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103-412: Megavirales Nucleocytoviricota is a phylum of viruses . Members of the phylum are also known as the nucleocytoplasmic large DNA viruses ( NCLDV ), which serves as the basis of the name of the phylum with the suffix - viricota for virus phylum. These viruses are referred to as nucleocytoplasmic because they are often able to replicate in both the host's cell nucleus and cytoplasm . The phylum
206-406: A host cell is often forced to rapidly produce thousands of copies of the original virus. When not inside an infected cell or in the process of infecting a cell, viruses exist in the form of independent viral particles, or virions , consisting of (i) genetic material , i.e., long molecules of DNA or RNA that encode the structure of the proteins by which the virus acts; (ii) a protein coat,
309-425: A virion , consists of nucleic acid surrounded by a protective coat of protein called a capsid . These are formed from protein subunits called capsomeres . 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. Virally-coded protein subunits will self-assemble to form
412-406: A PIM or MAPI clade ( Pimascovirales ) in trees built from conserved proteins. The sister clade to PIM/MAPI is a clade made out of Algavirales ( Phycodnaviridae , Pandoraviridae ), and possibly Imitervirales / Mimiviridae ("P2" thereafter). Poxviridae is consistently treated as a basal branch. Asfarviridae is either a sister group to Poxviridae (building together Pokkesviricetes ) or
515-606: A basic optical microscope. In 2013, the Pandoravirus genus was discovered in Chile and Australia, and has genomes about twice as large as Megavirus and Mimivirus. All giant viruses have dsDNA genomes and they are classified into several families: Mimiviridae , Pithoviridae, Pandoraviridae , Phycodnaviridae , and the Mollivirus genus. Some viruses that infect Archaea have complex structures unrelated to any other form of virus, with
618-418: 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. 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
721-581: 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 . In general, there are five main morphological virus types: The poxviruses are large, complex viruses that have an unusual morphology. The viral genome
824-639: A cellular structure, which is often seen as the basic unit of life. Viruses do not have their own metabolism and require a host cell to make new products. They therefore cannot naturally reproduce outside a host cell —although some bacteria such as rickettsia and chlamydia are considered living organisms despite the same limitation. Accepted forms of life use cell division to reproduce, whereas viruses spontaneously assemble within cells. They differ from autonomous growth of crystals as they inherit genetic mutations while being subject to natural selection. Virus self-assembly within host cells has implications for
927-444: A coastal water sample in Chile. It is mostly found infecting amoebae. It has a length of 1 micrometer long and .5 micrometer wide. Its genome can be up to 2.5 million base pairs long. The replication of this virus takes place in the cytoplasm. Like other giant viruses, it affects the host's nucleus and can take up to 15 hours to start infecting. Although it is found in water, it does not affect humans, it may actually help us by increasing
1030-493: 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. Recombination is common to both RNA and DNA viruses. 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
1133-401: A family of large viruses that replicate in crustacea. Members of this proposed family include Carcinus maenas virus 1 (CmV1), Dikerogammarus haemobaphes virus 1 (DhV1), and Panulirus argus virus 1 (PaV1). The general consensus is that Iridoviridae – Ascoviridae are closely related sister taxa in a clade. Pithovirus , Iridoviridae – Ascoviridae and Marseillevirus form
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#17330858951911236-559: A few species, or broad for viruses capable of infecting many. Viral infections in animals provoke an immune response that usually eliminates the infecting virus. Immune responses can also be produced by vaccines , which confer an artificially acquired immunity to the specific viral infection. Some viruses, including those that cause HIV/AIDS , HPV infection , and viral hepatitis , evade these immune responses and result in chronic infections. Several classes of antiviral drugs have been developed. The English word "virus" comes from
1339-549: A fluid, by Wendell Meredith Stanley , and the invention of the electron microscope in 1931 allowed their complex structures to be visualised. Scientific opinions differ on whether viruses are a form of life or organic structures that interact with living organisms. They have been described as "organisms at the edge of life", since they resemble organisms in that they possess genes , evolve by natural selection , and reproduce by creating multiple copies of themselves through self-assembly. Although they have genes, they do not have
1442-445: A genome size of only two kilobases; the largest—the pandoraviruses —have genome sizes of around two megabases which code for about 2500 proteins. Virus genes rarely have introns and often are arranged in the genome so that they overlap . In general, RNA viruses have smaller genome sizes than DNA viruses because of a higher error-rate when replicating, and have a maximum upper size limit. Beyond this, errors when replicating render
