54-829: Alphavirus is a genus of RNA viruses , the sole genus in the Togaviridae family. Alphaviruses belong to group IV of the Baltimore classification of viruses , with a positive-sense, single-stranded RNA genome. There are 32 alphavirus species, which infect various vertebrates such as humans, rodents, fish, birds, and larger mammals such as horses, as well as invertebrates . Alphaviruses that can infect both vertebrates and arthropods are referred dual-host alphaviruses, while insect-specific alphaviruses such as Eilat virus and Yada yada virus are restricted to their competent arthropod vector. Transmission between species and their vertebrate hosts (including human) occurs mainly via mosquitoes, making
108-497: A 5’ cap and a 3’ poly-A tail . The four non-structural protein genes are encoded in the 5′ two-thirds of the genome, while the three structural proteins are translated from a subgenomic mRNA colinear with the 3′ one-third of the genome. There are two open reading frames (ORFs) in the genome, nonstructural and structural. The first is non-structural and encodes proteins (nsP1–nsP4) necessary for transcription and replication of viral RNA. The second encodes three structural proteins:
162-495: A ribosome is about 20 nm. The nanometre is also commonly used to specify the wavelength of electromagnetic radiation near the visible part of the spectrum : visible light ranges from around 400 to 700 nm. The ångström , which is equal to 0.1 nm, was formerly used for these purposes. Since the late 1980s, in usages such as the 32 nm and the 22 nm semiconductor node , it has also been used to describe typical feature sizes in successive generations of
216-533: A +ve RNA ancestor and the -ve RNA viruses from within the dsRNA viruses. The closest relation to the -ve stranded RNA viruses is the Reoviridae . This is the single largest group of RNA viruses and has been organized by the ICTV into the phyla Kitrinoviricota , Lenarviricota , and Pisuviricota in the kingdom Orthornavirae and realm Riboviria . Positive-strand RNA viruses can also be classified based on
270-463: A 60–70 nanometer diameter. It is enveloped, spherical and has a positive-strand RNA genome of ~12 kilobases. The genome encodes two polyproteins. The first polyprotein consists of four non-structural units: in order from the N terminal to the C terminal - nsP1, nsP2, nsP3, and nsP4. The second is a structural polyprotein composed of five expression units: from the N terminal to the C terminal - Capsid, E3, E2, 6K and E1. A sub genomic positive strand RNA -
324-523: A disease. They could therefore be used to vaccinate against viral, bacterial, protozoan, and tumor antigens. Initially, the Togaviridae family included what are now called the Flaviviruses , within the Alphavirus genus. The flaviviruses were formed into their own family when sufficient differences with the alphaviruses were noted due to the development of sequencing. Rubella virus was formerly included in
378-606: A form of recombination. Recombination also occurs in the Reoviridae (dsRNA), e.g. reovirus; Orthomyxoviridae ((-)ssRNA), e.g. influenza virus ; and Coronaviridae ((+)ssRNA), e.g. SARS . Recombination in RNA viruses appears to be an adaptation for coping with genome damage. Recombination can occur infrequently between animal viruses of the same species but of divergent lineages. The resulting recombinant viruses may sometimes cause an outbreak of infection in humans. Classification
432-473: A human is bitten by the infected mosquito, the virus can gain entry into the bloodstream, causing viremia . The alphavirus can also get into the CNS where it is able to grow and multiply within the neurones. This can lead to encephalitis , which can be fatal. When an individual is infected with this particular virus, its immune system can play a role in clearing away the virus particles. Alphaviruses are able to cause
486-412: A key characteristic for accurate reference-free viral classification. There are three distinct groups of RNA viruses depending on their genome and mode of replication: Retroviruses (Group VI) have a single-stranded RNA genome but, in general, are not considered RNA viruses because they use DNA intermediates to replicate. Reverse transcriptase , a viral enzyme that comes from the virus itself after it
540-503: A non-conserved loop in the structure of E2, specific populations of cells have been targeted. Furthermore, the use of whole alphaviruses for gene therapy is of limited efficacy both because several internal alphaviral proteins are involved in the induction of apoptosis upon infection and also because the alphaviral capsid mediates only the transient introduction of mRNA into host cells. Neither of these limitations extend to alphaviral envelope pseudotypes of retroviruses or lentiviruses. However,
594-416: A number of key viral proteins and virion capsids of several dsRNA viruses, highlighting the significant parallels in the structure and replicative processes of many of these viruses. RNA viruses generally have very high mutation rates compared to DNA viruses , because viral RNA polymerases lack the proofreading ability of DNA polymerases . The genetic diversity of RNA viruses is one reason why it
