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Virology is the
scientific study
scientific study
of
virus
virus
essubmicroscopic, parasitic organisms of genetic material contained in a protein coatand virus-like agents. It focuses on the following aspects of viruses: their structure, classification and evolution, their ways to infect and exploit
host A host is a person responsible for guests at an event or for providing hospitality during it. Host may also refer to: Places *Host, Pennsylvania, a village in Berks County People *Jim Host (born 1937), American businessman *Michel Host (bo ...
cells Cell most often refers to: * Cell (biology), the functional basic unit of life Cell may also refer to: Closed spaces * Monastic cell, a small room, hut, or cave in which a monk or religious recluse lives * Prison cell, a room used to hold peopl ...
for reproduction, their interaction with host organism physiology and immunity, the diseases they cause, the techniques to isolate and culture them, and their use in research and therapy. Virology is a subfield of
microbiology Microbiology (from Greek , ''mīkros'', "small"; , ''bios'', "life Life is a characteristic that distinguishes physical entities that have biological processes, such as signaling and self-sustaining processes, from those that do not, e ...

microbiology
. The identification of the causative agent of tobacco mosaic disease as a novel
pathogen In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanisms, ...
by
Martinus Beijerinck The Laboratory of Microbiology in Delft, where Beijerinck worked from 1897 to 1921. Martinus Willem Beijerinck (, 16 March 1851 – 1 January 1931) was a Dutch microbiologist and botanist who was one of the founders of virology Virology i ...

Martinus Beijerinck
(1898) is now acknowledged as being the official beginning of the field of virology as a discipline distinct from
bacteriology Bacteriology is the branch and specialty of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactio ...
. He realized the source was neither a
bacterial Bacteria (; common noun bacteria, singular bacterium) are a type of biological cell. They constitute a large domain of prokaryotic microorganism A microorganism, or microbe,, ''mikros'', "small") and ''organism In biology, an ...
nor a
fungal A fungus (plural The plural (sometimes list of glossing abbreviations, abbreviated ), in many languages, is one of the values of the grammatical number, grammatical category of number. The plural of a noun typically denotes a quantity great ...
infection An infection is the invasion of an organism's body tissues by disease-causing agents, their multiplication, and the reaction of host A host is a person responsible for guests at an event or for providing hospitality during it. Host may a ...

infection
, but something completely different. Beijerinck used the word ‘
virus
virus
’ to describe the mysterious agent in his ‘ contagium vivum fluidum’ (‘contagious living fluid’).


Virus structure and classification

A major branch of virology is
virus classification Virus classification is the process of naming viruses and placing them into a Alpha taxonomy, taxonomic system similar to the classification systems used for cell (biology), cellular organisms. Viruses are classified by phenotypic characteristics, ...
. Viruses can be classified according to the host cell they infect:
animal virus Animal viruses are virus A virus is a submicroscopic infectious agent that Viral replication, replicates only inside the living Cell (biology), cells of an organism. Viruses infect all types of life forms, from animals and plants to microo ...
es,
plant virus Plant viruses are viruses that affect plants. Like all other viruses, plant viruses are obligate intracellular parasites that do not have the molecular machinery to Self-replication, replicate without a host (biology), host. Plant viruses can be ...

plant virus
es,
fungal A fungus (plural The plural (sometimes list of glossing abbreviations, abbreviated ), in many languages, is one of the values of the grammatical number, grammatical category of number. The plural of a noun typically denotes a quantity great ...

fungal
viruses, and
bacteriophage A bacteriophage (), also known informally as a ''phage'' (), is a virus A virus is a submicroscopic infectious agent that Viral replication, replicates only inside the living Cell (biology), cells of an organism. Viruses infect all t ...
s (viruses infecting
bacteria Bacteria (; common noun bacteria, singular bacterium) are a type of Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a Bacte ...
, which include the most complex viruses). Another classification uses the geometrical shape of their
capsid A capsid is the protein shell of a virus A virus is a submicroscopic infectious agent that Viral replication, replicates only inside the living Cell (biology), cells of an organism. Viruses infect all types of life forms, from animals ...
(often a
helix Image:Helix.svg, The right-handed helix (cos ''t'', sin ''t'', ''t'') from ''t'' = 0 to 4π with arrowheads showing direction of increasing ''t'' A helix (), plural helixes or helices (), is a shape like a corkscrew or spiral staircase. It is a ty ...

helix
or an
icosahedron In geometry Geometry (from the grc, γεωμετρία; ''wikt:γῆ, geo-'' "earth", ''wikt:μέτρον, -metron'' "measurement") is, with arithmetic, one of the oldest branches of mathematics. It is concerned with properties of space t ...

icosahedron
) or the virus's structure (e.g. presence or absence of a
lipid In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanisms ...
envelope An envelope is a common packaging Packaging is the art and technology of enclosing or protecting products for distribution, storage, sale, and use. Packaging also refers to the process of designing, evaluating, and producing packages. Packa ...
). Viruses range in size from about 30 nm to about 450 nm, which means that most of them cannot be seen with
light microscope The optical microscope, also referred to as a light microscope, is a type of microscope that commonly uses visible spectrum, visible light and a system of lens (optics), lenses to generate magnified images of small objects. Optical microscopes a ...
s. The shape and structure of viruses has been studied by
electron microscopy An electron microscope is a microscope that uses a beam of accelerated electrons as a source of illumination. As the wavelength of an electron can be up to 100,000 times shorter than that of visible light photons, electron microscopes have a high ...

electron microscopy
,
NMR spectroscopy Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a spectroscopic Spectroscopy is the study of the interaction between matter In classical physics and general che ...
, and
X-ray crystallography X-ray crystallography (XRC) is the experimental science determining the atomic and molecular structure of a crystal A crystal or crystalline solid is a solid material whose constituents (such as atoms, molecules, or ions) are arranged in a ...

