Virus

Virus
Coronavirinae
Virus classification
(unranked):	Virus
Realms
Adnaviria Duplodnaviria Monodnaviria Riboviria Ribozyviria Varidnaviria

A virus is a submicroscopic

The English word "virus" comes from the

Viruses are found wherever there is life and have probably existed since living cells first evolved.

There are three main hypotheses that aim to explain the origins of viruses:[25]

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",^[26][27] or "reduction hypothesis".^[28]

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

transposons (molecules of DNA that replicate and move around to different positions within the genes of the cell).^[29] 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.^[30] This is sometimes called the "vagrancy hypothesis",^[26][31] or the "escape hypothesis".^[28]

Co-evolution hypothesis

This is also called the "virus-first hypothesis"

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.^[35] In similar manner, the sputnik virophage is dependent on mimivirus, which infects the protozoan Acanthamoeba castellanii.^[36] 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.^[37][38]

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.[28] Viruses are now recognised as ancient and as having origins that pre-date the divergence of life into the three domains.^[39] This discovery has led modern virologists to reconsider and re-evaluate these three classical hypotheses.^[39]

The evidence for an ancestral world of RNA cells^[40] 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.^[40] 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.^[41]

Microbiology

Life properties

Scientific opinions differ on whether viruses are a form of life or organic structures that interact with living organisms.

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.^[50] 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.^[51][52] 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.^[53][54] 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^[55] and inovirus^[56] 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.^[57] 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.^[58]

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.^[59]

Enveloped

Some species of virus

severe acute respiratory syndrome coronavirus 2 (which causes COVID-19)^[60] use this strategy. Most enveloped viruses are dependent on the envelope for their infectivity.^[61]

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.^[62]

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.^[63]

Giant viruses

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.^[64] 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.^[65] In 2013, the Pandoravirus genus was discovered in Chile and Australia, and has genomes about twice as large as Megavirus and Mimivirus.^[66] All giant viruses have dsDNA genomes and they are classified into several families: Mimiviridae, Pithoviridae, Pandoraviridae, Phycodnaviridae, and the Mollivirus genus.^[67]

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.^[68]

Genome

An enormous variety of genomic structures can be seen among

A virus has either a DNA or an RNA genome and is called a DNA virus or an RNA virus, respectively. The vast majority of viruses have RNA genomes. Plant viruses tend to have single-stranded RNA genomes and bacteriophages tend to have double-stranded DNA genomes.^[73]

Viral genomes are circular, as in the

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.^[73]

For most viruses with RNA genomes and some with single-stranded DNA (ssDNA) genomes, the single strands are said to be either

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;^[75] the largest—the pandoraviruses—have genome sizes of around two megabases which code for about 2500 proteins.^[66] Virus genes rarely have introns and often are arranged in the genome so that they overlap.^[76]

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.^[24] 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.^[77] 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.^[78]

Genetic mutation and recombination

Viruses undergo genetic change by several mechanisms. These include a process called

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'.[83]

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.^[84] Recombination is common to both RNA and DNA viruses.^[85][86]

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.^[87] This process appears to be an adaptation for coping with genome damage.^[88]

Replication cycle

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.^[89] When infected, the host cell is forced to rapidly produce thousands of copies of the original virus.^[90]

Their life cycle differs greatly between species, but there are six basic stages in their life cycle:^[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

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.^[93] 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.^[94] 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.^[95]

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.^[96]

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.^[97]

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.^[98]

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".^[99] 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.^[100] 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.^[101]

Genome replication

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.^[102]

RNA viruses

Replication of

RNA replicase enzymes to create copies of their genomes.^[103]

Reverse transcribing viruses

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.^[104] 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.^[105]

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.^[121] The SARS-CoV-2 coronavirus that caused the COVID-19 pandemic is an example of a novel virus.^[122]

Classification

Classification seeks to describe the diversity of viruses by naming and grouping them on the basis of similarities. In 1962,

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.[129] Only a small part of the total diversity of viruses has been studied.^[130] As of 2022, 6 realms, 10 kingdoms, 17 phyla, 2 subphyla, 40 classes, 72 orders, 8 suborders, 264 families, 182 subfamilies, 2,818 genera, 84 subgenera, and 11,273 species of viruses have been defined by the ICTV.^[7]

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.^[7]

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

Baltimore classification

The Nobel Prize-winning biologist David Baltimore devised the Baltimore classification system.^[131][132] The ICTV classification system is used in conjunction with the Baltimore classification system in modern virus classification.^{[133][134][135]}