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#1733085792784648-574: A number of unassigned genera and species recognised in this group. There are three orders and 34 families recognised in this group. In addition, there are a number of unclassified species and genera. Satellite viruses An unclassified astrovirus/hepevirus-like virus has also been described. With the exception of the Hepatitis D virus , this group of viruses has been placed into a single phylum— Negarnaviricota . This phylum has been divided into two subphyla— Haploviricotina and Polyploviricotina . Within
702-471: Is structurally different from the class I fusion proteins found in influenza virus and HIV. The structure of the Semliki Forest virus revealed a structure that is similar to that of flaviviral glycoprotein E, with three structural domains in the same primary sequence arrangement. The E2 glycoprotein functions to interact with the nucleocapsid through its cytoplasmic domain, while its ectodomain
756-538: Is based principally on the type of genome (double-stranded, negative- or positive-single-strand) and gene number and organization. Currently, there are 5 orders and 47 families of RNA viruses recognized. There are also many unassigned species and genera. Related to but distinct from the RNA viruses are the viroids and the RNA satellite viruses . These are not currently classified as RNA viruses and are described on their own pages. A study of several thousand RNA viruses has shown
810-450: Is difficult to make effective vaccines against them. Retroviruses also have a high mutation rate even though their DNA intermediate integrates into the host genome (and is thus subject to host DNA proofreading once integrated), because errors during reverse transcription are embedded into both strands of DNA before integration. Some genes of RNA virus are important to the viral replication cycles and mutations are not tolerated. For example,
864-427: Is in vaccination. Alphaviruses are can be engineered to create replicon vectors which efficiently induce humoral and T-cell immune responses. In these contexts, replicons have been termed self-amplifying RNA . The replicons lack the ability to transmit to new cells as they lack the sequences encoding for structural proteins, which are replaced with a gene of interest such as an antigen for generation of immunity against
918-565: Is located at the base of a narrow cleft and is not readily accessible. Before cleavage, nsP3 creates a ring structure that encircles nsP2. These two proteins have an extensive interface. Mutations in nsP2 that produce noncytopathic viruses or a temperature sensitive phenotypes cluster at the P2/P3 interface region. P3 mutations opposite the location of the nsP2 noncytopathic mutations prevent efficient cleavage of P2/3. This in turn affects RNA infectivity altering viral RNA production levels. The virus has
972-605: Is not infectious by itself as it needs to be transcribed into positive-sense RNA; each virion can be transcribed to several positive-sense RNAs. Ambisense RNA viruses resemble negative-sense RNA viruses, except they translate genes from their negative and positive strands. The double-stranded (ds)RNA viruses represent a diverse group of viruses that vary widely in host range (humans, animals, plants, fungi , and bacteria ), genome segment number (one to twelve), and virion organization ( Triangulation number , capsid layers, spikes, turrets, etc.). Members of this group include
1026-611: Is responsible for binding a cellular receptor . Most alphaviruses lose the peripheral protein E3, but in Semliki viruses it remains associated with the viral surface. Four nonstructural proteins (nsP1–4) which are produced as a single polyprotein constitute the virus' replication machinery. The processing of the polyprotein occurs in a highly regulated manner, with cleavage at the P2/3 junction influencing RNA template use during genome replication. This site
1080-419: Is similar to mRNA and thus 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. Purified RNA of a positive-sense virus can directly cause infection though it may be less infectious than the whole virus particle. In contrast, purified RNA of a negative-sense virus
1134-619: Is to the Semliki Forest virus subgroup which is also found in the Old World. The following species are assigned to the genus: The seven complexes are: Barmah Forest virus is related to the Semliki Forest virus. Middelburg virus, although classified as a separate complex, may be a member of the Semliki Forest virus group. It seems likely that the genus evolved in the Old World from an insect-borne plant virus. Sindbis virus may have originated in South America. The equine encephalitis viruses and