X-ray crystallography
. The most useful and most widely used classification system distinguishes viruses according to the type of
nucleic acid Nucleic acids are biopolymers, macromolecules, essential to all Organism, known forms of life. They are composed of nucleotides, which are the monomers made of three components: a pentose, 5-carbon sugar, a phosphate group and a nitrogenous base. T ...

nucleic acid
they use as genetic material and the
viral replication Viral replication is the formation of biological viruses during the infection process in the target host cells. Viruses must first get into the cell before viral replication can occur. Through the generation of abundant copies of its genome and ...

viral replication
method they employ to coax host cells into producing more viruses: *
DNA virus A DNA virus is a virus A virus is a submicroscopic infectious agent that Viral replication, replicates only inside the living Cell (biology), cells of an organism. Viruses infect all types of life forms, from animals and plants to microo ...
es (divided into double-stranded DNA viruses and single-stranded DNA viruses), *
RNA virus An RNA virus is a virus A virus is a submicroscopic infectious agent that Viral replication, replicates only inside the living Cell (biology), cells of an organism. Viruses infect all types of life forms, from animals and plants to micr ...
es (divided into positive-sense single-stranded RNA viruses, negative-sense single-stranded RNA viruses and the much less common
double-stranded RNA viruses Double-stranded RNA viruses (dsRNA viruses) are a polyphyletic group of viruses A virus is a wikt:submicroscopic, submicroscopic infectious agent that Viral replication, replicates only inside the living Cell (biology), cells of an organis ...
), * reverse transcribing viruses ( double-stranded reverse-transcribing DNA viruses and single-stranded reverse-transcribing RNA viruses including
retrovirus A retrovirus is a type of virus that inserts a copy of its RNA genome into the DNA of a host cell that it invades, thus changing the genome of that cell. Once inside the host cell's cytoplasm, the virus uses its own reverse transcriptase enzy ...

retrovirus
es). Virologists also study ''subviral particles'', infectious entities notably smaller and simpler than viruses: *
viroid Viroids are small single-stranded, circular RNA Circular RNA (or circRNA) is a type of single-stranded RNA which, unlike linear RNA, forms a covalently closed continuous loop. In circular RNA, the 3' and 5' ends normally present in an RNA molec ...
s (naked
circular RNA Circular RNA (or circRNA) is a type of single-stranded RNA which, unlike linear RNA, forms a covalently closed continuous loop. In circular RNA, the 3' and 5' ends normally present in an RNA molecule have been joined together. This feature confers ...
molecules infecting plants), *
satellites alt=, A full-size model of the Earth observation satellite ERS 2 ">ERS_2.html" ;"title="Earth observation satellite ERS 2">Earth observation satellite ERS 2 In the context of spaceflight, a satellite is an object that has been intentionally ...
(nucleic acid molecules with or without a capsid that require a helper virus for infection and reproduction), and *
prion Prions are misfolded protein Protein folding is the physical process Physical changes are changes affecting the form of a chemical substance A chemical substance is a form of matter In classical physics and general chemistry, matter ...

prion
s (
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metabol ...

protein
s that can exist in a pathological conformation that induces other prion molecules to assume that same conformation).
Taxa In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanism ...
in virology are not necessarily
monophyletic 300px, A cladogram of the primates, showing a ''monophyletic'' taxon: ''the simians'' (in yellow); a ''paraphyletic'' taxon: ''the prosimians'' (in cyan, including the red patch); and a ''polyphyletic'' group: ''the night-active primates, i.e., ...

monophyletic
, as the evolutionary relationships of the various virus groups remain unclear. Three hypotheses regarding their origin exist: #Viruses arose from non-living matter, separately from yet in parallel to cells, perhaps in the form of self-replicating
RNA Ribonucleic acid (RNA) is a polymer A polymer (; Greek '' poly-'', "many" + '' -mer'', "part") is a substance or material consisting of very large molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of ...

RNA
ribozyme Ribozymes (ribonucleic acid enzymes) are RNA molecules that have the ability to catalyze specific biochemical reactions, including RNA splicing in gene expression, similar to the action of protein enzymes. The 1982 discovery of ribozymes demonst ...

ribozyme
s similar to
viroid Viroids are small single-stranded, circular RNA Circular RNA (or circRNA) is a type of single-stranded RNA which, unlike linear RNA, forms a covalently closed continuous loop. In circular RNA, the 3' and 5' ends normally present in an RNA molec ...
s. #Viruses arose by genome reduction from earlier, more competent cellular life forms that became parasites to host cells and subsequently lost most of their functionality; examples of such tiny parasitic prokaryotes are
Mycoplasma ''Mycoplasma'' (plural mycoplasmas or mycoplasmata) is a genus of bacteria Bacteria (; common noun bacteria, singular bacterium) are a type of Cell (biology), biological cell. They constitute a large domain (biology), domain of prokary ...
and Nanoarchaea. #Viruses arose from mobile genetic elements of cells (such as
transposon A transposable element (TE, transposon, or jumping gene) is a DNA sequence that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size. Transposition often resu ...
s,
retrotransposon Retrotransposons (also called Class I transposable elements or transposons via RNA intermediates) are a type of genetic component that copy and paste themselves into different genomic locations (transposon) by converting RNA back into DNA through t ...

retrotransposon
s or
plasmid A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from gDNA, chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; ...
s) that became encapsulated in protein capsids, acquired the ability to "break free" from the host cell and infect other cells. Of particular interest here is
mimivirus ''Mimivirus'' is a genus of giant viruses, in the family ''Mimiviridae''. Amoeba serve as their natural hosts. This genus contains a single identified species named ''Acanthamoeba polyphaga mimivirus'' (APMV), which serves as its type species. I ...

mimivirus
, a
giant virus A giant virus, sometimes referred to as a girus, is a very large virus A virus is a submicroscopic infectious agent that Viral replication, replicates only inside the living Cell (biology), cells of an organism. Viruses infect all types ...
that infects
amoebae An amoeba (; less commonly spelt ameba or amœba; plural ''am(o)ebas'' or ''am(o)ebae'' ), often called an amoeboid, is a type of cell or unicellular organism A unicellular organism, also known as a single-celled organism, is an organism ...
and encodes much of the molecular machinery traditionally associated with bacteria. Two possibilities are that it is a simplified version of a parasitic prokaryote or it originated as a simpler virus that acquired genes from its host. The evolution of viruses, which often occurs in concert with the evolution of their hosts, is studied in the field of
viral evolution Viral evolution is a subfield of evolutionary biology Evolutionary biology is the subfield of biology that studies the evolution, evolutionary processes (natural selection, common descent, speciation) that produced the Biodiversity, diversity o ...
. While viruses reproduce and evolve, they do not engage in
metabolism Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main purposes of metabolism are: the conversion of the energy in food to energy available to run cellu ...

metabolism
, do not move, and depend on a host cell for
reproduction Reproduction (or procreation or breeding) is the biological process Biological processes are those processes that are vital for an organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is ...

reproduction
. The often-debated question of whether they are alive or not is a matter of definition that does not affect the biological reality of viruses.


