Introduction to viruses: Difference between revisions

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{{short description|Non-technical introduction to viruses}}

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A '''virus''' is a tiny [[infectious agent]] that [[reproduction|reproduces]] inside the [[Cell (biology)|cells]] of living [[Host (biology)|hosts]]. When infected, the host cell is forced to rapidly produce thousands of identical copies of the original virus. Unlike most [[Organism|living things]], viruses do not have cells that divide; new viruses assemble in the infected host cell. But unlike simpler infectious agents like [[prion]]s, they contain [[Introduction to genetics|genes]], which allow them to [[Mutation|mutate]] and evolve. Over 4,800 [[List of virus species|species of viruses]] have been [[List of virus taxa|described in detail]]<ref name="pmid29754305">{{cite journal |vauthors=King AM, Lefkowitz EJ, Mushegian AR, Adams MJ, Dutilh BE, Gorbalenya AE, Harrach B, Harrison RL, Junglen S, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Nibert ML, Rubino L, Sabanadzovic S, Sanfaçon H, Siddell SG, Simmonds P, Varsani A, Zerbini FM, Davison AJ |s2cid=21670772 |title=Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee Taxonomy of Viruses (2018) |journal=Archives of Virology |volume=163 |issue=9 |date=September 2018 |page=2601 <!-- CITATION BOT DO NOT CHANGE THIS ... citation is specific to this page --> |pmid=29754305 |doi=10.1007/s00705-018-3847-1 |url=https://hal-pasteur.archives-ouvertes.fr/pasteur-01977332/file/King2018_Article_ChangesToTaxonomyAndTheInterna.pdf}}</ref> out of the millions in the environment. Their origin is unclear: some may have [[evolution|evolved]] from [[plasmid]]s—pieces of DNA that can move between cells—while others may have evolved from [[bacteria]].

Viruses are made of either two or three parts. All include [[gene]]s. These genes contain the encoded biological information of the virus and are built from either [[DNA]] or [[RNA]]. All viruses are also covered with a [[protein]] coat to protect the genes. Some viruses may also have an [[viral envelope|envelope]] of [[Lipid|fat-like substance]] that covers the protein coat, and makes them vulnerable to soap. A virus with this "viral envelope" uses it—along with specific [[Cell surface receptor|receptors]]—to enter a new host cell. Viruses vary in shape from the simple [[tobacco mosaic virus|helical]] and [[icosahedron|icosahedral]] to more [[bacteriophage|complex]] structures. Viruses range in size from 20 to 300 [[nanometre]]s; it would take 33,000 to 500,000 of them, sidelaid byend sideto end, to stretch to {{convert|1|cm|1}}.

Viruses spread in many ways. Although many are very specific about which host species or [[Tissue (biology)|tissue]] they attack, each [[species]] of virus relies on a particular method to copy itself. [[Plant pathology#Viruses, viroids and virus-like organisms|Plant viruses]] are often spread from plant to plant by insects and other [[organism]]s, known as ''[[Vector (epidemiology)|vectors]]''. Some [[Virus#Role in human disease|viruses of humans]] and other animals are spread by exposure to infected bodily fluids. Viruses such as [[influenza]] are spread through the air by droplets of moisture when people cough or sneeze. Viruses such as [[norovirus]] are transmitted by the [[fecal–oral route|faecal–oral route]], which involves the contamination of hands, food and water. [[Rotavirus]] is often spread by direct contact with infected children. The human immunodeficiency virus, [[HIV]], is transmitted by bodily fluids transferred during sex. Others, such as the [[dengue virus]], are spread by [[Hematophagy|blood-sucking insects]].

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In 1884, French [[microbiologist]] [[Charles Chamberland]] invented the [[Chamberland filter]] (or Chamberland–Pasteur filter), that contains pores smaller than [[bacteria]]. He could then pass a solution containing bacteria through the filter, and completely remove them. In the early 1890s, Russian [[biologist]] [[Dmitri Ivanovsky]] used this method to study what became known as the [[tobacco mosaic virus]]. His experiments showed that extracts from the crushed leaves of infected tobacco plants remain infectious after filtration.<ref>{{harvnb|Shors|2017|p=6}}</ref>