1545-506: 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. For most viruses with RNA genomes and some with single-stranded DNA (ssDNA) genomes, the single strands are said to be either positive-sense (called the 'plus-strand') or negative-sense (called the 'minus-strand'), depending on if they are complementary to
1648-403: A length of about 100–200 kilobase pairs. They infect lepidopteran insect larvae and can infect through parasitoid wasps. Once they infect they replicate and cause death in insect pest. Ascoviridae can have up to 180 genes in its genome. The replication of this virus takes place in the nucleus of the host cell. When it replicates, it causes the nucleus to increase in size and eventually burst. After,
1751-436: A life form, because they carry genetic material, reproduce, and evolve through natural selection , although they lack some key characteristics, such as cell structure, that are generally considered necessary criteria for defining life. Because they possess some but not all such qualities, viruses have been described as "organisms at the edge of life" and as replicators . Viruses spread in many ways. One transmission pathway
1854-472: A limited range of hosts and many are species-specific. Some, such as smallpox virus for example, can infect only one species—in this case humans, and are said to have a narrow host range . Other viruses, such as rabies virus, can infect different species of mammals and are said to have a broad range. The viruses that infect plants are harmless to animals, and most viruses that infect other animals are harmless to humans. The host range of some bacteriophages
1957-633: A member of the P2 clade. The ICTV classification, as of 2019, matches the general shape of the tree. The origin of the NCLDVs may predate that of their eukaryotic hosts, judging from their RNA polymerase structures. Virus A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism . Viruses infect all life forms , from animals and plants to microorganisms , including bacteria and archaea . Viruses are found in almost every ecosystem on Earth and are
2060-499: A member of the family Iridoviridae , encodes a protein (Rad2 homolog) that has a key role in the repair of DNA by homologous recombination , and in double-strand break repair . Order Pimascovirales . The Marseilleviridae viruses have double stranded DNA genomes that are about 368 kilobases long. Members of the family can have about 457 open reading frames (ORFs) in its genome. The host organisms are amoebae . Once it infects, viral replication takes place in virus factories in
2163-424: A mouth or cytostome , and there is no fixed place on the cell at which phagocytosis normally occurs. Some amoebae also feed by pinocytosis , imbibing dissolved nutrients through vesicles formed within the cell membrane. The size of amoeboid cells and species is extremely variable. The marine amoeboid Massisteria voersi is just 2.3 to 3 micrometres in diameter, within the size range of many bacteria. At
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#17330858951912266-408: A prime target for natural selection. 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'. Genetic recombination is a process by which a strand of DNA (or RNA) is broken and then joined to the end of
2369-513: A secondary loss of the amoeboid phase. In his scheme, the Sarcodina were divided into the more primitive Eosarcodina (with the phyla Reticulosa and Mycetozoa) and the more derived Neosarcodina (with the phyla Amoebozoa for lobose amoebae and Rhizopoda for filose amoebae). Shortly after, phylogenetic analyses disproved this hypothesis, as non-amoeboid zooflagellates and amoeboflagellates were found to be completely intermingled with amoebae. With
2472-428: A series of molecular phylogenetic analyses confirmed that Sarcodina was not a monophyletic group, and that amoebae evolved from flagellate ancestors. The protozoologist Thomas Cavalier-Smith proposed that the ancestor of most eukaryotes was an amoeboflagellate much like modern heteroloboseans , which in turn gave rise to a paraphyletic Sarcodina from which other groups (e.g., alveolates, animals, plants) evolved by
2575-412: A single viral particle that is released from the cell and is capable of infecting other cells of the same type. Viruses are found wherever there is life and have probably existed since living cells first evolved . The origin of viruses is unclear because they do not form fossils, so molecular techniques are used to infer how they arose. In addition, viral genetic material occasionally integrates into
2678-456: A small part of the total diversity of viruses has been studied. 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. The general taxonomic structure of taxon ranges and the suffixes used in taxonomic names are shown hereafter. As of 2022,
2781-605: A wide diversity of sizes and shapes, called ' morphologies '. In general, viruses are much smaller than bacteria and more than a thousand bacteriophage viruses would fit inside an Escherichia coli bacterium's cell. Many viruses that have been studied are spherical and have a diameter between 20 and 300 nanometres . Some filoviruses , which are filaments, have a total length of up to 1400 nm; their diameters are only about 80 nm. Most viruses cannot be seen with an optical microscope , so scanning and transmission electron microscopes are used to visualise them. To increase