Viral diseases and host defenses

One main motivation for the study of viruses is the fact that they cause many important infectious diseases, among them the
common cold The common cold, also known simply as a cold, is a viral infectious disease An infection is the invasion of an organism's body Tissue (biology), tissues by Pathogen, disease-causing agents, their multiplication, and the reaction of host (b ...
,
influenza Influenza, commonly known as "the flu", is an infectious disease caused by ''influenza viruses''. Symptoms range from mild to severe and often include fever, runny nose, sore throat, muscle pain, headache, coughing, and fatigue. These sympto ...

influenza
,
rabies Rabies is a viral disease A viral disease (or viral infection) occurs when an organism's body is invaded by pathogen In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical s ...
,
measles Measles is a highly contagious infectious disease caused by Measles morbillivirus, measles virus. Symptoms usually develop 10–12 days after exposure to an infected person and last 7–10 days. Initial symptoms typically include fever, often ...
, many forms of
diarrhea Diarrhea, also spelled diarrhoea, is the condition of having at least three loose, liquid, or watery bowel movement frame, Anatomy of the anus and rectum Defecation is the final act of digestion Digestion is the breakdown of large ins ...
,
hepatitis Hepatitis is inflammation of the liver tissue. Some people or animals with hepatitis have no symptoms, whereas others develop yellow discoloration of the skin and whites of the eyes (jaundice Jaundice, also known as icterus, is a yellowish o ...

hepatitis
,
Dengue fever Dengue fever is a mosquito-borne tropical disease caused by the dengue virus. Symptoms typically begin three to fourteen days after infection. These may include a high fever Fever, also referred to as pyrexia, is defined as having a tem ...
,
yellow fever Yellow fever is a viral disease of typically short duration. In most cases, symptoms include fever, chills, Anorexia (symptom), loss of appetite, nausea, muscle pains particularly in the back, and headaches. Symptoms typically improve within ...
,
polio Poliomyelitis, commonly shortened to polio, is an infectious disease An infection is the invasion of an organism's body Tissue (biology), tissues by Pathogen, disease-causing agents, their multiplication, and the reaction of host (biology) ...
,
smallpox Smallpox was an infectious disease An infection is the invasion of an organism's body Tissue (biology), tissues by Pathogen, disease-causing agents, their multiplication, and the reaction of host (biology), host tissues to the infectious a ...

smallpox
and
AIDS Human immunodeficiency virus infection and acquired immunodeficiency syndrome (HIV/AIDS) is a spectrum of conditions caused by infection An infection is the invasion of an organism's body Tissue (biology), tissues by Pathogen, disease-ca ...
.
Herpes simplex Herpes simplex is a viral disease, viral infection caused by the herpes simplex virus. Infections are categorized based on the part of the body infected. Herpes labialis, Oral herpes involves the face or mouth. It may result in small blisters ...
causes cold sores and genital herpes and is under investigation as a possible factor in
Alzheimer's Alzheimer's disease (AD), also referred to simply as Alzheimer's, is a neurodegeneration, neurodegenerative disease that usually starts slowly and progressively worsens. It is the cause of 60–70% of cases of dementia. The most common earl ...
. Some viruses, known as
oncovirus An oncovirus or oncogenic virus is a virus A virus is a submicroscopic infectious agent that Viral replication, replicates only inside the living Cell (biology), cells of an organism. Viruses infect all types of life forms, from animals ...
es, contribute to the development of certain forms of
cancer Cancer is a group of diseases A disease is a particular abnormal condition that negatively affects the structure or function of all or part of an organism, and that is not due to any immediate external injury. Diseases are often kn ...

cancer
. The best-studied example is the association between
Human papillomavirus Human papillomavirus infection (HPV infection) is an infection An infection is the invasion of an organism's body Tissue (biology), tissues by Pathogen, disease-causing agents, their multiplication, and the reaction of host (biology), host t ...
and
cervical cancer Cervical cancer is a cancer arising from the cervix. It is due to the abnormal growth of Cell (biology), cells that have the ability to invade or spread to other parts of the body. Early on, typically no symptoms are seen. Later symptoms may incl ...

