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.

中文翻译：

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在许多人类病毒中，产生 CpG 的突变代价高昂

突变可以发生在整个病毒基因组中，可能是有益的、中性的或有害的。我们对在 G 旁边产生 C 的突变感兴趣，产生 CpG 位点。CpG 位点在真核和病毒基因组中很少见。对于真核生物，人们认为 CpG 位点很少见，因为它们在甲基化时容易发生突变。在病毒方面，我们对 CpG 位点为何稀有知之甚少。先前对 HIV 的研究表明，产生 CpG 的过渡突变比类似的非产生 CpG 的突变成本更高。为了确定其他病毒是否也是这种情况，我们使用从 Genbank、HIV 数据库和病毒病原体获得的现有数据分析了各种病毒株、亚型和病毒基因中 CpG 产生和非 CpG 产生突变的等位基因频率资源。我们的结果表明，对于大多数病毒来说，CpG 站点确实是昂贵的。通过了解 CpG 站点的成本，我们可以进一步了解病毒的进化和适应。