At the same time, several other scientists showed that, although these agents (later called viruses) were different from bacteria and about one hundred times smaller, they could still cause disease. In 1899, Dutch microbiologist [[Martinus Beijerinck]] observed that the agent only multiplied when in [[cell division|dividing cells]]. He called it a "contagious living fluid" ({{lang-langx|la|text= [[contagium vivum fluidum]]}})—or a "soluble living germ" because he could not find any germ-like particles.<ref>{{harvnbsfn|CollierHowley|BalowsKnipe|SussmanEnquist|19982023|p=34}}</ref> In the early 20th century, English [[bacteriologist]] [[Frederick Twort]] discovered viruses that infect bacteria,<ref>{{harvnb|Shors|2017|p=827}}</ref> and French-Canadian microbiologist [[Félix d'Herelle]] described viruses that, when added to bacteria growing on [[agar]], would lead to the formation of whole areas of dead bacteria. Counting these dead areas allowed him to calculate the number of viruses in the suspension.<ref>{{cite journal | vauthors = D'Herelle F | title = On an invisible microbe antagonistic toward dysenteric bacilli: brief note by Mr. F. D'Herelle, presented by Mr. Roux. 1917 | journal = Research in Microbiology | volume = 158 | issue = 7 | pages = 553–554 | year = 2007 | pmid = 17855060 | doi = 10.1016/j.resmic.2007.07.005 | doi-access = free }}</ref>

The invention of the [[electron microscope]] in 1931 brought the first images of viruses.<ref>From ''Nobel Lectures, Physics 1981–1990'', (1993) Editor-in-Charge Tore Frängsmyr, Editor Gösta Ekspång, World Scientific Publishing Co., Singapore</ref> In 1935, American [[biochemist]] and [[virologist]] [[Wendell Meredith Stanley]] examined the tobacco mosaic virus (TMV) and found it to be mainly made from [[protein]].<ref>{{cite journal | vauthors = Stanley WM, Loring HS | year = 1936 | title = The isolation of crystalline tobacco mosaic virus protein from diseased tomato plants | journal = Science | volume = 83 | issue = 2143| page = 85 | pmid = 17756690 | doi = 10.1126/science.83.2143.85 |bibcode = 1936Sci....83...85S }}</ref> A short time later, this virus was shown to be made from protein and [[RNA]].<ref>{{cite journal | doi = 10.1126/science.89.2311.345 | vauthors = Stanley WM, Lauffer MA | year = 1939 | title = Disintegration of tobacco mosaic virus in urea solutions |journal = Science | volume = 89 | issue = 2311| pages = 345–347 | pmid = 17788438 |bibcode = 1939Sci....89..345S }}</ref> [[Rosalind Franklin]] developed [[X-ray crystallography|X-ray crystallographic pictures]] and determined the full structure of TMV in 1955.<ref name="pmid18702397">{{cite journal | vauthors = Creager AN, Morgan GJ | title = After the double helix: Rosalind Franklin's research on Tobacco mosaic virus | journal = Isis; an International Review Devoted to the History of Science and Its Cultural Influences | volume = 99 | issue = 2 | pages = 239–272 | date = June 2008 | pmid = 18702397 | doi = 10.1086/588626 | s2cid = 25741967 }}</ref> Franklin confirmed that viral proteins formed a spiral hollow tube, wrapped by RNA, and also showed that viral RNA was a single strand, not a double helix like DNA.<ref name="Johnson">{{cite journal |last1=Johnson |first1=Ben |title=Rosalind Franklin's contributions to virology |journal=Nature Portfolio Microbiology Community |date=25 July 2017 |url=https://microbiologycommunity.nature.com/posts/18900-rosalind-franklin-s-contributions-to-virology |access-date=7 January 2022 |language=en}}</ref>

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== Origins ==

{{Further|Virus#Origins}}

Viruses co-exist with life wherever it occurs. They have probably existed since living cells first evolved. Their origin remains unclear because they do not [[fossil]]ize, so [[Molecular biology|molecular techniques]] have been the best way to [[hypothesis]]e about how they arose. These techniques rely on the availability of ancient viral DNA or RNA, but most viruses that have been preserved and stored in laboratories are less than 90 years old.<ref>{{harvnb|Shors|2017|p=16}}</ref><ref>{{harvnb|Collier|Balows|Sussman|1998|pp=18–19}}</ref> Molecular methods have only been successful in tracing the ancestry of viruses that evolved in the 20th century.<ref name="pmid15476878">{{cite journal | vauthors = Liu Y, Nickle DC, Shriner D, Jensen MA, Learn GH, Mittler JE, Mullins JI | title = Molecular clock-like evolution of human immunodeficiency virus type 1 | journal = Virology | volume = 329 | issue = 1 | pages = 101–108 | date = November 2004 | pmid = 15476878 | doi = 10.1016/j.virol.2004.08.014| doi-access = free }}</ref> New groups of viruses might have repeatedly emerged at all stages of the evolution of life.<ref name=NRM_Krupovic2019>{{cite journal |vauthors= Krupovic M, Dooja W, Koonin EV |s2cid=169035711 |title=Origin of viruses: primordial replicators recruiting capsids from hosts. |journal=Nature Reviews Microbiology |volume=17 |issue=7 |pages=449–458 |date=2019 |doi=10.1038/s41579-019-0205-6 |pmid=31142823|url=https://hal-pasteur.archives-ouvertes.fr/pasteur-02557191/file/Krupovic_NRMICRO-19-022_MS_v3_clean.pdf }}</ref> There are three major [[Scientific theory|theories]] about the origins of viruses:<ref name=NRM_Krupovic2019 /><ref>{{harvnb|Collier|Balows|Sussman|1998|pp=11–21}}</ref>