2884-553: 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. An enormous variety of genomic structures can be seen among viral species ; as a group, they contain more structural genomic diversity than plants, animals, archaea, or bacteria. There are millions of different types of viruses, although fewer than 7,000 types have been described in detail. As of January 2021,
2987-416: 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 ". Whenever the host divides, the viral genome is also replicated. The viral genome is mostly silent within
3090-405: Is a major change in the genome of the virus. This can be a result of recombination or reassortment . The Influenza A virus is highly prone to reassortment; occasionally this has resulted in novel strains which have caused pandemics . RNA viruses often exist as quasispecies or swarms of viruses of the same species but with slightly different genome nucleoside sequences. Such quasispecies are
3193-558: Is a type of cell or unicellular organism with the ability to alter its shape, primarily by extending and retracting pseudopods . Amoebae do not form a single taxonomic group ; instead, they are found in every major lineage of eukaryotic organisms. Amoeboid cells occur not only among the protozoa , but also in fungi , algae , and animals . Microbiologists often use the terms "amoeboid" and "amoeba" interchangeably for any organism that exhibits amoeboid movement . In older classification systems, most amoebae were placed in
Nucleocytoviricota - Misplaced Pages Continue
3296-400: 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. Mimivirus is one of the largest characterised viruses, with
3399-439: Is caused by cessation of its normal activities because of suppression by virus-specific proteins, not all of which are components of the virus particle. The distinction between cytopathic and harmless is gradual. Some viruses, such as Epstein–Barr virus , can cause cells to proliferate without causing malignancy, while others, such as papillomaviruses , are established causes of cancer. Some viruses cause no apparent changes to
3502-402: Is controversy over whether the bornavirus , previously thought to cause neurological diseases in horses, could be responsible for psychiatric illnesses in humans. Amoeba An amoeba ( / ə ˈ m iː b ə / ; less commonly spelled ameba or amœba ; pl. : amoebas (less commonly, amebas ) or amoebae ( amebae ) / ə ˈ m iː b i / ), often called an amoeboid ,
3605-512: Is correct. 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. The first evidence of the existence of viruses came from experiments with filters that had pores small enough to retain bacteria. In 1892, Dmitri Ivanovsky used one of these filters to show that sap from a diseased tobacco plant remained infectious to healthy tobacco plants despite having been filtered. Martinus Beijerinck called
3708-505: Is estimated to code for 476 open reading frames. The viron is rod shaped with a length of 1,100 nm long and 500 nm in diameter. Order Chitovirales . The Poxviridae have a linear double-stranded DNA molecule that can have a length of up to 230 kilobases. The replication of these viruses takes place in the cytoplasm. Smallpox , cowpox , and other pox viruses belong to this family. Possibly order Pimascovirales . A new family has been proposed — Mininucleoviridae — for
3811-498: Is first recorded in 1728, long before the discovery of viruses by Dmitri Ivanovsky in 1892. The English plural is viruses (sometimes also vira ), whereas the Latin word is a mass noun , which has no classically attested plural ( vīra is used in Neo-Latin ). The adjective viral dates to 1948. The term virion (plural virions ), which dates from 1959, is also used to refer to
3914-607: Is identical in sequence to the viral mRNA and is thus a coding strand, while negative-sense viral ssDNA is complementary to the viral mRNA and is thus a template strand. Several types of ssDNA and ssRNA viruses have genomes that are ambisense in that transcription can occur off both strands in a double-stranded replicative intermediate. Examples include geminiviruses , which are ssDNA plant viruses and arenaviruses , which are ssRNA viruses of animals. Genome size varies greatly between species. The smallest—the ssDNA circoviruses, family Circoviridae —code for only two proteins and have
4017-411: Is known to infect algae, which means it is found in the ocean. Order Pimascovirales . The Pithoviridae have only two known representatives. These viruses infects amoebas and can survive in low temperatures. For years this virus was believed to be frozen, but due to climate change it has begun to show up again. This is a double stranded DNA virus with its size being 610 kilobases long. The genome
4120-431: Is limited to a single strain of bacteria and they can be used to trace the source of outbreaks of infections by a method called phage typing . The complete set of viruses in an organism or habitat is called the virome ; for example, all human viruses constitute the human virome . 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