The Baltimore classification of viruses is based on the mechanism of

• I:
  Poxviruses
  )
• II:
  Parvoviruses
  )
• III:
  Reoviruses
  )
• IV:
  Togaviruses
  )
• V:
  Rhabdoviruses
  )
• VI:
  ssRNA-RT viruses (+ strand or sense) RNA with DNA intermediate in life-cycle (e.g. Retroviruses
  )
• VII:
  Hepadnaviruses
  )

Examples of common human diseases caused by viruses include the

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^[139] 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.^[140] These latent viruses might sometimes be beneficial, as the presence of the virus can increase immunity against bacterial pathogens, such as Yersinia pestis.^[141]

Some viruses can cause lifelong or

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.^[145] 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.^[146]

Epidemiology is used to break the chain of infection in populations during outbreaks of viral diseases.^[150] 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.^[151] To control the outbreak of foot-and-mouth disease in cattle in Britain in 2001, thousands of cattle were slaughtered.^[152] Most viral infections of humans and other animals have incubation periods during which the infection causes no signs or symptoms.^[153] Incubation periods for viral diseases range from a few days to weeks, but are known for most infections.^[154] 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.^[154] This, too, is known for many viral infections, and knowledge of the length of both periods is important in the control of outbreaks.^[155] 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.^[156]

Epidemics and pandemics

A

Although viral pandemics are rare events, HIV—which evolved from viruses found in monkeys and chimpanzees—has been pandemic since at least the 1980s.[160] During the 20th century there were four pandemics caused by influenza virus and those that occurred in 1918, 1957 and 1968 were severe.^[161] Most researchers believe that HIV originated in sub-Saharan Africa during the 20th century;^[162] it is now a pandemic, with an estimated 37.9 million people now living with the disease worldwide.^[163] There were about 770,000 deaths from AIDS in 2018.^[164] 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.^[165] In 2007 there were 2.7 million new HIV infections and 2 million HIV-related deaths.^[166]

Ebola (top) and Marburg viruses (bottom)

Several highly lethal viral pathogens are members of the

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.^[169]

Severe acute respiratory syndrome (

Middle East respiratory syndrome (MERS) are caused by new types of coronaviruses. Other coronaviruses are known to cause mild infections in humans,^[170] 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.^[171]

A related coronavirus,

curfews were imposed in several major cities worldwide in response to the pandemic.^[175]

Cancer

Further information: 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 "

Merkel cell carcinoma.^[178]

Hepatitis viruses can develop into a chronic viral infection that leads to

Hodgkin's lymphoma, B lymphoproliferative disorder, and nasopharyngeal carcinoma.^[183] Merkel cell polyomavirus closely related to SV40 and mouse polyomaviruses that have been used as animal models for cancer viruses for over 50 years.^[184]

Host defence mechanisms

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.^[185]

RNA interference is an important innate defence against viruses.^[186] 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.^[187][188]

When the

immunity are carried out.^[190]

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

proteosome system.^[191]

A second defence of vertebrates against viruses is called

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.^[192] 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.^[193]

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.^[194] Other viruses, called 'neurotropic viruses', are disseminated by neural spread where the immune system may be unable to reach them due to immune privilege.^[195]

Prevention and treatment

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

antiviral drugs

that selectively interfere with viral replication.

Vaccines

Further information: 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

immunocompromised patients because they cannot cause the disease.^[204] The yellow fever virus vaccine, a live-attenuated strain called 17D, is probably the safest and most effective vaccine ever generated.^[205]

Antiviral drugs

Further information: Antiviral drug

acyclovir

Antiviral drugs are often

hydroxyl groups, which, along with phosphorus atoms, link together to form the strong "backbone" of the DNA molecule. This is called DNA chain termination.^[207] 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.^[208]

Other antiviral drugs in use target different stages of the viral life cycle. HIV is dependent on a proteolytic enzyme called the

protease inhibitors that inactivate this enzyme.^[209] There are around thirteen classes of antiviral drugs each targeting different viruses or stages of viral replication.^[206]

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.^[210] 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.^[211]

Infection in other species

Viruses infect all cellular life and, although viruses occur universally, each cellular species has its own specific range that often infects only that species.^[212] Some viruses, called satellites, can replicate only within cells that have already been infected by another virus.^[36]

