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{{otheruses1|biological infectious particles}}

{{Taxobox | color=violet
| name = Viruses
| image = Herpes_simpex_virus.jpg
| image_caption = Herpes simplex virus 1 (HSV-1)
| virus_group = I–VII
| subdivision_ranks = Groups
| subdivision = I: [[dsDNA virus]]es<br>
II: [[ssDNA virus]]es<br>
III: [[dsRNA virus]]es<br>
IV: [[positive-sense ssRNA virus|(+)ssRNA virus]]es<br>
V: [[negative-sense ssRNA virus|(-)ssRNA virus]]es<br>
VI: [[ssRNA-RT virus]]es<br>
VII: [[dsDNA-RT virus]]es
}}
A '''virus''' (from the [[Latin]] noun ''virus'', meaning [[toxin]] or [[poison]]) is a sub-[[microscopic]] particle (ranging in size from 20–300 [[Nano|n]][[Metre|m]]) that can [[infectious diseases|infect]] the [[cell (biology)|cell]]s of a [[biological]] [[organism]]. Viruses can replicate themselves only by infecting a host cell. They therefore cannot reproduce on their own. At the most basic level, viruses consist of [[genetic material]] contained within a protective [[protein]] coat called a [[capsid]]. They infect a wide variety of organisms: both [[eukaryote]]s (animals, plants, [[protist]]s, and [[fungi]]) and [[prokaryote]]s ([[bacteria]] and [[archaea]]). A virus that infects bacteria is known as a ''[[bacteriophage]]'', often shortened to ''phage''. The study of viruses is known as [[virology]] and people who study viruses are known as virologists. Viruses cause several serious human diseases, such as [[AIDS]], [[influenza]] and [[rabies]]. Therapy is difficult for viral diseases as [[antibiotic]]s have no effect on viruses and few [[antiviral drug]]s are known. The best way to prevent viral diseases is with a [[vaccine]], which produces [[immunity (medical)|immunity]].

It has been argued extensively whether viruses are living organisms. Most virologists consider them non-living,<ref>[http://school.discovery.com/lessonplans/programs/understandingviruses/ http://school.discovery.com/lessonplans/programs/understandingviruses/]</ref><ref>[http://www.tulane.edu/~dmsander/garryfavwebfaq.html http://www.tulane.edu/~dmsander/garryfavwebfaq.html]</ref><ref>[http://library.thinkquest.org/CR0212089/virus.htm http://library.thinkquest.org/CR0212089/virus.htm]</ref> as they do not meet all the criteria of the generally accepted definition of [[life]]. For example, unlike living organisms as defined, viruses do not respond to changes in the environment.

==Discovery==
[[Image:viren22.jpg|thumb|right|200px|Computer-generated image of virions]]
Viral diseases such as [[rabies]], [[yellow fever]] and [[smallpox]] have affected humans for many centuries. There is hieroglyphical evidence of [[polio]] in the ancient Egyptian empire,<ref name=Lewis_2000>{{cite journal | author = Lewis R | title = Polio Eradication Goal Extended | journal = The Scientist | year = 2000 | volume = 14 | issue = 24 | pages = 12 | url= http://www.the-scientist.com/article/display/12168/}}</ref> however, the cause of these diseases was unknown at the time. In 1717, [[Lady Mary Wortley Montagu|Mary Montagu]], the wife of an English ambassador to the [[Ottoman Empire]], observed local women [[inoculation|inoculating]] their children against [[smallpox]].<ref name=Behbehani_1983>{{cite journal |author=Behbehani AM |title=The smallpox story: life and death of an old disease |journal=Microbiol Rev |volume=47 |issue=4 |pages=455-509 |year=1983 |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=6319980 |pmid=6319980}}</ref> In the late 18th century, [[Edward Jenner]] observed and studied Miss Sarah Nelmes, a milkmaid who had previously caught [[cowpox]] and was subsequently found to be immune to [[smallpox]], a similar, but devastating virus. Jenner developed the first [[vaccine]] based on these findings; after lengthy (but successful) [[vaccination]] campaigns the [[World Health Organization]] (WHO) certified the eradication of [[smallpox]] in 1979.<ref name=WHO_Meeting_Agenda>{{cite web | title=Smallpox eradication: destruction of variola virus stocks | work= WHO: 52nd World Health Assembly | url=http://ftp.who.int/gb/pdf_files/WHA52/ew5.pdf | accessdate=2006-09-23}}</ref>

In the late 19th century [[Charles Chamberland]] developed a porcelain filter with pores small enough to filter bacteria, yet retain all viable viruses.<ref name=Horzinek_1997>{{cite journal | author = Horzinek MC| title = The birth of virology | journal = Antonie van Leeuwenhoek | year = 1997 | volume = 71 | pages = 15&ndash;20 | doi=10.1023/A:1000197505492 }}</ref> [[Dimitri Ivanovski]] used this filter to study [[tobacco mosaic virus]]. He published experiments showing that crushed leaf extracts of infected tobacco plants were still infectious after filtering through such filters. At about the same time, several others documented filterable disease-causing agents, with several independent experiments showing that viruses were different from bacteria, yet they could also cause disease in living organisms. These experiments showed that viruses are orders of magnitudes smaller than bacteria. The term ''virus'' was coined by the Dutch microbiologist [[Martinus Beijerinck]].

In the early 20th century, [[Frederick Twort]] discovered that bacteria could be attacked by viruses. [[Felix d'Herelle]], working independently, showed that a preparation of viruses caused areas of cellular death on thin [[cell culture]]s spread on [[agar]]. Counting the dead areas allowed him to estimate the original number of viruses in the suspension. The invention of [[Electron microscopy]] provided the first look at viruses. In 1935 [[Wendell Stanley]] crystallised the tobacco mosaic virus and found it to be mostly [[protein]]. A short time later the virus was separated into protein and [[nucleic acid]] parts. In 1939, [[Max Delbrück]] and [[E.L. Ellis]] demonstrated that, in contrast to cellular organisms, bacteriophage reproduce in "one step", rather than exponentially.

