Virus#Viral replication

{{See also|Plural form of words ending in -us}}

The English word "virus" comes from the Latin {{lang|la|vīrus}}, which refers to poison and other noxious liquids. {{lang|la|Vīrus}} comes from the same Indo-European root as Sanskrit {{lang|sa|viṣa}}, Avestan {{lang|ae|vīša}}, and Ancient Greek {{lang|grc|ἰός}} ({{Transliteration|grc|iós}}), which all mean "poison". The first attested use of "virus" in English appeared in 1398 in John Trevisa's translation of Bartholomeus Anglicus's De Proprietatibus Rerum.{{cite encyclopedia | chapter = Virus, n. | title = OED Online | publisher = Oxford University Press | date = March 2015 }}{{cite web | title=virus | vauthors=Harper D |year=2011 | work=The Online Etymology Dictionary |url=http://www.etymonline.com/index.php?term=virus|access-date=19 December 2014}} Virulent, from Latin virulentus ('poisonous'), dates to {{c.|1400}}.{{cite encyclopedia | chapter=Virulent, adj. | title=OED Online | publisher=Oxford University Press | date=March 2015 }}{{cite web

|title=virulent | vauthors=Harper D |year=2011 | work=The Online Etymology Dictionary |url=http://www.etymonline.com/index.php?term=virulent |access-date=19 December 2014}} A meaning of 'agent that causes infectious disease' is first recorded in 1728, long before the discovery of viruses by Dmitri Ivanovsky in 1892. The English plural is viruses (sometimes also vira),{{cite book | vauthors=Buschard K, Thon R | chapter=Diabetic Animal Models | title=Handbook of Laboratory Animal Science | edition=2nd | volume=II | series=Animal Models | veditors=Hau J, Van Hoosier Jr GL | publisher=CRC Press | date=2003 | pages=163, 166 }} whereas the Latin word is a mass noun, which has no classically attested plural (vīra is used in Neo-LatinWilliam T. Stearn: Botanical Latin. History, Grammar, Syntax, Terminology and Vocabulary. David & Charles, 3rd ed., 1983. Quote: "Virus: virus (s.n. II), gen. sing. viri, nom. pl. vira, gen. pl. vīrorum (to be distinguished from virorum, of men)."). The adjective viral dates to 1948.{{cite web |title=viral | vauthors=Harper D |year=2011 | work=The Online Etymology Dictionary |url=http://www.etymonline.com/index.php?term=viral |access-date=19 December 2014}} The term virion (plural virions), which dates from 1959,{{cite web |title=virion |vauthors=Harper D |year=2011

| work = The Online Etymology Dictionary |url=http://www.etymonline.com/index.php?term=virion |access-date=19 December 2014}} is also used to refer to a single viral particle that is released from the cell and is capable of infecting other cells of the same type.{{cite book | vauthors=Casjens S | veditors=Mahy BW, Van Regenmortel MH |title=Desk Encyclopedia of General Virology|publisher=Academic Press |location=Boston |year=2010|page=167|isbn=978-0-12-375146-1}}

{{See also|Viral evolution}}

Viruses are found wherever there is life and have probably existed since living cells first evolved.{{cite journal | vauthors=Iyer LM, Balaji S, Koonin EV, Aravind L | title=Evolutionary genomics of nucleo-cytoplasmic large DNA viruses | journal=Virus Research | volume=117 | issue=1 | pages=156–84 | date=April 2006 | pmid=16494962 | doi=10.1016/j.virusres.2006.01.009 | url=https://zenodo.org/record/1259447 }} The origin of viruses is unclear because they do not form fossils, so molecular techniques are used to infer how they arose.{{cite journal | vauthors=Sanjuán R, Nebot MR, Chirico N, Mansky LM, Belshaw R | title=Viral mutation rates | journal=Journal of Virology | volume=84 | issue=19 | pages=9733–9748 | date=October 2010 | pmid=20660197 | pmc=2937809 | doi=10.1128/JVI.00694-10 }} In addition, viral genetic material occasionally integrates into the germline of the host organisms, by which they can be passed on vertically to the offspring of the host for many generations. This provides an invaluable source of information for paleovirologists to trace back ancient viruses that existed as far back as millions of years ago.

There are three main hypotheses that aim to explain the origins of viruses:{{cite journal |vauthors=Krupovic M, Dolja VV, Koonin EV |title=Origin of viruses: primordial replicators recruiting capsids from hosts |journal=Nature Reviews. Microbiology |volume=17 |issue=7 |pages=449–58 |date=July 2019 |pmid=31142823 |doi=10.1038/s41579-019-0205-6|s2cid=256744818 |url=https://hal-pasteur.archives-ouvertes.fr/pasteur-02557191/file/Krupovic_NRMICRO-19-022_MS_v3_clean.pdf }}

; Regressive hypothesis: Viruses may have once been small cells that parasitised larger cells. Over time, genes not required by their parasitism were lost. The bacteria rickettsia and chlamydia are living cells that, like viruses, can reproduce only inside host cells. They lend support to this hypothesis, as their dependence on parasitism is likely to have caused the loss of genes that enabled them to survive outside a cell. This is also called the "degeneracy hypothesis",{{rp|16}}{{rp|11}} or "reduction hypothesis".{{rp|24}}

; Cellular origin hypothesis: Some viruses may have evolved from bits of DNA or RNA that "escaped" from the genes of a larger organism. The escaped DNA could have come from plasmids (pieces of naked DNA that can move between cells) or transposons (molecules of DNA that replicate and move around to different positions within the genes of the cell).{{rp|810}} Once called "jumping genes", transposons are examples of mobile genetic elements and could be the origin of some viruses. They were discovered in maize by Barbara McClintock in 1950.{{cite journal|vauthors=McClintock B|title=The origin and behavior of mutable loci in maize|journal=Proceedings of the National Academy of Sciences of the United States of America|volume=36|issue=6|pages=344–55|date=June 1950|pmid=15430309|pmc=1063197|doi=10.1073/pnas.36.6.344|bibcode=1950PNAS...36..344M|doi-access=free}} This is sometimes called the "vagrancy hypothesis",{{rp|16}}{{rp|11–12}} or the "escape hypothesis".{{cite book | veditors=Mahy WJ, Regenmortel MH |title=Desk Encyclopedia of General Virology |publisher=Academic Press |location=Oxford |year=2009 |isbn=978-0-12-375146-1}}{{rp|24}}

; Co-evolution hypothesis: This is also called the "virus-first hypothesis"{{rp|24}} and proposes that viruses may have evolved from complex molecules of protein and nucleic acid at the same time that cells first appeared on Earth and would have been dependent on cellular life for billions of years. Viroids are molecules of RNA that are not classified as viruses because they lack a protein coat. They have characteristics that are common to several viruses and are often called subviral agents.{{rp|55}} Viroids are important pathogens of plants.{{rp|791}} They do not code for proteins but interact with the host cell and use the host machinery for their replication.{{cite journal | vauthors=Tsagris EM, Martínez de Alba AE, Gozmanova M, Kalantidis K | title=Viroids | journal=Cellular Microbiology | volume=10 | issue=11 | pages=2168–79 | date=November 2008 | pmid=18764915 | doi=10.1111/j.1462-5822.2008.01231.x | s2cid=221581424 | doi-access=free }} The hepatitis delta virus of humans has an RNA genome similar to viroids but has a protein coat derived from hepatitis B virus and cannot produce one of its own. It is, therefore, a defective virus. Although hepatitis delta virus genome may replicate independently once inside a host cell, it requires the help of hepatitis B virus to provide a protein coat so that it can be transmitted to new cells.{{rp|460}} In similar manner, the sputnik virophage is dependent on mimivirus, which infects the protozoan Acanthamoeba castellanii.{{cite journal | vauthors=La Scola B, Desnues C, Pagnier I, Robert C, Barrassi L, Fournous G, Merchat M, Suzan-Monti M, Forterre P, Koonin E, Raoult D | title=The virophage as a unique parasite of the giant mimivirus | journal=Nature | volume=455 | issue=7209 | pages=100–04 | date=September 2008 | pmid=18690211 | doi=10.1038/nature07218 | bibcode=2008Natur.455..100L | s2cid=4422249 }} These viruses, which are dependent on the presence of other virus species in the host cell, are called "satellites" and may represent evolutionary intermediates of viroids and viruses.{{rp|777}}{{rp|55–57}}

In the past, there were problems with all of these hypotheses: the regressive hypothesis did not explain why even the smallest of cellular parasites do not resemble viruses in any way. The escape hypothesis did not explain the complex capsids and other structures on virus particles. The virus-first hypothesis contravened the definition of viruses in that they require host cells.{{rp|24}} Viruses are now recognised as ancient and as having origins that pre-date the divergence of life into the three domains.{{rp|28}} This discovery has led modern virologists to reconsider and re-evaluate these three classical hypotheses.{{rp|28}}

The evidence for an ancestral world of RNA cells{{rp|26}} and computer analysis of viral and host DNA sequences give a better understanding of the evolutionary relationships between different viruses and may help identify the ancestors of modern viruses. To date, such analyses have not proved which of these hypotheses is correct.{{rp|26}} It seems unlikely that all currently known viruses have a common ancestor, and viruses have probably arisen numerous times in the past by one or more mechanisms.Dimmock pp. 15–16

{{main|History of virology}}

The first evidence of the existence of viruses came from experiments with filters that had pores small enough to retain bacteria. In 1892, Dmitri Ivanovsky used one of these filters to show that sap from a diseased tobacco plant remained infectious to healthy tobacco plants despite having been filtered. Martinus Beijerinck called the filtered, infectious substance a "virus" and this discovery is considered to be the beginning of virology.

The subsequent discovery and partial characterization of bacteriophages by Frederick Twort and Félix d'Herelle further catalyzed the field, and by the early 20th century many viruses had been discovered. In 1926, Thomas Milton Rivers defined viruses as obligate parasites. Viruses were demonstrated to be particles, rather than a fluid, by Wendell Meredith Stanley, and the invention of the electron microscope in 1931 allowed their complex structures to be visualised.{{cite journal |vauthors=Zerbini FM, Kitajima EW |title=From Contagium vivum fluidum to Riboviria: A Tobacco Mosaic Virus-Centric History of Virus Taxonomy |journal=Biomolecules |volume=12 |issue=10 |date=September 2022 |page=1363 |pmid=36291572 |pmc=9599303 |doi=10.3390/biom12101363 |doi-access=free |url=}}

Scientific opinions differ on whether viruses are a form of life or organic structures that interact with living organisms.{{cite journal | vauthors=Koonin EV, Starokadomskyy P | title=Are viruses alive? The replicator paradigm sheds decisive light on an old but misguided question | journal=Studies in History and Philosophy of Biological and Biomedical Sciences | volume=59 | pages=125–34 | date=October 2016 | pmid=26965225 | pmc=5406846 | doi=10.1016/j.shpsc.2016.02.016 }} They have been described as "organisms at the edge of life", since they resemble organisms in that they possess genes, evolve by natural selection,{{cite journal | vauthors=Holmes EC | title=Viral evolution in the genomic age | journal=PLOS Biology | volume=5 | issue=10 | page=e278 | date=October 2007 | pmid=17914905 | pmc=1994994 | doi=10.1371/journal.pbio.0050278 | doi-access=free }} and reproduce by creating multiple copies of themselves through self-assembly. Although they have genes, they do not have a cellular structure, which is often seen as the basic unit of life. Viruses do not have their own metabolism and require a host cell to make new products. They therefore cannot naturally reproduce outside a host cell{{cite journal | vauthors=Wimmer E, Mueller S, Tumpey TM, Taubenberger JK | title=Synthetic viruses: a new opportunity to understand and prevent viral disease | journal=Nature Biotechnology | volume=27 | issue=12 | pages=1163–72 | date=December 2009 | pmid=20010599 | pmc=2819212 | doi=10.1038/nbt.1593 }}—although some bacteria such as rickettsia and chlamydia are considered living organisms despite the same limitation.{{cite journal | vauthors=Horn M | title=Chlamydiae as symbionts in eukaryotes | journal=Annual Review of Microbiology | volume=62 | pages=113–31 | year=2008 | pmid=18473699 | doi=10.1146/annurev.micro.62.081307.162818 }}{{cite journal | vauthors=Ammerman NC, Beier-Sexton M, Azad AF | title=Laboratory maintenance of Rickettsia rickettsii | journal=Current Protocols in Microbiology | volume=11 | issue=1 | pages=3A.5.1–3A.5.21 | date=November 2008 | pmid=19016440 | pmc=2725428 | doi=10.1002/9780471729259.mc03a05s11 | isbn=978-0471729259 }} Accepted forms of life use cell division to reproduce, whereas viruses spontaneously assemble within cells. They differ from autonomous growth of crystals as they inherit genetic mutations while being subject to natural selection. Virus self-assembly within host cells has implications for the study of the origin of life, as it lends further credence to the hypothesis that life could have started as self-assembling organic molecules. The virocell model first proposed by Patrick Forterre considers the infected cell to be the "living form" of viruses and that virus particles (virions) are analogous to spores.Forterre, P. The virocell concept and environmental microbiology. ISME J 7, 233–236 (2013). https://doi.org/10.1038/ismej.2012.110 Although the living versus non-living debate continues, the virocell model has gained some acceptance.{{cite journal |vauthors=DeLong JP, Al-Sammak MA, Al-Ameeli ZT, Dunigan DD, Edwards KF, Fuhrmann JJ, Gleghorn JP, Li H, Haramoto K, Harrison AO, Marston MF, Moore RM, Polson SW, Ferrell BD, Salsbery ME, Schvarcz CR, Shirazi J, Steward GF, Van Etten JL, Wommack KE |title=Towards an integrative view of virus phenotypes |journal=Nature Reviews. Microbiology |volume=20 |issue=2 |pages=83–94 |date=February 2022 |pmid=34522049 |doi=10.1038/s41579-021-00612-w |url=}}

{{Multiple image

| align = right

| direction = vertical

| width = 200

| image1=Virus size.png

| caption1= Virions of some of the most common human viruses with their relative size. The nucleic acids are not to scale.

| image2 = Hexon.svg

| caption2 = Diagram of how a virus capsid can be constructed using multiple copies of just two protein molecules

| image3 = TMV structure simple.png

| caption3 = Structure of tobacco mosaic virus: RNA coiled in a helix of repeating protein sub-units

| image4 = Icosahedral Adenoviruses.jpg

| caption4 = Structure of icosahedral adenovirus. Electron micrograph with an illustration to show shape

| image5 = Varicella (Chickenpox) Virus PHIL 1878 lores.jpg

| caption5 = Structure of chickenpox virus. They have a lipid envelope.

| image6 = CowpeaMosaicVirus3D.png

| caption6 = Structure of an icosahedral cowpea mosaic virus

| image7 = Ms2capsid surface.png

| caption7 = Bacteriophage Escherichia virus MS2 capsid. This spherical virus also has icosahedral symmetry.