Animal viruses

Main articles: Animal virus and Veterinary virology

Viruses are important pathogens of livestock. Diseases such as foot-and-mouth disease and

invertebrates, the honey bee is susceptible to many viral infections.^[215] Most viruses co-exist harmlessly in their host and cause no signs or symptoms of disease.^[6]

Plant viruses

Main article: Plant virus

There are many types of plant viruses, but often they cause only a loss of

vectors. These are usually insects, but some fungi, nematode worms, single-celled organisms, and parasitic plants are vectors.^[216] 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.^[217] Plant viruses cannot infect humans and other animals because they can reproduce only in living plant cells.^[218]

Originally from Peru, the potato has become a staple crop worldwide.[219] 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.^[220]

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.^[221] RNA interference is also an effective defence in plants.^[222] When they are infected, plants often produce natural disinfectants that kill viruses, such as salicylic acid, nitric oxide, and reactive oxygen molecules.^[223]

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.^[224]

Bacterial viruses

Main article: Bacteriophage

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,

T4 phage, in just over twenty minutes after injection over three hundred phages could be released.^[227]

The major way bacteria defend themselves from bacteriophages is by producing enzymes that destroy foreign DNA. These enzymes, called

acquired immunity to infection.^[231]

Some bacteriophages are called "

proviruses including HIV.^[232][234]

Archaeal viruses

Main article: Archaeal virus

Some viruses replicate within

repetitive DNA sequences within archaean genomes that are related to the genes of the viruses.^[236][237] 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.^[238]

Role in aquatic ecosystems

Main article:

Marine virus

Viruses are the most abundant biological entity in aquatic environments.

cyanophages infecting cyanobacteria and they are essential to the regulation of saltwater and freshwater ecosystems.^[240]

Bacteriophages are harmless to plants and animals, and are essential to the regulation of marine and freshwater ecosystems

foodchain in aquatic environments.^[242] 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.^[243] In particular, lysis of bacteria by viruses has been shown to enhance nitrogen cycling and stimulate phytoplankton growth.^[244] Viral activity may also affect the biological pump, the process whereby carbon is sequestered in the deep ocean.^[245]

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.[246] Viruses are also major agents responsible for the destruction of phytoplankton including harmful algal blooms,^[247] The number of viruses in the oceans decreases further offshore and deeper into the water, where there are fewer host organisms.^[245]

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.^[248][249]

Like any organism,

parvoviruses, circulate in marine mammal populations.^[245]

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.^[251][252]

Role in evolution

Main article: Horizontal gene transfer

Viruses are an important natural means of transferring genes between different species, which increases

last universal common ancestor into bacteria, archaea and eukaryotes.^[254] Viruses are still one of the largest reservoirs of unexplored genetic diversity on Earth.^[245]

Applications

Life sciences and medicine

H5N1

influenza virus

Viruses are important to the study of

translation, protein transport, and immunology

.

Geneticists often use viruses as

antibiotic resistance now found in some pathogenic bacteria.^[257]

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.^[258]

Virotherapy

Main article: Virotherapy

Virotherapy involves the use of genetically modified viruses to treat diseases.

clinical trials, the virus gained approval for the treatment of melanoma in late 2015.^[261] Viruses that have been reprogrammed to kill cancer cells are called oncolytic viruses.^[262]

Materials science and nanotechnology

From the viewpoint of a materials scientist, viruses can be regarded as organic

dimers that act as quenchers.^[265] Another example is the use of CPMV as a nanoscale breadboard for molecular electronics.^[266]

Synthetic viruses

Many viruses can be synthesised de novo ("from scratch"). The first synthetic virus was created in 2002.

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.^[268] 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.^[269]

Weapons

Further information: 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.^[270] 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.^[271] It may be used as a weapon,^[271] 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.^[271]

See also

• Cross-species transmission
• Glossary of virology
• Law of declining virulence
   – Disproved hypothesis of epidemiologist Theobald Smith
• Non-cellular life
• Retrozyme
• Smallest organisms
• Theory of virulence
   – Theory by biologist Paul W. Ewald
• Viral metagenomics
• Viroplasm
• Zoonosis

References

Notes

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Bibliography

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External links

Look up genogroup in Wiktionary, the free dictionary.

Look up virus in Wiktionary, the free dictionary.

• Media related to Viruses at Wikimedia Commons
• Data related to Virus at Wikispecies
• ViralZone A Swiss Institute of Bioinformatics resource for all viral families, providing general molecular and epidemiological information