4223-543: Is no vaccine developed to fight this virus. Order Pimascovirales . The Iridoviridae have linear double stranded DNA genomes up to 220 kilobases long and can code for about 211 proteins. The capsid of this virion is icosahedral shaped and can be up to 350 nm wide. The replication cycle of this virus begins in the nucleus of the host and end in the cytoplasm. Some viruses of this family are often found infecting fish and amphibians while other are found in insect and crustaceans. The Andrias davidianus ranavirus (ADRV),
Nucleocytoviricota - Misplaced Pages Continue
4326-558: Is notable for containing the giant viruses . There are nine families of NCLDVs that all share certain genomic and structural characteristics; however, it is uncertain whether the similarities of the different families of this group have a common viral ancestor. One feature of this group is a large genome and the presence of many genes involved in DNA repair , DNA replication , transcription , and translation . Typically, viruses with smaller genomes do not contain genes for these processes. Most of
4429-475: Is through disease-bearing organisms known as vectors : for example, viruses are often transmitted from plant to plant by insects that feed on plant sap , such as aphids ; and viruses in animals can be carried by blood-sucking insects. Many viruses spread in the air by coughing and sneezing, including influenza viruses , SARS-CoV-2 , chickenpox , smallpox , and measles . Norovirus and rotavirus , common causes of viral gastroenteritis , are transmitted by
4532-675: Is transferred across the amoeba's cell membrane by osmosis . Without a contractile vacuole, the cell would fill with excess water and, eventually, burst. Marine amoebae do not usually possess a contractile vacuole because the concentration of solutes within the cell are in balance with the tonicity of the surrounding water. The food sources of amoebae vary. Some amoebae are predatory and live by consuming bacteria and other protists . Some are detritivores and eat dead organic material. Amoebae typically ingest their food by phagocytosis , extending pseudopods to encircle and engulf live prey or particles of scavenged material. Amoeboid cells do not have
4635-787: The Acanthamoeba genome . These genes included Spo11 , Mre11 , Rad50 , Rad51 , Rad52 , Mnd1, Dmc1 , Msh and Mlh . This finding suggests that the ‘'Acanthamoeba'’ are capable of some form of meiosis and may be able to undergo sexual reproduction. The meiosis-specific recombinase , Dmc1 , is required for efficient meiotic homologous recombination , and Dmc1 is expressed in Entamoeba histolytica . The purified Dmc1 from E. histolytica forms presynaptic filaments and catalyses ATP -dependent homologous DNA pairing and DNA strand exchange over at least several thousand base pairs . The DNA pairing and strand exchange reactions are enhanced by
4738-400: The capsid , which surrounds and protects the genetic material; and in some cases (iii) an outside envelope of lipids . The shapes of these virus particles range from simple helical and icosahedral forms to more complex structures. Most virus species have virions too small to be seen with an optical microscope and are one-hundredth the size of most bacteria. The origins of viruses in
4841-474: The CD4 molecule—a chemokine receptor —which is most commonly found on the surface of CD4+ T-Cells . This mechanism has evolved to favour those viruses that infect only cells in which they are capable of replication. Attachment to the receptor can induce the viral envelope protein to undergo changes that result in the fusion of viral and cellular membranes, or changes of non-enveloped virus surface proteins that allow
4944-540: The International Committee on Taxonomy of Viruses (ICTV) was formed. The system proposed by Lwoff, Horne and Tournier was initially not accepted by the ICTV because the small genome size of viruses and their high rate of mutation made it difficult to determine their ancestry beyond order. As such, the Baltimore classification system has come to be used to supplement the more traditional hierarchy. Starting in 2018,
5047-675: The Latin vīrus , which refers to poison and other noxious liquids. Vīrus comes from the same Indo-European root as Sanskrit viṣa , Avestan vīša , and Ancient Greek ἰός ( iós ), which all mean "poison". The first attested use of "virus" in English appeared in 1398 in John Trevisa 's translation of Bartholomeus Anglicus 's De Proprietatibus Rerum . Virulent , from Latin virulentus ('poisonous'), dates to c. 1400 . A meaning of 'agent that causes infectious disease'
5150-484: The NCBI Virus genome database has more than 193,000 complete genome sequences, but there are doubtlessly many more to be discovered. A virus has either a DNA or an RNA genome and is called a DNA virus or an RNA virus , respectively. Most viruses have RNA genomes. Plant viruses tend to have single-stranded RNA genomes and bacteriophages tend to have double-stranded DNA genomes. Viral genomes are circular, as in
5253-516: The Radiolaria and Heliozoa , have stiff, needle-like, radiating axopodia (actinopoda) supported from within by bundles of microtubules . Free-living amoebae may be " testate " (enclosed within a hard shell), or "naked" (also known as gymnamoebae , lacking any hard covering). The shells of testate amoebae may be composed of various substances, including calcium , silica , chitin , or agglutinations of found materials like small grains of sand and