A major problem for early virologists was the inability to propagate viruses on sterile culture media, as is done with cellular microorganisms. This limitation required medical virologists to infect living animals with infectious material, which is dangerous. The first breakthrough came in 1931, when [[Ernest William Goodpasture]] demonstrated the growth of [[influenza]] and several other viruses in fertile chicken eggs. However, many viruses would not grow in chicken eggs, and a more flexible technique was needed for propagation of viruses. The solution came in 1949 when [[John Franklin Enders]], [[Thomas H. Weller]] and [[Frederick Chapman Robbins]] together developed a technique to grow [[polio virus]] in cultures of living animal cells. Their methods have since been extended and applied to the growth of many viruses and other infectious agents that do not grow on sterile culture media.

==Origins==
The origins of modern viruses are not entirely clear. It may be that no single mechanism can account for all viruses. They do not [[fossil]]ize well, so [[Molecular biology|molecular techniques]] have been the most useful means of hypothesising how they arose. Research in [[microfossil]] identification and molecular biology may yet discern fossil evidence dating to the [[Archean]] or [[Proterozoic]] [[eon (geology)|eons]]. Two main hypotheses currently exist.<ref name="prescott">{{cite book | title=Microbiology| last=Prescott| first=L| date=1993| publisher=Wm. C. Brown Publishers| id=0-697-01372-3}}</ref>

Small viruses with only a few genes may be runaway stretches of nucleic acid originating from the genome of a living organism. Their genetic material could have been derived from transferable genetic elements such as [[plasmid]]s or [[transposon]]s, which are prone to moving within, leaving, and entering genomes.

Viruses with larger genomes, such as [[poxvirus]]es, may have once been small cells which parasitised larger host cells. Over time, genes not required by their parasitic lifestyle would have been lost in a streamlining process known as ''retrograde-evolution'' or ''reverse-evolution''. The bacteria [[Rickettsia]] and [[Chlamydia]] are living cells that, like viruses, can only reproduce inside host cells. They lend credence to the streamlining hypothesis, as their parasitic lifestyle is likely to have caused the loss of genes that enabled them to survive outside a host cell.

It is hypothetically possible that viruses represent a primitive form of self replicating DNA and are a precursor to life as it is presently defined.

Other infectious particles which are even simpler in structure than viruses include [[viroid]]s, [[satellite (biology)|satellite]]s, and [[prion]]s.

==Classification==
{{details|Virus classification}}
{| class = "prettytable" style = "float:right; font-size:85%; margin-left:15px"
|+ Baltimore classification
! Group || Contains
|-
| I || [[dsDNA virus]]es
|-
| II || [[ssDNA virus]]es
|-
| III || [[dsRNA virus]]es
|-
| IV || [[positive-sense ssRNA virus|(+)ssRNA virus]]es
|-
| V || [[negative-sense ssRNA virus|(-)ssRNA virus]]es
|-
| VI || [[ssRNA-RT virus]]es
|-
| VII || [[dsDNA-RT virus]]es
|-
| colspan="2" | <small>''ss: single-stranded, ds: double stranded<br>RT: reverse transcribing''</small>
|}
In [[taxonomy]], the classification of viruses is rather difficult due to the lack of a fossil record and the dispute over whether they are living or non-living. They do not fit easily into any of the [[domain (biology)|domains]] of [[biological classification]] and therefore classification begins at the [[family (biology)|family]] rank. However, the domain name of [[Acytota]] (without cells) has been suggested. This would place viruses on a par with the other domains of [[Eubacteria]], [[Archaea]], and [[Eukarya]]. Not all families are currently classified into orders, nor all genera classified into families.

As an example of viral classification, the [[chicken pox]] virus belongs to family ''[[Herpesviridae]]'', subfamily ''[[Alphaherpesvirinae]]'' and genus ''[[Varicellovirus]]''. It remains unranked in terms of order. The general structure is as follows.

:[[Order (biology)|Order]] (''-virales'')
::[[Family (biology)|Family]] (''-viridae'')
:::[[Subfamily]] (''-virinae'')
::::[[Genus]] (''-virus'')
:::::[[Species]] (''-virus'')

The [[International Committee on Taxonomy of Viruses]] (ICTV) developed the current classification system and put in place guidelines that put a greater weighting on certain virus properties in order to maintain family uniformity. In determining order, taxonomists should consider the type of nucleic acid present, whether the nucleic acid is single- or double-stranded, and the presence or absence of an [[Envelope (biology)|envelope]]. After these three main properties, other characteristics can be considered: the type of host, the capsid shape, immunological properties and the type of disease it causes.

In addition to this classification system, the [[Nobel Prize]]-winning biologist [[David Baltimore]] devised the [[Virus classification#Baltimore classification|Baltimore classification]] system. This places a virus into one of seven ''Groups'', which distinguish viruses based on their mode of replication and genome type. The ICTV classification system is used in conjunction with the Baltimore classification system in modern virus classification.

== Structure ==
A complete virus particle, known as a '''virion''', is little more than a [[gene]] transporter, consisting in its simplest form of [[nucleic acid]] surrounded by a protective coat of [[protein]] called a [[capsid]]. A capsid is composed of proteins encoded by the viral [[genome]] and its shape serves as the basis for [[morphology (biology)|morphological]] distinction. Virally coded protein subunits - sometimes called '''protomers''' - will self-assemble to form the capsid, generally requiring the presence of the virus genome - however, many complex viruses code for proteins which assist in the construction of their capsid.<ref name=prescott> </ref> Proteins associated with nucleic acid are known as [[nucleoprotein]]s, and the association of viral capsid proteins with viral nucleic acid is called a '''nucleocapsid'''.

