Positive-strand RNA virus

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Positive-strand RNA virus
HCV EM picture 2.png
Hepatitis C virus
Virus classification
Group:
Group IV ((+)ssRNA)
Kingdom: Phylum: Class
Synonyms
  • Positive-sense RNA virus

Positive-strand RNA viruses (+ssRNA viruses) are a group of related viruses that have positive-sense, single-stranded genomes made of ribonucleic acid. The positive-sense genome can act as messenger RNA (mRNA) and can be directly translated into viral proteins by the host cell's ribosomes. Positive-strand RNA viruses encode an RNA-dependent RNA polymerase (RdRp) which is used during replication of the genome to synthesize a negative-sense antigenome that is then used as a template to create a new positive-sense viral genome.

Contents

Positive-strand RNA viruses are divided between the phyla Kitrinoviricota , Lenarviricota , and Pisuviricota (specifically classes Pisoniviricetes and Stelpavirictes ) all of which are in the kingdom Orthornavirae and realm Riboviria . [1] They are monophyletic and descended from a common RNA virus ancestor. In the Baltimore classification system, +ssRNA viruses belong to Group IV. [2]

Positive-sense RNA viruses include pathogens such as the Hepatitis C virus, West Nile virus, dengue virus, and the MERS, SARS, and SARS-CoV-2 coronaviruses, [3] as well as less clinically serious pathogens such as the coronaviruses and rhinoviruses that cause the common cold. [4] [5] [6]

Genome

Positive-strand RNA virus genomes usually contain relatively few genes, usually between three and ten, including an RNA-dependent RNA polymerase. [4] Coronaviruses have the largest known RNA genomes, between 27 and 32 kilobases in length, and likely possess replication proofreading mechanisms in the form of an exoribonuclease within nonstructural protein nsp14. [7]

Replication

Life cycle of Japanese encephalitis virus a +ssRNA virus: attachment, endocytosis, membrane fusion, uncoating, translation, RNA replication, assembly, maturation, and release. Pathogens-07-00068-g002.webp
Life cycle of Japanese encephalitis virus a +ssRNA virus: attachment, endocytosis, membrane fusion, uncoating, translation, RNA replication, assembly, maturation, and release.

Positive-strand RNA viruses have genetic material that can function both as a genome and as messenger RNA; it can be directly translated into protein in the host cell by host ribosomes. [8] The first proteins to be expressed after infection serve genome replication functions; they recruit the positive-strand viral genome to viral replication complexes formed in association with intracellular membranes. These complexes contain proteins of both viral and host cell origin, and may be associated with the membranes of a variety of organelles—often the rough endoplasmic reticulum, but also including membranes derived from mitochondria, vacuoles, the Golgi apparatus, chloroplasts, peroxisomes, plasma membranes, autophagosomal membranes, and novel cytoplasmic compartments. [4]

The replication of the positive-sense RNA genome proceeds through double-stranded RNA intermediates, and the purpose of replication in these membranous invaginations may be the avoidance of cellular response to the presence of dsRNA. In many cases subgenomic RNAs are also created during replication. [8] After infection, the entirety of the host cell's translation machinery may be diverted to the production of viral proteins as a result of the very high affinity for ribosomes by the viral genome's internal ribosome entry site (IRES) elements; in some viruses, such as poliovirus and rhinoviruses, normal protein synthesis is further disrupted by viral proteases degrading components required to initiate translation of cellular mRNA. [6]

All positive-strand RNA virus genomes encode RNA-dependent RNA polymerase, a viral protein that synthesizes RNA from an RNA template. Host cell proteins recruited by +ssRNA viruses during replication include RNA-binding proteins, chaperone proteins, and membrane remodeling and lipid synthesis proteins, which collectively participate in exploiting the cell's secretory pathway for viral replication. [4]

Recombination

Mechanisms of replicative and nonreplicative RNA recombination. Viruses-11-00859-g004.png
Mechanisms of replicative and nonreplicative RNA recombination.

