''Nidovirales'' is an order of enveloped,

positive-strand 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 int ...

es which infect

vertebrate Vertebrates () comprise all animal taxa within the subphylum Vertebrata () ( chordates with backbones), including all mammals, birds, reptiles, amphibians, and fish. Vertebrates represent the overwhelming majority of the phylum Chordata, ...

s and

invertebrate Invertebrates are a paraphyletic group of animals that neither possess nor develop a vertebral column (commonly known as a ''backbone'' or ''spine''), derived from the notochord. This is a grouping including all animals apart from the chordate ...

s. Host organisms include

mammal Mammals () are a group of vertebrate animals constituting the class Mammalia (), characterized by the presence of mammary glands which in females produce milk for feeding (nursing) their young, a neocortex (a region of the brain), fur or ...

bird Birds are a group of warm-blooded vertebrates constituting the class Aves (), characterised by feathers, toothless beaked jaws, the laying of hard-shelled eggs, a high metabolic rate, a four-chambered heart, and a strong yet lightweigh ...

reptile Reptiles, as most commonly defined are the animals in the class Reptilia ( ), a paraphyletic grouping comprising all sauropsids except birds. Living reptiles comprise turtles, crocodilians, squamates (lizards and snakes) and rhynchocephalians ( ...

amphibian Amphibians are tetrapod, four-limbed and ectothermic vertebrates of the Class (biology), class Amphibia. All living amphibians belong to the group Lissamphibia. They inhabit a wide variety of habitats, with most species living within terres ...

fish Fish are aquatic, craniate, gill-bearing animals that lack limbs with digits. Included in this definition are the living hagfish, lampreys, and cartilaginous and bony fish as well as various extinct related groups. Approximately 95% of li ...

arthropod Arthropods (, (gen. ποδός)) are invertebrate animals with an exoskeleton, a Segmentation (biology), segmented body, and paired jointed appendages. Arthropods form the phylum Arthropoda. They are distinguished by their jointed limbs and Arth ...

molluscs Mollusca is the second-largest phylum of invertebrate animals after the Arthropoda, the members of which are known as molluscs or mollusks (). Around 85,000 extant taxon, extant species of molluscs are recognized. The number of fossil sp ...

, and

helminths Parasitic worms, also known as helminths, are large macroparasites; adults can generally be seen with the naked eye. Many are intestinal worms that are soil-transmitted and infect the gastrointestinal tract. Other parasitic worms such as schi ...

. The order includes the families ''

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 coronav ...

'', ''

Arteriviridae ''Arteriviridae'' is a family of enveloped, positive-strand RNA viruses in the order ''Nidovirales'' which infect vertebrates. Host organisms include equids, pigs, Possums, nonhuman primates, and rodents. The family includes, for example, equ ...

Roniviridae ''Okavirus'' is a genus of enveloped positive-strand RNA viruses which infect crustaceans. Host organisms are mostly shrimp. It is the only genus in the family ''Roniviridae''. Viruses associated with the genus include: gill-associated virus (G ...

,'' and ''

Mesoniviridae ''Mesoniviridae'' is a family of enveloped, positive-strand RNA viruses in the order ''Nidovirales'' which infect mosquitoes. The family is named after the size of the genomes relative to other nidoviruses, with ''meso-'' coming from the Greek w ...

''. Member

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 Ivanovsky's 1 ...

es have a viral envelope and a

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

RNA genome 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 ...

which is

capped In sport, a cap is a player's appearance in a game at international level. The term dates from the practice in the United Kingdom of awarding a cap to every player in an international match of rugby football and association football. In the ea ...

and polyadenylated. Nidoviruses are named for the Latin ''nidus'', meaning nest, as all viruses in this order produce a 3' co-terminal nested set of

subgenomic mRNA Subgenomic mRNAs are essentially smaller sections of the original transcribed template strand. 3' to 5' DNA or RNA During transcription, the original template strand is usually read from the 3' to the 5' end from beginning to end. Subgenomic ...

s during infection.

