What are viruses?

Viruses are very small (submicroscopic) infectious particles (virions) composed of a protein coat and a nucleic acid core. They carry genetic information encoded in their nucleic acid, which typically specifies two or more proteins. Translation of the genome (to produce proteins) or transcription and replication (to produce more nucleic acid) takes place within the host cell and uses some of the host's biochemical "machinery". Viruses do not capture or store free energy and are not functionally active outside their host. They are therefore parasites (and usually pathogens) but are not usually regarded as genuine microorganisms.

Most viruses are restricted to a particular type of host. Some infect bacteria, and are known as bacteriophages, whereas others are known that infect algae, protozoa, fungi (mycoviruses), invertebrates, vertebrates or vascular plants. However, some viruses that are transmitted between vertebrate or plant hosts by feeding insects (vectors) can replicate within both their host and their vector. This web site is mostly concerned with those viruses that infect plants but we also provide some taxonomic and genome information about viruses of fungi, protozoa, vertebrates and invertebrates where these are related to plant viruses.

We also provide information about viroids, which are infectious RNA molecules that cause diseases in various plants. Their genomes are much smaller than those of viruses (up to 400 nucleotides of circular single-stranded RNA) and do not code for any proteins.

Why are viruses important?

Viruses cause many diseases of international importance. Amongst the human viruses, smallpox, polio, influenza, hepatitis, human immunodeficiency virus (HIV-AIDS), measles and the SARS coronavirus are particularly well known. While antibiotics can be very effective against diseases caused by bacteria, these treatments are ineffective against viruses and most control measures rely on vaccines (antibodies raised against some component of the virus) or relief of the symptoms to encourage the body's own defense system.

Viruses also cause many important plant diseases and are responsible for huge losses in crop production and quality in all parts of the world. Infected plants may show a range of symptoms depending on the disease but often there is leaf yellowing (either of the whole leaf or in a pattern of stripes or blotches), leaf distortion (e.g. curling) and/or other growth distortions (e.g. stunting of the whole plant, abnormalities in flower or fruit formation).

	Yellow mosaic symptoms on lettuce caused by Lettuce mosaic virus. Figure from Description 399 (photo: INRA Avignon, France).
	Yellow vein-banding symptoms on grapevine caused by Grapevine fanleaf virus. Figure from Description 385
	Fruit distortion on eggplant fruit caused by Tomato bushy stunt virus. A healthy fruit is shown on the left. Figure courtesy of F. Garcia Arenal, from Description 382.
	Bark scaling caused by Citrus psorosis virus. Figure from Description 401.

These symptoms and many others are further illustrated in the various virus Descriptions on this site. Sometimes the virus is restricted to certain parts of the plant (e.g. the vascular system; discrete spots on the leaf) but in others it spreads throughout the plant causing a systemic infection. Infection does not always result in visible symptoms (as witnessed by names such as Carnation latent virus and Lily symptomless virus, both members of the genus Carlavirus). Occasionally, virus infection can result in symptoms of ornamental value, such as 'breaking' of tulips or variegation of Abutilon.

Plant viruses cannot be directly controlled by chemical application. The major means of control (depending on the disease) include:

• Chemical or biological control of the vector (the organism transmitting the disease, often an insect): this can be very effective where the vectors need to feed for some time on a crop before the virus is transmitted but are of much less value where transmission occurs very rapidly and may already have taken place before the vector succumbs to the pesticide.
• Growing resistant crop varieties: in some crops and for some viruses there are highly effective sources of resistance that plant breeders have been using for many years. However, no such "natural" resistance has been identified for many others. Transgenic resistance has shown considerable promise for many plant-virus combinations following the discovery that the incorporation of part of the virus genome into the host plant may confer a substantial degree of resistance. For example, the use of this approach in Hawaii to control Papaya ringspot virus has been credited with saving the local papaya industry. However, this technology is controversial, particularly in Europe, and the extent to which it will be used commercially is currently uncertain.
• Use of virus-free planting material: in vegetatively propagated crops (e.g. potatoes, many fruit crops) and where viruses are transmitted through seed major efforts are made through breeding, certification schemes etc., to ensure that the planting material is virus-free.
• Exclusion: the prevention of disease establishment in areas where it does not yet occur. This is a major objective of plant quarantine procedures throughout the world as well as more local schemes.