Numerous positive-strand RNA viruses can undergo genetic recombination when at least two viral genomes are present in the same host cell. [9] The capability for recombination among +ssRNA virus pathogens of humans is common. RNA recombination appears to be a major driving force in determining genome architecture and the course of viral evolution among Picornaviridae (e.g. poliovirus). [10] In the Retroviridae (e.g. HIV), genome damage appears to be avoided during reverse transcription by strand switching, a form of recombination. [11] [12] [13] Recombination occurs in the Coronaviridae (e.g. SARS). [14] Recombination in RNA viruses appears to be an adaptation for coping with genome damage. [9] Recombination can also occur infrequently between +ssRNA viruses of the same species but of divergent lineages. The resulting recombinant viruses may sometimes cause an outbreak of infection in humans, as in the case of SARS and MERS. [14]

Positive-strand RNA viruses are common in plants. In tombusviruses and carmoviruses, RNA recombination occurs frequently during replication. [15] The ability of the RNA-dependent RNA polymerase of these viruses to switch RNA templates suggests a copy choice model of RNA recombination that may be an adaptive mechanism for coping with damage in the viral genome. [15] Other +ssRNA viruses of plants have also been reported to be capable of recombination, such as Brom mosaic bromovirus [16] and Sindbis virus. [17]

Classification

Phylogenetic tree with phylum branches highlighted. Negarnaviricota (brown), Duplornaviricota (green), Kitrinoviricota (pink), Pisuviricota (blue), and Lenarviricota (yellow). MBio.02329-18.F1.large.jpg
Phylogenetic tree with phylum branches highlighted. Negarnaviricota (brown), Duplornaviricota (green), Kitrinoviricota (pink), Pisuviricota (blue), and Lenarviricota (yellow).

Positive-strand RNA viruses are found in three phyla: Kitrinoviricota, Lenarviricota, and Pisuviricota, each of which are assigned to the kingdom Orthornavirae in the realm Riboviria . In the Baltimore classification system, which groups viruses together based on their manner of mRNA synthesis, +ssRNA viruses are group IV.[ citation needed ]

Kitrinoviricota

The first +ssRNA phylum is Kitrinoviricota . The phylum contains what have been referred to as the "alphavirus supergroup" and "flavivirus supergroup" along with various other short-genome viruses. Four classes in the phylum are recognized: Alsuviricetes , the alphavirus supergroup, which contains a large number of plant viruses and arthropod viruses; Flasuviricetes, which contains flaviviruses, Magsaviricetes , which contains nodaviruses and sinhaliviruses; and Tolucaviricetes , which primarily contains plant viruses. [18] [19]

Lenarviricota

Lenarviricota is the second +ssRNA phylum. It contains the class Leviviricetes , which infect prokaryotes, and the apparent descendants of leviviruses, which infect eukaryotes. The phylum is divided into four classes: Leviviricetes, which contains leviviruses and their relatives, Amabiliviricetes, which contains narnaviruses and their relatives, Howeltoviricetes, which contains mitoviruses and their relatives, and Miaviricetes, which contains botourmiaviruses and their relatives. Based on phylogenetic analysis of RdRp, all other RNA viruses are considered to comprise a sister clade in relation to Lenarviricota. [18] [19]

Pisuviricota

False-color Transmission electron micrograph of a SARS-CoV-2 virion. Coronaviruses like SARS-CoV-2 fall in the phylum Pisuviricota. Novel Coronavirus SARS-CoV-2 (50960620707) (cropped).jpg
False-color Transmission electron micrograph of a SARS-CoV-2 virion. Coronaviruses like SARS-CoV-2 fall in the phylum Pisuviricota .

The third phylum that contains +ssRNA viruses is Pisuviricota , which has been informally called the "picornavirus supergroup". The phylum contains a large assemblage of eukaryotic viruses known to infect animals, plants, fungi, and protists. The phylum contains three classes, two of which contain only +ssRNA viruses: Pisoniviricetes , which contains nidoviruses, picornaviruses, and sobeliviruses, and Stelpaviricetes , which contains potyviruses and astroviruses. The third class is Duplopiviricetes , whose members are double-stranded RNA viruses that are descended from +ssRNA viruses. [18] [19]

See also

Related Research Articles

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<span class="mw-page-title-main">RNA virus</span> Subclass of viruses

An RNA virus is a virus—other than a retrovirus—that has ribonucleic acid (RNA) as its genetic material. The nucleic acid is usually single-stranded RNA (ssRNA) but it may be double-stranded (dsRNA). Notable human diseases caused by RNA viruses include the common cold, influenza, SARS, MERS, COVID-19, Dengue Virus, hepatitis C, hepatitis E, West Nile fever, Ebola virus disease, rabies, polio, mumps, and measles.