cervical cancer
: almost all cases of cervical cancer are caused by certain strains of this sexually transmitted virus. Another example is the association of infection with hepatitis B and hepatitis C viruses and
liver cancer Liver cancer (also known as hepatic cancer, primary hepatic cancer, or primary hepatic malignancy) is cancer that starts in the liver. Liver cancer can be primary (starts in liver) or secondary (meaning cancer which has spread from elsewhere to the ...
. Some subviral particles also cause disease: the
transmissible spongiform encephalopathies Transmissible spongiform encephalopathies (TSEs) are a group of progressive, invariably fatal, conditions that are associated with prions and affect the brain (encephalopathy, encephalopathies) and nervous system of many animals, including humans ...
, which include
Kuru Kuru may refer to: Anthropology and history * Kuru (disease) Kuru is a very rare, incurable and fatal neurodegenerative disorder Neurodegeneration is the progressive loss of structure or function of neurons A neuron or nerve cell is an ...
,
Creutzfeldt–Jakob disease Creutzfeldt–Jakob disease (CJD), also known as subacute spongiform encephalopathy or neurocognitive disorder due to prion disease, is a fatal degenerative brain disorder. Early symptoms include memory problems, behavioral changes, poor coordi ...
and
bovine spongiform encephalopathy Bovine spongiform encephalopathy (BSE), commonly known as mad cow disease, is a neurodegenerative disease of cattle. Symptoms include abnormal behavior, trouble walking, and weight loss. Later in the course of the disease the cow becomes unable ...
("mad cow disease"), are caused by prions, hepatitis D is due to a
satellite virus A satellite is a subviral agent that depends on the coinfection of a host cell with a helper virus for its replication. Satellites can be divided into two major classes: satellite viruses and satellite nucleic acids. Satellite virus A ...
. The study of the manner in which viruses cause disease is
viral pathogenesis Viral pathogenesis is the study of the process and mechanisms by which viruses cause diseases in their target Host (biology), hosts, often at the cellular or molecular level. It is a specialized field of study in virology. Pathogenesis is a qualita ...
. The degree to which a virus causes disease is its
virulence Virulence is a pathogen In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, ...
. When the
immune system The immune system is a network of biological processes that protects an organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contiguous system that embodies the Life#Biolog ...
of a
vertebrate Vertebrates () comprise all species of animal Animals (also called Metazoa) are multicellular eukaryotic organisms that form the Kingdom (biology), biological kingdom Animalia. With few exceptions, animals Heterotroph, consume organic ma ...
encounters a virus, it may produce specific
antibodies An antibody (Ab), also known as an immunoglobulin (Ig), is a large, Y-shaped protein used by the immune system to identify and neutralize foreign objects such as pathogenic bacteria and Viral disease, viruses. The antibody recognizes a unique mo ...

antibodies
which bind to the virus and neutralize its infectivity or mark it for destruction. Antibody presence in
blood serum Serum () is the fluid and solute component of blood Blood is a body fluid in humans and other animals that delivers necessary substances such as nutrient A nutrient is a substance used by an organism to survive, grow, and reproduce. The re ...
is often used to determine whether a person has been exposed to a given virus in the past, with tests such as
ELISA The enzyme-linked immunosorbent assay (ELISA) (, ) is a commonly used analytical biochemistry Biochemistry or biological chemistry, is the study of chemical process In a scientific Science (from the Latin Latin (, or , ) is a class ...

ELISA
.
Vaccination Vaccination is the administration of a vaccine to help the immune system develop protection from a disease. Vaccines contain a microorganism or virus in a weakened, live or killed state, or proteins or toxins from the organism. In stimulating ...
s protect against viral diseases, in part, by eliciting the production of antibodies.
Monoclonal antibodies A monoclonal antibody (mAb or moAb) is an antibody An antibody (Ab), also known as an immunoglobulin (Ig), is a large, Y-shaped protein used by the immune system to identify and neutralize foreign objects such as pathogenic bacteria and Viral ...

Monoclonal antibodies
, specific to the virus, are also used for detection, as in
fluorescence microscopy A fluorescence microscope is an optical microscope that uses fluorescence instead of, or in addition to, scattering, reflection (physics), reflection, and attenuation or absorption (electromagnetic radiation), absorption, to study the properties ...

fluorescence microscopy
. The second defense of vertebrates against viruses,
cell-mediated immunity Cell-mediated immunity is an immune response that does not involve antibodies. Rather, cell-mediated immunity is the activation of phagocytes, antigen-specific cytotoxic T-lymphocytes A T cell is a type of lymphocyte. T cells are one of the im ...
, involves
immune cell White blood cells, also called leukocytes or leucocytes, are the cell (biology), cells of the immune system that are involved in protecting the body against both infectious disease and foreign invaders. All white blood cells are produced and der ...
s known as
T cell A T cell is a type of lymphocyte A lymphocyte is a type of white blood cell in the immune system The immune system is a network of biological processes that protects an organism In biology, an organism (from Ancient Greek, Greek: ...
s: the body's cells constantly display short fragments of their proteins on the cell's surface, and if a T cell recognizes a suspicious viral fragment there, the host cell is destroyed and the virus-specific T-cells proliferate. This mechanism is jump-started by certain vaccinations.
RNA interference RNA interference (RNAi) is a biological process in which RNA molecules are involved in sequence-specific suppression of gene expression by double-stranded RNA, through translation or transcriptional repression. Historically, RNAi was known by othe ...
, an important cellular mechanism found in plants, animals and many other
eukaryote Eukaryotes () are organisms whose Cell (biology), cells have a cell nucleus, nucleus enclosed within a nuclear envelope. Eukaryotes belong to the Domain (biology), domain Eukaryota or Eukarya; their name comes from the Greek language, Greek wi ...

eukaryote
s, most likely evolved as a defense against viruses. An elaborate machinery of interacting enzymes detects double-stranded RNA molecules (which occur as part of the life cycle of many viruses) and then proceeds to destroy all single-stranded versions of those detected RNA molecules. Every lethal viral disease presents a paradox: killing its host is obviously of no benefit to the virus, so how and why did it evolve to do so? Today it is believed that most viruses are relatively benign in their natural hosts; some viral infection might even be beneficial to the host.Dimmock NJ, Easton AJ, Leppard K, ''Introduction to Modern Virology'', (Oxford: Blackwell Publishers, 2007), ch 23 "Horizons in human virology", subch 23.3 "Subtle and insidious virus-host interactions", sec "Virus infections can give their host an evolutionary advantage"
p. 432.
/ref> The lethal viral diseases are believed to have resulted from an "accidental" jump of the virus from a species in which it is benign to a new one that is not accustomed to it (see
zoonosis A zoonosis (plural zoonoses, or zoonotic diseases) is an infectious disease caused by a pathogen (an infectious agent, such as a bacterium, virus, parasite or prion) that has jumped from an animal (usually a vertebrate Vertebrates () com ...
). For example, viruses that cause serious influenza in humans probably have pigs or birds as their natural host, and
HIV The human immunodeficiency viruses (HIV) are two species of '' Lentivirus'' (a subgroup of retrovirus) that infect humans. Over time, they cause AIDS, acquired immunodeficiency syndrome (AIDS), a condition in which progressive failure of the ...