In general, there are four main morphological virus types:

{| cellpadding=3 cellspacing=0 border=1 style="border-collapse:collapse"
|bgcolor="#dddddd"| '''Image'''
|bgcolor="#dddddd"| '''Helical viruses'''
|-
| [[Image:Tobacco mosaic virus structure.png|center|thumb|200px|Diagram of a helical capsid]]
| Helical capsids are composed of a single type of subunit stacked around a central axis to form a helical structure which may have a central cavity, or hollow tube. This arrangement results in rod-shaped or filamentous virions: these can be anything from short and highly rigid, to long and very flexible. The genetic material - generally single-stranded RNA, but also ssDNA in the case of certain phages - is bound into the protein helix, by charge interactions between the negatively-charged nucleic acid and positive charges on the protein. Overall, the length of a helical capsid is related to the length of the nucleic acid contained within it, while the diameter is dependent on the size and arrangement of protomers. The well-studied [[Tobacco mosaic virus]] is an example of a helical virus.
|-
|bgcolor="#dddddd"| '''Image'''
|bgcolor="#dddddd"| '''Icosahedral viruses'''
|-
| [[Image:Coronaviruses 004 lores.jpg|center|thumb|200px|Electron micrograph of icosahedral virions]]
| Icosahedral capsid symmetry results in a spherical appearance of viruses at low magnification but actually consists of capsomers arranged in a regular geometrical pattern, similar to a [[football (soccer)|soccer ball]], hence they are not truly "spherical". Capsomers are ring shaped structures constructed from five to six copies of protomers. These associate via [[chemical bond|non-covalent bonding]] to enclose the viral nucleic acid, though generally less intimately than helical capsids, and may involve one or more protomers.
Icosahedral architecture was employed by [[Buckminster Fuller|R. Buckminster-Fuller]] in his [[geodesic dome]], and is the most efficient way of creating an enclosed robust structure from multiple copies of a single protein.
The number of proteins required to form a spherical virus capsid is denoted by the T-number,<ref name="triang">{{Cite web|url=http://web.archive.org/web/20060223170529/http://rhino.bocklabs.wisc.edu/cgi-bin/virusworld/htdocs.pl?docname=triangulation.html|title=Virus triangulation numbers via Internet Archive|accessdate=2006-04-05}}</ref> where 60&times;''t'' proteins are necessary. In the case of the [[hepatitis B]] virus the T-number is 4, therefore 240 proteins assemble to form the capsid.
|-
|bgcolor="#dddddd"| '''Image'''
|bgcolor="#dddddd"| '''Enveloped viruses '''
|-
| [[Image:HIV Viron.png|thumb|center|200px|Diagram of enveloped [[HIV]]]]
| In addition to a protein capsid many viruses are able to envelope themselves in a modified form of one of the [[cell membranes]] - the outer membrane surrounding an infected host cell, or from internal membranes such as nuclear membrane or endoplasmic reticulum - thus gaining an outer lipid bilayer known as a [[viral envelope]]. This membrane is studded with proteins coded for by the viral genome and host genome; however the lipid membrane itself and any carbohydrates present are entirely host-coded. The Influenza virus and HIV use this strategy.

The viral envelope can give a virion a few distinct advantages over other capsid-only virions, such as protection from enzymes and certain chemicals. The proteins in it can include [[glycoprotein]]s functioning as [[receptor (biochemistry)|receptor molecules]], allowing host cells to recognise and bind these virions, resulting in the possible uptake of the virion into the cell. Most enveloped viruses are dependent upon the envelope for infectivity.
|-
|bgcolor="#dddddd"| '''Image'''
|bgcolor="#dddddd"| '''Complex viruses'''
|-
| [[Image:Tevenphage.png|thumb|center|200px|Diagram of a bacteriophage]]
| These viruses possess a capsid which is neither purely helical, nor purely icosahedral, and which may possess extra structures such as protein tails or a complex outer wall. Some [[bacteriophages]] have a complex structure consisting of an icosahedral head bound to a helical tail, the latter of which may have a hexagonal base plate with many protruding protein tail fibres.

The [[Poxvirus]]es are large, complex viruses which have an unusual [[morphology (biology)|morphology]]. The viral genome is associated with proteins within a central disk structure known as a [[nucleoid]]. The nucleoid is surrounded by a membrane and two lateral bodies of unknown function. The virus has an outer envelope with a thick layer of protein studded over its surface. The whole particle is slightly [[pleiomorphic]], ranging from ovoid to brick shape{{Fact|date=April 2007}}.
|}

[[Image:Relative scale.svg|thumb|300px|left|The range of sizes shown by viruses, relative to those of other organisms and [[biomolecule]]s]]
=== Size ===
To put viral size into perspective, a medium sized virion next to a flea is roughly equivalent to a human next to a mountain twice the size of [[Mount Everest]]. Some [[filovirus]]es have a total length of up to 1400&nbsp;nm, however their capsid diameters are only about 80&nbsp;nm. The majority of viruses which have been studied have a [[capsid]] diameter between 10 and 300 [[nanometres]]. While most viruses are unable to be seen with a [[light microscope]], some are as large or larger than the smallest bacteria and can be seen under high optical magnification. More commonly, both scanning and transmission [[electron microscope]]s are used to visualise virus particles.