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#17330857927841188-410: Is uncoated, converts the viral RNA into a complementary strand of DNA, which is copied to produce a double-stranded molecule of viral DNA. After this DNA is integrated into the host genome using the viral enzyme integrase , expression of the encoded genes may lead to the formation of new virions. Numerous RNA viruses are capable of genetic recombination when at least two viral genomes are present in
1242-607: Is viruses that use a homologous RNA-dependent polymerase for replication, are categorized by the International Committee on Taxonomy of Viruses (ICTV) into the realm Riboviria . This includes RNA viruses belonging to Group III , Group IV or Group V of the Baltimore classification system as well as Group VI. Group VI viruses are retroviruses , viruses with RNA genetic material that use DNA intermediates in their life cycle including HIV-1 and HIV-2 which cause AIDS . The majority of such RNA viruses fall into
1296-556: The International Bureau of Weights and Measures ; SI symbol: nm ), or nanometer ( American spelling ), is a unit of length in the International System of Units (SI), equal to one billionth ( short scale ) of a meter (0.000000001 m) and to 1000 picometres . One nanometre can be expressed in scientific notation as 1 × 10 m and as 1 / 1 000 000 000 m. The nanometre
1350-417: The rotaviruses , which are the most common cause of gastroenteritis in young children, and picobirnaviruses , which are the most common virus in fecal samples of both humans and animals with or without signs of diarrhea. Bluetongue virus is an economically important pathogen that infects cattle and sheep. In recent years, progress has been made in determining atomic and subnanometer resolution structures of
1404-763: The 'typovirus' group (apple chlorotic leaf spot virus, carlaviruses, potexviruses and tymoviruses). The alpha like supergroup can be further divided into three clades : the rubi-like, tobamo-like, and tymo-like viruses. Additional work has identified five groups of positive-stranded RNA viruses containing four, three, three, three, and one order(s), respectively. These fourteen orders contain 31 virus families (including 17 families of plant viruses) and 48 genera (including 30 genera of plant viruses). This analysis suggests that alphaviruses and flaviviruses can be separated into two families—the Togaviridae and Flaviridae, respectively—but suggests that other taxonomic assignments, such as
1458-407: The 26S RNA - is replicated from a negative-stranded RNA intermediate. This serves as template for the synthesis of viral structural proteins. Most alphaviruses have conserved domains involved in regulation of viral RNA synthesis. The nucleocapsid, 40 nanometers in diameter, contains 240 copies of the capsid protein and has a T = 4 icosahedral symmetry. The E1 and E2 viral glycoproteins are embedded in
1512-499: The Potexviridae. The evolution of the picornaviruses based on an analysis of their RNA polymerases and helicases appears to date to the divergence of eukaryotes . Their putative ancestors include the bacterial group II retroelements , the family of HtrA proteases and DNA bacteriophages . Partitiviruses are related to and may have evolved from a totivirus ancestor. Hypoviruses and barnaviruses appear to share an ancestry with
1566-499: The RNA-dependent RNA polymerase. Three groups have been recognised: A division of the alpha-like (Sindbis-like) supergroup on the basis of a novel domain located near the N termini of the proteins involved in viral replication has been proposed. The two groups proposed are: the 'altovirus' group (alphaviruses, furoviruses, hepatitis E virus, hordeiviruses, tobamoviruses, tobraviruses, tricornaviruses and probably rubiviruses); and
1620-456: The Semliki Forest virus subgroup (Semliki Forest, O'nyong-nyong and Ross River viruses); the eastern equine encephalitis virus subgroup (eastern equine encephalitis and Venezuelan equine encephalitis viruses) and the Sindbis virus subgroup. Sindbis virus, geographically restricted to the Old World, is more closely related to the eastern equine encephalitis subgroup, which are New World viruses, than it
1674-551: The Sindbis virus are related. The Old World and New World viruses appears to have diverged between 2000 and 3000 years ago. Divergence between the Venezuelan equine encephalitis virus and the eastern equine virus appears to have been ~1400 years ago. The fish infecting clade appears to be basal to the other species. The southern elephant seal virus appears to be related to the Sinbis clade. There are many alphaviruses distributed around
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1728-453: The alphaviruses a member of the collection of arboviruses – or arthropod -borne viruses. Alphavirus particles are enveloped, have a 70 nm diameter, tend to be spherical (although slightly pleomorphic ), and have a 40 nm isometric nucleocapsid . The alphaviruses are small, spherical, enveloped viruses with a genome of a single strand of positive-sense RNA. The total genome length ranges between 11,000 and 12,000 nucleotides, and has