HIV
is thought to derive from the benign non-human primate virus SIV. While it has been possible to prevent (certain) viral diseases by vaccination for a long time, the development of
antiviral drug Antiviral drugs are a class of medication used for treating viral infections. Most antivirals target specific viruses, while a broad-spectrum antiviral is effective against a wide range of viruses. Unlike most antibiotics, antiviral drugs do not d ...
s to ''treat'' viral diseases is a comparatively recent development. The first such drug was
interferon Interferons (IFNs, ) are a group of signaling proteins made and released by host cells in response to the presence of several viruses. In a typical scenario, a virus-infected cell will release interferons causing nearby cell (biology), cells t ...

interferon
, a substance that is naturally produced when an infection is detected and stimulates other parts of the immune system.


Molecular biology research and viral therapy

Bacteriophage A bacteriophage (), also known informally as a ''phage'' (), is a virus A virus is a submicroscopic infectious agent that Viral replication, replicates only inside the living Cell (biology), cells of an organism. Viruses infect all t ...

Bacteriophage
s, the viruses which infect
bacteria Bacteria (; common noun bacteria, singular bacterium) are a type of Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a Bacte ...
, can be relatively easily grown as
viral plaqueA viral plaque is a visible structure formed after introducing a viral sample to a cell culture grown on some Substrate (biology), nutrient medium. The virus will replicate and spread, generating regions of cell destruction known as plaques. For exam ...
s on bacterial cultures. Bacteriophages occasionally move genetic material from one bacterial cell to another in a process known as , and this
horizontal gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular A unicellular organism, also known as a single-celled organism, is an organism In biology, an organism (from Ancient G ...
is one reason why they served as a major research tool in the early development of
molecular biology Molecular biology is the branch of biology that seeks to understand the molecule, molecular basis of biological activity in and between Cell (biology), cells, including biomolecule, molecular synthesis, modification, mechanisms, and interactions ...
. The
genetic code The genetic code is the set of rules used by living cells Cell most often refers to: * Cell (biology), the functional basic unit of life Cell may also refer to: Closed spaces * Monastic cell, a small room, hut, or cave in which a monk or reli ...

genetic code
, the function of
ribozyme Ribozymes (ribonucleic acid enzymes) are RNA molecules that have the ability to catalyze specific biochemical reactions, including RNA splicing in gene expression, similar to the action of protein enzymes. The 1982 discovery of ribozymes demonst ...

ribozyme
s, the first
recombinant DNA Image:recombinant formation of plasmids.svg, 280px, Construction of recombinant DNA, in which a foreign DNA fragment is inserted into a plasmid vector. In this example, the gene indicated by the white color is inactivated upon insertion of the forei ...

recombinant DNA
and early genetic libraries were all arrived at using bacteriophages. Certain genetic elements derived from viruses, such as highly effective promoters, are commonly used in molecular biology research today. Growing animal viruses outside of the living host animal is more difficult. Classically, fertilized chicken eggs have often been used, but
cell culture Cell culture is the process by which cell (biology), cells are grown under controlled conditions, generally outside their natural environment. After the cells of interest have been Cell isolation, isolated from living tissue, they can subsequentl ...

cell culture
s are increasingly employed for this purpose today. Since some viruses that infect
eukaryote Eukaryotes () are organisms whose Cell (biology), cells have a cell nucleus, nucleus enclosed within a nuclear envelope. Eukaryotes belong to the Domain (biology), domain Eukaryota or Eukarya; their name comes from the Greek language, Greek wi ...

eukaryote
s need to transport their genetic material into the host cell's
nucleus ''Nucleus'' (plural nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central region of an atom *Cell nucleus, a central organelle of a eukaryotic cell, containing most of the cell's DNA ...

nucleus
, they are attractive tools for introducing new genes into the host (known as
transformation Transformation may refer to: Science and mathematics In biology and medicine * Metamorphosis, the biological process of changing physical form after birth or hatching * Malignant transformation, the process of cells becoming cancerous * Transf ...
or
transfection Transfection is the process of deliberately introducing naked or purified nucleic acids into eukaryotic Eukaryotes () are organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any indi ...

transfection
). Modified retroviruses are often used for this purpose, as they integrate their genes into the host's
chromosome A chromosome is a long DNA The structure of part of a DNA double helix Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of ...

chromosome
s. This approach of using viruses as gene vectors is being pursued in the
gene therapy Gene therapy is a Medicine, medical field which focuses on the genetic modification of cells to produce a therapeutic effect or the treatment of disease by repairing or reconstructing defective genetic material. The first attempt at modifying h ...

gene therapy
of genetic diseases. An obvious problem to be overcome in viral gene therapy is the rejection of the transforming virus by the immune system.
Phage therapy Phage therapy, viral phage therapy, or phagotherapy is the therapeutic use of bacteriophages to treat pathogenic bacterial infections. Bacteriophages, known as phages, are a form of viruses. Phages attach to bacterial cells, and inject a ...

Phage therapy
, the use of bacteriophages to combat bacterial diseases, was a popular research topic before the advent of
antibiotics An antibiotic is a type of antimicrobial substance active against bacteria. It is the most important type of antibacterial agent for fighting pathogenic bacteria, bacterial infections, and antibiotic medications are widely used in the therapy, ...
and has recently seen renewed interest.
Oncolytic virus An oncolytic virus is a virus A virus is a submicroscopic infectious agent that Viral replication, replicates only inside the living Cell (biology), cells of an organism. Viruses infect all types of life forms, from animals and plants to ...
es are viruses that preferably infect
cancer Cancer is a group of diseases A disease is a particular abnormal condition that negatively affects the structure or function of all or part of an organism, and that is not due to any immediate external injury. Diseases are often kn ...

cancer
cells. While early efforts to employ these viruses in the therapy of cancer failed, there have been reports in 2005 and 2006 of encouraging preliminary results.