; Regressive theory : Viruses may have once been small cells that [[parasitism|parasitised]] larger cells. Eventually, the genes they no longer needed for a parasitic way of life were lost. The bacteria ''[[Rickettsia]]'' and ''[[Chlamydia (bacterium)|Chlamydia]]'' are living cells that, like viruses, can reproduce only inside host cells. This lends credence to this theory, as their dependence on being parasites may have led to the loss of the genes that once allowed them to live on their own.<ref>{{harvnb|Collier|Balows|Sussman|1998|p=11}}</ref>

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[[File:Basic Scheme of Virus en.svg|thumb|Simplified diagram of the structure of a virus]]

A virus particle, also called a [[virion]], consists of genes made from DNA or RNA which are surrounded by a protective coat of protein called a [[capsid]].<ref name{{sfn|Howley|Knipe|Enquist|2023|pp="Topley50-and-Wilson33-55">52}}{{harvnb|Collier|Balows|Sussman|1998|pp=33–55}}</ref> The capsid is made of many smaller, identical protein molecules called [[capsomer]]s. The arrangement of the capsomers can either be [[truncated icosahedron|icosahedral]] (20-sidedfaced), [[helix|helical]], or more complex. There is an inner shell around the DNA or RNA called the [[nucleocapsid]], made out of proteins. Some viruses are surrounded by a bubble of [[lipid]] (fat) called an [[viral envelope|envelope]], which makes them vulnerable to soap and alcohol.<ref name="pmid11759024">{{cite journal |vauthors=Rotter ML |title=Arguments for alcoholic hand disinfection |journal=The Journal of Hospital Infection |volume=48 |issue=Suppl A |pages=S4–S8 |date=August 2001 |pmid=11759024 |doi=10.1016/s0195-6701(01)90004-0 }}</ref>

=== Size ===

[[File:Virus size.png|right|thumb|Virions of some of the most common human viruses with their relative size. The nucleic acids are not to scale.]]

Viruses are among the smallest infectious agents, and are too small to be seen by [[Optical microscope|light microscopy]]; most of them can only be seen by [[electron microscopy]]. Their sizes range from 20 to 300&nbsp;[[nanometre]]s; it would take 30,000&nbsp;to 500,000 of them, sidelaid byend sideto end, to stretch to one centimetre (0.4&nbsp;in).<ref name="Topley-and-Wilson33-55" >{{harvnb|Collier|Balows|Sussman|1998|pp=33–55}}</ref> In comparison, bacteria are typically around 1000&nbsp;nanometres (1&nbsp;[[micrometre|micrometer]]) in diameter, and host cells of higher organisms are typically a few tens of [[Micrometre|micrometer]]smicrometers. Some viruses, such as [[megavirus]]es and [[pandoravirus]]es, are relatively large viruses. At around 1000&nbsp;nanometres, these viruses, which infect [[amoeba]]e, were discovered in 2003 and 2013.<ref>{{cite journal |vauthors=Abergel C, Legendre M, Claverie JM |title=The rapidly expanding universe of giant viruses: Mimivirus, Pandoravirus, Pithovirus and Mollivirus |journal=FEMS Microbiol. Rev. |volume=39 |issue=6 |pages=779–796 |date=November 2015 |pmid=26391910 |doi=10.1093/femsre/fuv037 |doi-access=free }}</ref><ref>{{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=281–286 |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 }}</ref> They are around ten times wider (and thus a thousand times larger in volume) than [[influenza virus]]es, and the discovery of these "giant" viruses astonished scientists.<ref name="Zimmer">{{cite news | url=https://www.nytimes.com/2013/07/18/science/changing-view-on-viruses-not-so-small-after-all.html | title=Changing View on Viruses: Not So Small After All | work=The New York Times | date=18 July 2013 | access-date=20 December 2014 | vauthors = Zimmer C}}</ref>

=== Genes ===

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== Effects on the host cell ==