A notable exception to the normal viral size range is the recently discovered [[mimivirus]], with a diameter of 750&nbsp;nm which is larger than a ''[[Mycoplasma]]'' bacterium.<ref name=robertson>{{cite journal | author = Robertson J, Gomersall M, Gill P | title = Mycoplasma hominis: growth, reproduction, and isolation of small viable cells | journal = J Bacteriol. | volume = 124 | issue = 2 | pages = 1007 – 18 | year = 1975 | id = PMID 1102522}}</ref><ref name=claverie>{{cite journal | author = Claverie J, Ogata H, Audic S, Abergel C, Suhre K, Fournier P | title = Mimivirus and the emerging concept of "giant" virus | journal = Virus Res | volume = 117 | issue = 1 | pages = 133-44 | year = 2006 | pmid = 16469402}}</ref> They also hold the record for the largest viral genome size, possessing about 1000 genes (some bacteria only possess 400) on a genome approximately 1.2 [[megabase]]s in length.<ref name=raoult>{{cite journal | author = Raoult D, Audic S, Robert C, ''et al'' | title = The 1.2-megabase genome sequence of Mimivirus | journal = Science | volume = 306 | issue = 5700 | pages = 1344-50 | year = 2004 | pmid = 15486256}}</ref> Their large genome also contains many genes which are [[Homology (biology)|conserved]] in both prokaryotic and eukaryotic genes.<ref name="mimi1">{{Cite web|url=http://www.stanford.edu/group/virus/mimi/2005/Genome.htm|title=Mimiviridae genome|accessdate=2007-04-05|publisher=Stanford University}}</ref> The discovery of the virus has led many scientists to reconsider the controversial boundary between living organisms and viruses, which are currently considered as mere mobile genetic elements.

== Genome ==
{| class = "prettytable" style = "float:right; font-size:85%; margin-left:15px"
|+ Genomic diversity among viruses
! Property || Parameters
|-
| ''Nucleic acid'' ||
*DNA
*RNA
*Both DNA and RNA
|-
| ''Shape'' ||
*Linear
*Circular
*Segmented
|-
| ''Strandedness'' ||
*Single-stranded
*Double-stranded
*Double-stranded with regions of single-strandedness
|-
| ''[[Sense (molecular biology)|Sense]]'' ||
*Positive sense (+)
*Negative sense (-)
*Ambisense (+/-)
|}

An enormous variety of genomic structures can be seen among viral species; as a group they contain more structural genomic diversity than the entire kingdoms of either plants, animals, or bacteria<ref name="flint">{{cite book | title=Principles of Virology| edition=2nd edn |last=Flinth| coauthors=et al.| date=2004| publisher=ASM Press, New York| id=1-55581-259-7}}</ref>.

===Nucleic acid===
A virus may employ either [[DNA]] or [[RNA]] as the nucleic acid. Rarely do they contain both, however [[cytomegalovirus]] is an exception to this, possessing a DNA core with several [[mRNA]] segments.<ref name=prescott> </ref> Plant viruses tend to have single-stranded RNA and bacteriophages tend to have double-stranded DNA.<ref name="prescott"> </ref> Some virus species possess abnormal [[nucleotide]]s, such as ''hydroxymethylcytosine'' instead of [[cytosine]], as a normal part of their genome.<ref name="prescott"> </ref>

===Shape===
Viral genomes may be circular, such as [[polyomavirus]]es, or linear, such as [[adenovirus]]es. The type of nucleic acid is irrelevant to the shape of the genome. Among [[RNA virus]]es, the genome may be divided up into separate parts within the virion, or ''segmented''. All double-stranded RNA genomes, and some single-stranded RNA genomes, are segmented.<ref name=prescott> </ref> Each segment may code for one protein, and they are usually found together in one capsid. Not all segments are required to be in the same virion for the overall virus to be infectious, as demonstrated by the [[brome mosaic virus]].<ref name="prescott"> </ref>

===Strandedness===
A viral genome, irrespective of nucleic acid type, may be either single-stranded or double-stranded. Single-stranded genomes consist of an unpaired nucleic acid, analogous to one-half of a ladder split down the middle. Double-stranded genomes consist of 2 complimentary paired nucleic acids, analogous to a ladder. Some viruses, such as those belonging to the ''[[Hepadnaviridae]]'', contain a genome which is partially double-stranded and partially single-stranded.<ref name="flint"> </ref>

===Sense===
For viruses with RNA as their nucleic acid, the strands are said to be either [[positive-sense]] (also called plus-strand) or [[negative-sense]] (also called minus-strand) depending on whether it is complementary to viral mRNA. Positive-sense viral RNA is identical to viral mRNA and thus can be immediately [[translation (genetics)|translated]] by the host cell. Negative-sense viral RNA is complementary to mRNA and thus must be converted to positive-sense RNA by an [[RNA polymerase]] before translation. DNA nomenclature is similar to RNA nomenclature, in that the ''coding strand'' for the viral mRNA is complementary to it (-), and the ''non-coding strand'' is a copy of it (+).

===Genome size===
Genome size in terms of the weight of [[nucleotides]] varies between species. The smallest genomes code for only four proteins and weigh about 10<sup>6</sup> [[Atomic mass unit|dalton]]s, while the largest weigh about 10<sup>8</sup> daltons and code for over one hundred proteins.<ref name=prescott> </ref> [[RNA virus]]es generally have smaller genome sizes than [[DNA virus]]es due to a higher error-rate when replicating, resulting in a maximum upper size limit. Beyond this limit, too many errors in the genome when replicating render the virus useless or uncompetitive. In contrast, DNA viruses generally have larger genomes due to the high fidelity of their replication enzymes.<ref name="flint"> </ref>

==Replication==
Viral populations do not grow through [[cell division]], because they are acellular; instead, they use the machinery and metabolism of a host cell to produce multiple copies of themselves. A virus can still cause degenerative effects within a cell without causing its death; collectively these are termed '''cytopathic effects'''. Released virions can be passed between hosts through either direct contact, often via [[body fluids]], or through a [[vector (biology)|vector]]. In aqueous environments, viruses float free in the water.