Virus classification is the process of naming viruses and placing them into a taxonomic system similar to the classification systems used for cellular organisms.

<i>Parvoviridae</i> Family of viruses

Parvoviruses are a family of animal viruses that constitute the family Parvoviridae. They have linear, single-stranded DNA (ssDNA) genomes that typically contain two genes encoding for a replication initiator protein, called NS1, and the protein the viral capsid is made of. The coding portion of the genome is flanked by telomeres at each end that form into hairpin loops that are important during replication. Parvovirus virions are small compared to most viruses, at 23–28 nanometers in diameter, and contain the genome enclosed in an icosahedral capsid that has a rugged surface.

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<span class="mw-page-title-main">Picornavirus</span> Family of viruses

Picornaviruses are a group of related nonenveloped RNA viruses which infect vertebrates including fish, mammals, and birds. They are viruses that represent a large family of small, positive-sense, single-stranded RNA viruses with a 30 nm icosahedral capsid. The viruses in this family can cause a range of diseases including the common cold, poliomyelitis, meningitis, hepatitis, and paralysis.

<span class="mw-page-title-main">Viral replication</span> Formation of biological viruses during the infection process

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<i>Nidovirales</i> Order of positive-sense, single-stranded RNA viruses

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<span class="mw-page-title-main">RNA-dependent RNA polymerase</span> Enzyme that synthesizes RNA from an RNA template

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<span class="mw-page-title-main">Double-stranded RNA viruses</span> Type of virus according to Baltimore classification

Double-stranded RNA viruses are a polyphyletic group of viruses that have double-stranded genomes made of ribonucleic acid. The double-stranded genome is used as a template by the viral RNA-dependent RNA polymerase (RdRp) to transcribe a positive-strand RNA functioning as messenger RNA (mRNA) for the host cell's ribosomes, which translate it into viral proteins. The positive-strand RNA can also be replicated by the RdRp to create a new double-stranded viral genome.

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<span class="mw-page-title-main">Negative-strand RNA virus</span> Phylum of viruses

Negative-strand RNA viruses are a group of related viruses that have negative-sense, single-stranded genomes made of ribonucleic acid (RNA). They have genomes that act as complementary strands from which messenger RNA (mRNA) is synthesized by the viral enzyme RNA-dependent RNA polymerase (RdRp). During replication of the viral genome, RdRp synthesizes a positive-sense antigenome that it uses as a template to create genomic negative-sense RNA. Negative-strand RNA viruses also share a number of other characteristics: most contain a viral envelope that surrounds the capsid, which encases the viral genome, −ssRNA virus genomes are usually linear, and it is common for their genome to be segmented.

<i>Riboviria</i> Realm of viruses

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In virology, realm is the highest taxonomic rank established for viruses by the International Committee on Taxonomy of Viruses (ICTV), which oversees virus taxonomy. Six virus realms are recognized and united by specific highly conserved traits:

<i>Monodnaviria</i> Realm of viruses

Monodnaviria is a realm of viruses that includes all single-stranded DNA viruses that encode an endonuclease of the HUH superfamily that initiates rolling circle replication of the circular viral genome. Viruses descended from such viruses are also included in the realm, including certain linear single-stranded DNA (ssDNA) viruses and circular double-stranded DNA (dsDNA) viruses. These atypical members typically replicate through means other than rolling circle replication.

<i>Orthornavirae</i> Kingdom of viruses

Orthornavirae is a kingdom of viruses that have genomes made of ribonucleic acid (RNA), including genes which encode an RNA-dependent RNA polymerase (RdRp). The RdRp is used to transcribe the viral RNA genome into messenger RNA (mRNA) and to replicate the genome. Viruses in this kingdom share a number of characteristics which promote rapid evolution, including high rates of genetic mutation, recombination, and reassortment.

<i>Pisuviricota</i> Phylum of viruses

Pisuviricota is a phylum of RNA viruses that includes all positive-strand and double-stranded RNA viruses that infect eukaryotes and are not members of the phylum Kitrinoviricota,Lenarviricota or Duplornaviricota. The name of the group is a syllabic abbreviation of “picornavirus supergroup” with the suffix -viricota, indicating a virus phylum. Phylogenetic analyses suggest that Birnaviridae and Permutotetraviridae, both currently unassigned to a phylum in Orthornavirae, also belong to this phylum and that both are sister groups. Another proposed family of the phylum is unassigned Polymycoviridae in Riboviria.

References

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