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Satellites are subviral agents which lack genes that could encode functions needed for replication. Thus for their multiplication they depend on the co-infection of a host cell with a helper virus. Satellite genomes have a substantial portion or all of their nucleotide sequences distinct from those of the genomes of their helper virus.
According to this definition, two major classes of satellites may be distinguished. Satellite viruses encode a structural protein that encapsidates their genome and so have nucleoprotein components distinct from those of their helper viruses. Satellite nucleic acids encode either non-structural proteins, or no proteins at all, and are encapsidated by the CP of helper viruses.
In addition to the true satellites, this chapter also describes subviral agents (nucleic acids) that depend upon viruses in a variety of ways. Satellite-like nucleic acids resemble satellites because they do not encode a replicase but differ because they encode a function necessary for the biological success of the associated virus. They can therefore be considered as components that remedy a deficiency in a defective virus. They have sometimes been classified as part of the genome of the virus they assist but they can also be dispensable because they are not always found in association with their helper virus. Examples include RNAs associated with groundnut rosette virus (genus Umbravirus) or with beet necrotic yellow vein virus (genus Benyvirus), that contribute to vector transmissibility and DNAs associated with begomoviruses (betasatellites) that encode a pathogenicity determinant.
A final group of agents described are nucleic acids capable of autonomous replication and which therefore are not strictly satellites although the term has sometimes been loosely applied to them. These agents are dependent on their helper viruses for various functions such as encapsidation, cell-to-cell and long-distance movement and vector transmission. Examples are the alphasatellites (DNAs that encode a replication initiator protein) or the RNAs associated with some poleroviruses that appear to encode a carmovirus-like RdRp.
The distinction between satellite nucleic acids, satellite-like nucleic acids and virus genomic components can be subtle and these agents are not always easy to categorize.
Satellites are genetically distinct from their helper virus with a nucleotide sequence that is substantially different from that of their helper virus. However, the genomes of most satellites have short sequences, often at the termini, that are identical to the genome of the helper virus. This is presumably linked to the dependence of nucleic acids of both satellite and helper virus on the same viral polymerase and host-encoded proteins for replication. Satellites are distinct from defective interfering (DI) RNAs or defective RNAs because such RNAs are derived from their “helper” virus genomes. Nevertheless, satellite viruses may form their own DI RNAs that specifically interfere with the satellite virus genomic RNA, as has been shown for satellite panicum mosaic virus. Recombination can occur between satellites and their helper viruses. For example, chimeric molecules can be formed from a satellite RNA associated with turnip crinkle virus (genus Carmovirus) and parts of the helper virus genome.
Satellites do not constitute a homogeneous taxonomic group and are not formally classified into species and higher taxa by ICTV. The descriptions in this section are meant only to provide a classification framework and a nomenclature to assist in the description and identification of satellites and other virus-dependent nucleic acids. The arrangement adopted is based largely on features of the genetic material of the satellites. The physicochemical and biological features of the helper virus and of the helper virus host are important secondary characters.
There appears to be no taxonomic correlation between the viruses that are associated with satellites. Satellites would appear to have arisen independently a number of times during virus evolution. A further complication is that some viruses are associated with more than one satellite and some satellites are supported by more than one species of helper virus. Satellites can even depend on both a second satellite and a helper virus for multiplication.
The first satellites characterized were mostly ssRNA satellites that use ssRNA plant viruses as helpers. It can be very difficult to distinguish between satellite RNA and viral genomic RNA (e. g., dsRNA satellites of fungus viruses) and it is very likely that other satellites, some with novel combinations of characters, remain to be discovered.
Virus-dependent nucleic acids:
6a Alphasatellites (encoding a replication initiator protein)
6b Betasatellites (encoding a pathogenicity determinant)
8a Large linear single stranded satellite RNAs
8b Small linear single stranded satellite and satellite-like RNAs
8c Small circular single stranded satellite RNAs
8d Hepadnavirus-associated satellite-like RNAs (Deltavirus)
8e Polerovirus-associated RNAs
These satellites encode a structural protein to encapsidate their genomes. The satellite virus particles are antigenically, and usually morphologically, distinct from those of the helper virus. Five subgroups of satellite viruses are currently distinguished.
