This post was most recently updated on January 29th, 2015
Why DNA viruses replicate in the Nucleus?
Once the nucleocapsid of DNA virus enters the host cell, it proceeds to the nucleus where it mimics the genome of the host cell.
Usually, the viral genome is replicated using the host cell DNA polymerase, and the viral genome is transcribed by the host cell RNA polymerase.
The resulting transcripts carrying information encoding viral proteins is then transported to the cytoplasm and seen as a template by the host cell ribosomes. Some of these newly synthesized viral proteins are used as the protein capsid around newly replicated viral DNA molecules.
These new virions are released from the cell, where they target other host cells and trigger new rounds of infection.
As DNA viruses exploit the host cell machinery to complete their life cycles they carry small genomes encoding mostly viral structural proteins, like those for the capsid.
There are exceptions, notably the smallpox DNA virus encodes its own DNA replication machinery so it replicates in the cytoplasm.
Why RNA viruses replicate in the cytoplasm?
Host cell does not have a mechanism to replicate RNA (there is no host enzyme that uses RNA as a template for nucleic acid synthesis). So the genome of RNA virus must encode a viral enzyme that can replicate viral RNA.
As the enzymes used to replicate viral RNA are virally encoded, most RNA viruses replicate in the cytoplasm .
In case of Retroviruses (+ SS RNA) it replicates forming RNA: DNA hybrid double helix. The copying of RNA into DNA is carried out by viral enzyme reverse transcriptase and occurs in cytoplasm.
Reverse transcriptase also degrade RNA portion and copies remaining DNA strand into dsDNA. Once the ds viral DNA is synthesized, it is transported into the nucleus and is inserted and covalently linked to the host chromosomal DNA.