===Lytic or lysogenic===
Viruses may have a [[lytic cycle|lytic]] or a [[lysogenic cycle]], with some viruses capable of carrying out both.<ref name=prescott> </ref>

====Lytic cycle====
{{Main|Lytic cycle}}
In the lytic cycle, characteristic of virulent phages such as the [[T4 phage]], host cells will be induced by the virus to begin manufacturing the proteins necessary for virus reproduction. As well as proteins, the virus must also direct the replication of new genomes, the technique used for this varies greatly between virus species but depends heavily on the genome type. The final viral product is assembled spontaneously, though it may be aided by [[chaperone|molecular chaperone]]s. After the genome has been replicated and the new capsid assembled, the virus causes the cell to be broken open (lysed) to release the virus particles. Some viruses do not lyse the cell but instead exit the cell via the [[cell membrane]] in a process known as [[exocytosis]], taking a small portion of the membrane with them as a viral envelope. As soon as the cell is destroyed the viruses have to find a new host.

====Lysogenic cycle====
{{Main|Lysogenic cycle}}
In contrast, the lysogenic cycle does not result in immediate lysing of the host cell, instead the viral genome integrates into the host DNA and replicates along with it. The virus remains dormant but after the host cell has replicated several times, or if environmental conditions permit it, the virus will become active and enter the lytic phase. The lysogenic cycle allows the host cell to continue to survive and reproduce, and the virus is passed on to all of the cell’s offspring.

[[Image:Bacteriophage.jpg|thumb|200px|right|A falsely coloured electron micrograph of multiple [[bacteriophage]]s]]

===Bacteriophages===
'''[[Bacteriophage]]s''' infect specific bacteria by binding to [[receptor (biochemistry)|surface receptor molecule]]s and then enter the cell. Within a short amount of time, sometimes just minutes, bacterial [[polymerase]] starts translating viral mRNA into protein. These proteins go on to become either new virions within the cell, helper proteins which help assembly of new virions, or proteins involved in cell [[lysis]]. Viral enzymes aid in the breakdown of the cell membrane, and in the case of the [[T4 phage]], in just over twenty minutes after injection over three hundred phages will be released.

===DNA viruses===
Animal '''[[DNA virus]]es''', such as [[herpesvirus]]es, enter the host via [[endocytosis]], the process by which cells take in material from the external environment. Frequently after a chance collision with an appropriate surface receptor on a cell, the virus penetrates the cell, the viral genome is released from the capsid and host polymerases begin transcribing viral mRNA. New virions are assembled and released either by cell lysis or by budding off the cell membrane.

===RNA viruses===
Animal '''[[RNA viruses]]''' can be placed into about four different groups depending on their mode of replication. The [[Sense (molecular biology)|polarity]] of the RNA largely determines the replicative mechanism, as well as whether the genetic material is single-stranded or double-stranded. Some [[RNA virus]]es are actually DNA based but use an RNA-intermediate to replicate. RNA viruses are heavily dependent upon virally encoded [[RNA replicase]] to create copies of their genomes.

===Reverse transcribing viruses===
'''[[Reverse transcribing viruses]]''' are viruses that replicate using reverse transcription, which is the formation of DNA from an RNA template. Those viruses containing RNA genomes use a DNA intermediate to replicate, whereas those containing DNA genomes use an RNA intermediate during genome replication. Both types of reverse transcribing viruses use the [[reverse transcriptase]] enzyme to carry out the nucleic acid conversion.

==Lifeform debate==
[[Image:Rotavirus TEM B82-0337 lores.jpg|thumb|200px|right|Multiple [[rotavirus]] virions]]
Argument continues over whether viruses are truly alive. According to the [[United States Code]], they are considered [[microorganism]]s in the sense of biological weaponry and malicious use. Scientists, however, are divided. Things become complicated as they look at simple viruses, [[viroids]] and [[prions]]. Viruses resemble other organisms in that they possess nucleic acid, and can respond - in infected cells - to their environment in a limited fashion. They can also reproduce by creating multiple copies of themselves through simple self-assembly.

Viruses do not have a [[cell (biology)|cell]] structure, regarded as the basic unit of life. Additionally, although they reproduce, they do not metabolise on their own and therefore require a host cell to replicate and synthesise new products. Bacterial species such as [[Rickettsia]] and [[Chlamydia]], while living organisms, are even unable to reproduce outside of a host cell.

An argument can be made that all accepted forms of life use [[cell division]] to reproduce, whereas all viruses spontaneously assemble within cells. The comparison is drawn between viral self-assembly and the autonomous growth of non-living [[crystallization|crystal]]s. Virus self-assembly within host cells also has implications for the study of the [[origin of life]], as it lends credence to the hypothesis that life could have started as self-assembling organic molecules{{Fact|date=April 2007}}.

If viruses are considered alive, then the criteria specifying life will have been permanently changed, leading scientists to question what the basic prerequisite of life is. The standards required to call something artificially alive would be reduced and the prospect of creating [[artificial life]] would be enhanced. If viruses were said to be alive, the question could follow of whether even smaller infectious particles, such as [[viroid]]s and [[prion]]s, are alive.

