Family Secoviridae Virus

The Secoviridae are a family of Group IV (positive-sense ssRNA) plant-infecting viruses in the order Picornavirales.
Several plant viruses share features with animal and human viruses of the family Picornaviridae, including a conserved structure of both the virus particle and the viral genome, expressing viral proteins by proteolytic cleavage of large polyproteins and encoding replication proteins with conserved sequence motifs. Members of the family Comoviridae were originally described as the only plant picorna-like viruses. Other plant picorna-like viruses were later discovered and classified in the family Sequiviridae. Sequiviridae and Comoviridae are related to each other in phylogenetic studies and share the common property of encoding specialized proteins to enable their movement in the plant. Recently, it was proposed to regroup plant picorna-like viruses into a single family termed ‘secoviridae’. The proposed family amalgamates the families Comoviridae and Sequiviridae, and incorporates other plant picorna-like viruses currently classified in the genera Sadwavirus and Cheravirus, and the proposed genus ‘Torradovirus’.
Key concepts:

    Many plant viruses are related to the animal and human picornaviridae and to other picorna-like viruses infecting algae and arthropods.
    A recent update in the taxonomy of plant picorna-like viruses has lead to the creation of the family ‘secoviridae’ which amalgamates the families Comoviridae and Sequiviridae as well as the existing genera Cheravirus, Sequivirus and the proposed genus ‘torradovirus’.
    Secoviridae share many common characteristics including having both similar virus particle structures and genomic organizations, and requiring a specialized protein to facilitate their movement within the host plant.
    Secoviridae produce their proteins in the form of large polyproteins that are cleaved at specific sites by a viral proteinase.
    Replication of the viral RNA occurs in large protein complexes in association with intracellular membranes from the host.
    Plant cells infected with secoviridae generally display tubular structures that are composed of the viral movement protein, contain virus-like particles and traverse the cell wall. These tubular structures are probably involved in the movement of the virus from cell to cell.
    Secoviridae can be transmitted through seeds and pollen or with the help of nematode or arthropod vectors and their spread in the field is largely dependent on their mode of transmission.

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Family Potyviridae Virus

The Picornaviridae family (picornaviruses) causes a wider range of illnesses than most other, if not all, virus families. Infection with various picornaviruses may be asymptomatic or may cause clinical syndromes such as aseptic meningitis (the most common acute viral disease of the CNS), encephalitis, the common cold, febrile rash illnesses (hand-foot-and-mouth disease), conjunctivitis, herpangina, myositis and myocarditis, and hepatitis.

Poliomyelitis, caused by the enteroviral type species, was one of the first recorded infections; an Egyptian tomb carving showed a man with a foot-drop deformity typical of paralytic poliomyelitis.
Characteristics

The term Picornaviridae is derived from pico, which means small (typically, 18-30 nm), and RNA, referring to the single-stranded positive-sense RNA common to all members of the Picornaviridae family. All members of this family, whose RNA molecules range from 7.2-8.5 kilobases (kb) in size, lack a lipid envelope and are therefore resistant to ether, chloroform, and alcohol. However, ionizing radiation, phenol, and formaldehyde readily inactivate picornaviruses.

The viral capsid of picornaviruses consists of a densely packed icosahedral arrangement of 60 protomers. Each protomer consists of 4 polypeptides, etoposide (VP) 1, 2, 3, and 4, which all derive from the cleavage of a larger protein. The capsid-coat protein serves multiple functions, including (1) protecting the viral RNA from degradation by environmental RNAse, (2) determining host and tissue tropism by recognition of cell-specific cell-membrane receptors, (3) penetrating target cells and delivering the viral RNA into the cell cytoplasm, and (4) selecting and packaging viral RNA.

