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Positive-strand RNA viruses (+ssRNA viruses) are a group of related
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. Since Dmitri Ivanovsk ...
es that have
positive-sense In molecular biology and genetics, the sense of a nucleic acid molecule, particularly of a strand of DNA or RNA, refers to the nature of the roles of the strand and its complement in specifying a sequence of amino acids. Depending on the context ...
, 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. Positive-strand RNA viruses are divided between the phyla ''
Kitrinoviricota ''Kitrinoviricota'' is a phylum of RNA viruses that includes all positive-strand RNA viruses that infect eukaryotes and are not members of the phylum ''Pisuviricota'' or ''Lenarviricota.'' The name of the group derives from Greek ''κίτρινο ...
'', '' Lenarviricota'', and ''
Pisuviricota ''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 ...
'' (specifically classes ''
Pisoniviricetes ''Pisoniviricetes'' is a class of positive-strand RNA viruses which infect eukaryotes. A characteristic of the group is a conserved 3C- like protease from the PA clan of proteases for processing the translated polyprotein. The name of the gro ...
'' and '' Stelpavirictes'') all of which are in the kingdom '' Orthornavirae'' and realm '' Riboviria''. They are monophyletic and descended from a common RNA virus ancestor. In the
Baltimore classification Baltimore classification is a system used to classify viruses based on their manner of messenger RNA (mRNA) synthesis. By organizing viruses based on their manner of mRNA production, it is possible to study viruses that behave similarly as a d ...
system, +ssRNA viruses belong to Group IV. Positive-sense RNA viruses include
pathogen In biology, a pathogen ( el, πάθος, "suffering", "passion" and , "producer of") in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ ...
s such as the
Hepatitis C virus The hepatitis C virus (HCV) is a small (55–65 nm in size), enveloped, positive-sense single-stranded RNA virus of the family '' Flaviviridae''. The hepatitis C virus is the cause of hepatitis C and some cancers such as liver cancer (hepatoc ...
,
West Nile virus West Nile virus (WNV) is a single-stranded RNA virus that causes West Nile fever. It is a member of the family '' Flaviviridae'', from the genus '' Flavivirus'', which also contains the Zika virus, dengue virus, and yellow fever virus. The v ...
, dengue virus, and the MERS,
SARS Severe acute respiratory syndrome (SARS) is a viral respiratory disease of zoonotic origin caused by the severe acute respiratory syndrome coronavirus (SARS-CoV or SARS-CoV-1), the first identified strain of the SARS coronavirus species, ''seve ...
, and
SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) is a strain of coronavirus that causes COVID-19 (coronavirus disease 2019), the respiratory illness responsible for the ongoing COVID-19 pandemic. The virus previously had a ...
coronaviruses, as well as less clinically serious pathogens such as the coronaviruses and
rhinovirus The rhinovirus (from the grc, ῥίς, rhis "nose", , romanized: "of the nose", and the la, vīrus) is the most common viral infectious agent in humans and is the predominant cause of the common cold. Rhinovirus infection proliferates in tem ...
es that cause the common cold.


Genome

Positive-strand RNA virus genomes usually contain relatively few genes, usually between three and ten, including an RNA-dependent RNA polymerase. Coronaviruses have the largest known RNA genomes, between 27 and 32
kilobase A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DN ...
s in length, and likely possess replication proofreading mechanisms in the form of an
exoribonuclease An exoribonuclease is an exonuclease ribonuclease, which are enzymes that degrade RNA by removing terminal nucleotides from either the 5' end or the 3' end of the RNA molecule. Enzymes that remove nucleotides from the 5' end are called ''5'-3 ...
within
nonstructural protein In virology, a nonstructural protein is a protein encoded by a virus but that is not part of the viral particle. They typically include the various enzymes and transcription factors the virus uses to replicate itself, such as a viral protease ( 3CL ...
nsp14.