Viruses have an extensive range of structural and biochemical effects on the host cell.{{sfn | Oxford |Kellam|Collier| 2016 | p=34–36}} These are called ''[[cytopathic effect]]s''.{{sfn | Oxford |Kellam|Collier| 2016 | p=34}} Most virus infections eventually result in the death of the host cell. The causes of death include cell lysis (bursting), alterations to the cell's surface membrane and [[apoptosis]] (cell "suicide").<ref name="pmid28846635">{{cite journal |vauthors=Okamoto T, Suzuki T, Kusakabe S, Tokunaga M, Hirano J, Miyata Y, Matsuura Y |title=Regulation of Apoptosis during Flavivirus Infection |journal=Viruses |volume=9 |issue=9 |pages= 243|year= 2017 |pmid=28846635 |pmc=5618009 |doi=10.3390/v9090243|doi-access=free }}</ref> Often cell death is caused by cessation of its normal activity due to proteins produced by the virus, not all of which are components of the virus particle.<ref name="pmid18637511">{{cite book | vauthors = Alwine JC | title = Human Cytomegalovirus | chapter = Modulation of hostHost cellCell stressStress responsesResponses by humanHuman cytomegalovirusCytomegalovirus |series=Current journalTopics =in Curr.Microbiology Top.and Microbiol. Immunol.Immunology | volume = 325 | pages = 263–279263–79 | date = 2008 | pmid = 18637511 | doi = 10.1007/978-3-540-77349-8_15 | series = Current Topics in Microbiology and Immunology | isbn = 978-3-540-77348-1 }}</ref>

Some viruses cause no apparent changes to the infected cell. Cells in which the virus is [[virus latency|latent]] (inactive) show few signs of infection and often function normally.<ref name="pmid18164651">{{cite journal | vauthors = Sinclair J | title = Human cytomegalovirus: Latency and reactivation in the myeloid lineage | journal = J. Clin. Virol. | volume = 41 | issue = 3 | pages = 180–185 | date = March 2008 | pmid = 18164651 | doi = 10.1016/j.jcv.2007.11.014 }}</ref> This causes persistent infections and the virus is often dormant for many months or years. This is often the case with [[herpes simplex|herpes viruses]].<ref name="pmid6326635">{{cite journal | vauthors = Jordan MC, Jordan GW, Stevens JG, Miller G | title = Latent herpesviruses of humans | journal = Ann. Intern. Med. | volume = 100 | issue = 6 | pages = 866–880 | date = June 1984 | pmid = 6326635 | doi = 10.7326/0003-4819-100-6-866 }}</ref><ref name="pmid12076064">{{cite journal | vauthors = Sissons JG, Bain M, Wills MR | s2cid = 24879226 | title = Latency and reactivation of human cytomegalovirus | journal = J. Infect. | volume = 44 | issue = 2 | pages = 73–77 | date = February 2002 | pmid = 12076064 | doi = 10.1053/jinf.2001.0948}}</ref>

Some viruses, such as [[Epstein–Barr virus]], often cause cells to proliferate without causing [[malignancy]];<ref name="pmid18035323">{{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 = Autoimmun Rev | volume = 7 | issue = 2 | pages = 132–136 | date = December 2007 | pmid = 18035323 | doi = 10.1016/j.autrev.2007.02.018 | hdl = 11380/598275 | hdl-access = free }}</ref> but some other viruses, such as [[papillomavirus]], are an established cause of cancer.<ref name="pmid28798073">{{cite journal |vauthors=Graham SV |title=The human papillomavirus replication cycle, and its links to cancer progression: a comprehensive review |journal=Clinical Science |volume=131 |issue=17 |pages=2201–2221 |year= 2017 |pmid=28798073 |doi=10.1042/CS20160786 |doi-access=free }}</ref> When a cell's DNA is damaged by a virus such that the cell cannot repair itself, this often triggers apoptosis. One of the results of apoptosis is destruction of the damaged DNA by the cell itself. Some viruses have mechanisms to limit apoptosis so that the host cell does not die before progeny viruses have been produced; [[HIV]], for example, does this.<ref name="pmid10547702">{{cite journal | vauthors = Roulston A, Marcellus RC, Branton PE | title = Viruses and apoptosis | journal = Annu. Rev. Microbiol. | volume = 53 | pages = 577–628 | date = 1999 | pmid = 10547702 | doi = 10.1146/annurev.micro.53.1.577 }}</ref>

== Viruses and diseases ==

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{{for|more examples of diseases caused by viruses|List of infectious diseases}}

Common human diseases caused by viruses include the [[common cold]], [[influenza]], [[chickenpox]] and [[cold sores]]. Serious diseases such as [[Ebola]] and [[AIDS]] are also caused by viruses.<ref>{{harvnb|Shors|2017|p=271}}</ref> Many viruses cause little or no disease and are said to be "benign". The more harmful viruses are described as [[virulence|virulent]].<ref>{{cite journal|vauthors =Berngruber TW, Froissart R, Choisy M, Gandon S|year= 2013|title = Evolution of Virulence in Emerging Epidemics|journal = PLOS Pathogens|volume= 9 |issue= 3|pages= e1003209|doi= 10.1371/journal.ppat.1003209|pmid= 23516359|pmc= 3597519|doi-access= free}}</ref>

Viruses cause different diseases depending on the types of cell that they infect.