}}

{{Main|Virion}}

Viruses display a wide diversity of sizes and shapes, called 'morphologies'. In general, viruses are much smaller than bacteria and more than a thousand bacteriophage viruses would fit inside an Escherichia coli bacterium's cell.{{rp|98}} Many viruses that have been studied are spherical and have a diameter between 20 and 300 nanometres. Some filoviruses, which are filaments, have a total length of up to 1400 nm; their diameters are only about 80 nm.{{rp|33–55}} Most viruses cannot be seen with an optical microscope, so scanning and transmission electron microscopes are used to visualise them.{{rp|33–37}} To increase the contrast between viruses and the background, electron-dense "stains" are used. These are solutions of salts of heavy metals, such as tungsten, that scatter the electrons from regions covered with the stain. When virions are coated with stain (positive staining), fine detail is obscured. Negative staining overcomes this problem by staining the background only.{{cite journal | vauthors=Kiselev NA, Sherman MB, Tsuprun VL | title=Negative staining of proteins | journal=Electron Microscopy Reviews | volume=3 | issue=1 | pages=43–72 | year=1990 | pmid=1715774 | doi=10.1016/0892-0354(90)90013-I }}

A complete virus particle, known as a virion, consists of nucleic acid surrounded by a protective coat of protein called a capsid. These are formed from protein subunits called capsomeres.{{rp|40}} Viruses can have a lipid "envelope" derived from the host cell membrane. The capsid is made from proteins encoded by the viral genome and its shape serves as the basis for morphological distinction.{{cite journal | vauthors=Caspar DL, Klug A | title=Physical principles in the construction of regular viruses | journal=Cold Spring Harbor Symposia on Quantitative Biology | volume=27 | pages=1–24 | year=1962 | pmid=14019094 | doi=10.1101/sqb.1962.027.001.005 }}{{cite journal | vauthors=Crick FH, Watson JD | title=Structure of small viruses | journal=Nature | volume=177 | issue=4506 | pages=473–75 | date=March 1956 | pmid=13309339 | doi=10.1038/177473a0 | bibcode=1956Natur.177..473C | s2cid=5740221 }} Virally-coded protein subunits will self-assemble to form a capsid, in general requiring the presence of the virus genome. Complex viruses code for proteins that assist in the construction of their capsid. Proteins associated with nucleic acid are known as nucleoproteins, and the association of viral capsid proteins with viral nucleic acid is called a nucleocapsid. The capsid and entire virus structure can be mechanically (physically) probed through atomic force microscopy.{{cite journal | vauthors=Falvo MR, Washburn S, Superfine R, Finch M, Brooks FP, Chi V, Taylor RM | title=Manipulation of individual viruses: friction and mechanical properties | journal=Biophysical Journal | volume=72 | issue=3 | pages=1396–403 | date=March 1997 | pmid=9138585 | pmc=1184522 | doi=10.1016/S0006-3495(97)78786-1 | bibcode=1997BpJ....72.1396F }}{{cite journal | vauthors=Kuznetsov YG, Malkin AJ, Lucas RW, Plomp M, McPherson A | title=Imaging of viruses by atomic force microscopy | journal = The Journal of General Virology | volume=82 | issue = Pt 9 | pages = 2025–34 | date = September 2001 | pmid = 11514711 | doi = 10.1099/0022-1317-82-9-2025 | doi-access = free }} In general, there are five main morphological virus types:

; Helical: These viruses are composed of a single type of capsomere stacked around a central axis to form a helical structure, which may have a central cavity, or tube. This arrangement results in virions which can be short and highly rigid rods, or long and very flexible filaments. The genetic material (typically single-stranded RNA, but single-stranded DNA in some cases) is bound into the protein helix by 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, and the diameter is dependent on the size and arrangement of capsomeres. The well-studied tobacco mosaic virus{{rp|37}}and inovirus{{cite book | vauthors = Straus SK, Bo HE | title = Virus Protein and Nucleoprotein Complexes | chapter = Filamentous Bacteriophage Proteins and Assembly | series = Subcellular Biochemistry | volume=88 | pages = 261–79 | date = 2018 | pmid = 29900501 | doi = 10.1007/978-981-10-8456-0_12 | isbn = 978-981-10-8455-3 }} are examples of helical viruses.

; Icosahedral: Most animal viruses are icosahedral or near-spherical with chiral icosahedral symmetry. A regular icosahedron is the optimum way of forming a closed shell from identical subunits. The minimum number of capsomeres required for each triangular face is 3, which gives 60 for the icosahedron. Many viruses, such as rotavirus, have more than 60 capsomers and appear spherical but they retain this symmetry. To achieve this, the capsomeres at the apices are surrounded by five other capsomeres and are called pentons. Capsomeres on the triangular faces are surrounded by six others and are called hexons.{{rp|40,42}} Hexons are in essence flat and pentons, which form the 12 vertices, are curved. The same protein may act as the subunit of both the pentamers and hexamers or they may be composed of different proteins.{{cite journal | vauthors = Wilson DP | title = Protruding Features of Viral Capsids Are Clustered on Icosahedral Great Circles | journal = PLOS ONE | volume=11 | issue = 4 | pages = e0152319 | year = 2016 | pmid = 27045511 | pmc = 4821576 | doi = 10.1371/journal.pone.0152319 | bibcode = 2016PLoSO..1152319W | doi-access = free }}

; Prolate: This is an icosahedron elongated along the fivefold axis and is a common arrangement of the heads of bacteriophages. This structure is composed of a cylinder with a cap at either end.{{cite book | vauthors = Casens S |title=Desk Encyclopedia of General Virology|publisher=Academic Press |location=Boston |year=2009 |pages=167–74 |isbn=978-0-12-375146-1}}

; Enveloped:Some species of virus envelop themselves in a modified form of one of the cell membranes, either the outer membrane surrounding an infected host cell or internal membranes such as a 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; the lipid membrane itself and any carbohydrates present originate entirely from the host. Influenza virus, HIV (which causes AIDS), and severe acute respiratory syndrome coronavirus 2 (which causes COVID-19){{cite journal |vauthors=Dhama K, Khan S, Tiwari R, Sircar S, Bhat S, Malik YS, Singh KP, Chaicumpa W, Bonilla-Aldana DK, Rodriguez-Morales AJ |title=Coronavirus Disease 2019-COVID-19 |journal=Clinical Microbiology Reviews |volume=33 |issue=4 |date=September 2020 |pmid=32580969 |pmc=7405836 |doi=10.1128/CMR.00028-20 }} use this strategy. Most enveloped viruses are dependent on the envelope for their infectivity.{{rp|42–43}}

; Complex: These viruses possess a capsid that is neither purely helical nor purely icosahedral, and that may possess extra structures such as protein tails or a complex outer wall. Some bacteriophages, such as Enterobacteria phage T4, have a complex structure consisting of an icosahedral head bound to a helical tail, which may have a hexagonal base plate with protruding protein tail fibres. This tail structure acts like a molecular syringe, attaching to the bacterial host and then injecting the viral genome into the cell.{{cite journal | vauthors = Rossmann MG, Mesyanzhinov VV, Arisaka F, Leiman PG | title = The bacteriophage T4 DNA injection machine | journal = Current Opinion in Structural Biology | volume=14 | issue = 2 | pages = 171–80 | date = April 2004 | pmid = 15093831 | doi = 10.1016/j.sbi.2004.02.001 }}

The poxviruses are large, complex viruses that have an unusual morphology. The viral genome is associated with proteins within a central disc 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 virion is slightly pleomorphic, ranging from ovoid to brick-shaped.{{cite journal | vauthors = Long GW, Nobel J, Murphy FA, Herrmann KL, Lourie B | title = Experience with electron microscopy in the differential diagnosis of smallpox | journal = Applied Microbiology | volume=20 | issue = 3 | pages = 497–504 | date = September 1970 | doi = 10.1128/AEM.20.3.497-504.1970 | pmid = 4322005 | pmc = 376966 }}

{{main|Giant virus}}

Mimivirus is one of the largest characterised viruses, with a capsid diameter of 400 nm. Protein filaments measuring 100 nm project from the surface. The capsid appears hexagonal under an electron microscope, therefore the capsid is probably icosahedral.{{cite journal | vauthors = Suzan-Monti M, La Scola B, Raoult D | title = Genomic and evolutionary aspects of Mimivirus | journal = Virus Research | volume=117 | issue = 1 | pages = 145–55 | date = April 2006 | pmid = 16181700 | doi = 10.1016/j.virusres.2005.07.011 }} In 2011, researchers discovered the largest then known virus in samples of water collected from the ocean floor off the coast of Las Cruces, Chile. Provisionally named Megavirus chilensis, it can be seen with a basic optical microscope.{{cite journal | vauthors = Arslan D, Legendre M, Seltzer V, Abergel C, Claverie JM | title = Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae | journal = Proceedings of the National Academy of Sciences of the United States of America | volume=108 | issue = 42 | pages = 17486–91 | date = October 2011 | pmid = 21987820 | pmc = 3198346 | doi = 10.1073/pnas.1110889108 | bibcode = 2011PNAS..10817486A | doi-access = free }} In 2013, the Pandoravirus genus was discovered in Chile and Australia, and has genomes about twice as large as Megavirus and Mimivirus.{{cite journal | vauthors = Philippe N, Legendre M, Doutre G, Couté Y, Poirot O, Lescot M, Arslan D, Seltzer V, Bertaux L, Bruley C, Garin J, Claverie JM, Abergel C | s2cid = 16877147 | title = Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes | journal = Science | volume=341 | issue = 6143 | pages = 281–86 | date = July 2013 | pmid = 23869018 | doi = 10.1126/science.1239181 | bibcode = 2013Sci...341..281P | url = https://hal-cea.archives-ouvertes.fr/cea-00862677/file/phi.pdf }} All giant viruses have dsDNA genomes and they are classified into several families: Mimiviridae, Pithoviridae, Pandoraviridae, Phycodnaviridae, and the Mollivirus genus.{{cite journal | vauthors = Brandes N, Linial M | title = Giant Viruses-Big Surprises | journal = Viruses | volume=11 | issue = 5 | page = 404 | date = April 2019 | pmid = 31052218 | pmc = 6563228 | doi = 10.3390/v11050404 | doi-access = free }}

Some viruses that infect Archaea have complex structures unrelated to any other form of virus, with a wide variety of unusual shapes, ranging from spindle-shaped structures to viruses that resemble hooked rods, teardrops or even bottles. Other archaeal viruses resemble the tailed bacteriophages, and can have multiple tail structures.{{cite journal | vauthors = Prangishvili D, Forterre P, Garrett RA | title = Viruses of the Archaea: a unifying view | journal = Nature Reviews. Microbiology | volume=4 | issue = 11 | pages = 837–48 | date = November 2006 | pmid = 17041631 | doi = 10.1038/nrmicro1527 | s2cid = 9915859 }}

An enormous variety of genomic structures can be seen among viral species; as a group, they contain more structural genomic diversity than plants, animals, archaea, or bacteria. There are millions of different types of viruses, although fewer than 7,000 types have been described in detail.{{rp|49}} As of January 2021, the NCBI Virus genome database has more than 193,000 complete genome sequences,{{cite web |url=https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/|publisher=ncbi.nlm.nih.gov |title=NCBI Viral Genome database |access-date=15 January 2017}} but there are doubtlessly many more to be discovered.{{cite journal | vauthors = Pennisi E | author-link = Elizabeth Pennisi | title = Microbiology. Going viral: exploring the role of viruses in our bodies | journal = Science | volume=331 | issue = 6024 | page = 1513 | date = March 2011 | pmid = 21436418 | doi = 10.1126/science.331.6024.1513 | bibcode = 2011Sci...331.1513P }}{{cite journal | vauthors = Shi M, Lin XD, Tian JH, Chen LJ, Chen X, Li CX, Qin XC, Li J, Cao JP, Eden JS, Buchmann J, Wang W, Xu J, Holmes EC, Zhang YZ | title = Redefining the invertebrate RNA virosphere | journal = Nature | volume=540 | issue = 7634 | pages = 539–43 | date = December 2016 | pmid = 27880757 | doi = 10.1038/nature20167 | bibcode = 2016Natur.540..539S | s2cid = 1198891 }}

A virus has either a DNA or an RNA genome and is called a DNA virus or an RNA virus, respectively. Some RNA viruses, for example retroviruses, have a stage in their replication cycle where the genome is encoded in DNA.{{cite journal |vauthors=Levintov L, Vashisth H |title=Structural and computational studies of HIV-1 RNA |journal=RNA Biology |volume=21 |issue=1 |pages=1–32 |date=January 2024 |pmid=38100535 |pmc=10730233 |doi=10.1080/15476286.2023.2289709 |url=}} Most viruses have RNA genomes. Plant viruses tend to have single-stranded RNA genomes and bacteriophages tend to have double-stranded DNA genomes.{{rp|96–99}}

Viral genomes are circular, as in the polyomaviruses, or linear, as in the adenoviruses. The type of nucleic acid is irrelevant to the shape of the genome. Among RNA viruses and certain DNA viruses, the genome is often divided into separate parts, in which case it is called segmented. For RNA viruses, each segment often codes for only one protein and they are usually found together in one capsid. All segments are not required to be in the same virion for the virus to be infectious, as demonstrated by brome mosaic virus and several other plant viruses.{{rp|33–35}}

A viral genome, irrespective of nucleic acid type, is almost always either single-stranded (ss) or double-stranded (ds). 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 two complementary paired nucleic acids, analogous to a ladder. The virus particles of some virus families, such as those belonging to the Hepadnaviridae, contain a genome that is partially double-stranded and partially single-stranded.{{rp|96–99}}

For most viruses with RNA genomes and some with single-stranded DNA (ssDNA) genomes, the single strands are said to be either positive-sense (called the 'plus-strand') or negative-sense (called the 'minus-strand'), depending on if they are complementary to the viral messenger RNA (mRNA). Positive-sense viral RNA is in the same sense as viral mRNA and thus at least a part of it can be immediately 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-dependent RNA polymerase before translation. DNA nomenclature for viruses with genomic ssDNA is similar to RNA nomenclature, in that positive-strand viral ssDNA is identical in sequence to the viral mRNA and is thus a coding strand, while negative-sense viral ssDNA is complementary to the viral mRNA and is thus a template strand.{{rp|96–99}} Several types of ssDNA and ssRNA viruses have genomes that are ambisense in that transcription can occur off both strands in a double-stranded replicative intermediate. Examples include geminiviruses, which are ssDNA plant viruses and arenaviruses, which are ssRNA viruses of animals.{{cite book | vauthors = Saunders VA, Carter J |title=Virology: principles and applications |publisher=John Wiley & Sons |location=Chichester |year=2007 |page= 72 |isbn=978-0-470-02387-7}}

Genome size varies greatly between species. The smallest—the ssDNA circoviruses, family Circoviridae—code for only two proteins and have a genome size of only two kilobases;{{cite journal | vauthors = Belyi VA, Levine AJ, Skalka AM | title = Sequences from ancestral single-stranded DNA viruses in vertebrate genomes: the parvoviridae and circoviridae are more than 40 to 50 million years old | journal = Journal of Virology | volume=84 | issue = 23 | pages = 12458–62 | date = December 2010 | pmid = 20861255 | pmc = 2976387 | doi = 10.1128/JVI.01789-10 }} the largest—the pandoraviruses—have genome sizes of around two megabases which code for about 2500 proteins. Virus genes rarely have introns and often are arranged in the genome so that they overlap.{{cite journal | vauthors = Brandes N, Linial M | title = Gene overlapping and size constraints in the viral world | journal = Biology Direct | volume=11 | issue = 1 | page = 26 | date = May 2016 | pmid = 27209091 | pmc = 4875738 | doi = 10.1186/s13062-016-0128-3 | doi-access = free }}

In general, RNA viruses have smaller genome sizes than DNA viruses because of a higher error-rate when replicating, and have a maximum upper size limit. Beyond this, errors when replicating render the virus useless or uncompetitive. To compensate, RNA viruses often have segmented genomes—the genome is split into smaller molecules—thus reducing the chance that an error in a single-component genome will incapacitate the entire genome. In contrast, DNA viruses generally have larger genomes because of the high fidelity of their replication enzymes.{{cite journal | vauthors = Pressing J, Reanney DC | title = Divided genomes and intrinsic noise | journal = Journal of Molecular Evolution | volume=20 | issue = 2 | pages = 135–46 | year = 1984 | pmid = 6433032 | doi = 10.1007/BF02257374 | pmc = 7087551 | bibcode = 1984JMolE..20..135P }} Single-strand DNA viruses are an exception to this rule, as mutation rates for these genomes can approach the extreme of the ssRNA virus case.{{cite journal | vauthors = Duffy S, Holmes EC | title = Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses | journal = The Journal of General Virology | volume=90 | issue = Pt 6 | pages = 1539–47 | date = June 2009 | pmid = 19264617 | pmc = 4091138 | doi = 10.1099/vir.0.009266-0 }}