Two genera of Picornaviridae— enterovirus and rhinovirus —have an identical morphology but can be distinguished based on clinical, biophysical, and epidemiological studies. Enteroviruses grow at a wide pH range (ie, 3-10). After initial replication in the oropharynx, enteroviruses survive the acidic environment of the stomach. The small intestine is the major invasion site of enteroviruses, which replicate best at 37°C. Rhinoviruses replicate at a pH of 6-8. After initial replication in the nasal passages, the acidic environment of the stomach destroys rhinoviruses. Rhinoviruses optimally replicate at 33°C and primarily infect the nasal mucosa.[4]
Classification[1, 3, 2]

Enteroviruses have several subgroups: 3 serotypes of polioviruses, 23 serotypes of group A coxsackieviruses, 6 serotypes of group B coxsackieviruses, and at least 31 serotypes of echoviruses. (ECHO virus is a misnomer based on the acronym enteric cytopathic human orphan virus.) Viruses are grouped according to pathogenicity, host range, and serotype, which is based on serum neutralization. Some enteroviruses are not classified further but rather assigned a number, currently 68 to 71. Bovine, equine, simian, porcine, and rodent enteroviruses also exist.

Overall, the family Picornaviridae includes 9 genera. In addition to the major human enteroviral pathogens (poliovirus, enterovirus, coxsackievirus, echovirus), rhinoviruses (approximately 105 serotypes), the human hepatitis A virus (HAV), and several parechoviruses, Picornaviridae contains several other genera of viruses that infect nonhuman vertebrate hosts.

Cardiovirus (type species, encephalomyocarditis virus) is a classic infection in mice, although it has been observed to cause disease in humans.[5] Certain strains of this virus are associated with the development of diabetes in certain strains of mice and are used as a model for virus-associated insulin-requiring diabetes in humans.

Aphthovirus (type species, foot-and-mouth disease virus [FMDV]) creates a major worldwide economic problem, particularly in South America and Australia. FMDV, which has 7 serotypes, is largely controlled by the immunization or slaughter of infected animals. Aphthoviruses are more acid-labile than other picornaviruses.

The other genera include Parechovirus, Erbovirus (equine rhinitis B virus), Kobuvirus (Aichi virus), and Teschovirus (porcine teschovirus). Arthropod-infecting viruses, including Cricket paralysis virus, Drosophila C virus, and Tussock moth virus, are additional unclassified picornaviruses.

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Family Picornaviridae Virus

A picornavirus is a virus belonging to the family Picornaviridae. Picornaviruses are non-enveloped, positive-stranded RNA viruses with an icosahedral capsid. The genome RNA is unusual because it has a protein on the 5' end that is used as a primer for transcription by RNA polymerase. The name is derived from pico, meaning small, and RNA, referring to the ribonucleic acid genome, so "picornavirus" literally means small RNA virus.

Picornaviruses are separated into a number of genera and include many important pathogens of humans and animals. The diseases they cause are varied, ranging from acute "common-cold"-like illnesses, to poliomyelitis, to chronic infections in livestock. Additional species not belonging to any of the recognised genera continue to be described.

Taxonomy
Picornaviruses are separated into a number of genera. Contained within the picornavirus family are many organisms of importance as vertebrate and human pathogens, shown in the table below.

Enteroviruses infect the enteric tract, which is reflected in their name. On the other hand, rhinoviruses infect primarily the nose and the throat. Enteroviruses replicate at 37°C, whereas rhinoviruses grow better at 33°C, as this is the lower temperature of the nose. Enteroviruses are stable under acid conditions and thus they are able to survive exposure to gastric acid. In contrast, rhinoviruses are acid-labile (inactivated or destroyed by low pH conditions) and that is the reason why rhinovirus infections are restricted to the nose and throat.

Plant picornaviruses
The plant picornaviruses have a number of properties that are distinct from the animal viruses. They have been classified into the family Secoviridae containing the subfamily Comovirinae (genera Comovirus, Fabavirus and Nepovirus), and genera Sequivirus, Waikavirus, Cheravirus, Sadwavirus and Torradovirus (type species Tomato torrado virus).

Insect picornaviruses
A number of picorna like viruses have been described infecting insects. These include Perina nuda picorna-like virus of the tussock moth, infectious flacherie virus of the silkworm and Sacbrood virus of the honeybee, Plautia stali intestine virus kelp fly virus, Ectropis obliqua picorna-like virus, deformed wing virus, acute bee paralysis virus, Drosophila C virus, Rhopalosiphum padi virus, and Himetobi P virus. Most of these have been placed in a separate family - the Dicistroviridae.