==Viruses and disease==
:''For more examples of diseases caused by viruses see [[List of infectious diseases]]
Examples of common human diseases caused by viruses include the [[common cold]], [[influenza|the flu]], [[chickenpox]] and [[cold sores]]. Many serious diseases such as [[Ebola]], [[AIDS]], [[avian flu]] and [[SARS]] are also caused by viruses. The relative ability of viruses to cause disease is described in terms of [[virulence]]. Other diseases are under investigation as to whether they too have a virus as the causative agent, such as the possible connection between [[Human Herpesvirus Six]] (HHV6) and neurological diseases such as [[multiple sclerosis]] and [[chronic fatigue syndrome]]. Recently it was also shown that cervical cancer is partially caused by [[papillomavirus]], representing evidence in humans of a link existing between cancer and an infective agent.<ref name=BBC_1999>{{cite news | title=Human Papilloma Virus |url=http://news.bbc.co.uk/2/hi/health/medical_notes/429762.stm |publisher = BBC News |date=1999-08-26 |accessdate=2007-03-17 }}</ref> There is current controversy over whether the [[borna virus]], previously thought of as causing [[neurology|neurological]] disease in horses, could be responsible for [[psychiatry|psychiatric]] illness in humans.<ref name=Chen_1999>{{cite journal |author=Chen C, Chiu Y, Wei F, Koong F, Liu H, Shaw C, Hwu H, Hsiao K |title=High seroprevalence of Borna virus infection in schizophrenic patients, family members and mental health workers in Taiwan |journal=Mol Psychiatry |volume=4 |issue=1 |pages=33-8 |year=1999 |pmid=10089006}}</ref>

Viruses have many different mechanisms by which they produce disease in an organism, which largely depends on the species. Mechanisms at the cellular level primarily include cell [[lysis]], the breaking open and subsequent death of the cell. In [[multicellular organism]]s, if enough cells die the whole organism will start to suffer the effects. Although many viruses result in the disruption of healthy [[homeostasis]], resulting in disease, they may also exist relatively harmlessly within an organism. An example would include the ability of the [[herpes simplex virus]], which cause [[coldsore]]s, to remain in a dormant state within the human body.

=== Epidemics ===
[[Image:Ebola Virus TEM PHIL 1832 lores.jpg|thumb|200px|right|The [[Ebola]] virus]]
[[Image:Marburg virions TEM 275 lores.jpg|thumb|200px|right|The [[Marburg virus]]]]
{{details|List of epidemics}}
A number of highly lethal viral pathogens are members of the [[Filoviridae]]. Filoviruses are filament-like viruses that cause [[viral hemorrhagic fever]], and include the [[Ebola]] and [[Marburg virus]]es. The Marburg virus attracted widespread press attention in April 2005 for an outbreak in [[Angola]]. Beginning in October 2004 and continuing into 2005, the outbreak was the world's worst epidemic of any kind of viral hemorrhagic fever.<ref name="bbc">{{cite web| url=http://news.bbc.co.uk/2/hi/africa/4397891.stm| title=Marburg outbreak worst recorded| date = 2005-03-31 | accessdate=2007-04-05| publisher=BBC News}}</ref>

[[Indigenous peoples of the Americas|Native American]] populations were devastated by contagious diseases, particularly [[smallpox]], brought to the Americas by European colonists. It is unclear how many Native Americans were killed by foreign diseases after the arrival of Columbus in the Americas, but the numbers have been estimated to be close to 70% of the indigenous population.<ref name="smallpoxhistory">{{cite web|url=http://www.historylink.org/essays/output.cfm?file_id=5100|title=Smallpox epidemic ravages Native Americans on the northwest coast of North America in the 1770s|accessdate=2007-04-05|publisher=HistoryLink.org}}</ref> The damage done by this disease may have significantly aided European attempts to displace or conquer the native population.

=== Detection, purification and diagnosis ===
In the laboratory, several techniques for growing and detecting viruses exist. Purification of viral particles can be achieved using [[differential centrifugation]], [[isopycnic centrifugation]], precipitation with [[ammonium sulfate]] or [[ethylene glycol]], and removal of cell components from a homogenised cell mixture using [[organic solvent]]s or [[enzyme]]s to leave the virus particles in solution.

Assays to detect and quantify viruses include:
[[Image:Plaque assay macro.jpg|thumb|right|A [[viral plaque]] [[assay]]]]
* [[Hemagglutination assay]]s, which quantitatively measure how many virus particles are in a solution of [[red blood cells]] by the amount of [[Agglutination (biology)|agglutination]] the viruses cause between them. This occurs as many viruses are able to bind to the surface of one or more red blood cells.
* Direct counts using an [[electron microscope]]. A dilute mixture of virus particles and beads of known size are sprayed onto a special sheet and examined under high magnification. The virions are counted and the number extrapolated to estimate the number of virions in the undiluted mixture.
* [[Viral plaque|Plaque assays]] involve growing a thin layer of host cells onto a culture dish and adding a dilute mixture of virions onto it. The virions will infect and kill the cells they land on, producing holes in the cell layer known as plaques. The number of plaques can be counted and the number of infectious virions is estimated from it. Importantly, unlike other assays, the plaque assay is the only method that can accurately assess the number of infectious virus particles in a preparation of virus. Notably, most viruses exhibit low particle to PFU (plaque forming units) ratios - [[HIV]] is famous for this,; i.e. often hundreds or thousands of defective particles are generated for each one that can actually productively replicate in a permissive cell.

Detection and subsequent isolation of new viruses from patients is a specialised laboratory subject. Normally it requires the use of large facilities, expensive equipment, and trained specialists such as technicians, [[molecular biologist]]s, and [[virologist]]s. Often, this effort is undertaken by state and national governments and shared internationally through organizations like the [[World Health Organization]].

=== Prevention and treatment ===
Because viruses use the machinery of a host cell to reproduce and also reside within them, they are difficult to eliminate without killing the host cell. The most effective [[medicine|medical]] approaches to viral diseases so far are [[vaccination]]s to provide resistance to infection, and drugs which treat the symptoms of viral infections. Patients often ask for, and [[General Practitioner|physician]]s often prescribe, [[antibiotic]]s. These are useless against viruses, and their misuse against viral infections is one of the causes of [[antibiotic resistance]] in [[bacterium|bacteria]]. However, in life-threatening situations the prudent course of action is to begin a course of antibiotic treatment while waiting for test results to determine whether the patient's symptoms are caused by a virus or a bacterial infection{{Fact|date=April 2007}}.

