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About viruses and viral disease
The TWiVrific gang reveal how integration of a virophage into the nuclear genome of a marine protozoan enhances host survival after infection with a giant virus.
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Virophages (the name means virus eater) were first discovered to replicate only in amoeba infected with the giant mimiviruses or mamaviruses.  They reduce yields of the giant viruses, and also decrease killing of the host cell. Another virophage called mavirus has been found to integrate into the genome of its host and behaves like an inducible antiviral defense system (link to paper).
The host cell of the virophage mavirus is Cafeteria roenbergensis, Cro (pictured), a marine phagotropic flagellate, that is infected with the giant virus CroV (Cafeteria roenbergensis virus). When Cro cells are infected with a mixture of mavirus and CroV, the virophage integrates into the host cell genome. There it remains silent; the cells survive, and no virophage particles are produced. Such cells can be called lysogens, a name applied to bacteria containing integrated bacteriophage genomes, or prophages.
How does the mavirus genome integrate into the Cro cell? The viral genome encodes an integrase, an enzyme that cuts host DNA and inserts a copy of the viral genome. Retroviruses achieve the same feat via an integrase.
When Cro-mavirus lysogens are infected with CroV, the integrated mavirus genome is transcribed to RNA, the viral DNA replicates, and new virus particles are formed. These virophages inhibit the replication of CroV by 100-1000 fold. As a consequence, the host cell population survives.
These findings suggest that the virophage mavirus is altruistic: induction of the integrated genome leads to killing of the host cell, but other members of the cell population are protected. Altruism is not unknown in Nature, but how it evolved is an intriguing question.
All this work was done in a laboratory. It will be necessary to determine if integration of mavirus into Cro cells in the wild has any influence on the ecology of these organisms.
Satellites are subviral agents that differ from viroids because they depend on the presence of a helper virus for their propagation. Satellite viruses are particles that contain nucleic acid genomes encoding a structural protein that encapsidates the satellite genome. Satellite RNAs do not encode capsid protein, but are packaged by a protein encoded in the helper virus genome. Satellite genomes may be single-stranded RNA or DNA or circular RNA, and are replicated by enzymes provided by the helper virus. The origin of satellites remains obscure, but they are not derived from the helper virus.
Satellite viruses may infect plants, animals, or bacteria. An example of a satellite virus is satellite tobacco necrosis virus, which encodes a capsid protein that forms an icosahedral capsid that packages only the 1,260 nucleotide satellite RNA. The helper virus, tobacco necrosis virus, encodes an RNA polymerase that replicates its genome and that of the satellite.
Satellite RNAs do not encode a capsid protein and therefore require helper virus proteins for both genome encapsidation and replication. Satellite RNA genomes range in length from 220-1500 nucleotides, and have been placed into one of three classes. Class 1 satellite RNAs are 800-1500 nucleotide linear molecules with a single open reading frame encoding at least one non-structural protein. Class 2 satellite RNAs are linear, less than 700 nucleotides long and do not encode protein. Class 3 satellite RNAs are 350-400 nucleotide long circles without an open reading frame.
In plants, satellites and satellite viruses may attenuate or exacerbate disease caused by the helper virus. Examples of disease include necrosis and systemic chlorosis, or reduced chlorophyll production leading to leaves that are pale, yellow, or yellow-white. The symptoms induced by satellite RNAs are thought to be a consequence of silencing of host genes. For example, the Y-satellite RNA of cucumber mosaic virus causes systemic chlorosis in tobacco. This syndrome is caused by production of a small RNA from the Y-satellite RNA that has homology to a gene needed for chlorophyll biosynthesis. Production of this small RNA leads to degradation of the corresponding mRNA, causing the bright yellow leaves.
The giant DNA viruses including Acanthamoeba polyophaga mimivirus, Cafeteria roenbergensis virus, and others are associated with much smaller viruses (sputnik and mavirus, respectively) that depend upon the larger viruses for reproduction. For example, sputnik virus can only replicate in cells infected with mimivirus, and does so within viral factories. Whether these are satellite viruses or something new (they have been called virophages) has been a matter of controversy.
Like satellite viruses, sputnik and others have similar relationships with their helper viruses: they require their helper for their propagation, but their genomes are not derived from the helper, and they negatively impact helper reproduction. Others argue that the definition of satellite viruses as sub-viral agents cannot apply to these very large viruses. For example, sputnik virophage contains a circular dsDNA genome of 18,343 bp encoding 21 proteins encased in a 75 nm t=27 icosahedral capsid. Sputnik is dependent upon mimivirus not for DNA polymerase – it encodes its own – but probably for the transcriptional machinery of the helper virus. Those who favor the name virophage argue that dependence upon the cellular transcriptional machinery is a property of many autonomous viruses – the only difference is that Sputnik depends upon the machinery provided by another virus. It seems likely that a redefinition of what constitutes a satellite virus will be required to solve this disagreement.
Most known satellites are associated with plant viruses, but hepatitis delta satellite virus is associated with a human helper virus, hepatitis B virus. The genome (illustrated) is 1.7 kb – the smallest of any known animal virus – of circular single-stranded RNA that is 70% base paired and folds upon itself in a tight rod-like structure. The RNA molecule is replicated by cellular RNA polymerase II. These properties resemble those of viroid genomes. On the other hand, the genome encodes a protein (delta) that encapsidates the RNA, a property shared with satellite nucleic acids. The hepatitis delta satellite virus particle comprises the satellite nucleocapsid packaged within an envelope that contains the surface protein of the helper, hepatitis B virus.
Infection with hepatitis delta satellite virus only occurs in individuals infected with hepatitis B virus: it is globally distributed, present in about 5% of the 350 million carriers of hepatitis B virus. Acute co-infections of the two viruses can be more severe than infection with hepatitis B virus alone, leading to more cases of liver failure. In chronic hepatitis B virus infections, hepatitis delta satellite virus aggravates pre-existing liver disease, and may lead to more rapid progression to cirrhosis and death than monoinfections. Why co-infection with both viruses leads to more serious outcomes is not known.
Virophage is the name coined for viruses such as Sputnik and Mavirus that can only replicate in cells infected with a helper virus, whose replication they inhibit. I’ve never liked the name – it means virus eater – and neither does Brent Johnson, a virologist at Brigham Young University:
“I believe the term ‘virophage’ is unfortunate because it implies one virus is infecting another virus and eating it. The small virus isn’t infecting another virus, it’s just using it to assist in replication, which is consistent with the needs of a defective virus.” he explains. He prefers calling the giant viruses “megaviruses,” and considers the name “Megavirus-Associated Virus (MAV) more consistent with currently accepted virus nomenclature.”
For more discussion, see the article by Marsha Stone in the July 2011 Microbe.