File:Viruses-10-00497-g003.png

Viruses undergo genetic change by several mechanisms. These include a process called antigenic drift where individual bases in the DNA or RNA mutate to other bases. Most of these point mutations are "silent"—they do not change the protein that the gene encodes—but others can confer evolutionary advantages such as resistance to antiviral drugs.{{cite journal | vauthors = Sandbulte MR, Westgeest KB, Gao J, Xu X, Klimov AI, Russell CA, Burke DF, Smith DJ, Fouchier RA, Eichelberger MC | title = Discordant antigenic drift of neuraminidase and hemagglutinin in H1N1 and H3N2 influenza viruses | journal = Proceedings of the National Academy of Sciences of the United States of America | volume=108 | issue = 51 | pages = 20748–53 | date = December 2011 | pmid = 22143798 | pmc = 3251064 | doi = 10.1073/pnas.1113801108 | bibcode = 2011PNAS..10820748S | doi-access = free }}{{cite journal | vauthors = Moss RB, Davey RT, Steigbigel RT, Fang F | title = Targeting pandemic influenza: a primer on influenza antivirals and drug resistance | journal = The Journal of Antimicrobial Chemotherapy | volume=65 | issue = 6 | pages = 1086–93 | date = June 2010 | pmid = 20375034 | doi = 10.1093/jac/dkq100 | doi-access = free }} Antigenic shift occurs when there is a major change in the genome of the virus. This can be a result of recombination or reassortment. The Influenza A virus is highly prone to reassortment; occasionally this has resulted in novel strains which have caused pandemics.{{cite journal | vauthors = Hampson AW, Mackenzie JS | title = The influenza viruses | journal = The Medical Journal of Australia | volume=185 | issue = S10 | pages = S39–43 | date = November 2006 | doi = 10.5694/j.1326-5377.2006.tb00705.x | pmid = 17115950 | s2cid = 17069567 }} RNA viruses often exist as quasispecies or swarms of viruses of the same species but with slightly different genome nucleoside sequences. Such quasispecies are a prime target for natural selection.{{cite journal | vauthors = Metzner KJ | title = Detection and significance of minority quasispecies of drug-resistant HIV-1 | journal = Journal of HIV Therapy | volume=11 | issue = 4 | pages = 74–81 | date = December 2006 | pmid = 17578210 }}

Segmented genomes confer evolutionary advantages; different strains of a virus with a segmented genome can shuffle and combine genes and produce progeny viruses (or offspring) that have unique characteristics. This is called reassortment or 'viral sex'.Goudsmit, Jaap. Viral Sex. Oxford Univ Press, 1998. {{ISBN|978-0-19-512496-5}}

Genetic recombination is a process by which a strand of DNA (or RNA) is broken and then joined to the end of a different DNA (or RNA) molecule. This can occur when viruses infect cells simultaneously and studies of viral evolution have shown that recombination has been rampant in the species studied.{{cite journal | vauthors = Worobey M, Holmes EC | title = Evolutionary aspects of recombination in RNA viruses | journal = The Journal of General Virology | volume=80 | issue = 10 | pages = 2535–43 | date = October 1999 | pmid = 10573145 | doi = 10.1099/0022-1317-80-10-2535 | doi-access = free }} Recombination is common to both RNA and DNA viruses.{{cite journal | vauthors = Lukashev AN | title = Role of recombination in evolution of enteroviruses | journal = Reviews in Medical Virology | volume=15 | issue = 3 | pages = 157–67 | year = 2005 | pmid = 15578739 | doi = 10.1002/rmv.457 | s2cid = 26000112 }}{{cite journal | vauthors = Umene K | title = Mechanism and application of genetic recombination in herpesviruses | journal = Reviews in Medical Virology | volume=9 | issue = 3 | pages = 171–82 | date = July 1999 | pmid = 10479778 | doi = 10.1002/(SICI)1099-1654(199907/09)9:3<171::AID-RMV243>3.0.CO;2-A | s2cid = 43110533 }}

Coronaviruses have a single-strand positive-sense RNA genome. Replication of the genome is catalyzed by an RNA-dependent RNA polymerase. The mechanism of recombination used by coronaviruses likely involves template switching by the polymerase during genome replication.{{cite journal | vauthors = Su S, Wong G, Shi W, Liu J, Lai AC, Zhou J, Liu W, Bi Y, Gao GF | title = Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses | journal = Trends in Microbiology | volume=24 | issue = 6 | pages = 490–502 | date = June 2016 | pmid = 27012512 | pmc = 7125511 | doi = 10.1016/j.tim.2016.03.003 }} This process appears to be an adaptation for coping with genome damage.{{cite journal | vauthors = Barr JN, Fearns R | title = How RNA viruses maintain their genome integrity | journal = The Journal of General Virology | volume=91 | issue = Pt 6 | pages = 1373–87 | date = June 2010 | pmid = 20335491 | doi = 10.1099/vir.0.020818-0 }}

File:HepC replication.png

File:Phage injecting its genome into bacteria.svgs into bacterial cells (not to scale)]]

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, and they assemble in the cell.{{cite journal | vauthors = Freed EO | title = HIV-1 assembly, release and maturation | journal = Nature Reviews. Microbiology | volume=13 | issue = 8 | pages = 484–96 | date = August 2015 | pmid = 26119571 | pmc = 6936268 | doi = 10.1038/nrmicro3490 }} When infected, the host cell is forced to rapidly produce thousands of copies of the original virus.{{cite journal |vauthors=Yin J, Redovich J |title=Kinetic Modeling of Virus Growth in Cells |journal=Microbiology and Molecular Biology Reviews|volume=82 |issue=2|date=June 2018 |pmid=29592895 |pmc=5968458 |doi=10.1128/MMBR.00066-17}}

Their life cycle differs greatly between species, but there are six basic stages in their life cycle:{{rp|75–91}}

Attachment is a specific binding between viral capsid proteins and specific receptors on the host cellular surface. This specificity determines the host range and type of host cell of a virus. For example, HIV infects a limited range of human leucocytes. This is because its surface protein, gp120, specifically interacts with the CD4 molecule—a chemokine receptor—which is most commonly found on the surface of CD4+ T-Cells. This mechanism has evolved to favour those viruses that infect only cells in which they are capable of replication. Attachment to the receptor can induce the viral envelope protein to undergo changes that result in the fusion of viral and cellular membranes, or changes of non-enveloped virus surface proteins that allow the virus to enter.{{cite book | vauthors = Más V, Melero JA | chapter = Entry of Enveloped Viruses into Host Cells: Membrane Fusion | title = Structure and Physics of Viruses | volume=68 | pages = 467–87 | date = 2013 | pmid = 23737062 | doi = 10.1007/978-94-007-6552-8_16 | isbn = 978-94-007-6551-1 | series = Subcellular Biochemistry | pmc = 7121288 }}

Penetration or viral entry follows attachment: Virions enter the host cell through receptor-mediated endocytosis or membrane fusion. The infection of plant and fungal cells is different from that of animal cells. Plants have a rigid cell wall made of cellulose, and fungi one of chitin, so most viruses can get inside these cells only after trauma to the cell wall.{{rp|70}} Nearly all plant viruses (such as tobacco mosaic virus) can also move directly from cell to cell, in the form of single-stranded nucleoprotein complexes, through pores called plasmodesmata.{{cite journal | vauthors = Boevink P, Oparka KJ | title = Virus-host interactions during movement processes | journal = Plant Physiology | volume=138 | issue = 4 | pages = 1815–21 | date = August 2005 | pmid = 16172094 | pmc = 1183373 | doi = 10.1104/pp.105.066761 }} Bacteria, like plants, have strong cell walls that a virus must breach to infect the cell. Given that bacterial cell walls are much thinner than plant cell walls due to their much smaller size, some viruses have evolved mechanisms that inject their genome into the bacterial cell across the cell wall, while the viral capsid remains outside.{{rp|71}}

Uncoating is a process in which the viral capsid is removed: This may be by degradation by viral enzymes or host enzymes or by simple dissociation; the end-result is the releasing of the viral genomic nucleic acid.{{cite journal | vauthors = Blaas D | title = Viral entry pathways: the example of common cold viruses | journal = Wiener Medizinische Wochenschrift | volume=166 | issue = 7–8 | pages = 211–26 | date = May 2016 | pmid = 27174165 | pmc = 4871925 | doi = 10.1007/s10354-016-0461-2 }}

Replication of viruses involves primarily multiplication of the genome. Replication involves the synthesis of viral messenger RNA (mRNA) from "early" genes (with exceptions for positive-sense RNA viruses), viral protein synthesis, possible assembly of viral proteins, then viral genome replication mediated by early or regulatory protein expression. This may be followed, for complex viruses with larger genomes, by one or more further rounds of mRNA synthesis: "late" gene expression is, in general, of structural or virion proteins.{{cite journal | vauthors = Isomura H, Stinski MF | s2cid = 11448687 | title = Coordination of late gene transcription of human cytomegalovirus with viral DNA synthesis: recombinant viruses as potential therapeutic vaccine candidates | journal = Expert Opinion on Therapeutic Targets | volume=17 | issue = 2 | pages = 157–66 | date = February 2013 | pmid = 23231449 | doi = 10.1517/14728222.2013.740460 }}

Assembly – Following the structure-mediated self-assembly of the virus particles, some modification of the proteins often occurs. In viruses such as HIV, this modification (sometimes called maturation) occurs after the virus has been released from the host cell.{{cite journal | vauthors = Barman S, Ali A, Hui EK, Adhikary L, Nayak DP | title = Transport of viral proteins to the apical membranes and interaction of matrix protein with glycoproteins in the assembly of influenza viruses | journal = Virus Research | volume=77 | issue = 1 | pages = 61–69 | date = September 2001 | pmid = 11451488 | doi = 10.1016/S0168-1702(01)00266-0 }}

Release – Viruses can be released from the host cell by lysis, a process that kills the cell by bursting its membrane and cell wall if present: this is a feature of many bacterial and some animal viruses. Some viruses undergo a lysogenic cycle where the viral genome is incorporated by genetic recombination into a specific place in the host's chromosome. The viral genome is then known as a "provirus" or, in the case of bacteriophages a "prophage".{{rp|836}} Whenever the host divides, the viral genome is also replicated. The viral genome is mostly silent within the host. At some point, the provirus or prophage may give rise to the active virus, which may lyse the host cells.{{rp|243–259}} Enveloped viruses (e.g., HIV) typically are released from the host cell by budding. During this process, the virus acquires its envelope, which is a modified piece of the host's plasma or other, internal membrane.{{rp|185–187}}

The genetic material within virus particles, and the method by which the material is replicated, varies considerably between different types of viruses.

; DNA viruses: The genome replication of most DNA viruses takes place in the cell's nucleus. If the cell has the appropriate receptor on its surface, these viruses enter the cell either by direct fusion with the cell membrane (e.g., herpesviruses) or—more usually—by receptor-mediated endocytosis. Most DNA viruses are entirely dependent on the host cell's DNA and RNA synthesising machinery and RNA processing machinery. Viruses with larger genomes may encode much of this machinery themselves. In eukaryotes, the viral genome must cross the cell's nuclear membrane to access this machinery, while in bacteria it need only enter the cell.{{rp|118}}{{rp|78}}

; RNA viruses: Replication of RNA viruses usually takes place in the cytoplasm. RNA viruses can be placed into four different groups depending on their modes of replication. The polarity (whether or not it can be used directly by ribosomes to make proteins) of single-stranded RNA viruses largely determines the replicative mechanism; the other major criterion is whether the genetic material is single-stranded or double-stranded. All RNA viruses use their own RNA replicase enzymes to create copies of their genomes.{{rp|79}}

; Reverse transcribing viruses: Reverse transcribing viruses have ssRNA (Retroviridae, Metaviridae, Pseudoviridae) or dsDNA (Caulimoviridae, and Hepadnaviridae) in their particles. Reverse transcribing viruses with RNA genomes (retroviruses) use a DNA intermediate to replicate, whereas those with DNA genomes (pararetroviruses) use an RNA intermediate during genome replication. Both types use a reverse transcriptase, or RNA-dependent DNA polymerase enzyme, to carry out the nucleic acid conversion. Retroviruses integrate the DNA produced by reverse transcription into the host genome as a provirus as a part of the replication process; pararetroviruses do not, although integrated genome copies of especially plant pararetroviruses can give rise to infectious virus.{{cite journal | vauthors = Staginnus C, Richert-Pöggeler KR | title = Endogenous pararetroviruses: two-faced travelers in the plant genome | journal = Trends in Plant Science | volume=11 | issue = 10 | pages = 485–91 | date = October 2006 | pmid = 16949329 | doi = 10.1016/j.tplants.2006.08.008 | bibcode = 2006TPS....11..485S }} They are susceptible to antiviral drugs that inhibit the reverse transcriptase enzyme, e.g. zidovudine and lamivudine. An example of the first type is HIV, which is a retrovirus. Examples of the second type are the Hepadnaviridae, which includes Hepatitis B virus.{{rp|88–89}}

The range of structural and biochemical effects that viruses have on the host cell is extensive.{{rp|115–146}} These are called 'cytopathic effects'.{{rp|115}} Most virus infections eventually result in the death of the host cell. The causes of death include cell lysis, alterations to the cell's surface membrane and apoptosis.{{cite journal | vauthors = Roulston A, Marcellus RC, Branton PE | title = Viruses and apoptosis | journal = Annual Review of Microbiology | volume=53 | pages = 577–628 | year = 1999 | pmid = 10547702 | doi = 10.1146/annurev.micro.53.1.577 }} Often cell death is caused by cessation of its normal activities because of suppression by virus-specific proteins, not all of which are components of the virus particle.{{cite book | vauthors = Alwine JC | title = Human Cytomegalovirus | chapter = Modulation of Host Cell Stress Responses by Human Cytomegalovirus | series = Current Topics in Microbiology and Immunology | volume=325 | pages = 263–79 | year = 2008 | pmid = 18637511 | doi = 10.1007/978-3-540-77349-8_15 | isbn = 978-3-540-77348-1 }} The distinction between cytopathic and harmless is gradual. Some viruses, such as Epstein–Barr virus, can cause cells to proliferate without causing malignancy,{{cite journal | vauthors = Barozzi P, Potenza L, Riva G, Vallerini D, Quadrelli C, Bosco R, Forghieri F, Torelli G, Luppi M | title = B cells and herpesviruses: a model of lymphoproliferation | journal = Autoimmunity Reviews | volume=7 | issue = 2 | pages = 132–36 | date = December 2007 | pmid = 18035323 | doi = 10.1016/j.autrev.2007.02.018 }} while others, such as papillomaviruses, are established causes of cancer.{{cite journal | vauthors = Subramanya D, Grivas PD | s2cid = 1399003 | title = HPV and cervical cancer: updates on an established relationship | journal = Postgraduate Medicine | volume=120 | issue = 4 | pages = 7–13 | date = November 2008 | pmid = 19020360 | doi = 10.3810/pgm.2008.11.1928 }}

Some viruses cause no apparent changes to the infected cell. Cells in which the virus is latent and inactive show few signs of infection and often function normally.{{cite journal | vauthors = Sinclair J | title = Human cytomegalovirus: Latency and reactivation in the myeloid lineage | journal = Journal of Clinical Virology | volume=41 | issue = 3 | pages = 180–85 | date = March 2008 | pmid = 18164651 | doi = 10.1016/j.jcv.2007.11.014 }} This causes persistent infections and the virus is often dormant for many months or years. This is often the case with herpes viruses.{{cite journal | vauthors = Jordan MC, Jordan GW, Stevens JG, Miller G | title = Latent herpesviruses of humans | journal = Annals of Internal Medicine | volume=100 | issue = 6 | pages = 866–80 | date = June 1984 | pmid = 6326635 | doi = 10.7326/0003-4819-100-6-866 }}{{cite journal | vauthors = Sissons JG, Bain M, Wills MR | title = Latency and reactivation of human cytomegalovirus | journal = The Journal of Infection | volume=44 | issue = 2 | pages = 73–77 | date = February 2002 | pmid = 12076064 | doi = 10.1053/jinf.2001.0948 }}

Viruses are by far the most abundant biological entities on Earth and they outnumber all the others put together.{{cite book | vauthors = Crawford DH | chapter = Chapter 2: Viruses are Everywhere |title=Viruses: A Very Short Introduction |publisher=Oxford University Press, US |year=2011 |page = [https://archive.org/details/virusesveryshort0000craw/page/16 16] |isbn=978-0-19-957485-8 |chapter-url=https://archive.org/details/virusesveryshort0000craw/page/16 }} They infect all types of cellular life including animals, plants, bacteria and fungi.{{rp|49}} Different types of viruses can infect only a limited range of hosts and many are species-specific. Some, such as smallpox virus for example, can infect only one species—in this case humans,{{rp|643}} and are said to have a narrow host range. Other viruses, such as rabies virus, can infect different species of mammals and are said to have a broad range.{{rp|631}} The viruses that infect plants are harmless to animals, and most viruses that infect other animals are harmless to humans.{{rp|272}} The host range of some bacteriophages is limited to a single strain of bacteria and they can be used to trace the source of outbreaks of infections by a method called phage typing.{{cite journal | vauthors = Baggesen DL, Sørensen G, Nielsen EM, Wegener HC | title = Phage typing of Salmonella Typhimurium – is it still a useful tool for surveillance and outbreak investigation? | journal = Euro Surveillance | volume=15 | issue = 4 | page = 19471 | date = January 2010 | pmid = 20122382 | url = http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=19471 | access-date = 19 December 2014 }} The complete set of viruses in an organism or habitat is called the virome; for example, all human viruses constitute the human virome.{{cite journal | vauthors = Parker MT | title = An Ecological Framework of the Human Virome Provides Classification of Current Knowledge and Identifies Areas of Forthcoming Discovery | journal = The Yale Journal of Biology and Medicine | volume=89 | issue = 3 | pages = 339–51 | date = September 2016 | pmid = 27698618 | pmc = 5045143 }}

A novel virus is one that has not previously been recorded. It can be a virus that is isolated from its natural reservoir or isolated as the result of spread to an animal or human host where the virus had not been identified before. It can be an emergent virus, one that represents a new virus, but it can also be an extant virus that has not been previously identified.{{cite journal |vauthors=Woolhouse M, Scott F, Hudson Z, Howey R, Chase-Topping M |title=Human viruses: discovery and emergence |journal=Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences |volume=367 |issue=1604 |pages=2864–71 |date=October 2012 |pmid=22966141 |pmc=3427559 |doi=10.1098/rstb.2011.0354}} The SARS-CoV-2 coronavirus that caused the COVID-19 pandemic is an example of a novel virus.

