Why does methylation not occur in viral DNA? Can viral DNA undergo the process of methylation? If not then why does this process does not occur in viruses?
Hoelzer et al. give a review of the presence and role of cytosine methylation in DNA viruses of animals:
To understand the impact of cytosine methylation on the viral life cycle and the evolution of base composition, the particularities of each virus will need to be considered. Differences will inevitably exist between actively replicating viral DNA and that which is integrated into the host genome. The type of viral persistence will also be of importance. The integration of adeno- or polyomavirus DNA into the host genome is usually a terminal process since the viruses cannot liberate their genomes and are therefore no longer infectious. The evolutionary roles of methylation in these cases will likely differ from those seen in other viruses, such as Herpesviruses, which can liberate their genome after periods of latency. But differences may also exist between large and small viruses—with many larger viruses encoding their own replication machinery and additional proteins which modify host cell processes and immune responses. The susceptibility of the viral genome to methylation and immune recognition will also be affected by other factors, such as the location of replication within the cell and the specific intracellular trafficking route.
Viral DNA methylation has mostly been studied in large DNA virii, and the extent of methylation may be related to repression of viral replication. Bonvicini et al. writes that
Epigenetic mechanisms, and in particular the impact of cytosine methylation at CpG dinucleotides on the viral life cycle have been mainly studied for viruses that can establish latency and undergo reactivation, such as viruses in the Herpesviridae family, or for viruses that can integrate their genome into the host genome such as Retroviridae or Papillomaviridae. In general, a correlation has been found between the extent of CpG dinucleotides methylation of viral genomes and viral quiescence . Scarce information is on the contrary available on the possible occurrence and role of methylation for actively replicating viruses
Methylation played different roles for different types of organisms throughout evolution. For bacteria, methylation protects against self-digestion of DNA by restriction enzymes. In eukaryotes, methylation assumes many different roles (e.g., mutation-rate regulator, gene expression regulator, chromatin structure regulator, etc.). Insects have very little methylation and it is not entirely clear what they use it for. Viruses don't encode for methyltransferases that modify DNA. However, when a virus integrates into a host genome that is methylated, the viral DNA usually assumes the methylation pattern of the integration locus.