How are viruses transmitted?

Some important animal and human viruses can be spread through aerosols. The viruses have the "machinery" to enter the animal cells directly by fusing with the cell membrane (e.g. in the nasal lining or gut).

By contrast, plant cells have a robust cell wall and viruses cannot penetrate them unaided. Most plant viruses are therefore transmitted by a vector organism that feeds on the plant or (in some diseases) are introduced through wounds made, for example, during cultural operations (e.g. pruning). A small number of viruses can be transmitted through pollen to the seed (e.g. Barley stripe mosaic virus, genus Hordeivirus) while many that cause systemic infections accumulate in vegetatively-propagated crops. The major vectors of plant viruses are:

• Insects. This forms the largest and most significant vector group and particularly includes:
  • Aphids: transmit viruses from many different genera, including Potyvirus, Cucumovirus and Luteovirus.The picture shows the green peach aphid Myzus persicae, the vector of many plant viruses, including Potato virus Y. (Figure from Nuessly & Webb, Insect Management for Leafy Vegetables, ENY-475, September 2003, University of Florida, Institute of Food and Agricultural Sciences (UF/IFAS)).
    

  • Whiteflies: transmit viruses from several genera but particularly those in the genus Begomovirus. The picture shows Bemisia tabaci, the vector of many viruses including Tomato yellow leaf curl virus and Lettuce infectious yellows virus. (Figure from Description 369).
    

  • Hoppers: transmit viruses from several genera, including those in the families Rhabdoviridae and Reoviridae. The picture shows Micrutalis malleifera, the treehopper vector of Tomato pseudo-curly top virus. (Figure from Description 395).
    

  • Thrips: transmit viruses in the genus Tospovirus. The picture shows Frankinella occidentalis, the western flower thrips that is a major vector of Tomato spotted wilt virus..
    

  • Beetles: transmit viruses from several genera, including Comovirus and Sobemovirus

  The virus-vector relationships are of several types:

  • At one extreme, the association occurs within the feeding apparatus of the insect, where the virus can be rapidly adsorbed and then released into a different plant cell. The feeding insect looses the virus rapidly when feeding on a non-infected plant. Such a relationship is termed "non-persistent". The best studied examples are of potyvirus transmission by aphids.
  • At the other extreme, the virus is taken up into the vector, circulates within the vector body and is released through the salivary glands. The vector needs to feed on an infected plant for much longer and there is an interval (perhaps several hours) before it can transmit. Once it becomes viruliferous, the vector will remain so for many days and such a relationship is therefore termed "persistent" or "circulative". The best studied examples are of luteovirus transmission by aphids. In some examples of this type (e.g. some hoppers and thrips), the virus multiplies within the vector and this is termed "propagative".

• Nematodes: these are root-feeding parasites, some of which transmit viruses in the genera Nepovirus and Tobravirus. The picture shows an adult female of Paratrichodorus pachydermus, the vector of Tobacco rattle virus. (Figure from Description 398, courtesy of the Scottish Crop Research Station).
  

• Plasmodiophorids: these are root-infecting obligate parasites traditionally regarded as fungi but now known to be more closely related to protists. They transmit viruses in the genera Benyvirus, Bymovirus, Furovirus, Pecluvirus and Pomovirus. The picture shows Polymyxa graminis, the vector of several cereal viruses including Barley yellow mosaic virus, growing within a barley root cell. (Figure from Description 374).
  

• Mites: these transmit viruses in the genera Rymovirus and Tritimovirus. The picture shows Aceria tosichella, the vector of Wheat streak mosaic virus. (Figure from Description 393; bar represents 10 µm).
  