{{Main|Virus classification}}

{{Anchor|Genogroup}}

Classification seeks to describe the diversity of viruses by naming and grouping them on the basis of similarities. In 1962, André Lwoff, Robert Horne, and Paul Tournier were the first to develop a means of virus classification, based on the Linnaean hierarchical system.{{cite journal | vauthors = Lwoff A, Horne RW, Tournier P | title = [A virus system] | language = fr | journal = Comptes Rendus Hebdomadaires des Séances de l'Académie des Sciences | volume=254 | pages = 4225–27 | date = June 1962 | pmid = 14467544 }} This system based classification on phylum, class, order, family, genus, and species. Viruses were grouped according to their shared properties (not those of their hosts) and the type of nucleic acid forming their genomes.{{cite journal | vauthors = Lwoff A, Horne R, Tournier P | title = A system of viruses | journal = Cold Spring Harbor Symposia on Quantitative Biology | volume=27 | pages = 51–55 | year = 1962 | pmid = 13931895 | doi = 10.1101/sqb.1962.027.001.008 }} In 1966, the International Committee on Taxonomy of Viruses (ICTV) was formed. The system proposed by Lwoff, Horne and Tournier was initially not accepted by the ICTV because the small genome size of viruses and their high rate of mutation made it difficult to determine their ancestry beyond order. As such, the Baltimore classification system has come to be used to supplement the more traditional hierarchy.{{cite journal | vauthors = Fauquet CM, Fargette D | title = International Committee on Taxonomy of Viruses and the 3,142 unassigned species | journal = Virology Journal | volume=2 | page = 64 | date = August 2005 | pmid = 16105179 | pmc = 1208960 | doi = 10.1186/1743-422X-2-64 | doi-access = free }} Starting in 2018, the ICTV began to acknowledge deeper evolutionary relationships between viruses that have been discovered over time and adopted a 15-rank classification system ranging from realm to species.{{cite journal|author=International Committee on Taxonomy of Viruses Executive Committee|date=May 2020|title=The New Scope of Virus Taxonomy: Partitioning the Virosphere Into 15 Hierarchical Ranks|journal=Nat Microbiol|volume=5|issue=5|pages=668–74|doi=10.1038/s41564-020-0709-x|pmc=7186216|pmid=32341570}} Additionally, some species within the same genus are grouped into a genogroup.{{cite journal |vauthors=Khan MK, Alam MM |title=Norovirus Gastroenteritis Outbreaks, Genomic Diversity and Evolution: An Overview |journal=Mymensingh Medical Journal |volume=30 |issue=3 |pages=863–73 |date=July 2021 |pmid=34226482 |doi= |url=}}{{cite journal |vauthors=Eberle J, Gürtler L |title=HIV types, groups, subtypes and recombinant forms: errors in replication, selection pressure and quasispecies |journal=Intervirology |volume=55 |issue=2 |pages=79–83 |date=2012 |pmid=22286874 |doi=10.1159/000331993 |s2cid=5642060 |url=http://nbn-resolving.de/urn:nbn:de:bvb:19-epub-16666-3}}

The ICTV developed the current classification system and wrote guidelines that put a greater weight on certain virus properties to maintain family uniformity. A unified taxonomy (a universal system for classifying viruses) has been established.{{cite journal | vauthors = ((International Committee on Taxonomy of Viruses Executive Committee)) | title = The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks | journal = Nature Microbiology | volume=5 | issue = 5 | pages = 668–674 | date = May 2020 | pmid = 32341570 | pmc = 7186216 | doi = 10.1038/s41564-020-0709-x }} Only a small part of the total diversity of viruses has been studied.{{cite journal | vauthors = Delwart EL | title = Viral metagenomics | journal = Reviews in Medical Virology | volume=17 | issue = 2 | pages = 115–131 | year = 2007 | pmid = 17295196 | pmc = 7169062 | doi = 10.1002/rmv.532 }} As of 2024, 7 realms, 11 kingdoms, 22 phyla, 4 subphyla, 49 classes, 93 orders, 12 suborders, 368 families, 213 subfamilies, 3,769 genera, 86 subgenera, and 16,215 species of viruses have been defined by the ICTV.{{cite web|url=https://ictv.global/taxonomy|title=Virus Taxonomy: 2024 Release|website=talk.ictvonline.org|publisher=International Committee on Taxonomy of Viruses|access-date=10 March 2025}}

The general taxonomic structure of taxon ranges and the suffixes used in taxonomic names are shown hereafter. As of 2022, the ranks of subrealm, subkingdom, and subclass are unused, whereas all other ranks are in use.

:Realm (-viria)

::Subrealm (-vira)

:::Kingdom (-virae)

::::Subkingdom (-virites)

:::::Phylum (-viricota)

::::::Subphylum (-viricotina)

:::::::Class (-viricetes)

::::::::Subclass (-viricetidae)

:::::::::Order (-virales)

::::::::::Suborder (-virineae)

:::::::::::Family (-viridae)

::::::::::::Subfamily (-virinae)

:::::::::::::Genus (-virus)

::::::::::::::Subgenus (-virus)

:::::::::::::::Species

{{Main|Baltimore classification}}

File:VirusBaltimoreClassification.svg synthesis]]

The Nobel Prize-winning biologist David Baltimore devised the Baltimore classification system.{{cite journal | vauthors = Temin HM, Baltimore D | title = RNA-directed DNA synthesis and RNA tumor viruses | journal = Advances in Virus Research | volume=17 | pages = 129–86 | year = 1972 | pmid = 4348509 | doi = 10.1016/S0065-3527(08)60749-6 | isbn = 978-0120398171 }}{{cite journal | vauthors = Baltimore D | title = The strategy of RNA viruses | journal = Harvey Lectures | series = 70 Series | pages = 57–74 | year = 1974 | volume=70 | pmid = 4377923 }} The ICTV classification system is used in conjunction with the Baltimore classification system in modern virus classification.{{cite journal | vauthors = van Regenmortel MH, Mahy BW | title = Emerging issues in virus taxonomy | journal = Emerging Infectious Diseases | volume=10 | issue = 1 | pages = 8–13 | date = January 2004 | pmid = 15078590 | pmc = 3322749 | doi = 10.3201/eid1001.030279 }}{{cite journal | vauthors = Mayo MA | s2cid = 33422303 | title = Developments in plant virus taxonomy since the publication of the 6th ICTV Report. International Committee on Taxonomy of Viruses | journal = Archives of Virology | volume=144 | issue = 8 | pages = 1659–66 | year = 1999 | pmid = 10486120 | doi = 10.1007/s007050050620 | doi-access = free }}{{cite journal | vauthors = de Villiers EM, Fauquet C, Broker TR, Bernard HU, zur Hausen H | title = Classification of papillomaviruses | journal = Virology | volume=324 | issue = 1 | pages = 17–27 | date = June 2004 | pmid = 15183049 | doi = 10.1016/j.virol.2004.03.033 }}

The Baltimore classification of viruses is based on the mechanism of mRNA production. Viruses must generate mRNAs from their genomes to produce proteins and replicate themselves, but different mechanisms are used to achieve this in each virus family. Viral genomes may be single-stranded (ss) or double-stranded (ds), RNA or DNA, and may or may not use reverse transcriptase (RT). In addition, ssRNA viruses may be either sense (+) or antisense (−). This classification places viruses into seven groups:

{{Baltimore groups}}

{{See also|Viral disease}}

File:Viral infections and involved species.svg

Examples of common human diseases caused by viruses include the common cold, influenza, chickenpox, and cold sores. Many serious diseases such as rabies, Ebola virus disease, AIDS (HIV), avian influenza, and SARS are caused by viruses. The relative ability of viruses to cause disease is described in terms of virulence. Other diseases are under investigation to discover if they have a virus as the causative agent, such as the possible connection between human herpesvirus 6 (HHV6) and neurological diseases such as multiple sclerosis and chronic fatigue syndrome.{{cite journal | vauthors = Komaroff AL | title = Is human herpesvirus-6 a trigger for chronic fatigue syndrome? | journal = Journal of Clinical Virology | volume=37 |issue= Suppl 1 | pages = S39–46 | date = December 2006 | pmid = 17276367 | doi = 10.1016/S1386-6532(06)70010-5 }} There is controversy over whether the bornavirus, previously thought to cause neurological diseases in horses, could be responsible for psychiatric illnesses in humans.{{cite journal | vauthors = Chen CH, Chiu YL, Wei FC, Koong FJ, Liu HC, Shaw CK, Hwu HG, Hsiao KJ | s2cid = 19830976 | title = High seroprevalence of Borna virus infection in schizophrenic patients, family members and mental health workers in Taiwan | journal = Molecular Psychiatry | volume=4 | issue = 1 | pages = 33–38 | date = January 1999 | pmid = 10089006 | doi = 10.1038/sj.mp.4000484 | doi-access = free }}

Viruses have different mechanisms by which they produce disease in an organism, which depends largely on the viral species. Mechanisms at the cellular level primarily include cell lysis, the breaking open and subsequent death of the cell. In multicellular organisms, if enough cells die, the whole organism will start to suffer the effects. Although viruses cause disruption of healthy homeostasis, resulting in disease, they may exist relatively harmlessly within an organism. An example would include the ability of the herpes simplex virus, which causes cold sores, to remain in a dormant state within the human body. This is called latency{{cite journal | vauthors = Margolis TP, Elfman FL, Leib D, Pakpour N, Apakupakul K, Imai Y, Voytek C | title = Spontaneous reactivation of herpes simplex virus type 1 in latently infected murine sensory ganglia | journal = Journal of Virology | volume=81 | issue = 20 | pages = 11069–74 | date = October 2007 | pmid = 17686862 | pmc = 2045564 | doi = 10.1128/JVI.00243-07 }} and is a characteristic of the herpes viruses, including Epstein–Barr virus, which causes glandular fever, and varicella zoster virus, which causes chickenpox and shingles. Most people have been infected with at least one of these types of herpes virus.{{cite journal | vauthors = Whitley RJ, Roizman B | title = Herpes simplex virus infections | journal = Lancet | volume = 357 | issue = 9267 | pages = 1513–18 | date = May 2001 | pmid = 11377626 | doi = 10.1016/S0140-6736(00)04638-9 | s2cid = 9854903 }} These latent viruses might sometimes be beneficial, as the presence of the virus can increase immunity against bacterial pathogens, such as Yersinia pestis.{{cite journal | vauthors = Barton ES, White DW, Cathelyn JS, Brett-McClellan KA, Engle M, Diamond MS, Miller VL, Virgin HW | title = Herpesvirus latency confers symbiotic protection from bacterial infection | journal = Nature | volume = 447 | issue = 7142 | pages = 326–29 | date = May 2007 | pmid = 17507983 | doi = 10.1038/nature05762 | bibcode = 2007Natur.447..326B | s2cid = 4425405 }}

Some viruses can cause lifelong or chronic infections, where the viruses continue to replicate in the body despite the host's defence mechanisms.{{cite journal | vauthors = Bertoletti A, Gehring A | title = Immune response and tolerance during chronic hepatitis B virus infection | journal = Hepatology Research | volume = 37 |issue= Suppl 3 | pages = S331–38 | date = October 2007 | pmid = 17931183 | doi = 10.1111/j.1872-034X.2007.00221.x | s2cid = 13386004 }} This is common in hepatitis B virus and hepatitis C virus infections. People chronically infected are known as carriers, as they serve as reservoirs of infectious virus.{{cite journal | vauthors = Rodrigues C, Deshmukh M, Jacob T, Nukala R, Menon S, Mehta A | title = Significance of HBV DNA by PCR over serological markers of HBV in acute and chronic patients | journal = Indian Journal of Medical Microbiology | volume = 19 | issue = 3 | pages = 141–44 | year = 2001 | pmid = 17664817 }} In populations with a high proportion of carriers, the disease is said to be endemic.{{cite journal | vauthors = Nguyen VT, McLaws ML, Dore GJ | title = Highly endemic hepatitis B infection in rural Vietnam | journal = Journal of Gastroenterology and Hepatology | volume = 22 | issue = 12 | pages = 2093–100 | date = December 2007 | pmid = 17645465 | doi = 10.1111/j.1440-1746.2007.05010.x | s2cid = 29885790 }}

Viral epidemiology is the branch of medical science that deals with the transmission and control of virus infections in humans. Transmission of viruses can be vertical, which means from mother to child, or horizontal, which means from person to person. Examples of vertical transmission include hepatitis B virus and HIV, where the baby is born already infected with the virus.{{cite journal | vauthors = Fowler MG, Lampe MA, Jamieson DJ, Kourtis AP, Rogers MF | title = Reducing the risk of mother-to-child human immunodeficiency virus transmission: past successes, current progress and challenges, and future directions | journal = American Journal of Obstetrics and Gynecology | volume = 197 | issue = 3 Suppl | pages = S3–9 | date = September 2007 | pmid = 17825648 | doi = 10.1016/j.ajog.2007.06.048 | doi-access = free }} Another, more rare, example is the varicella zoster virus, which, although causing relatively mild infections in children and adults, can be fatal to the foetus and newborn baby.{{cite journal | vauthors = Sauerbrei A, Wutzler P | s2cid = 7973561 | title = The congenital varicella syndrome | journal = Journal of Perinatology | volume = 20 | issue = 8 Pt 1 | pages = 548–54 | date = December 2000 | pmid = 11190597 | doi = 10.1038/sj.jp.7200457 }}