===Potential uses in therapy===
[[Virotherapy]] uses viruses as vectors to treat various diseases, as they can specifically target cells and DNA. It shows promise in the treatment of cancer and as a method for gene therapy.{{Fact|date=April 2007}} Eastern European doctors have used [[phage therapy]] as an alternative to antibiotics for some time and interest in this approach is increasing, due to the high level of [[antibiotic resistance]] now found in some pathogenic bacteria.<ref name="pmid16258815">{{cite journal |author=Matsuzaki S, Rashel M, Uchiyama J, ''et al'' |title=Bacteriophage therapy: a revitalized therapy against bacterial infectious diseases |journal=J. Infect. Chemother. |volume=11 |issue=5 |pages=211-9 |year=2005 |pmid=16258815 |doi=10.1007/s10156-005-0408-9}}</ref>

==Applications==
[[Image:Polio EM PHIL 1875 lores.PNG|thumb|170px|right|[[Transmission electron microscopy|TEM]] [[micrograph]] of [[Poliovirus]] virions.]]
===Life sciences===
Viruses are important to the study of [[molecular biology|molecular]] and [[cellular biology]] as they provide simple systems that can be used to manipulate and investigate the functions of cells. The study and use of viruses have provided valuable information about many aspects of cell biology. For example, viruses have simplified the study of [[genetics]] and helped human understanding of the basic mechanisms of [[molecular genetics]], such as [[DNA replication]], [[transcription (genetics)|transcription]], [[RNA processing]], [[translation (genetics)|translation]], [[protein]] transport, and [[immunology]].

[[genetics|Geneticists]] regularly use viruses as [[vector (biology)|vectors]] to introduce genes into cells that they are studying. This is useful for making the cell produce a foreign substance, or to study the effect of introducing a new gene into the genome. In similar fashion, [[virotherapy]] uses viruses as vectors to treat various diseases, as they can specifically target cells and DNA. It shows promising use in the treatment of cancer and in [[gene therapy]].

===Materials science and nanotechnology===
Current trends in nanotechnology promise to make much more versatile use of viruses. From the viewpoint of a materials scientist, viruses can be regarded as organic nanoparticles{{Fact|date=April 2007}}. Their surface carries specific tools designed to cross the barriers of their host cells. The size and shape of viruses, and the number and nature of the functional groups on their surface, is precisely defined. As such, viruses are commonly used in materials science as scaffolds for covalently linked surface modifications. A particular quality of viruses is that they can be tailored by directed evolution. The powerful techniques developed by life sciences are becoming the basis of engineering approaches towards nanomaterials, opening a wide range of applications far beyond biology and medicine.<ref name=fischlechner >{{cite journal |author=Fischlechner M, Donath E |title=Viruses as Building Blocks for Materials and Devices |url=http://dx.doi.org/doi:10.1002/anie.200603445 |journal=Angewandte Chemie International Edition |volume= |issue= |pages= |year=2007 |doi=10.1002/anie.200603445}}</ref>

In April 2006 scientists at the [[Massachusetts Institute of Technology]] (MIT) created [[nanotechnology|nanoscale]] metallic wires using a [[Genetic engineering|genetically-modified]] virus.<ref name="mitvirusbattery">{{Cite web|url=http://web.mit.edu/newsoffice/2006/virus-battery.html|title=Researchers build tiny batteries with viruses|accessdate=2007-04-05|publisher=MIT News Office}}</ref> The MIT team was able to use the virus to create a working [[Battery (electricity)|battery]] with an [[energy density]] up to three times more than current materials. The potential exists for this technology to be used in [[liquid crystal]]s, [[solar cell]]s, [[fuel cells]], and other electronics in the future.

[[Image:Reconstructed Spanish Flu Virus.jpg|thumb|200px|right|The reconstructed [[1918 influenza]] virus]]

===Weapons===
{{details|Biological warfare}}
The ability of viruses to cause devastating [[epidemic]]s in human societies has led to the concern that viruses could be weaponized for [[biological warfare]]. Further concern was raised by the successful recreation of the infamous 1918 influenza virus in a laboratory.<ref name="cdcnews">{{Cite web|url=http://www.cdc.gov/OD/OC/MEDIA/pressrel/r051005.htm|title=Researchers Reconstruct 1918 Pandemic Influenza Virus; Effort Designed to Advance Preparedness|accessdate=2007-04-05|publisher=Centers for Disease Control}}</ref> The [[smallpox]] virus devastated numerous societies throughout history before its eradication. It currently exists in several secure laboratories in the world, and fears that it may be used as a weapon are not totally unfounded. The modern global human population has almost no established resistance to smallpox; if it were to be released, a massive loss of life could be sustained before the virus is brought under control.

== Etymology ==
The word is from the [[Latin]] ''virus'' referring to [[poison]] and other noxious substances, first used in English in 1392.<ref name=Etymology_Dictionary>{{cite web | title = virus | work = The Online Etymology Dictionary | url = http://www.etymonline.com/index.php?term=virus | accessdate = 2007-07-16}}</ref> ''Virulent'', from Latin ''virulentus'' "poisonous" dates to 1400.<ref name=OED>{{cite web | title = virulent, a. | work = The Oxford English Dictionary - Online | url = http://dictionary.oed.com | accessdate = 2007-07-16}}</ref> A meaning of "agent that causes infectious disease" is first recorded in 1728,<ref name=Etymology_Dictionary /> before the discovery of viruses by the [[Russians|Russian]]-[[Ukrainians|Ukrainian]] [[biologist]] [[Dmitry Ivanovsky]] in 1892. The adjective ''viral'' dates to 1948.<ref name=OED2>{{cite web | title = viral, a. | work = The Oxford English Dictionary - Online | url = http://dictionary.oed.com | accessdate = 2007-07-16}}</ref> Today, ''virus'' is used to describe the biological viruses discussed above and also as a [[metaphor]] for other parasitically-reproducing things, such as [[meme]]s or [[computer virus]]es (since 1972).<ref name=OED /> The [[neologism]] '''virion''' or viron is used to refer to a single infective viral particle.