Some viruses can cause lifelong or [[Chronic (medical)|chronic]] infections where the viruses continue to reproduce in the body despite the host's defence mechanisms.<ref>{{harvnb|Shors|2017|p=464}}</ref> This is common in hepatitis B virus and hepatitis C virus infections. People chronically infected with a virus are known as carriers. They serve as important reservoirs of the virus.<ref name="pmid31364248">{{cite journal |vauthors=Tanaka J, Akita T, Ko K, Miura Y, Satake M |title=Countermeasures against viral hepatitis B and C in Japan: An epidemiological point of view |journal=Hepatology Research |volume=49 |issue=9 |pages=990–1002 |date=September 2019 |pmid=31364248 |pmc=6852166 |doi=10.1111/hepr.13417 }}</ref><ref name="pmid32173241">{{cite journal |vauthors=Lai CC, Liu YH, Wang CY, Wang YH, Hsueh SC, Yen MY, Ko WC, Hsueh PR |title=Asymptomatic carrier state, acute respiratory disease, and pneumonia due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): Facts and myths |journal=Journal of Microbiology, Immunology, and Infection = Wei Mian Yu Gan Ran Za Zhi |volume= 53|issue= 3|pages= 404–412|date=March 2020 |pmid=32173241 |doi=10.1016/j.jmii.2020.02.012 |pmc=7128959 }}</ref>

==== Endemic ====

If the proportion of carriers in a given population reaches a given threshold, a disease is said to be [[Endemic (epidemiology)|endemic]].{{sfn | Oxford |Kellam|Collier| 2016 | p=63}} Before the advent of vaccination, infections with viruses were common and outbreaks occurred regularly. In countries with a temperate climate, viral diseases are usually seasonal. [[Poliomyelitis]], caused by [[poliovirus]] often occurred in the summer months.<ref name="pmid29961515">{{cite journal |vauthors=Strand LK |title=The Terrible Summer of 1952 … When Polio Struck Our Family |journal=Seminars in Pediatric Neurology |volume=26 |pages=39–44 |date=July 2018 |pmid=29961515 |doi=10.1016/j.spen.2017.04.001 |s2cid=49640682 }}</ref> By contrast colds, influenza and rotavirus infections are usually a problem during the winter months.<ref name="pmid22958213">{{cite journal |vauthors=Moorthy M, Castronovo D, Abraham A, Bhattacharyya S, Gradus S, Gorski J, Naumov YN, Fefferman NH, Naumova EN |title=Deviations in influenza seasonality: odd coincidence or obscure consequence? |journal=Clinical Microbiology and Infection |volume=18 |issue=10 |pages=955–962 |date=October 2012 |pmid=22958213 |pmc=3442949 |doi=10.1111/j.1469-0691.2012.03959.x }}</ref><ref name="pmid25777068">{{cite journal |vauthors=Barril PA, Fumian TM, Prez VE, Gil PI, Martínez LC, Giordano MO, Masachessi G, Isa MB, Ferreyra LJ, Ré VE, Miagostovich M, Pavan JV, Nates SV |title=Rotavirus seasonality in urban sewage from Argentina: effect of meteorological variables on the viral load and the genetic diversity |journal=Environmental Research |volume=138 |pages=409–415 |date=April 2015 |pmid=25777068 |doi=10.1016/j.envres.2015.03.004 |bibcode=2015ER....138..409B |hdl=11336/61497 |hdl-access=free }}</ref> Other viruses, such as [[measles virus]], caused outbreaks regularly every third year.<ref name="pmid25444814">{{cite journal |vauthors=Durrheim DN, Crowcroft NS, Strebel PM |title=Measles – The epidemiology of elimination |journal=Vaccine |volume=32 |issue=51 |pages=6880–6883 |date=December 2014 |pmid=25444814 |doi=10.1016/j.vaccine.2014.10.061 |doi-access=free |hdl=1959.13/1299149 |hdl-access=free }}</ref> In developing countries, viruses that cause respiratory and enteric infections are common throughout the year. Viruses carried by insects are a common cause of diseases in these settings. [[Zika]] and [[dengue virus]]es for example are transmitted by the female [[Aedes]] mosquitoes, which bite humans particularly during the mosquitoes' breeding season.<ref name="pmid32103776">{{cite journal |vauthors=Mbanzulu KM, Mboera LE, Luzolo FK, Wumba R, Misinzo G, Kimera SI |title=Mosquito-borne viral diseases in the Democratic Republic of the Congo: a review |journal=Parasites & Vectors |volume=13 |issue=1 |pagesarticle-number=103 |date=February 2020 |pmid=32103776 |pmc=7045448 |doi=10.1186/s13071-020-3985-7 |doi-access=free }}</ref>