Virology

Structure

Nidoviruses have a viral envelope and a positive-sense, single-stranded RNA genome which is capped and polyadenylated. The group expresses structural proteins separately from the nonstructural ones. The structural proteins are encoded at the 3’ region of the

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 ge ...

and are expressed from a set of

s. Member viruses encode one main

proteinase A protease (also called a peptidase, proteinase, or proteolytic enzyme) is an enzyme that catalysis, catalyzes (increases reaction rate or "speeds up") proteolysis, breaking down proteins into smaller polypeptides or single amino acids, and spurri ...

and between one and three accessory proteinases which are mainly involved in expressing the

replicase RNA-dependent RNA polymerase (RdRp) or RNA replicase is an enzyme that catalyzes the replication of RNA from an RNA template. Specifically, it catalyzes synthesis of the RNA strand complementary to a given RNA template. This is in contrast to ...

gene. These proteinases are also responsible for activating or inactivating specific proteins at the correct time in the virus life cycle, ensuring replication occurs at the right time.

Genome

Nidoviruses can be distinguished from other RNA viruses by a constellation of seven conserved domains—5'-TM2-3CLpro-TM3-RdRp-Zm-HEL1-NendoU-3'—with the first three being encoded in

ORF1a ORF1ab (also ORF1a/b) refers collectively to two open reading frames (ORFs), ORF1a and ORF1b, that are conserved in the genomes of nidoviruses, a group of viruses that includes coronaviruses. The genes express large polyproteins that undergo pr ...

and the remaining four in

ORF1b ORF1ab (also ORF1a/b) refers collectively to two open reading frames (ORFs), ORF1a and ORF1b, that are conserved in the genomes of nidoviruses, a group of viruses that includes coronaviruses. The genes express large polyproteins that undergo p ...

. TM2 and TM3 and

transmembrane A transmembrane protein (TP) is a type of integral membrane protein that spans the entirety of the cell membrane. Many transmembrane proteins function as gateways to permit the transport of specific substances across the membrane. They frequentl ...

domains; RdRp is the

RNA-dependent RNA polymerase RNA-dependent RNA polymerase (RdRp) or RNA replicase is an enzyme that catalyzes the replication of RNA from an RNA template. Specifically, it catalyzes synthesis of the RNA strand complementary to a given RNA template. This is in contrast to t ...

; Zm is a Zn-cluster binding domain fused with a

helicase Helicases are a class of enzymes thought to be vital to all organisms. Their main function is to unpack an organism's genetic material. Helicases are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separatin ...

(HEL1); 3CLpro is a 3C-like protease; and NendoU is an uridylate-specific

endonuclease Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain. Some, such as deoxyribonuclease I, cut DNA relatively nonspecifically (without regard to sequence), while many, typically called restriction endonucleases ...

. The 3CLpro has a catalytic

His His or HIS may refer to: Computing * Hightech Information System, a Hong Kong graphics card company * Honeywell Information Systems * Hybrid intelligent system * Microsoft Host Integration Server Education * Hangzhou International School, in ...

- Cys dyad, and is related to the

SARS coronavirus main proteinase The 3C-like protease (3CLpro) or main protease (Mpro), formally known as C30 endopeptidase or 3-chymotrypsin-like protease, is the main protease found in coronaviruses. It cleaves the coronavirus polyprotein at eleven conserved sites. It is a cy ...

(Mpro). Most, but not all, nidovirus subgenomic RNAs contain a 5′ leader sequence derived from the 5′ end of the genomic RNA. The

frameshift Ribosomal frameshifting, also known as translational frameshifting or translational recoding, is a biological phenomenon that occurs during translation that results in the production of multiple, unique proteins from a single mRNA. The process can ...

that generates

ORF ORF or Orf may refer to: * Norfolk International Airport, IATA airport code ORF * Observer Research Foundation, an Indian research institute * One Race Films, a film production company founded by Vin Diesel * Open reading frame, a portion of the ...