Virology
Picornaviruses are classed under Baltimore's viral classification system as group IV viruses as they contain a single stranded, positive sense RNA genome of between 7.2 and 9.0 kb (kilobases) in length. Like most positive sense RNA genomes, the genetic material alone is infectious; although substantially less virulent than if contained within the viral particle, the RNA can have increased infectivity when transfected into cells.

Structure
The capsid is an arrangement of 60 protomers in a tightly packed Icosahedral structure. Each protometer consists of 4 polypeptides known as VP (viral protein)1, 2, 3 and 4. VP2 and VP4 polypeptides originate from one protomer known as VP0 that is cleaved to give the different capsid components. The Icosahedral is said to have a triangulation number of 3, this means that in the icosahedral structure each of the 60 triangles that make up the capsid are split into 3 little triangles with a subunit on the corner. Depending on the type and degree of dehydration the viral particle is around 27-30 nm in diameter. The viral genome is around 2500 nm in length so we can therefore conclude that it must be tightly packaged within the capsid along with substances such as sodium ions in order to cancel out the negative charges on the RNA caused by the phosphate groups.

Genome
The genome itself is the same sense as mammalian mRNA, being read 5' to 3'. Unlike mammalian mRNA picornaviruses do not have a 5' cap but a virally encoded protein known as VPg. However, like mammalian mRNA, the genome does have a poly(A) tail at the 3' end. There is an un-translated region (UTR) at both ends of the picornavirus genome. The 5' UTR is longer, being around 600-1200 nucleotides (nt) in length, compared to that of the 3' UTR, which is around 50-100 nt. It is thought that the 5' UTR is important in translation and the 3' in negative strand synthesis; however the 5' end may also have a role to play in virulence of the virus. The rest of the genome encodes structural proteins at the 5' end and non-structural proteins at the 3' end in a single polyprotein.

Replication
The viral particle binds to cell surface receptors. This causes a conformational change in the viral capsid proteins, and myristic acid are released. These acids form a pore in the cell membrane through which RNA is injected. Once inside the cell, the RNA un-coats and the (+) strand RNA genome is replicated through a double-stranded RNA intermediate that is formed using viral RDRP (RNA-Dependent RNA polymerase). Translation by host cell ribosomes is not initiated by a 5' G cap as usual, but rather is initiated by an IRES (Internal Ribosome Entry Site). The viral lifecycle is very rapid with the whole process of replication being completed on average within 8 hours. However as little as 30 minutes after initial infection, cell protein synthesis declines to almost zero output – essentially the macromolecular synthesis of cell proteins is “shut off”. Over the next 1–2 hours there is a loss of margination of chromatin and homogeneity in the nucleus, before the viral proteins start to be synthesized and a vacuole appears in the cytoplasm close to the nucleus that gradually starts to spread as the time after infection reaches around 3 hours. After this time the cell plasma membrane becomes permeable, at 4–6 hours the virus particles assemble, and can sometimes be seen in the cytoplasm. At around 8 hours the cell is effectively dead and lyses to release the viral particles.

Experimental data from single step growth-curve-like experiments have allowed scientists to look at the replication of the picornaviruses in great detail. The whole of replication occurs within the host cell cytoplasm and infection can even happen in cells that do not contain a nucleus (known as enucleated cells) and those treated with actinomycin D (this antibiotic would inhibit viral replication if this occurred in the nucleus.)

History
In 1897, foot-and-mouth disease virus (FMDV), the first animal virus, was discovered. FMDV is the prototypic member of the Aphthovirus genus in the Picornaviridae family.[3] The plaque assay was developed using poliovirus. Both RNA dependent RNA polymerase and polyprotein synthesis were discovered by studying poliovirus infected cells.