Sequencing of viruses

As most viruses are too small to be seen by a light microscope, sequencing is one of the main tools in virology to identify and study the virus. Traditional Sanger sequencing and next-generation sequencing (NGS) are used to sequence viruses in basic and clinical research, as well as for the diagnosis of emerging viral infections, molecular epidemiology of viral pathogens, and drug-resistance testing. There are more than 2.3 million unique viral sequences in GenBank. Recently, NGS has surpassed traditional Sanger as the most popular approach for generating viral genomes.


Other uses of viruses

A new application of genetically engineered viruses in
nanotechnology Nanotechnology, also shortened to nanotech, is the use of matter on an atomic, molecular, and Supramolecular complex, supramolecular scale for industrial purposes. The earliest, widespread description of nanotechnology referred to the particul ...

nanotechnology
was recently described; see the uses of viruses in material science and nanotechnology. For use in mapping neurons see the Pseudorabies#Applications in Neuroscience, applications of pseudorabies in neuroscience.


History

File:Martinus Willem Beijerinck in his laboratory.jpg, upalt=An old, bespectacled man wearing a suit and sitting at a bench by a large window. The bench is covered with small bottles and test tubes. On the wall behind him is a large old-fashioned clock below which are four small enclosed shelves on which sit many neatly labelled bottles.,
Martinus Beijerinck The Laboratory of Microbiology in Delft, where Beijerinck worked from 1897 to 1921. Martinus Willem Beijerinck (, 16 March 1851 – 1 January 1931) was a Dutch microbiologist and botanist who was one of the founders of virology Virology i ...

Martinus Beijerinck
in his laboratory in 1921 The word ''virus'' appeared in 1599 and originally meant "venom". A very early form of vaccination known as variolation was developed several thousand years ago in China. It involved the application of materials from
smallpox Smallpox was an infectious disease An infection is the invasion of an organism's body Tissue (biology), tissues by Pathogen, disease-causing agents, their multiplication, and the reaction of host (biology), host tissues to the infectious a ...

smallpox
sufferers in order to immunize others. In 1717 Lady Mary Wortley Montagu observed the practice in Istanbul and attempted to popularize it in Britain, but encountered considerable resistance. In 1796 Edward Jenner developed a much safer method, using cowpox to successfully immunize a young boy against smallpox, and this practice was widely adopted. Vaccinations against other viral diseases followed, including the successful
rabies Rabies is a viral disease A viral disease (or viral infection) occurs when an organism's body is invaded by pathogen In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical s ...
vaccination by Louis Pasteur in 1886. The nature of viruses, however, was not clear to these researchers. In 1892, the Russian biologist Dmitry Ivanovsky used a Chamberland filter to try to isolate the bacteria that caused tobacco mosaic virus, tobacco mosaic disease. His experiments showed that crushed leaf extracts from infected tobacco plants remained infectious after filtration. Ivanovsky reported a minuscule infectious agent or toxin, capable of passing the filter, may be being produced by a bacterium. In 1898
Martinus Beijerinck The Laboratory of Microbiology in Delft, where Beijerinck worked from 1897 to 1921. Martinus Willem Beijerinck (, 16 March 1851 – 1 January 1931) was a Dutch microbiologist and botanist who was one of the founders of virology Virology i ...

Martinus Beijerinck
repeated Ivanovski's work but went further and passed the "filterable agent" from plant to plant, found the action undiminished, and concluded it infectiousreplicating in the hostand thus not a mere toxin. He called it '' contagium vivum fluidum''. The question of whether the agent was a "living fluid" or a particle was however still open. In 1903 it was suggested for the first time that by viruses might cause cancer. In 1908 Bang and Ellerman showed that a filterable virus could transmit chicken leukemia, data largely ignored till the 1930s when leukemia became regarded as cancerous. In 1911 Peyton Rous reported the transmission of chicken sarcoma, a solid tumor, with a virus, and thus Rous became "father of tumor virology". The virus was later called Rous sarcoma virus, Rous sarcoma virus 1 and understood to be a
retrovirus A retrovirus is a type of virus that inserts a copy of its RNA genome into the DNA of a host cell that it invades, thus changing the genome of that cell. Once inside the host cell's cytoplasm, the virus uses its own reverse transcriptase enzy ...

retrovirus
. Several other cancer-causing retroviruses have since been described. The existence of viruses that infect bacteria (
bacteriophage A bacteriophage (), also known informally as a ''phage'' (), is a virus A virus is a submicroscopic infectious agent that Viral replication, replicates only inside the living Cell (biology), cells of an organism. Viruses infect all t ...
s) was first recognized by Frederick Twort in 1911, and, independently, by Félix d'Herelle in 1917. As bacteria could be grown easily in culture, this led to an explosion of virology research. The cause of the devastating Spanish flu pandemic of 1918 was initially unclear. In late 1918, French scientists showed that a "filter-passing virus" could transmit the disease to people and animals, fulfilling Koch's postulates. In 1926 it was shown that scarlet fever is caused by a bacterium that is infected by a certain bacteriophage. While plant viruses and bacteriophages can be grown comparatively easily, animal viruses normally require a living host animal, which complicates their study immensely. In 1931 it was shown that influenza virus could be grown in fertilized chicken eggs, a method that is still used today to produce vaccines. In 1937, Max Theiler managed to grow the
yellow fever Yellow fever is a viral disease of typically short duration. In most cases, symptoms include fever, chills, Anorexia (symptom), loss of appetite, nausea, muscle pains particularly in the back, and headaches. Symptoms typically improve within ...
virus in chicken eggs and produced a vaccine from an attenuated virus strain; this vaccine saved millions of lives and is still being used today. Max Delbrück, an important investigator in the area of bacteriophages, described the basic "life cycle" of a virus in 1937: rather than "growing", a virus particle is assembled from its constituent pieces in one step; eventually it leaves the host cell to infect other cells. The Hershey–Chase experiment in 1952 showed that only DNA and not protein enters a bacterial cell upon infection with enterobacteria phage T2, bacteriophage T2. transduction (genetics), Transduction of bacteria by bacteriophages was first described in the same year. In 1949 John F. Enders, Thomas Huckle Weller, Thomas Weller and Frederick Robbins reported growth of poliovirus in cultured human embryonal cells, the first significant example of an animal virus grown outside of animals or chicken eggs. This work aided Jonas Salk in deriving a polio vaccine from deactivated polio viruses; this vaccine was shown to be effective in 1955. The first virus that could be crystalized and whose structure could, therefore, be elucidated in detail was tobacco mosaic virus (TMV), the virus that had been studied earlier by Ivanovski and Beijerink. In 1935, Wendell Meredith Stanley, Wendell Stanley achieved its crystallization for
electron microscopy An electron microscope is a microscope that uses a beam of accelerated electrons as a source of illumination. As the wavelength of an electron can be up to 100,000 times shorter than that of visible light photons, electron microscopes have a high ...