Replication

Positive-strand RNA viruses have genetic material that can function both as a
genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding g ...
and as messenger RNA; it can be directly translated into
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...
in the
host cell In biology and medicine, a host is a larger organism that harbours a smaller organism; whether a parasitic, a mutualistic, or a commensalist ''guest'' (symbiont). The guest is typically provided with nourishment and shelter. Examples include a ...
by host ribosomes. The first proteins to be expressed after infection serve genome replication functions; they recruit the positive-strand viral genome to
viral replication Viral replication is the formation of biological viruses during the infection process in the target host cells. Viruses must first get into the cell before viral replication can occur. Through the generation of abundant copies of its genome an ...
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 The endoplasmic reticulum (ER) is, in essence, the transportation system of the eukaryotic cell, and has many other important functions such as protein folding. It is a type of organelle made up of two subunits – rough endoplasmic reticulum ( ...
, but also including membranes derived from mitochondria,
vacuole A vacuole () is a membrane-bound organelle which is present in plant and fungal cells and some protist, animal, and bacterial cells. Vacuoles are essentially enclosed compartments which are filled with water containing inorganic and organic m ...
s, the
Golgi apparatus The Golgi apparatus (), also known as the Golgi complex, Golgi body, or simply the Golgi, is an organelle found in most eukaryotic cells. Part of the endomembrane system in the cytoplasm, it packages proteins into membrane-bound vesicles ...
, chloroplasts, peroxisomes, plasma membranes, autophagosomal membranes, and novel
cytoplasm In cell biology, the cytoplasm is all of the material within a eukaryotic cell, enclosed by the cell membrane, except for the cell nucleus. The material inside the nucleus and contained within the nuclear membrane is termed the nucleoplasm. ...
ic compartments. The replication of the positive-sense RNA genome proceeds through
double-stranded RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydr ...
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. 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 An internal ribosome entry site, abbreviated IRES, is an RNA element that allows for translation initiation in a cap-independent manner, as part of the greater process of protein synthesis. In eukaryotic translation, initiation typically occurs at ...
(IRES) elements; in some viruses, such as
poliovirus A poliovirus, the causative agent of polio (also known as poliomyelitis), is a serotype of the species '' Enterovirus C'', in the family of ''Picornaviridae''. There are three poliovirus serotypes: types 1, 2, and 3. Poliovirus is composed of a ...
and
rhinovirus The rhinovirus (from the grc, ῥίς, rhis "nose", , romanized: "of the nose", and the la, vīrus) is the most common viral infectious agent in humans and is the predominant cause of the common cold. Rhinovirus infection proliferates in tem ...
es, normal protein synthesis is further disrupted by viral
protease A protease (also called a peptidase, proteinase, or proteolytic enzyme) is an enzyme that catalyzes (increases reaction rate or "speeds up") proteolysis, breaking down proteins into smaller polypeptides or single amino acids, and spurring the ...
s degrading components required to initiate translation of cellular mRNA. 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 protein RNA-binding proteins (often abbreviated as RBPs) are proteins that bind to the double or single stranded RNA in cells and participate in forming ribonucleoprotein complexes. RBPs contain various structural motifs, such as RNA recognition motif ...
s, chaperone proteins, and membrane remodeling and
lipid synthesis Lipid metabolism is the synthesis and degradation of lipids in cells, involving the breakdown or storage of fats for energy and the synthesis of structural and functional lipids, such as those involved in the construction of cell membranes. In anim ...
proteins, which collectively participate in exploiting the cell's
secretory pathway 440px Secretion is the movement of material from one point to another, such as a secreted chemical substance from a cell or gland. In contrast, excretion is the removal of certain substances or waste products from a cell or organism. The classica ...
for viral replication.


Recombination

Numerous positive-strand RNA viruses can undergo genetic recombination when at least two viral genomes are present in the same host cell. 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 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&nbs ...
'' (e.g. poliovirus). In the ''
Retroviridae A retrovirus is a type of virus that inserts a DNA copy of its RNA genome into the DNA of a host cell that it invades, thus changing the genome of that cell. Once inside the host cell's cytoplasm, the virus uses its own reverse transcriptase ...
'' (e.g.
HIV The human immunodeficiency viruses (HIV) are two species of ''Lentivirus'' (a subgroup of retrovirus) that infect humans. Over time, they cause acquired immunodeficiency syndrome (AIDS), a condition in which progressive failure of the immune ...
), genome damage appears to be avoided during reverse transcription by strand switching, a form of recombination. Recombination occurs in the ''
Coronaviridae ''Coronaviridae'' is a family of enveloped, positive-strand RNA viruses which infect amphibians, birds, and mammals. The group includes the subfamilies '' Letovirinae'' and ''Orthocoronavirinae;'' the members of the latter are known as coronavi ...
'' (e.g.
SARS Severe acute respiratory syndrome (SARS) is a viral respiratory disease of zoonotic origin caused by the severe acute respiratory syndrome coronavirus (SARS-CoV or SARS-CoV-1), the first identified strain of the SARS coronavirus species, ''seve ...
). Recombination in RNA viruses appears to be an adaptation for coping with genome damage. 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. Positive-strand RNA viruses are common in plants. In
tombusvirus ''Tombusvirus'' is a genus of viruses, in the family '' Tombusviridae''. Plants serve as natural hosts. There are 17 species in this genus. Symptoms associated with this genus include mosaic. The name of the genus comes from ''Tomato bushy stunt ...
es and carmoviruses, RNA recombination occurs frequently during replication. 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. Other +ssRNA viruses of plants have also been reported to be capable of recombination, such as Brom mosaic bromovirus and
Sindbis virus ''Sindbis virus'' (SINV) is a member of the ''Togaviridae'' family, in the ''Alphavirus'' genus. The virus was first isolated in 1952 in Cairo, Egypt. The virus is transmitted by mosquitoes (''Culex'' and Culiseta). SINV is linked to Pogosta di ...
.