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#17330858951915356-559: The class or subphylum Sarcodina, a grouping of single-celled organisms that possess pseudopods or move by protoplasmic flow. However, molecular phylogenetic studies have shown that Sarcodina is not a monophyletic group whose members share common descent . Consequently, amoeboid organisms are no longer classified together in one group. The best known amoeboid protists are Chaos carolinense and Amoeba proteus , both of which have been widely cultivated and studied in classrooms and laboratories. Other well known species include
5459-539: The common cold , influenza , chickenpox , and cold sores . Many serious diseases such as rabies , Ebola virus disease , AIDS (HIV) , avian influenza , and SARS are caused by viruses. The relative ability of viruses to cause disease is described in terms of virulence . Other diseases are under investigation to discover if they have a virus as the causative agent, such as the possible connection between human herpesvirus 6 (HHV6) and neurological diseases such as multiple sclerosis and chronic fatigue syndrome . There
5562-817: The eukaryotic family tree, these results suggest that meiosis was present early in eukaryotic evolution. Furthermore, these findings are consistent with the proposal of Lahr et al. that the majority of amoeboid lineages are anciently sexual. Some amoebae can infect other organisms pathogenically , causing disease: Amoeba have been found to harvest and grow the bacteria implicated in plague . Amoebae can likewise play host to microscopic organisms that are pathogenic to people and help in spreading such microbes. Bacterial pathogens (for example, Legionella ) can oppose absorption of food when devoured by amoebae. The currently generally utilized and best-explored amoebae that host other organisms are Acanthamoeba castellanii and Dictyostelium discoideum. Microorganisms that can overcome
5665-407: The evolutionary history of life are still unclear. Some viruses may have evolved from plasmids , which are pieces of DNA that can move between cells. Other viruses may have evolved from bacteria. In evolution, viruses are an important means of horizontal gene transfer , which increases genetic diversity in a way analogous to sexual reproduction . Viruses are considered by some biologists to be
5768-422: The faecal–oral route , passed by hand-to-mouth contact or in food or water. The infectious dose of norovirus required to produce infection in humans is fewer than 100 particles. HIV is one of several viruses transmitted through sexual contact and by exposure to infected blood. The variety of host cells that a virus can infect is called its host range : this is narrow for viruses specialized to infect only
5871-406: The frustules of diatoms . To regulate osmotic pressure , most freshwater amoebae have a contractile vacuole which expels excess water from the cell. This organelle is necessary because freshwater has a lower concentration of solutes (such as salt) than the amoeba's own internal fluids ( cytosol ). Because the surrounding water is hypotonic with respect to the contents of the cell, water
5974-430: The germline of the host organisms, by which they can be passed on vertically to the offspring of the host for many generations. This provides an invaluable source of information for paleovirologists to trace back ancient viruses that existed as far back as millions of years ago. There are three main hypotheses that aim to explain the origins of viruses: In the past, there were problems with all of these hypotheses:
6077-567: The plasma membrane that surrounds the cell. The appearance and internal structure of pseudopods are used to distinguish groups of amoebae from one another. Amoebozoan species, such as those in the genus Amoeba , typically have bulbous (lobose) pseudopods, rounded at the ends and roughly tubular in cross-section. Cercozoan amoeboids, such as Euglypha and Gromia , have slender, thread-like (filose) pseudopods. Foraminifera emit fine, branching pseudopods that merge with one another to form net-like (reticulose) structures. Some groups, such as
6180-454: The polyomaviruses , or linear, as in the adenoviruses . The type of nucleic acid is irrelevant to the shape of the genome. Among RNA viruses and certain DNA viruses, the genome is often divided into separate parts, in which case it is called segmented. For RNA viruses, each segment often codes for only one protein and they are usually found together in one capsid. All segments are not required to be in
6283-447: The three domains . This discovery has led modern virologists to reconsider and re-evaluate these three classical hypotheses. The evidence for an ancestral world of RNA cells 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
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#17330858951916386-529: The 20th century. For convenience, all amoebae were grouped as Sarcodina and generally divided into morphological categories , on the basis of the form and structure of their pseudopods . Amoebae with pseudopods supported by regular arrays of microtubules (such as the freshwater Heliozoa and marine Radiolaria ) were classified as Actinopoda , whereas those with unsupported pseudopods were classified as Rhizopoda . The Rhizopods were further subdivided into lobose, filose, plasmodial and reticulose, according to