electron microscopy
and showed that it remains active even after crystallization. Clear X-ray diffraction pictures of the crystallized virus were obtained by Bernal and Fankuchen in 1941. Based on such pictures, Rosalind Franklin proposed the full structure of the tobacco mosaic virus in 1955. Also in 1955, Heinz Fraenkel-Conrat and Robley Williams showed that purified TMV
RNA Ribonucleic acid (RNA) is a polymer A polymer (; Greek '' poly-'', "many" + '' -mer'', "part") is a substance or material consisting of very large molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of ...

RNA
and its
capsid A capsid is the protein shell of a virus A virus is a submicroscopic infectious agent that Viral replication, replicates only inside the living Cell (biology), cells of an organism. Viruses infect all types of life forms, from animals ...
(coat) protein can self-assemble into functional virions, suggesting that this assembly mechanism is also used within the host cell, as Delbrück had proposed earlier. In 1963, the Hepatitis B, Hepatitis B virus was discovered by Baruch Blumberg who went on to develop a hepatitisB vaccine. In 1965, Howard Temin described the first
retrovirus A retrovirus is a type of virus that inserts a copy of its RNA genome into the DNA of a host cell that it invades, thus changing the genome of that cell. Once inside the host cell's cytoplasm, the virus uses its own reverse transcriptase enzy ...

retrovirus
: a virus whose RNA genome was reverse transcription, reverse transcribed into complementary DNA (cDNA), then integrated into the host's genome and expressed from that template. The viral enzyme reverse transcriptase, which along with integrase is a distinguishing trait of retroviruses, was first described in 1970, independently by Howard Temin and David Baltimore. The first retrovirus infecting humans was identified by Robert Gallo in 1974. Later it was found that reverse transcriptase is not specific to retroviruses;
retrotransposon Retrotransposons (also called Class I transposable elements or transposons via RNA intermediates) are a type of genetic component that copy and paste themselves into different genomic locations (transposon) by converting RNA back into DNA through t ...

retrotransposon
s which code for reverse transcriptase are abundant in the genomes of all eukaryotes. Ten to forty percent of the human genome derives from such retrotransposons. In 1975 the functioning of oncoviruses was clarified considerably. Until that time, it was thought that these viruses carried certain genes called oncogenes which, when inserted into the host's genome, would cause cancer. J. Michael Bishop, Michael Bishop and Harold Varmus showed that the oncogene of Rous sarcoma virus is in fact not specific to the virus but is contained in the genome of healthy animals of many species. The oncovirus can switch this pre-existing benign proto-oncogene on, turning it into a true oncogene that causes cancer. 1976 saw the first recorded outbreak of Ebola virus disease, a highly lethal virally transmitted disease. In 1977, Frederick Sanger achieved the first complete sequencing of the genome of any organism, the bacteriophage Phi X 174. In the same year, Richard J. Roberts, Richard Roberts and Phillip Allen Sharp, Phillip Sharp independently showed that the genes of adenovirus contain introns and therefore require gene splicing. It was later realized that almost all genes of eukaryotes have introns as well. A worldwide vaccination campaign led by the UN World Health Organization resulted in the eradication of
smallpox Smallpox was an infectious disease An infection is the invasion of an organism's body Tissue (biology), tissues by Pathogen, disease-causing agents, their multiplication, and the reaction of host (biology), host tissues to the infectious a ...

smallpox
in 1979. In 1982, Stanley Prusiner discovered
prion Prions are misfolded protein Protein folding is the physical process Physical changes are changes affecting the form of a chemical substance A chemical substance is a form of matter In classical physics and general chemistry, matter ...

prion
s and showed that they cause scrapie. The first cases of
AIDS Human immunodeficiency virus infection and acquired immunodeficiency syndrome (HIV/AIDS) is a spectrum of conditions caused by infection An infection is the invasion of an organism's body Tissue (biology), tissues by Pathogen, disease-ca ...
were reported in 1981, and
HIV The human immunodeficiency viruses (HIV) are two species of '' Lentivirus'' (a subgroup of retrovirus) that infect humans. Over time, they cause AIDS, acquired immunodeficiency syndrome (AIDS), a condition in which progressive failure of the ...

HIV
, the retrovirus causing it, was identified in 1983 by Luc Montagnier, Françoise Barré-Sinoussi and Robert Gallo. Tests detecting HIV infection by detecting the presence of HIV antibody were developed. Subsequent tremendous research efforts turned HIV into the best studied virus. Kaposi's sarcoma-associated herpesvirus, Human Herpes Virus 8, the cause of Kaposi's sarcoma which is often seen in AIDS patients, was identified in 1994. Several antiretroviral drugs were developed in the late 1990s, decreasing AIDS mortality dramatically in developed countries. Treatment that exists for HIV includes a multitude of different drugs collectively termed Highly Active Antiretroviral Therapy (HAART). HAART attacks many different aspects of the HIV virus, effectively reducing its effects below the limit of detection. However, when the administration of HAART is discontinued, HIV will bounce back. This is because HAART does not attack latently infected HIV cells, which can reactivate. The Hepatitis C virus was identified using novel molecular cloning techniques in 1987, leading to screening tests that dramatically reduced the incidence of post-blood transfusion, transfusion
hepatitis Hepatitis is inflammation of the liver tissue. Some people or animals with hepatitis have no symptoms, whereas others develop yellow discoloration of the skin and whites of the eyes (jaundice Jaundice, also known as icterus, is a yellowish o ...