Satellite virus particles are found in bees infected with the helper, chronic bee-paralysis virus (CBPV; a virus not yet classified). Particles are about 12 nm in diameter and serologically unrelated to those of CBPV. The satellite interferes with CBPV replication.
Chronic bee-paralysis satellite virus
These satellite virus particles are found in plant hosts in association with taxonomically diverse helper viruses. The T=1 isometric particles are about 17 nm in diameter. The capsid consists of 60 copies of a single protein of 17–24 kDa, which is encoded by the satellite virus genome (positive sense ssRNA). The genomes of some satellite viruses contain a second ORF.
Satellite viruses associated with viruses in the familyTombusviridae
Maize white line mosaic satellite virus
Panicum mosaic satellite virus
Tobacco necrosis satellite virus
Satellite viruses associated with viruses in the familyVirgaviridae
Tobacco mosaic satellite virus
Satellite virus particles are found in Macrobrachium rosenbergii (giant river prawn) infected with Macrobrachium rosenbergii nodavirus (MrNV; a virus not yet classified but clearly related to viruses in the family Nodaviridae). The XSV (extra small virus) satellite virus particles are about 15 nm in diameter and serologically unrelated to those of MrNV. XSV is a positive-sense single-stranded RNA, about 800 bases in size, encoding a 17 kDa capsid protein. The mixed infection of MrNV and XSV is implicated in white spot disease of prawns.
Macrobrachium rosenbergii nodavirus XSV (extra small virus)
Adenovirus-associated (AAV) satellite virus particles are found in humans, domesticated animals, fowl and in tissue or cell cultures as co-infections with a helper virus. The single stranded 5 kb DNA genome encodes three structural proteins (VP1, −2 and −3). The 26 nm T=1 particles have a 10:1:1 ratio of VP3:VP2:VP1. Smaller particles about 12 nm in diameter only contain the 60 kDa VP3 protein. AAV satellite viruses are dependent on adenoviruses (or herpesviruses) for replication and cap functions. This group of satellites is anomalous, having been placed in a genus Dependovirus within the family Parvoviridae, although they meet all definitions for an authentic satellite virus. For more details see the section on genus Dependovirus.
See tables for the genus Dependovirus in the Parvoviridae chapter.
Acanthamoeba polyphaga mimivirus (genus Mimivirus) is an extremely large (ca. 1.2 Mbp) virus with a dsDNA genome that infects amoebae of the genus Acanthamoeba. A mimivirus strain (sometimes called mamavirus) isolated from A. castellanii supports a 50 nm T=27 satellite virus, referred to as Sputnik (=satellite in Russian). The satellite virus has a circular dsDNA genome of 18 kbp that is predicted to code for about 22 proteins. Sputnik does not replicate in either host in the absence of the helper virus.
Acanthamoeba castellanii mamavirus-associated satellite virus (Sputnik)
This category includes a diverse range of DNA and RNA molecules that do not encode a capsid protein but are packaged in capsids encoded by their helper virus. Those that encode a function necessary for the biological success of the associated virus are described as “satellite-like”.
These molecules are not strictly satellites because they encode a rolling-circle replication initiator protein (known as the replication-associated protein [Rep]) with similarity to the master Rep encoding genomic components (DNA-R) of nanoviruses. They are capable of autonomous replication in host cells, have a stem-loop region containing the ubiquitous nonanucleotide TAA/GTATTAC, and depend on their helper viruses for encapsidation, movement in plants and insect transmission. Some are associated with viruses in the genus Begomovirus and are typically about 1.4 kb, half the size of their helper viruses. Others are associated with multipartite genome viruses of the family Nanoviridae and are approximately the same size (ca. 1 kb) as the genomic components of their helper viruses (but are not derived from them). The presence of alphasatellites in begomovirus and nanovirid infections may reduce symptom severity, suggesting interference akin to that seen with defective interfering DNAs. Recent results have shown that the Rep encoded by at least some alphasatellites associated with begomoviruses suppresses host defenses based on RNA interference.