See also
Dicistroviridae
VPg
Animal viruses

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Family Marnaviridae Virus

Marnaviridae is a family of Virus which a single sort is known, Marnavirus . The infected species type to the microscopic alga Heterosigma akashiwo . contains Genome ARN monocatenary positive and therefore Classification of Baltimore is included in Group IV of . virus particles present/display one isometric Cápside with icosahedral symmetry and lack envelope . The length of the genome is of approximately 9000 Nucleotides

An RNA virus is a virus that has RNA (ribonucleic acid) as its genetic material. This nucleic acid is usually single-stranded RNA (ssRNA) but may be double-stranded RNA (dsRNA). The ICTV classifies RNA viruses as those that belong to Group III, Group IV or Group V of the Baltimore classification system of classifying viruses, and does not consider viruses with DNA intermediates as RNA viruses. Notable human diseases caused by RNA viruses include SARS, influenza and hepatitis C. Another term for RNA viruses that explicitly excludes retroviruses is ribovirus.

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 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 polymerase before translation. As such, purified RNA of a positive-sense virus can directly cause infection though it may be less infectious than the whole virus particle. Purified RNA of a negative-sense virus is not infectious by itself as it needs to be transcribed into positive-sense RNA, however each virion can be transcribed to several positive-sense RNAs. Ambisense RNA viruses resemble negative-sense RNA viruses, except they also translate genes from the positive strand.

Double-stranded RNA viruses
Further information: Double-stranded RNA viruses
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 (T-number, capsid layers, or turrets). Members of this group include the rotaviruses, renowned globally as the most common cause of gastroenteritis in young children, and bluetongue virus, an economically important pathogen of cattle and sheep. In recent years, remarkable progress has been made in determining, at atomic and subnanometeric levels, the structures of a number of key viral proteins and of the virion capsids of several dsRNA viruses, highlighting the significant parallels in the structure and replicative processes of many of these viruses.

Mutation rates
RNA viruses generally have very high mutation rates compared to DNA viruses, because viral RNA polymerases lack the proof-reading ability of DNA polymerases] This is one reason why it is difficult to make effective vaccines to prevent diseases caused by RNA viruses. 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, 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.

Replication
Animal RNA viruses are classified into three distinct groups depending on their genome and mode of replication (and the numerical groups based on the older Baltimore classification):

    Double-stranded RNA viruses (Group III) contain from one to a dozen different RNA molecules, each of which codes for one or more viral proteins.
    Positive-sense ssRNA viruses (Group IV) have their genome directly utilized as if it were mRNA, producing a single protein which is modified by host and viral proteins to form the various proteins needed for replication. One of these includes RNA-dependent RNA polymerase, which copies the viral RNA to form a double-stranded replicative form, in turn this directs the formation of new virions.
    Negative-sense ssRNA viruses (Group V) must have their genome copied by an RNA polymerase to form positive-sense RNA. This means that the virus must bring along with it the RNA-dependent RNA polymerase enzyme. The positive-sense RNA molecule then acts as viral mRNA, which is translated into proteins by the host ribosomes. The resultant protein goes on to direct the synthesis of new virions, such as capsid proteins and RNA replicase, which is used to produce new negative-sense RNA molecules.

Retroviruses (Group VI) have a single-stranded RNA genome but are generally not considered RNA viruses because they use DNA intermediates to replicate. Reverse transcriptase, a viral enzyme that comes from the virus itself after it 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, expression of the encoded genes may lead the formation of new virions.
Classification

Classification of the positive strand RNA viruses is based on the RNA dependent RNA polymerase. Three groups have been recognised:

I. Bymoviruses, comoviruses, nepoviruses, nodaviruses, picornaviruses, potyviruses, sobemoviruses and a subset of luteoviruses (beet western yellows virus and potato leafroll virus) - the picorna like group (Picornavirata).

II. Carmoviruses, dianthoviruses, flaviviruses, pestiviruses, tombusviruses, single-stranded RNA bacteriophages, hepatitis C virus and a subset of luteoviruses (barley yellow dwarf virus) - the flavi like group (Flavivirata).

III. Alphaviruses, carlaviruses, furoviruses, hordeiviruses, potexviruses, rubiviruses, tobraviruses, tricornaviruses, tymoviruses, apple chlorotic leaf spot virus, beet yellows virus and hepatitis E virus - the alpha like group (Rubivirata).