6489-450: The Austrian zoologist Ludwig Karl Schmarda used "sarcode" as the conceptual basis for his division Sarcodea, a phylum -level group made up of "unstable, changeable" organisms with bodies largely composed of "sarcode". Later workers, including the influential taxonomist Otto Bütschli , amended this group to create the class Sarcodina, a taxon that remained in wide use throughout most of
6592-720: The BER pathway early in the Mimivirus life cycle. Cafeteria roenbergensis, a giant virus of the Mimiviridae family, also encodes enzymes for DNA repair. Traditionally only these viruses have been grouped into a family Mimiviridae . Later it appeared that the viruses of the Organic Lake Phycodna Group (OLPG) are more related to Mimiviruses than to Phycodnaviruses . For this reason it has been proposed adding them to legacy Mimiviridae as new subfamily Mesomimivirinae in order to form
6695-527: The ICTV began to acknowledge deeper evolutionary relationships between viruses that have been discovered over time and adopted a 15-rank classification system ranging from realm to species. Additionally, some species within the same genus are grouped into a genogroup . 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. Only
6798-671: The addition of many flagellates to Rhizopoda and the removal of some amoebae, the name was rejected in favour of a new name Cercozoa . As such, both names Rhizopoda and Sarcodina were finally abandoned as formal taxa, but they remained useful as descriptive terms for amoebae. The phylum Amoebozoa was conserved, as it still primarily included amoeboid organisms, and now included the Mycetozoa. Today, amoebae are dispersed among many high-level taxonomic groups. The majority of traditional sarcodines are placed in two eukaryote supergroups : Amoebozoa and Rhizaria . The rest have been distributed among
6901-484: The basis of similarities. In 1962, André Lwoff , Robert Horne , and Paul Tournier were the first to develop a means of virus classification, based on the Linnaean hierarchical system. This system based classification on phylum , class , order , family , genus , and species . Viruses were grouped according to their shared properties (not those of their hosts) and the type of nucleic acid forming their genomes. In 1966,
7004-560: The common species now known as Amoeba proteus . The term "Proteus animalcule" remained in use throughout the 18th and 19th centuries, as an informal name for any large, free-living amoeboid. In 1822, the genus Amiba (from the Greek ἀμοιβή amoibe , meaning "change") was erected by the French naturalist Bory de Saint-Vincent . Bory's contemporary, C. G. Ehrenberg , adopted the genus in his own classification of microscopic creatures, but changed
7107-410: The contrast between viruses and the background, electron-dense "stains" are used. These are solutions of salts of heavy metals, such as tungsten , that scatter the electrons from regions covered with the stain. When virions are coated with stain (positive staining), fine detail is obscured. Negative staining overcomes this problem by staining the background only. A complete virus particle, known as
7210-446: The cytoplasm. It was found that the genome of the family Marseilleviridae codes for about 28 different proteins. The capsid of the marseillevirus is about 250 nm wide with a geometry shape of an icosahedral. The replication of this virus usually occurs near the nucleus once it infects the amoeba. Once the virus infects it can cause a shape change in the host's nucleus. Order Imitervirales . The Megaviridae contains some of
7313-686: The cytoplasm. Within the genome, DNA repair enzymes can be found. These are used when the DNA is harmed such as when it is exposed to ionizing radiation or UV light. Three enzymes employed in DNA base excision repair were characterized from Mimivirus. The pathway of DNA base excision repair (BER) was experimentally reconstituted using the purified recombinant proteins AP endonuclease (mvAPE), uracil-DNA glycosylase (mvUDG), and DNA polymerase X protein (mvPolX). When reconstituted in vitro, mvAPE, mvUDG and mvPolX were found to function cohesively to repair uracil-containing DNA mainly by long patch base excision repair. Thus these processes likely participate in
7416-471: The defenses of one-celled organisms can shelter and multiply inside them, where they are shielded from unfriendly outside conditions by their hosts. The earliest record of an amoeboid organism was produced in 1755 by August Johann Rösel von Rosenhof , who named his discovery "Der Kleine Proteus" ("the Little Proteus"). Rösel's illustrations show an unidentifiable freshwater amoeba, similar in appearance to
7519-430: The eukaryotic meiosis-specific recombination accessory factor (heterodimer) Hop2-Mnd1. These processes are central to meiotic recombination, suggesting that E. histolytica undergoes meiosis. Studies of Entamoeba invadens found that, during the conversion from the tetraploid uninucleate trophozoite to the tetranucleate cyst, homologous recombination is enhanced. Expression of genes with functions related to
7622-431: The extreme of the ssRNA virus case. Viruses undergo genetic change by several mechanisms. These include a process called antigenic drift where individual bases in the DNA or RNA mutate to other bases. Most of these point mutations are "silent"—they do not change the protein that the gene encodes—but others can confer evolutionary advantages such as resistance to antiviral drugs . Antigenic shift occurs when there