The Latin word is from a [[Proto-Indo-European language|Proto-Indo-European]] root *{{PIE|weis-}} "to melt away, to flow," used of foul or malodorous fluids. It is a cognate of [[Sanskrit]] ''{{IAST|viṣh}}'' "poison", [[Avestan]] ''viš-'' "poison", Greek ''ios'' "poison", [[Old Church Slavonic]] ''višnja'' "cherry", [[Old Irish]] ''fi'' "poison", [[Welsh language|Welsh]] ''gwy'' "fluid"; Latin ''viscum'' (see [[viscous]]) "sticky substance" is also from the same root.

The English plural form of ''virus'' is ''viruses''. No reputable dictionary gives any other form, including such "reconstructed" Latin plural forms as ''viri'' (which actually means ''men''), and no plural form appears in the Latin corpus (See [[plural of virus]]). ''Virus'' does not have a traditional Latin plural because its original sense, ''poison'' is a [[mass noun]] like the English word ''furniture'', and, as pointed out above, English use of ''virus'' to denote the agent of a disease predates the discovery that these agents are microscopic parasites and thus in principle countable.

== Philosophy ==

Viruses have attracted attention of philosophers and critics because of their position at the margins of life and their unique method of propagation. [[Susan Sontag]] argues that viruses have been used detrimentally as metaphors for social phenomena.<ref>[[Susan Sontag|Sontag, Susan]] (1978). [[Illness as Metaphor]]. Farrar Straus & Giroux.</ref> [[Gilles Deleuze]] and [[Félix Guattari]] use the virus as an example of [[Rhizome (philosophy)|rhizomatic]] being because of its nomadic movement through host organisms. They note that viruses can be responsible for [[Horizontal gene transfer|"aparallel evolution"]], which they see as disruptive to arborescent phylogentic trees. <ref>[[Gilles Deleuze|Deleuze, Gilles]] and [[Félix Guattari]] (1987) [1980]. ''[[A Thousand Plateaus]]''. University of Minnesota Press.</ref>

==See also==
{{Wikibookspar||Viruses, Prions, and Viroids (General Biology)|}}
{{Commons|Category:Viruses|Virus}}
{{Wiktionary}}
*[[List of viruses]]
*[[Nanobes]]
*[[Nanobacteria]]
*[[Provirus]]
*[[Transduction]]
*[[Bioaerosol]]
*[[Oncolytic virus]]<br clear="all" />

==Footnotes==
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==References==
<div class="references-small" style="-moz-column-count:2; column-count:2;">
* [http://viperdb.scripps.edu/ Icosahedral virus structure]
* Villarreal, Luis P. (2005). "Viruses and the Evolution of Life." Washington, ASM Press.
* [http://www.virology.net/ All the Virology on the WWW]
* [http://www-micro.msb.le.ac.uk/109/structure.html University of Leicester online notes] - Virus Structure
* [http://www.plazamedicine.com/index.html Chronic Active Human Herpesvirus-6 (HHV-6) Infection: A New Disease Paradigm]
* Gelderblom, Hans R. (1996). [http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mmed.chapter.2252 41. Structure and Classification of Viruses] in ''[http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mmed Medical Microbiology] 4th ed.'' Samuel Baron ed. The University of Texas Medical Branch at Galveston. ISBN 0-9631172-1-1
* Radetsky, Peter (1994). ''The Invisible Invaders: Viruses and the Scientists Who Pursue Them.'' Backbay Books, ISBNs 0316732168 (hc), 0316732176 (pb).
* Theiler, Max and Downs, W. G. (1973). ''The Arthropod-Borne Viruses of Vertebrates: An Account of the Rockefeller Foundation Virus Program 1951-1970''. Yale University Press.
* {{NCBI-scienceprimer}}</div>

==External links==
*[http://www.duesberg.com HIV] - HIV/AIDS Research
*[http://www.vrc.nih.gov Vaccine Research Center (VRC)] - Information concerning vaccine research studies
*[http://www.home-air-purifier-expert.com/bioaerosols.html Chart of viral pathogens which contribute to indoor air pollution]
*[http://www.isracast.com/tech_news/260106_tech.aspx Viruses: The new cancer hunters] - An IsraCast article on virotherapy
*[http://www.virology.net/Big_Virology/BVHomePage.html The Big Picture Book of Viruses] - Pictures and general information on many viruses
*[http://www.sciam.com/article.cfm?chanID=sa006&articleID=00023290-03BC-1F5D-905980A84189EEDF Scientific American Magazine (October 2003 Issue) Tumor-Busting Viruses]
* [http://www.vbrc.org Detailed genomic and bioinformatic information about Category A, B, and C priority pathogens at NIH-funded database].
* [http://www.larger-than-life.org/modules.php?name=Content&pa=showpage&pid=8 Assorted information about Viruses]
* [http://www.cosmosmagazine.com/node/1024 "A few good viruses"], a feature story on how viruses are being 'hijacked' for the benefit of humanity. [[Cosmos Magazine|''Cosmos Magazine'']], by Hamish Clarke, 7 February 2007

[[Category:English words and phrases of foreign origin]]
[[Category:Latin words and phrases]]
[[Category:Virology|*]]
[[Category:Viruses| ]]

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Revision as of 13:52, 13 September 2007

ik wil helemaal geen virus

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