CpG-creating Mutations are Costly in Many Human Viruses

Abstract

<jats:title>Abstract</jats:title><jats:p>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.</jats:p>

Global SNP analysis of 11,183 SARS‐CoV‐2 strains reveals high genetic diversity

“…Among all 119 SNPs across the genome, there are 60 positions with nucleotide substitutions from C to T, accounting for half of SNPs (Figure 1). It has been reported that transition mutations are much more common than transversion mutations in viruses (Caudill et al, 2019). (43), and among all non-synonymous mutation sites, 9 were mutated from T to I, 6 from A to V and 6 also from S to L (Data not shown).…”