Horizontal transmission is the most common mechanism of spread of viruses in populations.{{cite journal |vauthors=Antonovics J, Wilson AJ, Forbes MR, Hauffe HC, Kallio ER, Leggett HC, Longdon B, Okamura B, Sait SM, Webster JP |title=The evolution of transmission mode |journal=Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences |volume=372 |issue=1719 |date=May 2017 |pmid=28289251 |pmc=5352810 |doi=10.1098/rstb.2016.0083}} Horizontal transmission can occur when body fluids are exchanged during sexual activity, by exchange of saliva or when contaminated food or water is ingested. It can also occur when aerosols containing viruses are inhaled or by insect vectors such as when infected mosquitoes penetrate the skin of a host. Most types of viruses are restricted to just one or two of these mechanisms and they are referred to as "respiratory viruses" or "enteric viruses" and so forth. The rate or speed of transmission of viral infections depends on factors that include population density, the number of susceptible individuals, (i.e., those not immune),{{cite journal | vauthors = Garnett GP | title = Role of herd immunity in determining the effect of vaccines against sexually transmitted disease | journal = The Journal of Infectious Diseases | volume = 191 |issue= Suppl 1 | pages = S97–106 | date = February 2005 | pmid = 15627236 | doi = 10.1086/425271 | doi-access = free }} the quality of healthcare and the weather.{{cite journal | vauthors = Platonov AE | title = [The influence of weather conditions on the epidemiology of vector-borne diseases by the example of West Nile fever in Russia] | language = ru | journal = Vestnik Rossiiskoi Akademii Meditsinskikh Nauk | issue = 2 | pages = 25–29 | year = 2006 | pmid = 16544901 }}

Epidemiology is used to break the chain of infection in populations during outbreaks of viral diseases.{{rp|264}} Control measures are used that are based on knowledge of how the virus is transmitted. It is important to find the source, or sources, of the outbreak and to identify the virus. Once the virus has been identified, the chain of transmission can sometimes be broken by vaccines. When vaccines are not available, sanitation and disinfection can be effective. Often, infected people are isolated from the rest of the community, and those that have been exposed to the virus are placed in quarantine.{{rp|894}} To control the outbreak of foot-and-mouth disease in cattle in Britain in 2001, thousands of cattle were slaughtered.{{cite journal |vauthors=Jewell CP, Keeling MJ, Roberts GO |title=Predicting undetected infections during the 2007 foot-and-mouth disease outbreak |journal=Journal of the Royal Society, Interface |volume=6 |issue=41 |pages=1145–51 |date=December 2009 |pmid=19091686 |pmc=2817150 |doi=10.1098/rsif.2008.0433 }} Most viral infections of humans and other animals have incubation periods during which the infection causes no signs or symptoms.{{rp|170}} Incubation periods for viral diseases range from a few days to weeks, but are known for most infections.{{rp|170–172}} Somewhat overlapping, but mainly following the incubation period, there is a period of communicability—a time when an infected individual or animal is contagious and can infect another person or animal.{{rp|170–172}} This, too, is known for many viral infections, and knowledge of the length of both periods is important in the control of outbreaks.{{rp|272}} When outbreaks cause an unusually high proportion of cases in a population, community, or region, they are called epidemics. If outbreaks spread worldwide, they are called pandemics.{{rp|891}}

{{See also|1918 flu pandemic|AIDS|Ebola virus disease|COVID-19 pandemic}}

{{Further|List of epidemics}}

File:Reconstructed Spanish Flu Virus.jpg image of a recreated 1918 influenza virus]]

A pandemic is a worldwide epidemic. The 1918 flu pandemic, which lasted until 1919, was a category 5 influenza pandemic caused by an unusually severe and deadly influenza A virus. The victims were often healthy young adults, in contrast to most influenza outbreaks, which predominantly affect juvenile, elderly, or otherwise-weakened patients.{{rp|409–415}} Older estimates say it killed 40–50 million people,{{cite journal | vauthors = Patterson KD, Pyle GF | title = The geography and mortality of the 1918 influenza pandemic | journal = Bulletin of the History of Medicine | volume = 65 | issue = 1 | pages = 4–21 | year = 1991 | pmid = 2021692 }} while more recent research suggests that it may have killed as many as 100 million people, or 5% of the world's population in 1918.{{cite journal | vauthors = Johnson NP, Mueller J | title = Updating the accounts: global mortality of the 1918-1920 "Spanish" influenza pandemic | journal = Bulletin of the History of Medicine | volume = 76 | issue = 1 | pages = 105–15 | year = 2002 | pmid = 11875246 | doi = 10.1353/bhm.2002.0022 | s2cid = 22974230 }}

Although viral pandemics are rare events, HIV—which evolved from viruses found in monkeys and chimpanzees—has been pandemic since at least the 1980s.{{cite journal | vauthors = Eisinger RW, Fauci AS | title = 1 | journal = Emerging Infectious Diseases | volume = 24 | issue = 3 | pages = 413–16 | date = March 2018 | pmid = 29460740 | pmc = 5823353 | doi = 10.3201/eid2403.171797 }} During the 20th century there were four pandemics caused by influenza virus and those that occurred in 1918, 1957 and 1968 were severe.{{cite journal | vauthors = Qin Y, Zhao MJ, Tan YY, Li XQ, Zheng JD, Peng ZB, Feng LZ | title = [History of influenza pandemics in China during the past century] | language = zh | journal = Zhonghua Liu Xing Bing Xue Za Zhi = Zhonghua Liuxingbingxue Zazhi | volume = 39 | issue = 8 | pages = 1028–31 | date = August 2018 | doi = 10.3760/cma.j.issn.0254-6450.2018.08.003 | doi-broken-date = 13 March 2025 | pmid = 30180422}} Most researchers believe that HIV originated in sub-Saharan Africa during the 20th century;{{cite journal | vauthors = Gao F, Bailes E, Robertson DL, Chen Y, Rodenburg CM, Michael SF, Cummins LB, Arthur LO, Peeters M, Shaw GM, Sharp PM, Hahn BH | title = Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes | journal = Nature | volume = 397 | issue = 6718 | pages = 436–41 | date = February 1999 | pmid = 9989410 | doi = 10.1038/17130 | bibcode = 1999Natur.397..436G | s2cid = 4432185 | doi-access = free }} it is now a pandemic, with an estimated 37.9 million people now living with the disease worldwide.{{cite web|title=Fact Sheet|url=https://www.unaids.org/sites/default/files/media_asset/2019-UNAIDS-data_en.pdf|work=UNAIDS.org|year=2018|access-date=12 December 2019}} There were about 770,000 deaths from AIDS in 2018.{{cite web|title=UN AIDS DATA2019|url=https://www.unaids.org/en/resources/fact-sheet|work=UNAIDS.org|year=2019|access-date=5 December 2019}} The Joint United Nations Programme on HIV/AIDS (UNAIDS) and the World Health Organization (WHO) estimate that AIDS has killed more than 25 million people since it was first recognised on 5 June 1981, making it one of the most destructive epidemics in recorded history.{{cite journal | vauthors = Mawar N, Saha S, Pandit A, Mahajan U | title = The third phase of HIV pandemic: social consequences of HIV/AIDS stigma & discrimination & future needs | journal = The Indian Journal of Medical Research | volume = 122 | issue = 6 | pages = 471–84 | date = December 2005 | pmid = 16517997 | url = http://www.icmr.nic.in/ijmr/2005/december/1201.pdf | access-date = 19 December 2014 | url-status = dead | archive-url = https://web.archive.org/web/20160304023223/http://www.icmr.nic.in/ijmr/2005/december/1201.pdf | archive-date = 4 March 2016 }} In 2007 there were 2.7 million new HIV infections and 2 million HIV-related deaths.{{cite web|url=http://data.unaids.org/pub/GlobalReport/2008/jc1510_2008_global_report_pp29_62_en.pdf |title=Status of the global HIV epidemic |year=2008 |publisher=UNAIDS |access-date=19 December 2014 |url-status=dead |archive-url=https://web.archive.org/web/20151122231422/http://data.unaids.org/pub/GlobalReport/2008/jc1510_2008_global_report_pp29_62_en.pdf |archive-date=22 November 2015 }}

{{Multiple image

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Several highly lethal viral pathogens are members of the Filoviridae. Filoviruses are filament-like viruses that cause viral hemorrhagic fever, and include ebolaviruses and marburgviruses. Marburg virus, first discovered in 1967, attracted widespread press attention in April 2005 for an outbreak in Angola.{{cite journal | vauthors = Towner JS, Khristova ML, Sealy TK, Vincent MJ, Erickson BR, Bawiec DA, Hartman AL, Comer JA, Zaki SR, Ströher U, Gomes da Silva F, del Castillo F, Rollin PE, Ksiazek TG, Nichol ST | title = Marburgvirus genomics and association with a large hemorrhagic fever outbreak in Angola | journal = Journal of Virology | volume = 80 | issue = 13 | pages = 6497–516 | date = July 2006 | pmid = 16775337 | pmc = 1488971 | doi = 10.1128/JVI.00069-06 }} Ebola virus disease has also caused intermittent outbreaks with high mortality rates since 1976 when it was first identified. The worst and most recent one is the 2013–2016 West Africa epidemic.{{Cite web|url=http://apps.who.int/iris/bitstream/10665/134771/1/roadmapsitrep_24Sept2014_eng.pdf?ua=1|title=World Health Organisation report, 24 September 2014}}

Except for smallpox, most pandemics are caused by newly evolved viruses. These "emergent" viruses are usually mutants of less harmful viruses that have circulated previously either in humans or other animals.{{cite web|url=https://virologyj.biomedcentral.com/articles/sections/emerging-viruses|title=Virology Journal|website=Virology Journal}}

Severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) are caused by new types of coronaviruses. Other coronaviruses are known to cause mild infections in humans,{{cite book |vauthors=Weiss SR, Leibowitz JL |title=Coronavirus pathogenesis |volume=81|pages=85–164 |year=2011 |pmid=22094080 |doi=10.1016/B978-0-12-385885-6.00009-2 |series=Advances in Virus Research |pmc=7149603 |isbn=978-0-12-385885-6}} so the virulence and rapid spread of SARS infections—that by July 2003 had caused around 8,000 cases and 800 deaths—was unexpected and most countries were not prepared.{{cite journal | vauthors = Wong AT, Chen H, Liu SH, Hsu EK, Luk KS, Lai CK, Chan RF, Tsang OT, Choi KW, Kwan YW, Tong AY, Cheng VC, Tsang DN | title = From SARS to Avian Influenza Preparedness in Hong Kong | journal = Clinical Infectious Diseases | volume = 64 | issue = suppl_2 | pages = S98–S104 | date = May 2017 | pmid = 28475794 | doi = 10.1093/cid/cix123 | doi-access = free }}

A related coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2), thought to have originated in bats, emerged in Wuhan, China in November 2019 and spread rapidly around the world. Infections with the virus caused the COVID-19 pandemic that started in 2020.{{cite journal | vauthors = Ashour HM, Elkhatib WF, Rahman MM, Elshabrawy HA | title=Insights into the Recent 2019 Novel Coronavirus (SARS-CoV-2) in Light of Past Human Coronavirus Outbreaks | journal=Pathogens | volume=9 | issue=3 | page=186 | date=March 2020 | pmid=32143502 | doi=10.3390/pathogens9030186 | pmc=7157630 | doi-access=free }}{{cite journal | vauthors=Deng SQ, Peng HJ | title = Characteristics of and Public Health Responses to the Coronavirus Disease 2019 Outbreak in China | journal = Journal of Clinical Medicine | volume = 9 | issue = 2 | page = 575 | date = February 2020 | pmid = 32093211 | pmc = 7074453 | doi = 10.3390/jcm9020575 | doi-access = free }}{{cite journal | vauthors = Han Q, Lin Q, Jin S, You L | title=Coronavirus 2019-nCoV: A brief perspective from the front line | journal=The Journal of Infection | volume=80 | issue=4 | pages=373–77 | date=April 2020 | pmid=32109444 | doi=10.1016/j.jinf.2020.02.010 | pmc=7102581 }} Unprecedented restrictions in peacetime were placed on international travel,{{cite news|url=https://www.nytimes.com/article/coronavirus-travel-restrictions.html|title=Coronavirus Travel Restrictions, Across the Globe| vauthors = Londoño E, Ortiz A|newspaper=The New York Times |date=16 March 2020}} and curfews were imposed in several major cities worldwide in response to the pandemic.{{cite web| url= http://www.cidrap.umn.edu/news-perspective/2020/03/us-takes-more-big-pandemic-response-steps-europe-covid-19-cases-soar |title=US takes more big pandemic response steps; Europe COVID-19 cases soar|website=CIDRAP|date=15 March 2020 }}

{{Further|Oncovirus}}

Viruses are an established cause of cancer in humans and other species. Viral cancers occur only in a minority of infected persons (or animals). Cancer viruses come from a range of virus families, including both RNA and DNA viruses, and so there is no single type of "oncovirus" (an obsolete term originally used for acutely transforming retroviruses). The development of cancer is determined by a variety of factors such as host immunity{{cite journal | vauthors = Einstein MH, Schiller JT, Viscidi RP, Strickler HD, Coursaget P, Tan T, Halsey N, Jenkins D | title = Clinician's guide to human papillomavirus immunology: knowns and unknowns | journal = The Lancet. Infectious Diseases | volume = 9 | issue = 6 | pages = 347–56 | date = June 2009 | pmid = 19467474 | doi = 10.1016/S1473-3099(09)70108-2 }} and mutations in the host.{{cite journal | vauthors = Shuda M, Feng H, Kwun HJ, Rosen ST, Gjoerup O, Moore PS, Chang Y | title = T antigen mutations are a human tumor-specific signature for Merkel cell polyomavirus | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 105 | issue = 42 | pages = 16272–77 | date = October 2008 | pmid = 18812503 | pmc = 2551627 | doi = 10.1073/pnas.0806526105 | bibcode = 2008PNAS..10516272S | doi-access = free }} Viruses accepted to cause human cancers include some genotypes of human papillomavirus, hepatitis B virus, hepatitis C virus, Epstein–Barr virus, Kaposi's sarcoma-associated herpesvirus and human T-lymphotropic virus. The most recently discovered human cancer virus is a polyomavirus (Merkel cell polyomavirus) that causes most cases of a rare form of skin cancer called Merkel cell carcinoma.{{cite journal | vauthors = Pulitzer MP, Amin BD, Busam KJ | title = Merkel cell carcinoma: review | journal = Advances in Anatomic Pathology | volume = 16 | issue = 3 | pages = 135–44 | date = May 2009 | pmid = 19395876 | doi = 10.1097/PAP.0b013e3181a12f5a | s2cid = 36110778 }}

Hepatitis viruses can develop into a chronic viral infection that leads to liver cancer.{{cite journal | vauthors = Koike K | title = Hepatitis C virus contributes to hepatocarcinogenesis by modulating metabolic and intracellular signaling pathways | journal = Journal of Gastroenterology and Hepatology | volume = 22 |issue= Suppl 1 | pages = S108–11 | date = June 2007 | pmid = 17567457 | doi = 10.1111/j.1440-1746.2006.04669.x | s2cid = 25399220 }}{{cite book | vauthors = Hu J, Ludgate L | title = Aids-Associated Viral Oncogenesis | chapter = HIV–HBV and HIV–HCV Coinfection and Liver Cancer Development | series = Cancer Treatment and Research | volume = 133 | pages = 241–52 | year = 2007 | pmid = 17672044 | doi = 10.1007/978-0-387-46816-7_9 | isbn = 978-0-387-46804-4 }} Infection by human T-lymphotropic virus can lead to tropical spastic paraparesis and adult T-cell leukaemia.{{cite journal | vauthors = Bellon M, Nicot C | title = Telomerase: a crucial player in HTLV-I-induced human T-cell leukemia | journal = Cancer Genomics & Proteomics | volume = 4 | issue = 1 | pages = 21–25 | year = 2007 | pmid = 17726237 }} Human papillomaviruses are an established cause of cancers of cervix, skin, anus, and penis.{{cite journal | vauthors = Schiffman M, Castle PE, Jeronimo J, Rodriguez AC, Wacholder S | title = Human papillomavirus and cervical cancer | journal = Lancet | volume = 370 | issue = 9590 | pages = 890–907 | date = September 2007 | pmid = 17826171 | doi = 10.1016/S0140-6736(07)61416-0 | s2cid = 20196938 }} Within the Herpesviridae, Kaposi's sarcoma-associated herpesvirus causes Kaposi's sarcoma and body-cavity lymphoma, and Epstein–Barr virus causes Burkitt's lymphoma, Hodgkin's lymphoma, B lymphoproliferative disorder, and nasopharyngeal carcinoma.{{cite journal | vauthors = Klein E, Kis LL, Klein G | title = Epstein-Barr virus infection in humans: from harmless to life endangering virus-lymphocyte interactions | journal = Oncogene | volume = 26 | issue = 9 | pages = 1297–305 | date = February 2007 | pmid = 17322915 | doi = 10.1038/sj.onc.1210240 | doi-access = free }} Merkel cell polyomavirus closely related to SV40 and mouse polyomaviruses that have been used as animal models for cancer viruses for over 50 years.{{cite journal | vauthors = Zur Hausen H | title = Novel human polyomaviruses – re-emergence of a well known virus family as possible human carcinogens | journal = International Journal of Cancer | volume = 123 | issue = 2 | pages = 247–50 | date = July 2008 | pmid = 18449881 | doi = 10.1002/ijc.23620 | s2cid = 9482506 | doi-access = free }}