How are viruses classified?

The highest level of virus classification recognises six major groups, based on the nature of the genome:

• Double-stranded DNA (dsDNA): there are no plant viruses in this group, which is defined to include only those viruses that replicate without an RNA intermediate (see Reverse-transcribing viruses, below). It includes those viruses with the largest known genomes (up to about 400,000 base pairs) and there is only one genome component, which may be linear or circular. Well-known viruses in this group include the herpes and pox viruses.
• Single-stranded DNA (ssDNA): there are two families of plant viruses in this group and both of these have small circular genome components, often with two or more segments.
• Reverse-transcribing viruses: these have dsDNA or ssRNA genomes and their replication includes the synthesis of DNA from RNA by the enzyme reverse transcriptase; many integrate into their host genomes. The group includes the retroviruses, of which Human immunodeficiency virus (HIV), the cause of AIDS, is a member. There is a single family of plant viruses in this group and this is characterised by a single component of circular dsDNA, the replication of which is via an RNA intermediate.
• Double-stranded RNA (dsRNA): some plant viruses and many of the mycoviruses are included in this group.
• Negative sense single-stranded RNA (ssRNA-): in this group, some or all of the genes are translated into protein from an RNA strand complementary to that of the genome (as packaged in the virus particle). There are some plant viruses in this group and it also includes the viruses that cause measles, influenza and rabies.
• Positive sense single-stranded RNA (ssRNA+): the majority of plant viruses are included in this group. It also includes the SARS coronavirus and many other viruses that cause respiratory diseases (including the "common cold"), and the causal agents of polio and foot-and-mouth disease.

Within each of these groups, many different characteristics are used to classify the viruses into families, genera and species. Typically, a combination of characters are used and some of the most important are:

• Particle morphology: the shape and size of particles as seen under the electron microscope.
• Genome properties: this includes the number of genome components and the translation strategy. Where genome sequences have been determined, the relatedness of different sequences is often an important factor in discriminating between species.
• Biological properties: this may include the type of host and also the mode of transmission.
• Serological properties: the relatedness (or otherwise) of the virion protein(s).

Particle morphology: Amongst plant viruses, the most frequently encountered shapes are:

Isometric: apparently spherical and (depending on the species) from about 18nm in diameter upwards. The example here shows Tobacco necrosis virus, genus Necrovirus with particles 26 nm in diameter.
Rod-shaped: about 20-25 nm in diameter and from about 100 to 300 nm long. These appear rigid and often have a clear central canal (depending on the staining method used). Some viruses have two or more different lengths of particle and these contain different genome components. The example here shows Tobacco mosaic virus, genus Tobamovirus with particles 300 nm long.
Filamentous: usually about 12 nm in diameter and more flexuous than the rod-shaped particles. They can be up to 1000 nm long, or even longer in some instances. Some viruses have two or more different lengths of particle and these contain different genome components. The example here shows Potato virus Y, genus Potyvirus with particles 740 nm long.
Geminate: twinned isometric particles about 30 x 18 nm. These particles are diagnostic for viruses in the family Geminiviridae which are widespread in many crops especially in tropical regions. The example here shows Maize streak virus, genus Mastrevirus.
Bacilliform: Short round-ended rods. These come in various forms up to about 30 nm wide and 300 nm long. The example here shows Cocoa swollen shoot virus, genus Badnavirus with particles 28 x 130 nm.

Further details can be found in the genus description pages and on the Rothamsted Electron Micrographs of Plant Viruses page.