1b frameshift occurs at a UUUAAAC heptanucleotide 'slippery' sequence located upstream of the ORF1a stop codon and a putative RNA

pseudoknot __NOTOC__ A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot was first recognized in the turnip yellow ...

structure. Many proteins have been identified on the genomes of ''Nidovirales'', but their function has not yet been determined. Other enzymes that may be present in the genome include

papain Papain, also known as papaya proteinase I, is a cysteine protease () enzyme present in papaya (''Carica papaya'') and mountain papaya (''Vasconcellea cundinamarcensis''). It is the namesake member of the papain-like protease family. It has wide ...

-like proteases, ADP-ribose/poly(ADP-ribose)-binding or ADP-ribose 1''-phosphate phosphatase activities and

cyclic nucleotide phosphodiesterase 3′,5′-cyclic-nucleotide phosphodiesterases (EC 3.1.4.17) are a family of phosphodiesterases. Generally, these enzymes hydrolyze a nucleoside 3′,5′-cyclic phosphate to a nucleoside 5′-phosphate: :nucleoside 3′,5′-cyclic phosphate + ...

Phylogenetics

The order ''Nidovirales'' can be divided into two

clade A clade (), also known as a monophyletic group or natural group, is a group of organisms that are monophyletic – that is, composed of a common ancestor and all its lineal descendants – on a phylogenetic tree. Rather than the English term, ...

s depending on the size of the genome: those with large genomes (26.3–31.7 kilobases) which included the ''Coronaviridae'' and ''Roniviridae'' (the large nidoviruses) and those with small genomes (the small nidoviruses)—a clade that includes the distantly related ''Arteriviridae'' (12.7–15.7 kb). The large nidoviruses encode both a 2'-O-

methyltransferase Methyltransferases are a large group of enzymes that all methylate their substrates but can be split into several subclasses based on their structural features. The most common class of methyltransferases is class I, all of which contain a Ross ...

and a 3'–5'

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 ...

(ExoN)—the latter being very unusual for an RNA virus. They also encode a superfamily 1

, uridylate-specific endonuclease (an enzyme unique to nidoviruses) and several proteases. Nidoviruses as a group have the largest RNA genomes of viruses. Group member planarian secretory cell nidovirus (PSCNV) has the largest known nonsegmented RNA genome of 41.1kb. Its host is the

planarian A planarian is one of the many flatworms of the traditional class Turbellaria. It usually describes free-living flatworms of the order Tricladida (triclads), although this common name is also used for a wide number of free-living platyhelmint ...

flatworm The flatworms, flat worms, Platyhelminthes, or platyhelminths (from the Greek πλατύ, ''platy'', meaning "flat" and ἕλμινς (root: ἑλμινθ-), ''helminth-'', meaning "worm") are a phylum of relatively simple bilaterian, unsegment ...

Taxonomy

The following suborders and families are recognized (-''virineae'' denotes

suborder Order ( la, ordo) is one of the eight major hierarchical taxonomic ranks in Linnaean taxonomy. It is classified between family and class. In biological classification, the order is a taxonomic rank used in the classification of organisms and ...

s and -''viridae'' denotes families): Taxonomy tree of the order Nidovirales

* '' Abnidovirineae'' ** '' Abyssoviridae'' * '' Arnidovirineae'' ** ''

'' ** '' Cremegaviridae'' ** '' Gresnaviridae'' ** '' Olifoviridae'' * '' Cornidovirineae'' ** ''

'' * '' Mesnidovirineae'' ** '' Medioniviridae'' ** ''

'' * '' Monidovirineae'' ** '' Mononiviridae'' * '' Nanidovirinae'' ** '' Nanghoshaviridae'' ** '' Nanhypoviridae'' * '' Ronidovirineae'' ** '' Euroniviridae'' ** ''

'' * '' Tornidovirineae'' ** '' Tobaniviridae''

References

External links

Nidovirales
��ICTVdB—The Universal Virus Database, version 4. *
NIH/MeSH
* "The Nidoviruses" {{Authority control Animal virology Virus orders Riboviria