{{See also|Immune system}}

The body's first line of defence against viruses is the innate immune system. This comprises cells and other mechanisms that defend the host from infection in a non-specific manner. This means that the cells of the innate system recognise, and respond to, pathogens in a generic way, but, unlike the adaptive immune system, it does not confer long-lasting or protective immunity to the host.{{cite book | vauthors = Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walters P |title=Molecular Biology of the Cell | edition = 4th |publisher=Garland Science |year=2002 |location=New York and London |url=https://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=mboc4.TOC&depth=2 |isbn=0-8153-3218-1 }}

RNA interference is an important innate defence against viruses.{{cite journal | vauthors = Ding SW, Voinnet O | title = Antiviral immunity directed by small RNAs | journal = Cell | volume = 130 | issue = 3 | pages = 413–26 | date = August 2007 | pmid = 17693253 | pmc = 2703654 | doi = 10.1016/j.cell.2007.07.039 }} Many viruses have a replication strategy that involves double-stranded RNA (dsRNA). When such a virus infects a cell, it releases its RNA molecule or molecules, which immediately bind to a protein complex called a dicer that cuts the RNA into smaller pieces. A biochemical pathway—the RISC complex—is activated, which ensures cell survival by degrading the viral mRNA. Rotaviruses have evolved to avoid this defence mechanism by not uncoating fully inside the cell, and releasing newly produced mRNA through pores in the particle's inner capsid. Their genomic dsRNA remains protected inside the core of the virion.{{cite journal | vauthors = Patton JT, Vasquez-Del Carpio R, Spencer E | title = Replication and transcription of the rotavirus genome | journal = Current Pharmaceutical Design | volume = 10 | issue = 30 | pages = 3769–77 | year = 2004 | pmid = 15579070 | doi = 10.2174/1381612043382620 }}{{cite journal | vauthors = Jayaram H, Estes MK, Prasad BV | title = Emerging themes in rotavirus cell entry, genome organization, transcription and replication | journal = Virus Research | volume = 101 | issue = 1 | pages = 67–81 | date = April 2004 | pmid = 15010218 | doi = 10.1016/j.virusres.2003.12.007 }}

When the adaptive immune system of a vertebrate encounters a virus, it produces specific antibodies that bind to the virus and often render it non-infectious. This is called humoral immunity. Two types of antibodies are important. The first, called IgM, is highly effective at neutralising viruses but is produced by the cells of the immune system only for a few weeks. The second, called IgG, is produced indefinitely. The presence of IgM in the blood of the host is used to test for acute infection, whereas IgG indicates an infection sometime in the past.{{cite journal | vauthors = Greer S, Alexander GJ | title = Viral serology and detection | journal = Baillière's Clinical Gastroenterology | volume = 9 | issue = 4 | pages = 689–721 | date = December 1995 | pmid = 8903801 | doi = 10.1016/0950-3528(95)90057-8 }} IgG antibody is measured when tests for immunity are carried out.{{cite journal | vauthors = Matter L, Kogelschatz K, Germann D | title = Serum levels of rubella virus antibodies indicating immunity: response to vaccination of subjects with low or undetectable antibody concentrations | journal = The Journal of Infectious Diseases | volume = 175 | issue = 4 | pages = 749–55 | date = April 1997 | pmid = 9086126 | doi = 10.1086/513967 | doi-access = free }}

Antibodies can continue to be an effective defence mechanism even after viruses have managed to gain entry to the host cell. A protein that is in cells, called TRIM21, can attach to the antibodies on the surface of the virus particle. This primes the subsequent destruction of the virus by the enzymes of the cell's proteosome system.{{cite journal | vauthors = Mallery DL, McEwan WA, Bidgood SR, Towers GJ, Johnson CM, James LC | title = Antibodies mediate intracellular immunity through tripartite motif-containing 21 (TRIM21) | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 107 | issue = 46 | pages = 19985–90 | date = November 2010 | pmid = 21045130 | pmc = 2993423 | doi = 10.1073/pnas.1014074107 | bibcode = 2010PNAS..10719985M | doi-access = free }}

File:Rotavirus with antibody.jpges: the one on the right is coated with antibodies that prevent its attachment to cells and infecting them.]]

A second defence of vertebrates against viruses is called cell-mediated immunity and involves immune cells known as T cells. The body's cells constantly display short fragments of their proteins on the cell's surface, and, if a T cell recognises a suspicious viral fragment there, the host cell is destroyed by 'killer T' cells and the virus-specific T-cells proliferate. Cells such as the macrophage are specialists at this antigen presentation.{{cite journal | vauthors = Cascalho M, Platt JL | title = Novel functions of B cells | journal = Critical Reviews in Immunology | volume = 27 | issue = 2 | pages = 141–51 | year = 2007 | pmid = 17725500 | doi = 10.1615/critrevimmunol.v27.i2.20 }} The production of interferon is an important host defence mechanism. This is a hormone produced by the body when viruses are present. Its role in immunity is complex; it eventually stops the viruses from reproducing by killing the infected cell and its close neighbours.{{cite journal | vauthors = Le Page C, Génin P, Baines MG, Hiscott J | title = Interferon activation and innate immunity | journal = Reviews in Immunogenetics | volume = 2 | issue = 3 | pages = 374–86 | year = 2000 | pmid = 11256746 }}

Not all virus infections produce a protective immune response in this way. HIV evades the immune system by constantly changing the amino acid sequence of the proteins on the surface of the virion. This is known as "escape mutation" as the viral epitopes escape recognition by the host immune response. These persistent viruses evade immune control by sequestration, blockade of antigen presentation, cytokine resistance, evasion of natural killer cell activities, escape from apoptosis, and antigenic shift.{{cite journal | vauthors = Hilleman MR | title = Strategies and mechanisms for host and pathogen survival in acute and persistent viral infections | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 101 |issue= Suppl 2 | pages = 14560–66 | date = October 2004 | pmid = 15297608 | pmc = 521982 | doi = 10.1073/pnas.0404758101 | bibcode = 2004PNAS..10114560H | doi-access = free }} Other viruses, called 'neurotropic viruses', are disseminated by neural spread where the immune system may be unable to reach them due to immune privilege.{{cite book |vauthors=Libbey JE, Fujinami RS |title=Neurovirology |chapter=Adaptive immune response to viral infections in the central nervous system |series=Handbook of Clinical Neurology |volume=123 |pages=225–47 |date=2014 |pmid=25015488 |pmc=4370180 |doi=10.1016/B978-0-444-53488-0.00010-9|isbn=978-0444534880 }}

Because viruses use vital metabolic pathways within host cells to replicate, they are difficult to eliminate without using drugs that cause toxic effects to host cells in general. The most effective medical approaches to viral diseases are vaccinations to provide immunity to infection, and antiviral drugs that selectively interfere with viral replication.

{{Further|Vaccination}}

Vaccination is a cheap and effective way of preventing infections by viruses. Vaccines were used to prevent viral infections long before the discovery of the actual viruses. Their use has resulted in a dramatic decline in morbidity (illness) and mortality (death) associated with viral infections such as polio, measles, mumps and rubella.{{cite journal | vauthors = Asaria P, MacMahon E | title = Measles in the United Kingdom: can we eradicate it by 2010? | journal = BMJ | volume = 333 | issue = 7574 | pages = 890–95 | date = October 2006 | pmid = 17068034 | pmc = 1626346 | doi = 10.1136/bmj.38989.445845.7C }} Smallpox infections have been eradicated.{{cite book | vauthors = Lane JM | title = Mass Vaccination: Global Aspects — Progress and Obstacles | chapter = Mass vaccination and surveillance/containment in the eradication of smallpox | series = Current Topics in Microbiology and Immunology | volume = 304 | pages = 17–29 | year = 2006 | pmid = 16989262 | doi = 10.1007/3-540-36583-4_2 | pmc = 7120753 | isbn = 978-3-540-29382-8 }} Vaccines are available to prevent over thirteen viral infections of humans,{{cite journal | vauthors = Arvin AM, Greenberg HB | title = New viral vaccines | journal = Virology | volume = 344 | issue = 1 | pages = 240–49 | date = January 2006 | pmid = 16364754 | doi = 10.1016/j.virol.2005.09.057 | doi-access = free }} and more are used to prevent viral infections of animals.{{cite journal | vauthors = Pastoret PP, Schudel AA, Lombard M | title = Conclusions--future trends in veterinary vaccinology | journal = Revue Scientifique et Technique | volume = 26 | issue = 2 | pages = 489–94, 495–501, 503–09 | date = August 2007 | pmid = 17892169 | doi = 10.20506/rst.26.2.1759 }} Vaccines can consist of live-attenuated or killed viruses, viral proteins (antigens), or RNA.{{cite journal | vauthors = Palese P | title = Making better influenza virus vaccines? | journal = Emerging Infectious Diseases | volume = 12 | issue = 1 | pages = 61–65 | date = January 2006 | pmid = 16494719 | pmc = 3291403 | doi = 10.3201/eid1201.051043 | author-link = Peter Palese }}{{cite journal |vauthors=Anand P, Stahel VP |title=Review the safety of Covid-19 mRNA vaccines: a review |journal=Patient Safety in Surgery |volume=15 |issue=1 |page=20 |date=May 2021 |pmid=33933145 |pmc=8087878 |doi=10.1186/s13037-021-00291-9 |url= |doi-access=free }} Live vaccines contain weakened forms of the virus, which do not cause the disease but, nonetheless, confer immunity. Such viruses are called attenuated. Live vaccines can be dangerous when given to people with a weak immunity (who are described as immunocompromised), because in these people, the weakened virus can cause the original disease.{{cite journal | vauthors = Thomssen R | title = Live attenuated versus killed virus vaccines | journal = Monographs in Allergy | volume = 9 | pages = 155–76 | year = 1975 | pmid = 1090805 }} Biotechnology and genetic engineering techniques are used to produce subunit vaccines. These vaccines use only the capsid proteins of the virus. Hepatitis B vaccine is an example of this type of vaccine.{{cite journal | vauthors = McLean AA | title = Development of vaccines against hepatitis A and hepatitis B | journal = Reviews of Infectious Diseases | volume = 8 | issue = 4 | pages = 591–98 | year = 1986 | pmid = 3018891 | doi = 10.1093/clinids/8.4.591 }} Subunit vaccines are safe for immunocompromised patients because they cannot cause the disease.{{cite journal | vauthors = Casswall TH, Fischler B | s2cid = 40821818 | title = Vaccination of the immunocompromised child | journal = Expert Review of Vaccines | volume = 4 | issue = 5 | pages = 725–38 | date = October 2005 | pmid = 16221073 | doi = 10.1586/14760584.4.5.725 }} The yellow fever virus vaccine, a live-attenuated strain called 17D, is probably the safest and most effective vaccine ever generated.{{cite journal | vauthors = Barnett ED, Wilder-Smith A, Wilson ME | s2cid = 19352868 | title = Yellow fever vaccines and international travelers | journal = Expert Review of Vaccines | volume = 7 | issue = 5 | pages = 579–87 | date = July 2008 | pmid = 18564013 | doi = 10.1586/14760584.7.5.579 }}

{{Further|Antiviral drug}}

File:Guanosine aciclovir comparison.svg and the antiviral drug acyclovir]]

Antiviral drugs are often nucleoside analogues (fake DNA building-blocks), which viruses mistakenly incorporate into their genomes during replication.{{cite journal |vauthors=De Clercq E, Li G |title=Approved Antiviral Drugs over the Past 50 Years |journal=Clinical Microbiology Reviews |volume=29 |issue=3 |pages=695–747 |date=July 2016 |pmid=27281742 |pmc=4978613 |doi=10.1128/CMR.00102-15}} The life-cycle of the virus is then halted because the newly synthesised DNA is inactive. This is because these analogues lack the hydroxyl groups, which, along with phosphorus atoms, link together to form the strong "backbone" of the DNA molecule. This is called DNA chain termination.{{cite journal | vauthors = Magden J, Kääriäinen L, Ahola T | title = Inhibitors of virus replication: recent developments and prospects | journal = Applied Microbiology and Biotechnology | volume = 66 | issue = 6 | pages = 612–21 | date = March 2005 | pmid = 15592828 | doi = 10.1007/s00253-004-1783-3 | pmc = 7082807 }} Examples of nucleoside analogues are aciclovir for Herpes simplex virus infections and lamivudine for HIV and hepatitis B virus infections. Aciclovir is one of the oldest and most frequently prescribed antiviral drugs.{{cite journal | vauthors = Mindel A, Sutherland S | title = Genital herpes - the disease and its treatment including intravenous acyclovir | journal = The Journal of Antimicrobial Chemotherapy | volume = 12 |issue= Suppl B | pages = 51–59 | date = September 1983 | pmid = 6355051 | doi = 10.1093/jac/12.suppl_b.51 }}

Other antiviral drugs in use target different stages of the viral life cycle. HIV is dependent on a proteolytic enzyme called the HIV-1 protease for it to become fully infectious. There is a large class of drugs called protease inhibitors that inactivate this enzyme.{{cite journal | vauthors = Palmisano L, Vella S | title = A brief history of antiretroviral therapy of HIV infection: success and challenges | journal = Annali dell'Istituto Superiore di Sanità | volume = 47 | issue = 1 | pages = 44–48 | date = 2011 | pmid = 21430338 | doi = 10.4415/ANN_11_01_10 }} There are around thirteen classes of antiviral drugs each targeting different viruses or stages of viral replication.

Hepatitis C is caused by an RNA virus. In 80% of people infected, the disease is chronic, and without treatment, they are infected for the remainder of their lives. There are effective treatments that use direct-acting antivirals.{{cite journal |vauthors=Falade-Nwulia O, Suarez-Cuervo C, Nelson DR, Fried MW, Segal JB, Sulkowski MS |title=Oral Direct-Acting Agent Therapy for Hepatitis C Virus Infection: A Systematic Review |journal=Annals of Internal Medicine |volume=166 |issue=9 |pages=637–48 |date=May 2017 |pmid=28319996 |pmc=5486987 |doi=10.7326/M16-2575}} The treatment of chronic carriers of the hepatitis B virus has also been developed by using similar strategies that include lamivudine and other anti-viral drugs.{{cite journal |vauthors=Nguyen MH, Wong G, Gane E, Kao JH, Dusheiko G |title=Hepatitis B Virus: Advances in Prevention, Diagnosis, and Therapy |journal=Clinical Microbiology Reviews |volume=33 |issue=2 |pages= |date=March 2020 |pmid=32102898 |pmc=7048015 |doi=10.1128/CMR.00046-19}}

Viruses infect all cellular life and, although viruses occur universally, each cellular species has its own specific range that often infects only that species.{{rp|3}} Some viruses, called satellites, can replicate only within cells that have already been infected by another virus.