Genome properties: Important features include:

• Nature of the genome: circular (as in all known plant DNA viruses) or linear.
• Number of genome components: This varies from a single component (e.g. in the genera Potyvirus and Tobamovirus) to 11 (in some members of the genus Nanovirus). Individual components vary in size from about 1kb (Nanovirus components) to about 20 kb (in the genus Closterovirus).
• Number of genes: These vary considerably. Most plant viruses have at least 3 genes: 1 (or more) concerned with replication of the nucleic acid, 1 (or more) concerned with cell-to-cell movement of the virus and 1 (or more) encoding a structural protein that is assembled into the virus particle (usually called the "coat" or "capsid" protein). There may also be additional genes that have a regulatory function or which are required for transmission between plants (association with a vector).
• Translation strategy: A variety of strategies are employed to translate the genes from the genome components either directly or via mRNA intermediates and (in some cases) to permit different amounts of protein to be produced from the different genes. These are summarised for each genus in the genus description pages but 3 examples here serve to illustrate some of the variety:
  • Genus Potyvirus: in this very large genus, there is one ssRNA component that encodes one large (c. 350 kDa) polyprotein. This is cleaved by 3 different proteases (all encoded by the virus itself) into 10 different mature proteins. The two proteins at the C-terminus of the polyprotein are respectively an RNA-dependent RNA polymerase (NIb, involved in replication of the virus) and the (single) coat protein (CP). Many of the proteins have multiple functions. The genome organisation of a typical member is shown here, indicating the 10 mature proteins and the nine cleavage sites (arrowed).
    

  • Genus Furovirus: in this genus there are two ssRNA components. The 5'-proximal gene on each RNA is translated directly from the genomic RNA: on RNA1 (the larger RNA component) this gene encodes a replication protein and on RNA2 it is the coat protein. The stop codons of both of these genes are "leaky" and in a small percentage of cases, translation continues to produce a larger ("readthrough") protein. On RNA1, the replication protein is extended to include an RNA-dependent RNA polymerase (RdRp) while the readthrough region of the coat protein is probably required for particle assembly and for transmission by the plasmodiophorid vector. There is a further (3'-proximal) gene on each of the RNAs and these are translated from shorter RNA molecules transcribed from the 3'-end of the genomic RNA ("subgenomic" mRNAs). That from RNA1 is a cell-to-cell movement protein (MP) that enables the virus to move between adjacent plant cells via the plasmodesmata while the function of the product from RNA2 is uncertain but may involve supression of the host plant defence reaction. The genome organisation of a typical member is shown here
    

  • Genus Fijivirus: in this genus there are 10 components of dsRNA. Most of the components encode a single protein and at least 3 of these are structural proteins assembled into the complex virion.
• Genome relatedness: the degree of nucleotide identity (or amino acid identity in the protein sequence) between sequences is often used to examine the relationship between different viruses or isolates. For example, recent studies in the genus Carlavirus show that when different species are compared, they have less than 73% nucleotide identity (or 80% amino acid identity) in their coat proteins.

Biological properties:

• In some families, the type of host is a useful feature for classification. For example, in the family Reoviridae, there are currently 3 genera with plant-infecting members (Fijivirus, Oryzavirus, Phytoreovirus), 1 genus of mycoviruses (Mycoreovirus), 1 genus containing viruses of fish and cephalopods (Aquareovirus), two genera that are restricted to insects (Cypovirus and Entomoreovirus) and 5 genera of vertebrate viruses that sometimes also infect insects.
• The mode of transmission is also a useful characteristic of some groups of plant viruses. For example in the family Potyviridae, members of the largest genus (Potyvirus) are transmitted by aphids, while viruses in the genera Rymovirus and Tritimovirus are transmitted by mites of the genus Abacarus or Aceria respectively, those in the genus Ipomovirus are transmitted by whiteflies and those in the genus Bymovirus by plasmodiphorids (root-infecting parasites once considered to be fungi but probably more closely related to protists).

Serological properties: Many viruses are good antigens (elicit strong antibody production when purified preparations are injected into a mammal) and this property has been widely exploited to produce specific antibodies that can be used for virus detection and for examining relationships between viruses. Earlier studies used agar diffusion plates but in the last 20 years these have been largely superseded by ELISA (enzyme-linked immunosorbent assay) procedures. Although serological properties are still important, their significance in taxonomy has declined to some extent now that nucleotide sequence data are available.