Virus Genomes

The genomes of viruses are just like every other genome, they contain all the genes necessary to replicate a virus. However, viruses are very lazy, and just use most of the host cell's machinery to make what they need to replicate. Kind of like that time you let that carnie into your house, then when you came back your dryer was gone…and there were twelve carnies and a ring toss game in its place.

Viruses encode a minimum of two proteins, while other proteins they encode aid in the process of virus survival. Those two proteins are

• Replicase – an enzyme that replicates the genome

• Capsid – a protein that protects the genome.

Other types of genes that a virus would encode include (in order of common genes to more rare):

• Protease – enzyme that processes viral proteins and allows assembly or maturation to infect other virus cells.

• Glycoprotein – (enveloped viruses only) allows virus to enter a cell, targets specific cell types for virus, and aids in virus assembly.

• Host shutoff proteins – virus proteins that shut off host activities so only virus genes get made.

• Anti-host defense proteins – this varies in number of different genes, depending on the virus. These proteins prevent the host defense mechanism from stopping virus replication.

These genes are encoded on either RNA or DNA polymers, and are either single stranded or double stranded

Figure 2: Types of virus genomes

Wow, that was a lot, right? Well, it gets worse. While most genomes are non-segmented (the genome is all on one piece of RNA or DNA), some genomes are segmented, meaning there are several fragments of DNA/RNA that make a complete virus genome. Also, some genomes are linear, meaning that there is a beginning and end to the genome, while other genomes are circular (no beginning and no end, Kind of like that friendship song, except by "friends" we mean "piles of microscopic goo").

That seems like a lot of information overload, and we sympathize. For something so small and seemingly simple (like "I can't believe it's not butter"), viruses are very complex (like the ingredients of "I can't believe it's not butter"). The important thing is that if you can tell the difference between RNA and DNA virus, and if it is linear or circular, and if it is segmented or non-segmented, you can immediately tell a lot about a virus. So, we attached a table to serve as a cheat sheet for virus genomes.

Virus Type	Genome	Example	What It Tells Us
I	dsDNA	Adenoviruses, Herpesviruses, and Poxviruses	Virus can use host machinery to make mRNA, and even replicate virus
II	ssDNA (+)	Parvoviruses	Need DNA polymerase to make negative strand, can use host machinery to make mRNA
III	dsRNA	Reoviruses	Needs RNA polymerase to replicate itself as well as make mRNA
IV	ssRNA (+)	Poliovirus and Ebola Virus	Needs RNA polymerase to replicate itself. Genome also serves as mRNA.
V	ssRNA (-)	Influenza virus, Hantavirus	Needs RNA polymerase to replicate itself as well as make mRNA
-	ssRNA (+)	Retroviruses, HIV	Makes cDNA that integrates into host genome, which makes mRNA and proteins
-	Segmented	Influenza	When making viruses, can mix and match segments to allow virus to more easily evolve
-	Non-segmented	HIV, Poxvirus	Evolution is more difficult. Requires more error-prone polymerase
-	Linear		Needs a primer to start replication from one end of genome.
-	Circular	Poxvirus, Herpesvirus	Replication starts anywhere on the genome (but often has a specific origin of replication)