{{Main|Animal virus|Veterinary virology}}

Viruses are important pathogens of livestock. Diseases such as foot-and-mouth disease and bluetongue are caused by viruses.{{cite journal | vauthors = Goris N, Vandenbussche F, De Clercq K | title = Potential of antiviral therapy and prophylaxis for controlling RNA viral infections of livestock | journal = Antiviral Research | volume = 78 | issue = 1 | pages = 170–78 | date = April 2008 | pmid = 18035428 | doi = 10.1016/j.antiviral.2007.10.003 }} Companion animals such as cats, dogs, and horses, if not vaccinated, are susceptible to serious viral infections. Canine parvovirus is caused by a small DNA virus and infections are often fatal in pups.{{cite journal | vauthors = Carmichael LE | title = An annotated historical account of canine parvovirus | journal = Journal of Veterinary Medicine. B, Infectious Diseases and Veterinary Public Health | volume = 52 | issue = 7–8 | pages = 303–11 | year = 2005 | pmid = 16316389 | doi = 10.1111/j.1439-0450.2005.00868.x }} Like all invertebrates, the honey bee is susceptible to many viral infections.{{cite journal | vauthors = Chen Y, Zhao Y, Hammond J, Hsu HT, Evans J, Feldlaufer M | title = Multiple virus infections in the honey bee and genome divergence of honey bee viruses | journal = Journal of Invertebrate Pathology | volume = 87 | issue = 2–3 | pages = 84–93 | date = October–November 2004 | pmid = 15579317 | doi = 10.1016/j.jip.2004.07.005 | bibcode = 2004JInvP..87...84C | url = http://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1395&context=usdaarsfacpub }} Most viruses co-exist harmlessly in their host and cause no signs or symptoms of disease.{{rp|4}}

{{Main|Plant virus}}

File:Pepper mild mottle virus.png infected by mild mottle virus]]

There are many types of plant viruses, but often they cause only a loss of yield, and it is not economically viable to try to control them. Plant viruses are often spread from plant to plant by organisms, known as vectors. These are usually insects, but some fungi, nematode worms, single-celled organisms, and parasitic plants are vectors.{{cite book | vauthors = Hull R |title=Matthews' Plant Virology |date=2002 |publisher=Academic Press |isbn=978-0123611604 |pages=555–56 |edition=4th |chapter-url=https://www.sciencedirect.com/science/article/pii/B9780123611604500633 |access-date=21 February 2022 |chapter= Chapter 12: Transmission 2: Mechanical, Seed, Pollen and Epidemiology|doi=10.1016/B978-012361160-4/50063-3 }} When control of plant virus infections is considered economical, for perennial fruits, for example, efforts are concentrated on killing the vectors and removing alternate hosts such as weeds.{{rp|802}} Plant viruses cannot infect humans and other animals because they can reproduce only in living plant cells.{{rp|799–807}}

Originally from Peru, the potato has become a staple crop worldwide.{{cite journal |vauthors=Zaheer K, Akhtar MH |title=Potato Production, Usage, and Nutrition – A Review |journal=Critical Reviews in Food Science and Nutrition |volume=56 |issue=5 |pages=711–21 |date=2016 |pmid=24925679 |doi=10.1080/10408398.2012.724479 |s2cid=33074838 }} The potato virus Y causes disease in potatoes and related species including tomatoes and peppers. In the 1980s, this virus acquired economical importance when it proved difficult to control in seed potato crops. Transmitted by aphids, this virus can reduce crop yields by up to 80 per cent, causing significant losses to potato yields.{{cite journal |vauthors=Fuentes S, Jones RA, Matsuoka H, Ohshima K, Kreuze J, Gibbs AJ |title=Potato virus Y; the Andean connection |journal=Virus Evolution |volume=5 |issue=2 |date=July 2019 |pages=vez037 |pmid=31559020 |pmc=6755682 |doi=10.1093/ve/vez037}}

Plants have elaborate and effective defence mechanisms against viruses. One of the most effective is the presence of so-called resistance (R) genes. Each R gene confers resistance to a particular virus by triggering localised areas of cell death around the infected cell, which can often be seen with the unaided eye as large spots. This stops the infection from spreading.{{cite journal | vauthors = Dinesh-Kumar SP, Tham WH, Baker BJ | title = Structure-function analysis of the tobacco mosaic virus resistance gene N | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 97 | issue = 26 | pages = 14789–94 | date = December 2000 | pmid = 11121079 | pmc = 18997 | doi = 10.1073/pnas.97.26.14789 | bibcode = 2000PNAS...9714789D | doi-access = free }} RNA interference is also an effective defence in plants.{{rp|809}}> When they are infected, plants often produce natural disinfectants that kill viruses, such as salicylic acid, nitric oxide, and reactive oxygen molecules.{{cite journal | vauthors = Soosaar JL, Burch-Smith TM, Dinesh-Kumar SP | title = Mechanisms of plant resistance to viruses | journal = Nature Reviews. Microbiology | volume = 3 | issue = 10 | pages = 789–98 | date = October 2005 | pmid = 16132037 | doi = 10.1038/nrmicro1239 | s2cid = 27311732 }}

Plant virus particles or virus-like particles (VLPs) have applications in both biotechnology and nanotechnology. The capsids of most plant viruses are simple and robust structures and can be produced in large quantities either by the infection of plants or by expression in a variety of heterologous systems. Plant virus particles can be modified genetically and chemically to encapsulate foreign material and can be incorporated into supramolecular structures for use in biotechnology.{{cite book| vauthors = Lomonossoff GP |chapter = Virus Particles and the Uses of Such Particles in Bio- and Nanotechnology|year=2011|title=Recent Advances in Plant Virology|publisher=Caister Academic Press|isbn= 978-1-904455-75-2}}

{{Main|Bacteriophage}}

File:Phage.jpg

Bacteriophages are a common and diverse group of viruses and are the most abundant biological entity in aquatic environments—there are up to ten times more of these viruses in the oceans than there are bacteria,{{cite journal | vauthors = Wommack KE, Colwell RR | title = Virioplankton: viruses in aquatic ecosystems | journal = Microbiology and Molecular Biology Reviews | volume = 64 | issue = 1 | pages = 69–114 | date = March 2000 | pmid = 10704475 | pmc = 98987 | doi = 10.1128/MMBR.64.1.69-114.2000 }} reaching levels of 250,000,000 bacteriophages per millilitre of seawater.{{cite journal | vauthors = Bergh O, Børsheim KY, Bratbak G, Heldal M | title = High abundance of viruses found in aquatic environments | journal = Nature | volume = 340 | issue = 6233 | pages = 467–68 | date = August 1989 | pmid = 2755508 | doi = 10.1038/340467a0 | bibcode = 1989Natur.340..467B | s2cid = 4271861 }} These viruses infect specific bacteria by binding to surface receptor molecules and then entering the cell. Within a short amount of time, in some cases, 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 could be released.{{rp|834–835}}

The major way bacteria defend themselves from bacteriophages is by producing enzymes that destroy foreign DNA. These enzymes, called restriction endonucleases, cut up the viral DNA that bacteriophages inject into bacterial cells.{{cite journal | vauthors = Bickle TA, Krüger DH | title = Biology of DNA restriction | journal = Microbiological Reviews | volume = 57 | issue = 2 | pages = 434–50 | date = June 1993 | pmid = 8336674 | pmc = 372918 | doi = 10.1128/MMBR.57.2.434-450.1993 }} Bacteria also contain a system that uses CRISPR sequences to retain fragments of the genomes of viruses that the bacteria have come into contact with previously, which allows them to block the virus's replication through a form of RNA interference.{{cite journal | vauthors = Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P | title = CRISPR provides acquired resistance against viruses in prokaryotes | journal = Science | volume = 315 | issue = 5819 | pages = 1709–12 | date = March 2007 | pmid = 17379808 | doi = 10.1126/science.1138140 | bibcode = 2007Sci...315.1709B | hdl = 20.500.11794/38902 | s2cid = 3888761 | hdl-access = free }}{{cite journal | vauthors = Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, Dickman MJ, Makarova KS, Koonin EV, van der Oost J | title = Small CRISPR RNAs guide antiviral defense in prokaryotes | journal = Science | volume = 321 | issue = 5891 | pages = 960–64 | date = August 2008 | pmid = 18703739 | pmc = 5898235 | doi = 10.1126/science.1159689 | bibcode = 2008Sci...321..960B }} This genetic system provides bacteria with acquired immunity to infection.{{cite journal | vauthors = Mojica FJ, Rodriguez-Valera F | title = The discovery of CRISPR in archaea and bacteria | journal = The FEBS Journal | volume = 283 | issue = 17 | pages = 3162–69 | date = September 2016 | pmid = 27234458 | doi = 10.1111/febs.13766 | hdl = 10045/57676 | s2cid = 42827598 | hdl-access = free }}

Some bacteriophages are called "temperate" because they cause latent infections and do not immediately destroy their host cells. Instead, their DNA is incorporated with the host cell's as a prophage. These latent infections become productive when the prophage DNA is activated by stimuli such as changes in the environment. The intestines of animals, including humans, contain temperate bacteriophages, which are activated by various stimuli including changes in diet and antibiotics.{{cite journal |vauthors=Hu J, Ye H, Wang S, Wang J, Han D |title=Prophage Activation in the Intestine: Insights Into Functions and Possible Applications |journal=Frontiers in Microbiology |volume=12 |issue= |pages=785634 |date=2021 |pmid=34966370 |pmc=8710666 |doi=10.3389/fmicb.2021.785634 |doi-access=free }} Although first observed in bacteriophages, many other viruses are known to form proviruses including HIV.{{cite book |vauthors=Weiss RA |title=Viruses, Genes, and Cancer |chapter=Exchange of Genetic Sequences Between Viruses and Hosts |series=Current Topics in Microbiology and Immunology |volume=407 |pages=1–29 |date=2017 |pmid=28550453 |doi=10.1007/82_2017_21|isbn=978-3-319-61803-6 }}{{cite journal |vauthors=Russ E, Iordanskiy S |title=Endogenous Retroviruses as Modulators of Innate Immunity |journal=Pathogens |volume=12 |issue=2 |date=January 2023 |page=162 |pmid=36839434 |pmc=9963469 |doi=10.3390/pathogens12020162 |doi-access=free }}

{{Main|Archaeal virus}}

Some viruses replicate within archaea: these are DNA viruses with unusual and sometimes unique shapes.{{cite journal | vauthors = Lawrence CM, Menon S, Eilers BJ, Bothner B, Khayat R, Douglas T, Young MJ | title = Structural and functional studies of archaeal viruses | journal = The Journal of Biological Chemistry | volume = 284 | issue = 19 | pages = 12599–603 | date = May 2009 | pmid = 19158076 | pmc = 2675988 | doi = 10.1074/jbc.R800078200 | doi-access = free }} These viruses have been studied in most detail in the thermophilic archaea, particularly the orders Sulfolobales and Thermoproteales.{{cite journal | vauthors = Prangishvili D, Garrett RA | title = Exceptionally diverse morphotypes and genomes of crenarchaeal hyperthermophilic viruses | journal = Biochemical Society Transactions | volume = 32 | issue = Pt 2 | pages = 204–08 | date = April 2004 | pmid = 15046572 | doi = 10.1042/BST0320204 | s2cid = 20018642 | url = https://curis.ku.dk/ws/files/51497971/0320204.pdf }} Defences against these viruses involve RNA interference from repetitive DNA sequences within archaean genomes that are related to the genes of the viruses.{{cite journal | vauthors = Mojica FJ, Díez-Villaseñor C, García-Martínez J, Soria E | title = Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements | journal = Journal of Molecular Evolution | volume = 60 | issue = 2 | pages = 174–82 | date = February 2005 | pmid = 15791728 | doi = 10.1007/s00239-004-0046-3 | bibcode = 2005JMolE..60..174M | s2cid = 27481111 }}{{cite journal | vauthors = Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV | title = A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action | journal = Biology Direct | volume = 1 | page = 7 | date = March 2006 | pmid = 16545108 | pmc = 1462988 | doi = 10.1186/1745-6150-1-7 | doi-access = free }} Most archaea have CRISPR–Cas systems as an adaptive defence against viruses. These enable archaea to retain sections of viral DNA, which are then used to target and eliminate subsequent infections by the virus using a process similar to RNA interference.{{cite journal | vauthors = van der Oost J, Westra ER, Jackson RN, Wiedenheft B | title = Unravelling the structural and mechanistic basis of CRISPR-Cas systems | journal = Nature Reviews. Microbiology | volume = 12 | issue = 7 | pages = 479–92 | date = July 2014 | pmid = 24909109 | pmc = 4225775 | doi = 10.1038/nrmicro3279 }}

{{Main|Marine virus}}

Viruses are the most abundant biological entity in aquatic environments. There are about ten million of them in a teaspoon of seawater.{{cite journal | vauthors = Dávila-Ramos S, Castelán-Sánchez HG, Martínez-Ávila L, Sánchez-Carbente MD, Peralta R, Hernández-Mendoza A, Dobson AD, Gonzalez RA, Pastor N, Batista-García RA | title = A Review on Viral Metagenomics in Extreme Environments | journal = Frontiers in Microbiology | volume = 10 | page = 2403 | date = 2019 | pmid = 31749771 | pmc = 6842933 | doi = 10.3389/fmicb.2019.02403 | doi-access = free }} Most of these viruses are bacteriophages infecting heterotrophic bacteria and cyanophages infecting cyanobacteria and they are essential to the regulation of saltwater and freshwater ecosystems.{{cite journal |vauthors=Zhang QY, Gui JF |s2cid=53564176 |title=Diversity, evolutionary contribution and ecological roles of aquatic viruses |journal=Science China Life Sciences |volume=61 |issue=12 |pages=1486–1502 |date=December 2018 |pmid=30443861 |doi=10.1007/s11427-018-9414-7 }}

Bacteriophages are harmless to plants and animals, and are essential to the regulation of marine and freshwater ecosystems{{cite journal | vauthors = Weitz JS, Wilhelm SW |title=An ocean of viruses |journal=The Scientist |volume=27 |issue=7 |pages=35–39 |year=2013 |url=https://www.the-scientist.com/?articles.view/articleNo/36120/title/An-Ocean-of-Viruses/ }} are important mortality agents of phytoplankton, the base of the foodchain in aquatic environments.{{cite journal | vauthors = Suttle CA | title = Viruses in the sea | journal = Nature | volume = 437 | issue = 7057 | pages = 356–61 | date = September 2005 | pmid = 16163346 | doi = 10.1038/nature04160 | bibcode = 2005Natur.437..356S | s2cid = 4370363 }} They infect and destroy bacteria in aquatic microbial communities, and are one of the most important mechanisms of recycling carbon and nutrient cycling in marine environments. The organic molecules released from the dead bacterial cells stimulate fresh bacterial and algal growth, in a process known as the viral shunt.{{cite journal | vauthors = Wilhelm SW, Suttle CA |title=Viruses and nutrient cycles in the sea: viruses play critical roles in the structure and function of aquatic food webs |journal=BioScience |volume=49 |issue=10 |pages=781–88 |year=1999 |doi=10.2307/1313569|jstor=1313569 |doi-access=free }} In particular, lysis of bacteria by viruses has been shown to enhance nitrogen cycling and stimulate phytoplankton growth.{{cite journal | vauthors = Shelford EJ, Suttle CA |title=Virus-mediated transfer of nitrogen from heterotrophic bacteria to phytoplankton |journal=Biogeosciences |volume=15 |issue=3 |pages=809–15 |year=2018 |url=https://www.biogeosciences.net/15/809/2018/bg-15-809-2018.html |doi=10.5194/bg-15-809-2018|bibcode=2018BGeo...15..809S |doi-access=free }} Viral activity may also affect the biological pump, the process whereby carbon is sequestered in the deep ocean.{{cite journal | vauthors = Suttle CA | title = Marine viruses – major players in the global ecosystem | journal = Nature Reviews. Microbiology | volume = 5 | issue = 10 | pages = 801–12 | date = October 2007 | pmid = 17853907 | doi = 10.1038/nrmicro1750 | s2cid = 4658457 }}

Microorganisms constitute more than 90% of the biomass in the sea. It is estimated that viruses kill approximately 20% of this biomass each day and that there are 10 to 15 times as many viruses in the oceans as there are bacteria and archaea.{{cite journal | vauthors = Wigington CH, Sonderegger D, Brussaard CP, Buchan A, Finke JF, Fuhrman JA, Lennon JT, Middelboe M, Suttle CA, Stock C, Wilson WH, Wommack KE, Wilhelm SW, Weitz JS | s2cid = 52829633 | title = Re-examination of the relationship between marine virus and microbial cell abundances | journal = Nature Microbiology | volume = 1 | issue = 15024 | page = 15024 | date = January 2016 | pmid = 27572161 | doi = 10.1038/nmicrobiol.2015.24 | url = http://www.vliz.be/imisdocs/publications/23/301523.pdf }} Viruses are also major agents responsible for the destruction of phytoplankton including harmful algal blooms,{{cite journal | vauthors = Brussaard CP | title = Viral control of phytoplankton populations – a review | journal = The Journal of Eukaryotic Microbiology | volume = 51 | issue = 2 | pages = 125–38 | year = 2004 | pmid = 15134247 | doi = 10.1111/j.1550-7408.2004.tb00537.x | s2cid = 21017882 }}

The number of viruses in the oceans decreases further offshore and deeper into the water, where there are fewer host organisms.