Classification

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 Baltimore classification is a system used to classify viruses based on their manner of messenger RNA (mRNA) synthesis. By organizing viruses based on their manner of mRNA production, it is possible to study viruses that behave similarly as a d ...
system, which groups viruses together based on their manner of mRNA synthesis, +ssRNA viruses are group IV.


''Kitrinoviricota''

The first +ssRNA phylum is ''
Kitrinoviricota ''Kitrinoviricota'' is a phylum of RNA viruses that includes all positive-strand RNA viruses that infect eukaryotes and are not members of the phylum ''Pisuviricota'' or ''Lenarviricota.'' The name of the group derives from Greek ''κίτρινο ...
''. The phylum contains what have been referred to as the "
alphavirus ''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 alphaviruses ...
supergroup" and "
flavivirus ''Flavivirus'' is a genus of positive-strand RNA viruses in the family ''Flaviviridae''. The genus includes the West Nile virus, dengue virus, tick-borne encephalitis virus, yellow fever virus, Zika virus and several other viruses which may cau ...
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 virus Plant viruses are viruses that affect plants. Like all other viruses, plant viruses are obligate intracellular parasites that do not have the molecular machinery to replicate without a host. Plant viruses can be pathogenic to higher plants. ...
es and arthropod viruses; ''Flasuviricetes'', which contains flaviviruses, '' Magsaviricetes'', which contains nodaviruses and sinhaliviruses; and '' Tolucaviricetes'', which primarily contains plant viruses.


''Lenarviricota''

'' Lenarviricota'' is the second +ssRNA phylum. It contains the class '' Leviviricetes'', which infect
prokaryote A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Conne ...
s, 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''.


''Pisuviricota''

The third phylum that contains +ssRNA viruses is ''
Pisuviricota ''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 ...
'', 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 ''Pisoniviricetes'' is a class of positive-strand RNA viruses which infect eukaryotes. A characteristic of the group is a conserved 3C- like protease from the PA clan of proteases for processing the translated polyprotein. The name of the gro ...
'', which contains nidoviruses, picornaviruses, and sobeliviruses, and '' Stelpaviricetes'', which contains
potyviruses ''Potyvirus'' is a genus of positive-strand RNA viruses in the family ''Potyviridae''. Plants serve as natural hosts. The genus is named after member virus ''potato virus Y''. Potyviruses account for about thirty percent of the currently known p ...
and astroviruses. The third class is ''
Duplopiviricetes ''Durnavirales'' is an order of double-stranded RNA viruses which infect eukaryotes. The name of the group derives from Italian ''duplo'' which means double (a reference to double-stranded), ''rna'' for the type of virus, and -''virales'' which i ...
'', whose members are double-stranded RNA viruses that are descended from +ssRNA viruses.


See also

* Double-stranded RNA virus *
Negative-strand RNA virus Negative-strand RNA viruses (−ssRNA viruses) are a group of related viruses that have negative-sense, single-stranded genomes made of ribonucleic acid. They have genomes that act as complementary strands from which messenger RNA (mRNA) is s ...
*
Sense (molecular biology) In molecular biology and genetics, the sense of a nucleic acid molecule, particularly of a strand of DNA or RNA, refers to the nature of the roles of the strand and its complement in specifying a sequence of amino acids. Depending on the contex ...


References

{{Taxonbar, from=Q9094478 Positive-sense single-stranded RNA viruses