1782-500: The assistance of another virus to complete their life cycle—are also known. Their taxonomy has yet to be settled. The following four genera have been proposed for positive sense single stranded RNA satellite viruses that infect plants— Albetovirus , Aumaivirus , Papanivirus and Virtovirus . A family— Sarthroviridae which includes the genus Macronovirus —has been proposed for the positive sense single stranded RNA satellite viruses that infect arthropods . There are twelve families and
1836-594: The basis for the seven antigenic complexes, 32 species and many subtypes and varieties. The E2 protein is the site of most neutralizing epitopes, while the E1 protein contains more conserved, cross-reactive epitopes. A study of this taxon suggests that this group of viruses had a marine origin—specifically the Southern Ocean—and that they have subsequently spread to both the Old and New World. There are three subgroups in this genus:
1890-405: The centre to the vertices, E1 fills the space between the vertices, and E3, if present, is at the distal end of the spike. Upon exposure of the virus to the acidity of the endosome , E1 dissociates from E2 to form an E1 homotrimer , which is necessary for the fusion step to drive the cellular and viral membranes together. The alphaviral glycoprotein E1 is a class II viral fusion protein, which
1944-485: The core nucleocapsid protein C, and the envelope proteins P62 and E1, which associate as a heterodimer . The viral membrane-anchored surface glycoproteins are responsible for receptor recognition and entry into target cells through membrane fusion . The proteolytic maturation of P62 into E2 and E3 causes a change in the viral surface. Together the E1, E2, and sometimes E3, glycoprotein "spikes" form an E1/E2 dimer or an E1/E2/E3 trimer, where E2 extends from
1998-551: The cytoplasm, specifically in areas termed "spherules" separated by plasma membrane invaginations from the rest. Each complex occupies one such area of about 50-nm in inner diameter. Virions mature by budding through the plasma membrane, where virus-encoded surface glycoproteins E2 and E1 are assimilated. These two glycoproteins are the targets of numerous serologic reactions and tests including neutralization and hemagglutination inhibition. The alphaviruses show various degrees of antigenic cross-reactivity in these reactions and this forms
2052-417: The expression of Sindbis virus envelopes may lead to apoptosis, and their introduction into host cells upon infection by Sindbis virus envelope pseudotyped retroviruses may also lead to cell death. The toxicity of Sindbis viral envelopes may be the cause of the very low production titers realized from packaging cells constructed to produce Sindbis pseudotypes. Another branch of research involving alphaviruses
2106-477: The families Caliciviridae , Flaviviridae , and Picornaviridae and a second that includes the families Alphatetraviridae , Birnaviridae , Cystoviridae , Nodaviridae , and Permutotretraviridae . These viruses have multiple types of genome ranging from a single RNA molecule up to eight segments. Despite their diversity it appears that they may have originated in arthropods and to have diversified from there. A number of satellite viruses—viruses that require
2160-608: The family Togaviridae in its own genus Rubivirus , but is now classified in its own family Matonaviridae . Alphavirus is now the sole genus in the family. RNA virus An RNA virus is a virus characterized by a ribonucleic acid ( RNA ) based genome . The genome can be single-stranded RNA ( ssRNA ) or double-stranded (dsRNA). Notable human diseases caused by RNA viruses include influenza , SARS , MERS , COVID-19 , Dengue virus , hepatitis C , hepatitis E , West Nile fever , Ebola virus disease , rabies , polio , mumps , and measles . All known RNA viruses, that
2214-432: The genes that they carry into the expansive range of potential host cells that are recognized and infected by the alphaviral envelope proteins E2 and E1. The stable integration of viral genes is mediated by the retroviral interiors of these vectors. There are limitations to the use of alphaviruses in the field of gene therapy due to their lack of targeting, however, through the introduction of variable antibody domains in
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2268-453: The kingdom Orthornavirae and the rest have a positioning not yet defined . The realm does not contain all RNA viruses: Deltavirus , Avsunviroidae , and Pospiviroidae are taxa of RNA viruses that were mistakenly included in 2019, but corrected in 2020. RNA viruses can be further classified according to the sense or polarity of their RNA into negative-sense and positive-sense , or ambisense RNA viruses. Positive-sense viral RNA
2322-484: The lipid bilayer. Single E1 and E2 molecules associate to form heterodimers. The E1–E2 heterodimers form one-to-one contacts between the E2 protein and the nucleocapsid monomers. The E1 and E2 proteins mediate contact between the virus and the host cell. Several receptors have been identified. These include prohibitin , phosphatidylserine , glycosaminoglycans and ATP synthase β subunit (ref needed). Replication occurs within