In January 2018, scientists reported that 800 million viruses, mainly of marine origin, are deposited daily from the Earth{{'s}} atmosphere onto every square meter of the planet's surface, as the result of a global atmospheric stream of viruses, circulating above the weather system but below the altitude of usual airline travel, distributing viruses around the planet.{{cite news | vauthors = Robbins J |title=Trillions Upon Trillions of Viruses Fall From the Sky Each Day |url=https://www.nytimes.com/2018/04/13/science/virosphere-evolution.html |date=13 April 2018 |work=The New York Times |access-date=14 April 2018 }}{{cite journal | vauthors = Reche I, D'Orta G, Mladenov N, Winget DM, Suttle CA | title = Deposition rates of viruses and bacteria above the atmospheric boundary layer | journal = The ISME Journal | volume = 12 | issue = 4 | pages = 1154–62 | date = April 2018 | pmid = 29379178 | pmc = 5864199 | doi = 10.1038/s41396-017-0042-4 | bibcode = 2018ISMEJ..12.1154R }}

Like any organism, marine mammals are susceptible to viral infections. In 1988 and 2002, thousands of harbour seals were killed in Europe by phocine distemper virus.{{cite journal | vauthors = Hall AJ, Jepson PD, Goodman SJ, Harkonen T | year = 2006 | title = Phocine distemper virus in the North and European Seas – data and models, nature and nurture | journal = Biological Conservation | volume = 131 | issue = 2| pages = 221–29 | doi=10.1016/j.biocon.2006.04.008| bibcode = 2006BCons.131..221H }} Many other viruses, including caliciviruses, herpesviruses, adenoviruses and parvoviruses, circulate in marine mammal populations.

In December 2022, scientists reported the first observation of virovory via an experiment on pond water containing chlorovirus, which commonly infects green algae in freshwater environments. When all other microbial food sources were removed from the water, the ciliate Halteria was observed to have increased in number due to the active consumption of chlorovirus as a food source instead of its typical bacterivore diet.{{cite journal | vauthors = DeLong JP, Van Etten JL, Al-Ameeli Z, Agarkova IV, Dunigan DD | title = The consumption of viruses returns energy to food chains | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 120 | issue = 1 | pages = e2215000120 | date = January 2023 | pmid = 36574690 | pmc = 9910503 | doi = 10.1073/pnas.2215000120 | doi-access = free | s2cid = 255219850 | bibcode = 2023PNAS..12015000D }}{{cite news | vauthors = Irving M |title=First "virovore" discovered: An organism that eats viruses |url=https://newatlas.com/science/first-virovore-eats-viruses/ |access-date=29 December 2022 |publisher=New Atlas |date=28 December 2022 |archive-url=https://web.archive.org/web/20221229023549/https://newatlas.com/science/first-virovore-eats-viruses/ |archive-date=29 December 2022}}

{{Main|Horizontal gene transfer}}

Viruses are an important natural means of transferring genes between different species, which increases genetic diversity and drives evolution.{{cite journal | vauthors = Canchaya C, Fournous G, Chibani-Chennoufi S, Dillmann ML, Brüssow H | title = Phage as agents of lateral gene transfer | journal = Current Opinion in Microbiology | volume = 6 | issue = 4 | pages = 417–24 | date = August 2003 | pmid = 12941415 | doi = 10.1016/S1369-5274(03)00086-9 }}{{cite journal |vauthors=Broecker F, Moelling K |title=What viruses tell us about evolution and immunity: beyond Darwin? |journal=Annals of the New York Academy of Sciences |volume=1447 |issue=1 |pages=53–68 |date=2019 |pmid=31032941 |pmc=6850104 |doi=10.1111/nyas.14097 |bibcode=2019NYASA1447...53B |doi-access=free}}Lauer, A. (2021). Viruses, Underestimated Drivers of Ecology and Evolution of Life. In: Hurst, C.J. (eds) Microbes: The Foundation Stone of the Biosphere. Advances in Environmental Microbiology, vol 8. Springer, Cham. https://doi.org/10.1007/978-3-030-63512-1_28 It is thought that viruses played a central role in early evolution, before the diversification of the last universal common ancestor into bacteria, archaea and eukaryotes.{{cite journal | vauthors = Forterre P, Philippe H | title = The last universal common ancestor (LUCA), simple or complex? | journal = The Biological Bulletin | volume = 196 | issue = 3 | pages = 373–75; discussion 375–77 | date = June 1999 | pmid = 11536914 | doi = 10.2307/1542973 | jstor = 1542973 }} Viruses are still one of the largest reservoirs of unexplored genetic diversity on Earth.

File:Influenza virus research.jpg influenza virus]]

Viruses are important to the study of molecular and cell biology as they provide simple systems that can be used to manipulate and investigate the functions of cells.{{rp|8}} The study and use of viruses have provided valuable information about aspects of cell biology.{{cite book | vauthors = Lodish H, Berk A, Zipursky SL, Matsudaira P, Baltimore D, Darnell J | chapter-url = https://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=Viruses&rid=mcb.section.1408#1422 | chapter = Viruses: Structure, Function, and Uses | title = Molecular Cell Biology | edition = 4th | location = New York | publisher = W. H. Freeman | date = 2000 }} For example, viruses have been useful in the study of genetics and helped our understanding of the basic mechanisms of molecular genetics, such as DNA replication, transcription, RNA processing, translation, protein transport, and immunology.

Geneticists often use viruses as 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. Similarly, 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. Eastern European scientists have used phage therapy as an alternative to antibiotics for some time, and interest in this approach is increasing, because of the high level of antibiotic resistance now found in some pathogenic bacteria.{{cite journal | vauthors = Matsuzaki S, Rashel M, Uchiyama J, Sakurai S, Ujihara T, Kuroda M, Ikeuchi M, Tani T, Fujieda M, Wakiguchi H, Imai S | title = Bacteriophage therapy: a revitalized therapy against bacterial infectious diseases | journal = Journal of Infection and Chemotherapy | volume = 11 | issue = 5 | pages = 211–19 | date = October 2005 | pmid = 16258815 | doi = 10.1007/s10156-005-0408-9 | s2cid = 8107934 }}

The expression of heterologous proteins by viruses is the basis of several manufacturing processes that are currently being used for the production of various proteins such as vaccine antigens and antibodies. Industrial processes have been recently developed using viral vectors and several pharmaceutical proteins are currently in pre-clinical and clinical trials.{{cite book| vauthors = Gleba YY, Giritch A |chapter = Plant Viral Vectors for Protein Expression|year=2011|title=Recent Advances in Plant Virology|publisher=Caister Academic Press|isbn= 978-1-904455-75-2}}

{{main|Virotherapy}}

Virotherapy involves the use of genetically modified viruses to treat diseases.{{cite journal | vauthors = Jefferson A, Cadet VE, Hielscher A | title = The mechanisms of genetically modified vaccinia viruses for the treatment of cancer | journal = Critical Reviews in Oncology/Hematology | volume = 95 | issue = 3 | pages = 407–16 | date = September 2015 | pmid = 25900073 | doi = 10.1016/j.critrevonc.2015.04.001 }} Viruses have been modified by scientists to reproduce in cancer cells and destroy them but not infect healthy cells. Talimogene laherparepvec (T-VEC), for example, is a modified herpes simplex virus that has had a gene, which is required for viruses to replicate in healthy cells, deleted and replaced with a human gene (GM-CSF) that stimulates immunity. When this virus infects cancer cells, it destroys them and in doing so the presence the GM-CSF gene attracts dendritic cells from the surrounding tissues of the body. The dendritic cells process the dead cancer cells and present components of them to other cells of the immune system.{{cite journal | vauthors = Karimkhani C, Gonzalez R, Dellavalle RP | s2cid = 38864550 | title = A review of novel therapies for melanoma | journal = American Journal of Clinical Dermatology | volume = 15 | issue = 4 | pages = 323–37 | date = August 2014 | pmid = 24928310 | doi = 10.1007/s40257-014-0083-7 }} Having completed successful clinical trials, the virus gained approval for the treatment of melanoma in late 2015.{{cite news|url=https://www.reuters.com/article/us-amgen-fda-idUSKCN0SL2YH20151027|title=FDA approves Amgen's injected immunotherapy for melanoma|date=27 October 2015|work=Reuters|access-date=24 January 2020|language=en}} Viruses that have been reprogrammed to kill cancer cells are called oncolytic viruses.{{cite journal | vauthors = Burke J, Nieva J, Borad MJ, Breitbach CJ | title = Oncolytic viruses: perspectives on clinical development | journal = Current Opinion in Virology | volume = 13 | pages = 55–60 | date = August 2015 | pmid = 25989094 | doi = 10.1016/j.coviro.2015.03.020 }}

From the viewpoint of a materials scientist, viruses can be regarded as organic nanoparticles.{{cite journal | vauthors = Dogic Z | title = Filamentous Phages As a Model System in Soft Matter Physics | journal = Frontiers in Microbiology | volume = 7 | page = 1013 | date = 2016 | pmid = 27446051 | pmc = 4927585 | doi = 10.3389/fmicb.2016.01013 | doi-access = free }} Their surface carries specific tools that enable them 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 are 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.{{cite journal | vauthors = Fischlechner M, Donath E | title = Viruses as building blocks for materials and devices | journal = Angewandte Chemie | volume = 46 | issue = 18 | pages = 3184–93 | year = 2007 | pmid = 17348058 | doi = 10.1002/anie.200603445 }} Because of their size, shape, and well-defined chemical structures, viruses have been used as templates for organising materials on the nanoscale. Examples include the work at the Naval Research Laboratory in Washington, D.C., using Cowpea mosaic virus (CPMV) particles to amplify signals in DNA microarray based sensors. In this application, the virus particles separate the fluorescent dyes used for signalling to prevent the formation of non-fluorescent dimers that act as quenchers.{{cite journal | vauthors = Soto CM, Blum AS, Vora GJ, Lebedev N, Meador CE, Won AP, Chatterji A, Johnson JE, Ratna BR | title = Fluorescent signal amplification of carbocyanine dyes using engineered viral nanoparticles | journal = Journal of the American Chemical Society | volume = 128 | issue = 15 | pages = 5184–89 | date = April 2006 | pmid = 16608355 | doi = 10.1021/ja058574x | bibcode = 2006JAChS.128.5184S | url = https://figshare.com/articles/journal_contribution/3226522 }} Another example is the use of CPMV as a nanoscale breadboard for molecular electronics.{{cite journal | vauthors = Blum AS, Soto CM, Wilson CD, Brower TL, Pollack SK, Schull TL, Chatterji A, Lin T, Johnson JE, Amsinck C, Franzon P, Shashidhar R, Ratna BR | title = An engineered virus as a scaffold for three-dimensional self-assembly on the nanoscale | journal = Small | volume = 1 | issue = 7 | pages = 702–06 | date = July 2005 | pmid = 17193509 | doi = 10.1002/smll.200500021 }}

Many viruses can be synthesised de novo ("from scratch"). The first synthetic virus was created in 2002.{{cite journal | vauthors = Cello J, Paul AV, Wimmer E | s2cid = 5810309 | title = Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template | journal = Science | volume = 297 | issue = 5583 | pages = 1016–18 | date = August 2002 | pmid = 12114528 | doi = 10.1126/science.1072266 | bibcode = 2002Sci...297.1016C | doi-access = free }} Although somewhat of a misconception, it is not the actual virus that is synthesised, but rather its DNA genome (in case of a DNA virus), or a cDNA copy of its genome (in case of RNA viruses). For many virus families the naked synthetic DNA or RNA (once enzymatically converted back from the synthetic cDNA) is infectious when introduced into a cell. That is, they contain all the necessary information to produce new viruses. This technology is now being used to investigate novel vaccine strategies.{{cite journal | vauthors = Coleman JR, Papamichail D, Skiena S, Futcher B, Wimmer E, Mueller S | title = Virus attenuation by genome-scale changes in codon pair bias | journal = Science | volume = 320 | issue = 5884 | pages = 1784–87 | date = June 2008 | pmid = 18583614 | pmc = 2754401 | doi = 10.1126/science.1155761 | bibcode = 2008Sci...320.1784C }} The ability to synthesise viruses has far-reaching consequences, since viruses can no longer be regarded as extinct, as long as the information of their genome sequence is known and permissive cells are available. As of June 2021, the full-length genome sequences of 11,464 different viruses, including smallpox, are publicly available in an online database maintained by the National Institutes of Health.{{cite web |url=https://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?taxid=10239 |title=NIH viral genome database |publisher=Ncbi.nlm.nih.gov |access-date=28 June 2021}}

{{Further|Biological warfare}}

The ability of viruses to cause devastating epidemics in human societies has led to the concern that viruses could be weaponised for biological warfare. Further concern was raised by the successful recreation of the infamous 1918 influenza virus in a laboratory.{{cite journal |vauthors=Zilinskas RA |title=A brief history of biological weapons programmes and the use of animal pathogens as biological warfare agents |journal=Revue Scientifique et Technique (International Office of Epizootics) |volume=36 |issue=2 |pages=415–22 |date=August 2017 |pmid=30152475 |doi=10.20506/rst.36.2.2662 }}

The smallpox virus devastated numerous societies throughout history before its eradication. There are only two centres in the world authorised by the WHO to keep stocks of smallpox virus: the State Research Center of Virology and Biotechnology VECTOR in Russia and the Centers for Disease Control and Prevention in the United States.{{cite journal | vauthors = Artenstein AW, Grabenstein JD | s2cid = 33855724 | title = Smallpox vaccines for biodefense: need and feasibility | journal = Expert Review of Vaccines | volume = 7 | issue = 8 | pages = 1225–37 | date = October 2008 | pmid = 18844596 | doi = 10.1586/14760584.7.8.1225 | pmc = 9709930 }} It may be used as a weapon, as the vaccine for smallpox sometimes had severe side-effects, it is no longer used routinely in any country. Thus, much of the modern human population has almost no established resistance to smallpox and would be vulnerable to the virus.

{{div col|colwidth=18em}}

• Cross-species transmission
• Glossary of virology
• {{annotated link|Law of declining virulence}}
• Non-cellular life
• Gene transfer agent
• Retrozyme
• Smallest organisms
• {{annotated link|Theory of virulence}}
• Viral metagenomics
• Viroplasm
• Zoonosis

{{div col end}}

{{Reflist|refs =

{{cite book | vauthors = Collier L, Balows A, Sussman M | date = 1998 | title = Topley and Wilson's Microbiology and Microbial Infections | edition = 9th | volume = 1 | series = Virology | veditors = Mahy B, Collier LA | isbn = 0-340-66316-2 }}

{{cite book | vauthors = Dimmock NJ, Easton AJ, Leppard K | date = 2007 | title = Introduction to Modern Virology | edition = 6th | publisher = Blackwell Publishing | isbn = 978-1-4051-3645-7 }}

{{cite book | vauthors = Krasner R | title=The microbial challenge: a public health perspective | publisher=Jones & Bartlett Learning | publication-place=Burlington, Mass | year=2014 | isbn=978-1-4496-7375-8 | oclc=794228026 | page=}}

{{cite book | vauthors = Shors T | date = 2017 | title = Understanding Viruses | publisher = Jones and Bartlett Publishers | isbn = 978-1-284-02592-7}}

}}

{{Wiktionary|genogroup}}

{{Wiktionary}}

• {{Commons category-inline}}
• {{Wikispecies-inline}}
• [http://viralzone.expasy.org/ ViralZone] A Swiss Institute of Bioinformatics resource for all viral families, providing general molecular and epidemiological information

{{Virus topics}}

{{Self-replicating organic structures}}

{{Organisms et al.}}

{{portal bar|Biology|Evolutionary biology|Medicine|Science|Viruses}}

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Category:1898 in biology

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Category:Epidemiology

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Category:Infectious diseases

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Category:Zoonoses