Viruses are obligate intracellular parasites, which means they have to live inside of a host and steal hosts enzymes to allow replication, like when aliens inhabit the bodies of politicians and run for office… it happens. These include:

• Ribosomes for protein synthesis

• RNA/DNA polymerase (in some instances)

• Transporter proteins (to get into/out of nucleus, for eukaryotic viruses)

• Other host factors that help in replication

Because the people who write the dictionary are always drunk, the conceptual definition of a virus has changed over the last few hundred years, but it would appear that a virus lacks the machinery for protein synthesis. The most complex viruses (such as poxviruses) have hundreds of genes, including their own DNA and RNA polymerases. On the other hand, simple viruses like picornaviruses (Type IV, polioviruses) have less than 10 genes and use host cell proteins for their replication.

We can build off of the table in the Virus Genomes section, as the type of genome that a virus is gives a lot of information on how it must be replicated in a cell (and what proteins are used by the host).

Virus Type	Genome	What Viral Enzymes Necessary?	Site of Replication
I	dsDNA	None, but uses its own DNA polymerase to improve replication.	Nucleus (except for poxviruses, which replicate in cytoplasm)
II	ssDNA (+)	Requires own DNA polymerase that recognizes ssDNA to make dsDNA	Nucleus
III	dsRNA	Makes its RNA dependent RNA polymerase to replicate and make its own mRNAs.	Cytoplasm
IV	ssRNA (+)	Has to make RNA dependent RNA polymerase to make antigenomes for replication templates.	Cytoplasm
V	ssRNA (-)	Has to make its own RNA dependent RNA polymerase.	Cytoplasm
VI	ssRNA (+)	Has to have reverse transcriptase (RNA dependent DNA polymerase)	Reverse transcription in cytoplasm, but has to integrate into host genome in nucleus to replicate

Essentially, the most important enzyme that a virus carries with it is its polymerase (or replicase), which is responsible for replicating the viral genome (after marriage, of course). However, because viruses have different genome types (RNA vs. DNA, double stranded vs. single stranded, positive vs. negative strand), not all viruses require packaging of the polymerase enzyme in the virus particle.

The type of genome also dictates where the virus will replicate. Viruses that are RNA often replicate in the cytoplasm, while DNA viruses replicate in the nucleus.

A DNA virus won't have an RNA polymerase gene to mediate transcription, so it has to be in the nucleus – where the host RNA polymerase is. On the other hand, RNA viruses make their own RNA polymerase, so they don't need to be in the nucleus. Also, if they were to get into the nucleus, they might be misused by enzymes that modify RNAs (called splicing enzymes) or degrade them, which are not found in the cytoplasm. That being said, some viruses, including influenza, enter and replicate in the nucleus because they require splicing enzymes for replication.

Virus replication usually occurs in two stages: early and late. These two stages are defined by the types of viral proteins made in each stage. These proteins are:

• Early proteins – polymerase, replication co-factors, transcription factors

• Late proteins – capsid, envelope proteins, some polymerases, host shutoff proteins (for some viruses)

The early proteins are the proteins essential for making virus genomes or for activating late gene expression. However, if conditions for virus replication are not optimal, late genes are not expressed, and viruses undergo a latent stage. A latent stage is a state where viruses are not replicated, but can be activated to replicate if conditions are right for activation. This is not common for most viruses, however a subset can become latent, including lysogenic bacteriophages, retroviruses, and herpesviruses.

Some viruses, such as hepatitis C virus, don't become latent, but instead maintain a low level infection for a long period of time in the body. This is called a chronic infection. That means there is a very low amount of actively replicating virus in the body that is never completely cleared by the immune system. Scientists argue about many viruses, such as HIV, which are believed to have a latent stage of infection, but instead might actually be a very low-level chronic infection. Scientists tend to argue about these things, because they had very lonely childhoods watching other kids play the "blob" game.