7725-446: The filtered, infectious substance a "virus" and this discovery is considered to be the beginning of virology. The subsequent discovery and partial characterization of bacteriophages by Frederick Twort and Félix d'Herelle further catalyzed the field, and by the early 20th century many viruses had been discovered. In 1926, Thomas Milton Rivers defined viruses as obligate parasites. Viruses were demonstrated to be particles, rather than
7828-399: The form of single-stranded nucleoprotein complexes, through pores called plasmodesmata . 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
7931-406: The host. At some point, the provirus or prophage may give rise to the active virus, which may lyse the host cells. 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. The genetic material within virus particles, and the method by which
8034-517: The infected cell. Cells in which the virus is latent and inactive show few signs of infection and often function normally. This causes persistent infections and the virus is often dormant for many months or years. This is often the case with herpes viruses . Viruses are by far the most abundant biological entities on Earth and they outnumber all the others put together. They infect all types of cellular life including animals, plants, bacteria and fungi . Different types of viruses can infect only
8137-435: The largest viruses ever discovered. They have linear double stranded DNA genomes with a length of 1,259,197 base pairs, which is larger than some small bacteria. Within this genome 1,100 proteins are coded. 74.76% of the base pairs are represented by thymine and adenine. The Megaviridae virus can be found infecting acanthamoeba or other protozoan clades. Once the virus infects the host, the replication cycle takes place in
8240-510: The major steps of meiotic recombination also increase during encystations. These findings in E. invadens , combined with evidence from studies of E. histolytica indicate the presence of meiosis in the Entamoeba . Dictyostelium discoideum in the supergroup Amoebozoa can undergo mating and sexual reproduction including meiosis when food is scarce. Since the Amoebozoa diverged early from
8343-416: The material is replicated, varies considerably between different types of viruses. The range of structural and biochemical effects that viruses have on the host cell is extensive. These are called ' cytopathic effects '. Most virus infections eventually result in the death of the host cell. The causes of death include cell lysis, alterations to the cell's surface membrane and apoptosis . Often cell death
8446-489: The more comprehensive family Megaviridae . For this reason, the term Mimiviridae was used sensu lato synonymous with Megaviridae . However, since the ICTV has created a new order Imitervirales officially containing the (legacy) Mimiviridae , proposed Mesomimivirinae are proposed to be upgraded as a new family Mesomimiviridae , i. e. as sister family of legacy Mimiviridae (within this order). Possibly order Algavirales . Pandoraviridae Discovered in 2013 from
8549-407: The morphology of their pseudopods. During the 1980s, taxonomists reached the following classification, based exclusively on morphological comparisons: Archezoa Percolozoa (Heterolobosea) other excavates Eosarcodina Neosarcodina Apusozoa → Choanozoa → Animals , Fungi Actinopoda Alveolata → Plants , Chromista In the final decades of the 20th century,
8652-465: The most likely location. Host organisms typically include protozoa , invertebrates and eukaryotic algae . The class Pokkesviricetes infects familiar vertebrates, including multiple farm animals and humans. Order Pimascovirales . Members of the family Ascoviridae come in different shapes. Some can be rod-shaped, while others are oval. They measure up to 130 nm wide and 400 nm long. These viruses have circular double stranded DNA that have
8755-416: The most numerous type of biological entity. Since Dmitri Ivanovsky 's 1892 article describing a non-bacterial pathogen infecting tobacco plants and the discovery of the tobacco mosaic virus by Martinus Beijerinck in 1898, more than 11,000 of the millions of virus species have been described in detail. The study of viruses is known as virology , a subspeciality of microbiology . When infected,
8858-461: The original virus. Their life cycle differs greatly between species, but there are six basic stages in their life cycle: Attachment is a specific binding between viral capsid proteins and specific receptors on the host cellular surface. This specificity determines the host range and type of host cell of a virus. For example, HIV infects a limited range of human leucocytes . This is because its surface protein, gp120 , specifically interacts with
8961-540: The other extreme, the shells of deep-sea xenophyophores can attain 20 cm in diameter. Most of the free-living freshwater amoebae commonly found in pond water , ditches, and lakes are microscopic , but some species, such as the so-called "giant amoebae" Pelomyxa palustris and Chaos carolinense , can be large enough to see with the naked eye. Recent evidence indicates that several Amoebozoa lineages undergo meiosis . Orthologs of genes employed in meiosis of sexual eukaryotes have recently been identified in
9064-416: The polymerase during genome replication. This process appears to be an adaptation for coping with genome damage. 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. When infected, the host cell is forced to rapidly produce thousands of copies of