==== Pandemic and emergent ====

[[File:SIV primates.jpg|right|400px|thumb|Left to right: the [[African green monkey]], source of [[Simian immunodeficiency virus|SIV]]; the [[sooty mangabey]], source of [[HIV-2]]; and the [[Common chimpanzee|chimpanzee]], source of [[HIV-1]]]]

[[File:Orgin and evolution of SARS.jpg|thumb|Origin and evolution of (A) SARS-CoV, (B) MERS-CoV, and (C) SARS-CoV-2 in different hosts. All the viruses came from bats as coronavirus-related viruses before mutating and adapting to intermediate hosts and then to humans and causing the diseases [[SARS]], [[MERS]] and [[COVID-19]]. (<small>Adapted from Ashour et al. (2020)</small> <ref name="pmid32143502">{{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 (Basel, Switzerland) |volume=9 |issue=3 |pages= 186|date=March 2020 |pmid=32143502 |doi=10.3390/pathogens9030186 |pmc=7157630 |doi-access=free }}</ref>)]]

Although viral [[pandemic]]s are rare events, HIV—which evolved from viruses found in monkeys and chimpanzees—has been pandemic since at least the 1980s.<ref name="pmid29460740">{{cite journal |vauthors=Eisinger RW, Fauci AS |title=Ending the HIV/AIDS Pandemic1 |journal=Emerging Infectious Diseases |volume=24 |issue=3 |pages=413–416 |date=March 2018 |pmid=29460740 |pmc=5823353 |doi=10.3201/eid2403.171797 }}</ref> During the 20th century there were four pandemics caused by influenza virus and those that occurred in [[Spanish flu|1918]], [[1957–1958 influenza pandemic|1957]] and [[Hong Kong flu|1968]] were severe.<ref name="pmid30180422">{{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=1028–1031 |date=August 2018 |pmid=30180422 |doi=10.3760/cma.j.issn.0254-6450.2018.08.003 |doi-broken-date=1 July 2025 |pmid=30180422 }}</ref> Before its eradication, smallpox was a cause of pandemics for more than 3,000 years.<ref name="pmid26060873">{{cite journal |vauthors=Nishiyama Y, Matsukuma S, Matsumura T, Kanatani Y, Saito T |title=Preparedness for a smallpox pandemic in Japan: public health perspectives |journal=Disaster Medicine and Public Health Preparedness |volume=9 |issue=2 |pages=220–223 |date=April 2015 |pmid=26060873 |doi=10.1017/dmp.2014.157 |s2cid=37149836 }}</ref> Throughout history, human migration has aided the spread of pandemic infections; first by sea and in modern times also by air.<ref name="pmid30878442">{{cite journal |vauthors=Houghton F |title=Geography, global pandemics & air travel: Faster, fuller, further & more frequent |journal=Journal of Infection and Public Health |volume=12 |issue=3 |pages=448–449 |date=2019 |pmid=30878442 |doi=10.1016/j.jiph.2019.02.020 |pmc=7129534 }}</ref>

With the exception of smallpox, most pandemics are caused by newly evolved viruses. These [[Emergent virus|"emergent"]] viruses are usually mutants of less harmful viruses that have circulated previously either in humans or in other animals.<ref>{{Cite web|url=https://virologyj.biomedcentral.com/articles/sections/emerging-viruses|title=Virology Journal|website=Virology Journal}}</ref>

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[[Severe acute respiratory syndrome]] (SARS) and [[Middle East respiratory syndrome]] (MERS) are caused by new types of [[coronavirus]]es. Other coronaviruses are known to cause mild infections in humans,<ref name="pmid22094080">{{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}}</ref> 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.<ref name="pmid28475794">{{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 DC |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 }}</ref>