Ageratum yellow vein alphasatellite
Ageratum yellow vein India alphasatellite
Ageratum yellow vein Kenya alphasatellite
Ageratum yellow vein Pakistan alphasatellite
Ageratum yellow vein Singapore alphasatellite
Cotton leaf curl Dabwali alphasatellite
Cotton leaf curl Gezira alphasatellite
Cotton leaf curl Multan alphasatellite
Cotton leaf curl Shadadpur alphasatellite
Duranta leaf curl alphasatellite
Gossypium darwinii symptomless alphasatellite
Gossypium davidsonii symptomless alphasatellite
Gossypium mustilinum symptomless alphasatellite
Hibiscus leaf curl alphasatellite
Malvastrum yellow mosaic alphasatellite
Malvastrum yellow mosaic Hainan alphasatellite
Okra leaf curl alphasatellite
Okra leaf curl Barombi alphasatellite
Okra leaf curl Burkina Faso alphasatellite
Okra leaf curl Mali alphasatellite
Sida yellow vein Vietnam alphasatellite
Tobacco curly shoot alphasatellite
Tomato leaf curl Pakistan alphasatellite
Tomato yellow leaf curl China alphasatellite
Babu- and nanovirus-associated alphasatellites
Banana bunchy top S1 alphasatellite
Banana bunchy top S2 alphasatellite
Banana bunchy top S3 alphasatellite
Banana bunchy top W1 alphasatellite
Banana bunchy top Y alphasatellite
Faba bean necrotic yellows C1 alphasatellite
Faba bean necrotic yellows C11 alphasatellite
Faba bean necrotic yellows C7 alphasatellite
Faba bean necrotic yellows C9 alphasatellite
Milk vetch dwarf C1 alphasatellite
Milk vetch dwarf C10 alphasatellite
Milk vetch dwarf C2 alphasatellite
Milk vetch dwarf C3 alphasatellite
Subterranean clover stunt C2 alphasatellite
Subterranean clover stunt C6 alphasatellite
Coconut foliar decay alphasatellite
These are satellite-like circular ssDNA components, usually about 1.3 kb in size that are associated with viruses in the genus Begomovirus. Although initially identified only in association with monopartite begomoviruses, recently they have been increasingly identified in association with bipartite begomoviruses. All betasatellites have a stem-loop region containing the ubiquitous nonanucleotide TAATATTAC and an associated highly conserved sequence located immediately upstream (the function of which remains uncertain), a conserved ORF (termed βC1; encoding a protein that is a pathogenicity determinant and a suppressor of host defenses based on RNA interference), and an A-rich region that may reflect size adaptation for maintenance of the component by the helper begomovirus. The betasatellite DNAs readily recombine with the helper begomovirus genome and such recombinants may retain a biological activity similar to the parental betasatellite. Pairwise comparisons between sequences have shown that a sequence identity of about 78% is an appropriate demarcation threshold for distinguishing between betasatellites.
