Seven types of viral genomes

Professor David Baltimore, who won the Nobel prize in medicine in 1975 for his work on retroviruses, is credited with this classification of viruses. It's often referred to as the Baltimore scheme. Baltimore didn't actually find the seventh category; that was added later, but that's how science works.

There are only* seven known types of genomes in all of virology. They differ in whether the genetic material is DNA or RNA, whether it is single- or double-stranded, and a couple of other features. We'll go through all of those below, but there is one very important principle to remember about all viruses:

The viral genome must ultimately be converted to mRNA in order to be transcribed by the ribosomes of the host cell.

That simple rule governs much of the infectious behavior of viruses of various genome types, as we shall see. The seven genomic classes of viruses are:

* The word "only" is ironic here. All life forms on Earth use the same genetic system — double-stranded DNA — to store and use genetic information. While viruses aren't alive, they employ a much broader range of genetic storage.

Symbols used on this page

In the sections below, we'll use this symbol

to represent a viral protein translated from an mRNA by the host ribosome, and this symbol

to represent a newly-constituted virus particle with its genetic material inside, surrounded by a protein or protein-membrane coat.

Overview: Viral genome types

Here is a graphical overview of the seven Baltimore virus classes. Notice that, one way or another, all classes must either contain or transcribe a messenger RNA that encodes its proteins. If mRNAs cannot be made, the virus can't be reproduced.

Type I:   double-strand DNA

We know that in all living organisms (we don't consider viruses to be alive), DNA carries the instructions for proteins and a few RNAs, all that is needed to support cellular life. The (-) or non-coding strand of DNA is used to form a complement (+) RNA strand, the "message." That messenger RNA (mRNA) will be translated into the protein it encodes on the ribosomes in the cytoplasm of the host cell.

$$\text{-DNA } \: \rightarrow \: \text{ mRNA } \: \rightarrow \: \text{ protein}$$

The genetic material of double-stranded DNA viruses is a mimic of the dsDNA already present in the nucleus of any cell. If it can get into the nucleus, it can be transcribed by the host RNA polymerase (RNAp).

Generally, access to the nucleus is through a channel called the nuclear pore complex (NPC), and each virus has its own unique way of getting through this selective gateway. Some bypass it and get through the nuclear membrane another way. A nice review of these pathways can be found in: Fay & Pante, Frontiers in Microbiology (6), 467 (2015).

dsDNA viral replication schematic

Type II:   Single-strand (+) DNA

In this genome class, the viral code is contained on a single (+) strand of DNA. The genomes of ssDNA viruses are rather spare, usually encoding a single coat protein (CP) and a replication associated protein (Rep), an endonuclease*. Most ssDNA viruses have circular genomes which are transcribed by host RNAp (with various kinds of help from the Rep enzyme) in a process called rolling circle replication, in which new transcripts come off the circular template as the polymerase works around. The resulting linked transcripts are later processed for translation. Because host RNAp is involved, the viral genetic material must access the host cell nucleus.

ssDNA viral replication schematic

Type III:   Double-strand RNA

Double-strand RNA viruses contain base-paired RNA. When pulled apart, the (+) strand(s) can be used directly as mRNA to make viral proteins and form new particles. The (+) strand can also be converted, using RNA-dependent RNA polymerase (RdRp) into more dsRNA.

dsRNA viral replication schematic

Type IV:   Single-strand (+) RNA

with -RNA intermediate

Single-strand (+) RNAs are messenger RNAs, and thus ready for translation to proteins once released into the cytoplasm of the host cell. An RNA polymerase (RNAp) contained in the capsid copies the (+) strands to (-) strands, which are in turn copied to make more (+) strands.

A wide variety of pathogenic viruses are (+) RNA viruses. They include

Type V:   Single-strand (-) RNA

The single-strand (-) RNA's, which can come in a single piece or several fragments, depending on the virus, must be copied to a (+) strand in order to be translated into protein or into more (-) strands to build more viruses.

Host cells do not possess the polymerase, an RNA-dependent RNA polymerase (RNAp), that does this copying; it has to be supplied, as an intact enzyme, inside the viral capsid. When new viruses are formed, a new copy of the RNAp is packaged inside the VP with the new (-)RNAs.

The RNA-dependent RNAp can produce either translation-ready mRNAs for protein construction, or non-messenger (+) RNAs that are used to make new (-) RNAs for new viruses.

Flu & reassortment

The influenza viruses are good examples of (-) RNA viruses that have segmented genomes. Flu virus particles have a genome that consists of eight segments of 10,000 - 15,000 bases (10-15 Kb) each. One of the reasons that flu virus has a higher rate of phenotypic variablity and a higher rate of formation of infectious variants than most other viruses is that its genome is susceptible to reassortment. It works like this (see figure): Imagine that two different flu viruses infect the same cell. In the figure, one has red RNA segments and the other blue.

ss -RNA viral replication schematic

Type VI:   Single (+) strand RNA with (-) DNA intermediate

This is the genome of the retroviruses, like HIV, which can insert a copy of their genome into the host DNA. A single-strand of RNA is copied by reverse transcriptase (RT), an enzyme carried by the virus that does not exist in cells. These viruses are called retroviruses because the can perform the reverse operation of transcription, copying an RNA strand to a DNA strand.

The DNA copy is duplicated by the cellular machinery in the nucleus to form a double helix, which is then inserted into the host-cell genome.

retrovirus replication schematic

Type VII:   Gapped DNA

This genome class compares most closely with that of dsDNA viruses (type I). In order for it to produce mRNAs in the host cell, the gaps must be repaired to yield intact dsDNA that can then be transcribed.

This involves a series of steps, some of which are unique to gapped-DNA viruses and some of which strongly resemble the replication of retoroviral (type xx) viruses: The protein and RNA must be removed, the missing part(s) of the (+) strand of DNA must be repaired to produce a dsDNA that can be transcribed. Then, in order to build more viruses, both new capping proteins and RNAs must be made and attached, and some process to build the gapped (+) strand from an intact (-) strand must be deployed.

Gapped DNA viral replication schematic