A related coronavirus emerged in [[Wuhan]], China, in November 2019 and spread rapidly around the world. Thought to have originated in bats and subsequently named [[severe acute respiratory syndrome coronavirus 2]], infections with the virus cause a disease called [[COVID-19]], that varies in severity from mild to deadly,<ref name="WHOReport24Feb2020">{{cite report | title = Report of the WHO-China Joint Mission on Coronavirus Disease 2019 (COVID-19) | date = 16–24 February 2020 | url = https://www.who.int/docs/default-source/coronaviruse/who-china-joint-mission-on-covid-19-final-report.pdf | publisher = [[World Health Organization]] (WHO) | access-date = 21 March 2020}}</ref> and led to a [[COVID-19 pandemic|pandemic in 2020]].<ref name="pmid32143502">{{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 (Basel, Switzerland) |volume=9 |issue=3 |pages= 186|date=March 2020 |pmid=32143502 |doi=10.3390/pathogens9030186 |pmc=7157630 |doi-access=free }}</ref><ref name="pmid32093211">{{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 |pages= 575|date=February 2020 |pmid=32093211 |doi=10.3390/jcm9020575 |pmc=7074453 |doi-access=free }}</ref><ref name="pmid32109444">{{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= 373–377|date=February 2020 |pmid=32109444 |doi=10.1016/j.jinf.2020.02.010 |pmc=7102581 }}</ref> Restrictions unprecedented in peacetime were placed on international travel,<ref>{{Cite news|url=https://www.nytimes.com/article/coronavirus-travel-restrictions.html|title=Coronavirus Travel Restrictions, Across the Globe| vauthors = Londoño E, Ortiz A |work=The New York Times |date=16 March 2020|via=NYTimes.com}}</ref> and [[curfews]] imposed in several major cities worldwide.<ref>{{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 }}</ref>

=== In plants ===

{{Main|Plant pathology}}

[[File:Pepper mild mottle virus.png|thumb|125px|[[Capsicum|Peppers]] infected by [[pepper mild mottle virus]]]]

There are many types of [[plant virus]], but often they only cause a decrease in [[crop yield|yield]], and it is not economically viable to try to control them. Plant viruses are frequently spread from plant to plant by organisms called "[[Vector (epidemiology)|vectors]]". These are normally insects, but some [[fungi]], [[nematode]] worms and [[protozoa|single-celled organisms]] have also been shown to be vectors. When control of plant virus infections is considered economical (perennial fruits, for example) efforts are concentrated on killing the vectors and removing alternate hosts such as weeds.<ref>{{harvnb|Shors|2017|p=822}}</ref> Plant viruses are harmless to humans and other animals because they can only reproduce in living plant cells.<ref>{{harvnb|Shors|2017|pp=802–803}}</ref>

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[[File:PhageExterior.svg|thumb|upright=0.6|The structure of a typical bacteriophage]]

Bacteriophages are viruses that infect bacteria and [[archaea]].{{sfn | Oxford |Kellam|Collier| 2016 | p=19}} They are important in [[marine ecology]]: as the infected bacteria burst, carbon compounds are released back into the environment, which stimulates fresh organic growth. Bacteriophages are useful in scientific research because they are harmless to humans and can be studied easily. These viruses can be a problem in industries that produce food and drugs by [[Industrial fermentation|fermentation]] and depend on healthy bacteria. Some bacterial infections are becoming difficult to control with antibiotics, so there is a growing interest in [[phage therapy]], the use of bacteriophages to treat infections in humans.<ref>{{harvnb|Shors|2017|p=803}}</ref>

=== Host resistance ===

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==== Antiviral drugs ====

{{Main|Antiviral drug}}

[[File:Guanosine-acyclovir- aciclovir comparison.pngsvg|thumb|upright|The structure of the DNA base [[guanosine]] and the antiviral drug [[aciclovir]] which functions by mimicking it]]

Since the mid-1980s, the development of [[antiviral drug]]s has increased rapidly, mainly driven by the AIDS pandemic. Antiviral drugs are often [[nucleoside analogue]]s, which masquerade as DNA building blocks ([[nucleoside]]s). When the replication of virus DNA begins, some of the fake building blocks are used. This prevents DNA replication because the drugs lack the essential features that allow the formation of a DNA chain. When DNA production stops the virus can no longer reproduce.<ref>{{harvnb|Shors|2017|pp=514–515}}</ref> Examples of nucleoside analogues are [[aciclovir]] for [[Herpesviridae|herpes virus]] infections and [[lamivudine]] for HIV and [[hepatitis B virus]] infections. Aciclovir is one of the oldest and most frequently prescribed antiviral drugs.<ref>{{harvnb|Shors|2017|p=514}}</ref>

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== Role in ecology ==

Viruses are the most abundant biological entity in aquatic environments;<ref name="pmid16984643">{{cite journal | vauthors = Koonin EV, Senkevich TG, Dolja VV | title = The ancient Virus World and evolution of cells | journal = Biol. Direct | volume = 1 | page= 29 | date = September 2006 | pmid = 16984643 | pmc = 1594570 | doi = 10.1186/1745-6150-1-29 | doi-access = free }}</ref> one teaspoon of seawater contains about ten million viruses,<ref name="pmid31749771">{{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 |pages=2403 |date=2019 |pmid=31749771 |pmc=6842933 |doi=10.3389/fmicb.2019.02403 |doi-access=free }}</ref> and they are essential to the regulation of saltwater and freshwater ecosystems.<ref>{{harvnb|Shors|2017|p=5}}</ref> Most are bacteriophages,<ref name="pmid29867096">{{cite journal |vauthors=Breitbart M, Bonnain C, Malki K, Sawaya NA |s2cid=46927784 |title=Phage puppet masters of the marine microbial realm |journal=Nature Microbiology |volume=3 |issue=7 |pages=754–766 |date=July 2018 |pmid=29867096 |doi=10.1038/s41564-018-0166-y }}</ref> which are harmless to plants and animals. They infect and destroy the bacteria in aquatic microbial communities and this is the most important mechanism of recycling carbon in the marine environment. The organic molecules released from the bacterial cells by the viruses stimulate fresh bacterial and algal growth.<ref>{{harvnb|Shors|2017|pp=25–26}}</ref>