hepatitis
. The first attempts at
gene therapy Gene therapy is a Medicine, medical field which focuses on the genetic modification of cells to produce a therapeutic effect or the treatment of disease by repairing or reconstructing defective genetic material. The first attempt at modifying h ...

gene therapy
involving viral vectors began in the early 1980s, when retroviruses were developed that could insert a foreign gene into the host's genome. They contained the foreign gene but did not contain the viral genome and therefore could not reproduce. Tests in mice were followed by tests in humans, beginning in 1989. The first human studies attempted to correct the genetic disease severe combined immunodeficiency (SCID), but clinical success was limited. In the period from 1990 to 1995, gene therapy was tried on several other diseases and with different viral vectors, but it became clear that the initially high expectations were overstated. In 1999 a further setback occurred when 18-year-old Jesse Gelsinger died in a gene therapy trial. He suffered a severe immune response after having received an adenovirus vector. Success in the gene therapy of two cases of X-linked Severe combined immunodeficiency, SCID was reported in 2000. In 2002 it was reported that poliovirus had been synthetically assembled in the laboratory, representing the first synthetic organism. Assembling the 7741-base genome from scratch, starting with the virus's published RNA sequence, took about two years. In 2003 a faster method was shown to assemble the 5386-base genome of the bacteriophage Phi X 174 in two weeks. The giant
mimivirus ''Mimivirus'' is a genus of giant viruses, in the family ''Mimiviridae''. Amoeba serve as their natural hosts. This genus contains a single identified species named ''Acanthamoeba polyphaga mimivirus'' (APMV), which serves as its type species. I ...

mimivirus
, in some sense an intermediate between tiny prokaryotes and ordinary viruses, was described in 2003 and DNA sequencing, sequenced in 2004. The strain of Influenza A virus subtype H1N1 that killed up to 50 million people during the Spanish flu pandemic in 1918 was reconstructed in 2005. Sequence information was pieced together from preserved tissue samples of flu victims; viable virus was then synthesized from this sequence. The 2009 flu pandemic involved another strain of Influenza A H1N1, commonly known as "swine flu". By 1985, Harald zur Hausen had shown that two strains of
Human papillomavirus Human papillomavirus infection (HPV infection) is an infection An infection is the invasion of an organism's body Tissue (biology), tissues by Pathogen, disease-causing agents, their multiplication, and the reaction of host (biology), host t ...
(HPV) cause most cases of
cervical cancer Cervical cancer is a cancer arising from the cervix. It is due to the abnormal growth of Cell (biology), cells that have the ability to invade or spread to other parts of the body. Early on, typically no symptoms are seen. Later symptoms may incl ...

cervical cancer
. Two vaccines protecting against these strains were released in 2006. In 2006 and 2007 it was reported that introducing a small number of specific transcription factor genes into normal skin cells of mice or humans can turn these cells into pluripotency, pluripotent stem cells, known as induced pluripotent stem cells. The technique uses modified retroviruses to transform the cells; this is a potential problem for human therapy since these viruses integrate their genes at a random location in the host's genome, which can interrupt other genes and potentially causes cancer. In 2008, Sputnik virophage was described, the first known ''virophage'': it uses the machinery of a helper virus to reproduce and inhibits reproduction of that helper virus. Sputnik reproduces in amoeba infected by mamavirus, a relative of the mimivirus mentioned above and the largest known virus to date. An endogenous retrovirus (ERV) is a viral element in the genome that was derived from a
retrovirus A retrovirus is a type of virus that inserts a copy of its RNA genome into the DNA of a host cell that it invades, thus changing the genome of that cell. Once inside the host cell's cytoplasm, the virus uses its own reverse transcriptase enzy ...

retrovirus
whose genome has been incorporated into the germ-line genome of some organism and is therefore copied with each reproduction of that organism. It is estimated that about 9 percent of the human genome originates from ERVs. In 2015 it was shown that proteins from an ERV are actively expressed in 3-day-old human embryos and appear to play a role in embryonal development and protect embryos from infection by other viruses. Since the invention of Organ-on-a-chip in 2010s, the engineering approach has found application in the study of many diseases. The approach has also been introduced to virology and chip models are being developed. Examples include the invention of Influenza model by Donald E. Ingber group, the invention of Ebola virus disease model by Alireza Mashaghi group, and the invention of viral hepatitis model by Marcus Dorner group.H. Tang et al., Human Organs-on-Chips for Virology, Trends in Microbiology (2020)
/ref> The organ chip approach will likely replace animal models for human virology.


See also

*Animal virology *Astrovirology *:Viral diseases *Glossary of virology *Introduction to viruses *List of infectious diseases#Viral infectious diseases, List of viral diseases *List of viruses *Medical microbiology *Virus classification *Wikipedia:WikiProject Viruses *Endothelial Cell Tropism


References


Further reading

* (freely searchable online book) * (freely searchable online book) *


External links

*ICTV
International Committee on Taxonomy of Viruses
earchable virus taxonomy, updated versions in 2007 and 2008. Explanations of the virus species concept and viral taxonomy. *David Sander
All the Virology on the WWW
ollection of links, pictures, lecture notes. Many of the links on this site are broken and it does not appear to be being maintained.
Online lectures in virology
University of South Carolina
Microbes.info
is a microbiology information portal containing a vast collection of resources including articles, news, frequently asked questions, and links pertaining to the field of microbiology.

from the Washington University in St. Louis.
Wong's Virology

Vaccine Research Center (VRC)
nformation concerning vaccine research studies *This Week in Virology Podcast by Vincent Racaniello]

*Virulogy, Ton E. van den Bogaard University Maastricht, the Netherlands

{{Authority control Virology, Viruses