得的现有数据，分析了各种病毒株、亚型和基因中产生CpG和不产生CpG的突变的等位基因频率。我们的结果表明，对于大多数病毒来说，CpG位点确实代价高昂。通过了解CpG位点的代价，我们可以进一步深入了解病毒的进化和适应性。