The alpha like groups 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 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 the Potexviridae.

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.

These proposals were based on an analysis of the RNA polymerases and are still under consideration. To date they have not been broadly accepted because of doubts over the suitability of a single gene to determine the taxonomy of the clade.

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Virus Family Iflaviridae

General Description

This genus (the sole member of the family Iflaviridae, contains viruses of invertebrates that belong in the picornavirus "superfamily", and which share a number of features, both of virion structure and genomic organisation, of members of the families Picornaviridae and Dicistroviridae but which form a distinct group in phylogenetic analyses. It is named from the type member, Infectious flacherie virus.

Morphology

Virions isometric (icosahedral), not enveloped 30 nm in diameter.

Genome

Monopartite, linear, positive sense single-stranded RNA of 8.5-10 kb. There is a genome-linked protein (VPg) at the 5'-terminus and a 3'-polyA tail.

Genus Genomic Organization

The RNA encodes a single polyprotein of 330-350 kDa that is subsequently processed into the functional products. The 3 (or sometimes 4) coat proteins are encoded near the N-terminus.

Type Member Genomic Organization

The RNA encodes a single polyprotein of 346 kDa that is subsequently processed into the functional products. The 3 coat proteins are encoded near the N-terminus and the non-structural proteins contain the recognised motifs for the RNA helicase, cysteine protease and the RNA polymerase.

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Family Dicistroviridae Virus

The Dicistroviridae are a family of Group IV (positive-sense ssRNA) insect-infecting viruses. Some of the insects commonly infected by dicistroviruses include aphids, leafhoppers, flies, bees, ants, silkworms.

Taxonomy

Although many dicistroviruses were initially placed in the Picornaviridae they have since been reclassified into their own family. The name (Dicistro) is derived from the characteristic di-cistronic arrangement of the genome.

This family is a member of the 'picornavirus-like superfamily' (Comoviridae, Iflavirus, Picornaviridae, Potyviridae and Sequiviridae). Within this superfamily the gene order is the gene order of the non-structural proteins Hel(helicase)-Pro(protease)-RdRp(polymerase). The Dicistroviridae can be distinguished from the members of the taxa by the location of the their genome's organisation: the structural proteins are located at the 3' end rather than the 5' end (as found in Iflavirus, Picornaviridae and Sequiviridae) and by having 2 genomic segments rather than a single one (as in the Comoviridae).

This family has been divided into two genera and a number of as yet unclassified species.

    Genus Cripavirus:

        Aphid lethal paralysis virus

        Black queen cell virus

        Cricket paralysis virus (type species)

        Drosophila C virus

        Himetobi P virus

        Homalodisca coagulata virus-1

        Plautia stali intestine virus

        Rhopalosiphum padi virus

        Triatoma virus

    Genus: Aparavirus

        Acute bee paralysis virus (type species)

        Israeli acute paralysis virus

        Kashmir bee virus

        Solenopsis invicta virus 1

        Taura syndrome virus

Other species:

    Cloudy wing virus

    Blackberry virus Z

    Acheta domesticus virus

    Ervivirus

    Mud crab dicistrovirus

The Dicistroviridae are a family of Group IV (positive-sense ssRNA) insect-infecting viruses. Some of the insects commonly infected by dicistroviruses include aphids, leafhoppers, flies, bees, ants, silkworms.

Notable species

    Aphid lethal paralysis virus

    Black queen cell virus – a Western honey bee virus

    Bombyx mori infectious flacherie virus (BmIFV) – a silkworm virus

    Cricket paralysis virus

    Drosophila C virus

    Himetobi P virus

    Plautia stali intestine virus

    Rhopalosiphum padi virus

    Taura syndrome virus

    Triatoma virus

    Homalodisca coagulata virus 1 (HoCV-1) – a sharpshooter virus

    Solenopsis invicta virus 1 (SINV-1) – a Red imported fire ant virus

RNA structural elements

Many of the Dicistroviridae genomes contains structured RNA elements. For example, the Cripaviruses have an internal ribosome entry site, which mimics a Met-tRNA and is used in the initiation of translation

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