2376-427: The parent unit name metre (from Greek μέτρον , [metrοn] Error: {{Lang}}: Non-latn text/Latn script subtag mismatch ( help ) , "unit of measurement"). Nanotechnologies are based on physical processes which occur on a scale of nanometres (see nanoscopic scale ). The nanometre is often used to express dimensions on an atomic scale: the diameter of a helium atom, for example, is about 0.06 nm, and that of
2430-406: The pestiviruses, hepatitis C virus, rubiviruses, hepatitis E virus, and arteriviruses, may be incorrect. The coronaviruses and toroviruses appear to be distinct families in distinct orders and not distinct genera of the same family as currently classified. The luteoviruses appear to be two families rather than one, and apple chlorotic leaf spot virus appears not to be a closterovirus but a new genus of
2484-466: The potyvirus and sobemovirus lineages respectively. This analysis also suggests that the dsRNA viruses are not closely related to each other but instead belong to four additional classes—Birnaviridae, Cystoviridae, Partitiviridae, and Reoviridae—and one additional order (Totiviridae) of one of the classes of positive ssRNA viruses in the same subphylum as the positive-strand RNA viruses. One study has suggested that there are two large clades: One includes
2538-412: The presence of at least five main taxa: a levivirus and relatives group; a picornavirus supergroup; an alphavirus supergroup plus a flavivirus supergroup; the dsRNA viruses; and the -ve strand viruses. The lentivirus group appears to be basal to all the remaining RNA viruses. The next major division lies between the picornasupragroup and the remaining viruses. The dsRNA viruses appear to have evolved from
2592-583: The preventive measures of choice. Alphaviruses are of interest to gene therapy researchers, in particular the Ross River virus, Sindbis virus , Semliki Forest virus , and Venezuelan equine encephalitis virus have all been used to develop viral vectors for gene delivery. Of particular interest are the chimeric viruses that may be formed with alphaviral envelopes and retroviral capsids. Such chimeras are termed pseudotyped viruses. Alphaviral envelope pseudotypes of retroviruses or lentiviruses are able to integrate
2646-425: The production of interferons . Antibodies and T cells are also involved. The neutralizing antibodies also play an important role to prevent further infection and spread. Diagnoses is based on clinical samples from which the virus can be easily isolated and identified. There are no alphavirus vaccines currently available. Vector control with repellents, protective clothing, breeding site destruction, and spraying are
2700-434: The region of the hepatitis C virus genome that encodes the core protein is highly conserved , because it contains an RNA structure involved in an internal ribosome entry site . On average, dsRNA viruses show a lower sequence redundancy relative to ssRNA viruses. Contrarily, dsDNA viruses contain the most redundant genome sequences while ssDNA viruses have the least. The sequence complexity of viruses has been shown to be
2754-454: The same host cell. Very rarely viral RNA can recombine with host RNA. RNA recombination appears to be a major driving force in determining genome architecture and the course of viral evolution among Picornaviridae ( (+)ssRNA ), e.g. poliovirus . In the Retroviridae ((+)ssRNA), e.g. HIV , damage in the RNA genome appears to be avoided during reverse transcription by strand switching,
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#17330857927842808-485: The subphylum Haploviricotina four classes are currently recognised: Chunqiuviricetes , Milneviricetes , Monjiviricetes and Yunchangviricetes . In the subphylum Polyploviricotina two classes are recognised: Ellioviricetes and Insthoviricetes . Six classes, seven orders and twenty four families are currently recognized in this group. A number of unassigned species and genera are yet to be classified. Nanometer The nanometre (international spelling as used by
2862-540: The world with the ability to cause human disease. Infectious arthritis , encephalitis , rashes and fever are the most commonly observed symptoms. Larger mammals such as humans and horses are usually dead-end hosts or play a minor role in viral transmission; however, in the case of Venezuelan equine encephalitis the virus is mainly amplified in horses. In most other cases the virus is maintained in nature in mosquitoes, rodents and birds. Terrestrial alphavirus infections are spread by insect vectors such as mosquitoes. Once
2916-507: Was formerly known as the " millimicrometre " – or, more commonly, the " millimicron " for short – since it is 1 / 1000 of a micrometer . It was often denoted by the symbol mμ or, more rarely, as μμ (however, μμ should refer to a millionth of a micron). The name combines the SI prefix nano- (from the Ancient Greek νάνος , nanos , "dwarf") with
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