Ageratum leaf curl Cameroon betasatellite
Ageratum yellow leaf curl betasatellite
Ageratum yellow vein betasatellite
Ageratum yellow vein Sri Lanka betasatellite
Alternanthera yellow vein betasatellite
Bean leaf curl China betasatellite
Bhendi yellow vein betasatellite
Cardiospemum yellow leaf curl betasatellite
Chilli leaf curl betasatellite
Cotton leaf curl Gezira betasatellite
Cotton leaf curl Multan betasatellite
Croton yellow vein mosaic betasatellite
Emilia yellow vein betasatellite
Erectites yellow mosaic betasatellite
Eupatorium yellow vein betasatellite
Honeysuckle yellow vein betasatellite
Honeysuckle yellow vein Japan betasatellite
Honeysuckle yellow vein Kochi betasatellite
Honeysuckle yellow vein mosaic betasatellite
Honeysuckle yellow vein mosaic Hyogo betasatellite
Honeysuckle yellow vein mosaic Nara betasatellite
Kenaf leaf curl betasatellite
Leucas zeylanica yellow vein betasatellite
Lindernia anagallis yellow vein betasatellite
Ludwigia yellow vein betasatellite
Luffa leaf distortion betasatellite
Malvastrum leaf curl betasatellite
Malvastrum yellow vein betasatellite
Malvastrum yellow vein Yunnan betasatellite
Mesta yellow vein mosaic betasatellite
Okra leaf curl betasatellite
Papaya leaf curl betasatellite
Radish leaf curl betasatellite
Sida leaf curl betasatellite
Sida yellow mosaic China betasatellite
Sida yellow vein betasatellite
Sida yellow vein mosaic betasatellite
Sida yellow vein Vietnam betasatellite
Siegesbeckia yellow vein betasatellite
Siegesbeckia yellow vein Guangxi betasatellite
Tobacco curly shoot betasatellite
Tobacco leaf curl betasatellite
Tomato leaf curl Bangalore betasatellite
Tomato leaf curl Bangladesh betasatellite
Tomato leaf curl betasatellite
Tomato leaf curl China betasatellite
Tomato leaf curl Java betasatellite
Tomato leaf curl Joydebpur betasatellite
Tomato leaf curl Karnataka betasatellite
Tomato leaf curl Laos betasatellite
Tomato leaf curl Maharastra betasatellite
Tomato leaf curl Patna betasatellite
Tomato leaf curl Philippines betasatellite
Tomato leaf curl virus satellite
Tomato yellow dwarf betasatellite
Tomato yellow leaf curl China betasatellite
Tomato yellow leaf curl Thailand betasatellite
Tomato yellow leaf curl Vietnam betasatellite
Tomato yellow leaf curl Yunnan betasatellite
Vernonia yellow vein betasatellite
Zinnia leaf curl betasatellite
Most satellites in this category are found in association with viruses in the families Totiviridae and Partitiviridae. The dsRNAs range in size from 0.5 to 1.8 kbp and are encapsidated using the helper virus capsid protein. These particles often also contain a positive sense single stranded copy of the dsRNA. The satellite dsRNAs associated with helper viruses in the genus Totivirus encode a secreted preprotoxin that is lethal to sensitive cells (virus-free or containing helper virus only). The presence of satellites in helper totivirus cultures imparts self-protection against the secreted toxin and confers ecological advantage by killing competing virus- or satellite-free fungi. The satellite dsRNAs associated with partitiviruses do not code for functional proteins and their biological significance is not known.
Satellites associated with viruses in the familyTotiviridae
M satellites of Saccharomyces cerevisiae L-A virus
M satellites of Ustilago maydis virus H
Satellites of Trichomonas vaginalis T1 virus
M satellite of Zygosaccharomyces balii virus
Satellites associated with viruses in the familyPartitiviridae
Satellite of Atkinsonella hypoxylon virus
Satellites of Discula destructiva virus 1
Satellite of Gremmeniella abietina virus MS1
Satellite of Penicillium stoloniferum virus F
Satellites of Amasya cherry disease-associated virus
Satellites of cherry chlorotic rusty spot -associated virus
Satellites associated with viruses in the familyReoviridae
Bombyx mori cypovirus 1 satellite RNA
* Abbreviations: Sat, satellite; Seg, segment.
This category comprises satellites with genomes that are 0.8 to 1.5 kb in size and encode a non-structural protein that, at least in some cases, is essential for satellite RNA multiplication. Little sequence homology exists between the satellites and their helpers, some satellites can be exchanged among different helper viruses. These satellites rarely modify the disease induced in host plants by the helper virus. Most are associated with helper viruses in the family Secoviridae.
Satellite RNAs associated with viruses in the familySecoviridae
Arabis mosaic virus large satellite RNA
Beet ringspot virus satellite RNA (TBRV-S serotype satellite RNA)
Blackcurrant reversion virus satellite RNA
Chicory yellow mottle virus large satellite RNA
Grapevine Bulgarian latent virus satellite RNA
Grapevine fanleaf virus satellite RNA
Myrobalan latent ringspot virus satellite RNA
Strawberry latent ringspot virus satellite RNA
Tomato black ring virus satellite RNA (TBRV-G serotype satellite RNA)
Satellite RNAs associated with viruses in the familyAlphaflexiviridae
Bamboo mosaic virus satellite RNA
Beet necrotic yellow vein virus RNA5*
* Non-essential genome component that may be regarded as a satellite-like RNA. Beet necrotic yellow vein virus is a member of the genus Benyvirus.