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 fifteen times as many viruses in the oceans as there are bacteria and archaea. They are mainly responsible for the rapid destruction of harmful [[algal bloom]]s,<ref name="pmid16163346">{{cite journal | vauthors = Suttle CA | title = Viruses in the sea | journal = Nature | volume = 437 | issue = 7057 | pages = 356–361 | date = September 2005 | pmid = 16163346 | doi = 10.1038/nature04160 |bibcode = 2005Natur.437..356S | s2cid = 4370363 }}</ref> which often kill other marine life.<ref>{{cite web|url=https://www.cdc.gov/hab/redtide/|title=Harmful Algal Blooms: Red Tide: Home &#124; CDC HSB|publisher=www.cdc.gov|access-date=23 August 2009}}</ref>

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Their effects are far-reaching; by increasing the amount of respiration in the oceans, viruses are indirectly responsible for reducing the amount of carbon dioxide in the atmosphere by approximately 3 [[gigatonne]]s of carbon per year.<ref name="pmid17853907" />

Marine mammals are also susceptible to viral infections. In 1988 and 2002, thousands of harbour seals were killed in Europe by [[phocine distemper virus]].<ref>{{cite journal | vauthors = Hall A, Jepson P, Goodman S, Harkonen T | title= Phocine distemper virus in the North and European Seas&nbsp;– Data and models, nature and nurture | journal= Biological Conservation | volume= 131 | issue= 2 | pages= 221–229 | year= 2006 |doi = 10.1016/j.biocon.2006.04.008 | bibcode= 2006BCons.131..221H }}</ref> Many other viruses, including [[caliciviruses]], [[Herpesviridae|herpesviruses]], adenoviruses[[adenovirus]]es and parvoviruses[[parvovirus]]es, circulate in marine mammal populations.<ref name="pmid17853907" />

Viruses can also serve as an alternative food source for microorganisms which engage in [[Virovore|virovory]], supplying nucleic acids, nitrogen, and phosphorus through their consumption.<ref name="New Virovore">{{Cite journal |lastlast1=DeLong |firstfirst1=John P. |last2=Van Etten |first2=James L. |last3=Al-Ameeli |first3=Zeina |last4=Agarkova |first4=Irina V. |last5=Dunigan |first5=David D. |date=2023-01-03 |title=The consumption of viruses returns energy to food chains |url=https://pnas.org/doi/10.1073/pnas.2215000120 |journal=Proceedings of the National Academy of Sciences |language=en |volume=120 |issue=1 |pages=e2215000120 |doi=10.1073/pnas.2215000120 |doi-access=free |pmid=36574690 |pmc=9910503 |bibcode=2023PNAS..12015000D |issn=0027-8424}}</ref><ref name="First Virovore">{{cite news |last1=Irving |first1=Michael |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}}</ref>

== See also ==

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=== Bibliography ===

{{Refbegin}}

*{{cite book | editor-last = Collier | editor-first =Leslie |editor-last2=Balows| editor-first2 =Albert | editor-last3 =Sussman | editor-first3 =Max | name-list-style = vanc | title = Topley & Wilson's Microbiology and Microbial Infections | publisher = Arnold | year = 1998 | isbn = 0-340-66316-2 |edition=9th|volume=1, ''Virology''}}

* {{cite book | last1=Howley | first1=Peter M. | last2=Knipe | first2=David M. | last3=Enquist | first3=Lynn W. | title=Fields Virology: Fundamentals | publisher=LWW | publication-place=Philadelphia | date=2023-09-25 | isbn=978-1-9751-1251-6}}

*{{cite book | last1=Oxford

| first1=John |last2=Kellam|first2=Paul|last3=Collier|first3=Leslie|

title=Human Virology | publisher=Oxford University Press | publication-place=Oxford | year=2016 | isbn=978-0-19-871468-2 | oclc=968152575}}

*{{cite book | last = Shors | first = Teri | name-list-style = vanc | title = Understanding Viruses | publisher = Jones and Bartlett Publishers | year = 2017 | isbn = 978-1284025927 }}

{{Refend}}