9167-420: The production of oxygen in aquatic environments. Order Algavirales . The Phycodnaviridae are icosahedral in shape with a double-stranded DNA molecule. Some members of this family can have a linear double-stranded DNA while others have a circular double stranded DNA. The genome has been found to be up to 560 kilobases in length. Up to 50% of the DNA can be represented by guanine or cytosine. This virus
9270-960: The ranks of subrealm, subkingdom, and subclass are unused, whereas all other ranks are in use. The Nobel Prize-winning biologist David Baltimore devised the Baltimore classification system. The ICTV classification system is used in conjunction with the Baltimore classification system in modern virus classification. The Baltimore classification of viruses is based on the mechanism of mRNA production. Viruses must generate mRNAs from their genomes to produce proteins and replicate themselves, but different mechanisms are used to achieve this in each virus family. Viral genomes may be single-stranded (ss) or double-stranded (ds), RNA or DNA, and may or may not use reverse transcriptase (RT). In addition, ssRNA viruses may be either sense (+) or antisense (−). This classification places viruses into seven groups: Examples of common human diseases caused by viruses include
9373-422: 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. Viruses are now recognised as ancient and as having origins that pre-date the divergence of life into
9476-479: 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 . The SARS-CoV-2 coronavirus that caused the COVID-19 pandemic is an example of a novel virus. Classification seeks to describe the diversity of viruses by naming and grouping them on
9579-451: The same virion for the virus to be infectious, as demonstrated by brome mosaic virus and several other plant viruses. 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
9682-440: The so-called "brain-eating amoeba" Naegleria fowleri , the intestinal parasite Entamoeba histolytica , which causes amoebic dysentery , and the multicellular "social amoeba" or slime mould Dictyostelium discoideum . Amoeba do not have cell walls, which allows for free movement. Amoeba move and feed by using pseudopods, which are bulges of cytoplasm formed by the coordinated action of actin microfilaments pushing out
9785-427: The spelling to Amoeba . In 1841, Félix Dujardin coined the term " sarcode " (from Greek σάρξ sarx , "flesh," and εἶδος eidos , "form") for the "thick, glutinous, homogeneous substance" which fills protozoan cell bodies. Although the term originally referred to the protoplasm of any protozoan, it soon came to be used in a restricted sense to designate the gelatinous contents of amoeboid cells. Thirty years later,
9888-399: 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. 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
9991-457: The study of the origin of life , as it lends further credence to the hypothesis that life could have started as self-assembling organic molecules . The virocell model first proposed by Patrick Forterre considers the infected cell to be the "living form" of viruses and that virus particles (virions) are analogous to spores . Although the living versus non-living debate continues, the virocell model has gained some acceptance. Viruses display
10094-446: The viral messenger RNA (mRNA). Positive-sense viral RNA is in the same sense as viral mRNA and thus at least a part of it can be immediately translated by the host cell. Negative-sense viral RNA is complementary to mRNA and thus must be converted to positive-sense RNA by an RNA-dependent RNA polymerase before translation. DNA nomenclature for viruses with genomic ssDNA is similar to RNA nomenclature, in that positive-strand viral ssDNA
10197-824: The viral capsid remains outside. 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. 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. Assembly – Following
10300-452: The virion starts to form and spread. Order Asfuvirales . A member of the family Asfarviridae is known as an asfarvirus. This virus is the cause of African swine fever. Some of the symptoms for this flu include fever, high pulse, fast breathing, and it can cause death. These symptoms can be similar to those from hog cholera, the difference is that the African swine flu can not be cured. There
10403-503: The virus to enter. 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. Nearly all plant viruses (such as tobacco mosaic virus) can also move directly from cell to cell, in
10506-460: 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. Single-strand DNA viruses are an exception to this rule, as mutation rates for these genomes can approach
10609-702: The viruses in this family also replicate in both the host's nucleus and cytoplasm , thus the name nucleocytoplasmic. There are 47 NCLDV core genes currently recognised. These include four key proteins involved in DNA replication and repair: the enzymes DNA polymerase family B, the topoisomerase II A, the FLAP endonuclease and the processing factor proliferating cell nuclear antigen . Other proteins include DNA dependent RNA polymerase II and transcription factor II B. The following classes and orders are recognized, under which are families mentioned in this article: The unrecognized families are parenthesized and placed in
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