These satellites have a strictly linear genome of less than 0.7 kb that does not encode functional proteins. Some satellites can attenuate the symptoms induced by helper virus infection, whereas other satellites can exacerbate the symptoms.
Satellite RNAs associated with viruses in the familyTombusviridae
Artichoke mottled crinkle virus satellite RNA
Black beet scorch virus satellite RNA
Carnation Italian ringspot virus satellite RNA
Cymbidium ringspot virus satellite RNA
Panicum mosaic virus satellite RNA
Pelargonium leaf curl virus satellite RNA
Petunia asteroid mosaic virus satellite RNA
Tobacco necrosis virus small satellite RNA
Tomato bushy stunt virus satellite RNA (several types)
Satellite RNAs associated with viruses in the familyBromoviridae
Cucumber mosaic virus satellite RNA (several types)
Peanut stunt virus satellite RNA
Satellite RNAs associated with viruses in the genus Umbravirus†
Carrot mottle mimic virus satellite RNA
Groundnut rosette virus satellite RNA*
Pea enation mosaic virus satellite RNA
Tobacco bushy top virus satellite RNA*
* These may be regarded as a satellite-like RNAs as they appear to be essential components of a disease complex.
† These in turn depend upon viruses in the family Luteoviridae for their encapsidation and transmission.
These satellites have genomes that are about 350 nt long. Both circular and linear forms of the genome are found in infected cells. In some cases (e.g. the satellite RNA associated with tobacco ringspot virus, genus Nepovirus), replication involves self-cleavage of circular progeny molecules by an RNA-catalyzed reaction.
Arabis mosaic virus small satellite RNA
Chicory yellow mottle virus satellite RNA
Tobacco ringspot virus satellite RNA
Satellite RNAs associated with viruses in the familyLuteoviridae
Cereal yellow dwarf virus-RPV satellite RNA
Satellite RNAs associated with viruses in the genusSobemovirus
Lucerne transient streak virus satellite RNA
Rice yellow mottle virus satellite
Solanum nodiflorum mottle virus satellite RNA
Subterranean clover mottle virus satellite RNA (2 types)
Velvet tobacco mottle virus satellite RNA
Cherry small circular viroid-like RNA
Hepatitis D virus (HDV, genus Deltavirus) has a single molecule of circular, negative sense 1.7 kb ssRNA that encodes a 24 kDa small protein (S-HDAg) and a 27 kDa large protein (L-HDAg). The ribonucleoprotein of HDV RNA and both HDAgs, are packaged within an envelope containing lipid and helper virus antigens. For complete replication and transmission, HDV also requires a host DNA dependent RNA polymerase II and HBsAg, a protein encoded by its helper virus, human hepatitis B virus (genus Orthohepadnavirus). HDV RNA is encapsidated in distinct virions by the HBsAg capsid protein of the helper virus. HDV is a serious human pathogen and has until now been classified as a virus, although it meets the definitions of a satellite-like RNA. For more details see the chapter on genus Deltavirus.
See chapter for genus Deltavirus.
These ssRNA genomes are about 2.8–3 kb long and have two major ORFs. It is likely that the second ORF, which contains the classic RdRp motifs of the carmovirus supergroup, is translated by readthrough of the ORF1 amber stop codon. Additional small ORFs have been identified in some members. The RNA is capable of autonomous replication but appears to depend on a virus of the genus Polerovirus as helper virus for aphid transmission by encapsidating this RNA with the polerovirus coat protein to form aphid-transmissible hybrid virions. Some members increase the severity of disease symptoms.
Beet western yellows virus ST9-associated RNA
Carrot red leaf virus-associated RNA
Tobacco vein distorting virus-associated RNA
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