{{Short description|Order of positive-sense, single-stranded RNA viruses}} {{Virusbox | image = Nidovirales life cycle.webp | image_alt = Electron micrograph of negatively stained Nam Dinh virus particles | image_caption = Life cycle of nidoviruses | taxon = Nidovirales | synonyms = | synonyms_ref = }}
'''''Nidovirales''''' is an order of enveloped, positive-strand RNA viruses which infect vertebrates and invertebrates. Host organisms include mammals, birds, reptiles, amphibians, fish, arthropods, molluscs, and helminths.<ref>{{Cite journal|last1=Ogando|first1=Natacha S.|last2=Ferron|first2=Francois|last3=Decroly|first3=Etienne|last4=Canard|first4=Bruno|last5=Posthuma|first5=Clara C.|last6=Snijder|first6=Eric J.|date=2019|title=The Curious Case of the Nidovirus Exoribonuclease: Its Role in RNA Synthesis and Replication Fidelity|journal=Frontiers in Microbiology|language=en|volume=10|page=1813|doi=10.3389/fmicb.2019.01813|pmid=31440227|pmc=6693484|issn=1664-302X|doi-access=free}}</ref> The order includes the families ''Coronaviridae'', ''Arteriviridae, Roniviridae,'' ''Tobaniviridae'', and ''Mesoniviridae''.<ref>{{Cite web|title=International Committee on Taxonomy of Viruses (ICTV)|url=https://ictv.global/taxonomy|access-date=2020-06-08|website=talk.ictvonline.org|language=en}}</ref>
Member viruses have a viral envelope and a positive-sense, single-stranded RNA genome which is capped and polyadenylated.<ref name=":0">{{cite book|chapter=Order - Nidovirales|date=2012-01-01|chapter-url=http://www.sciencedirect.com/science/article/pii/B9780123846846000665|title=Virus Taxonomy|pages=784–794|editor-last=King|editor-first=Andrew M. Q.|publisher=Elsevier|doi=10.1016/B978-0-12-384684-6.00066-5|language=en|isbn=978-0-12-384684-6|s2cid=218627729 |access-date=2020-06-08|editor2-last=Adams|editor2-first=Michael J.|editor3-last=Carstens|editor3-first=Eric B.|editor4-last=Lefkowitz|editor4-first=Elliot J.|doi-access=free|pmc=7150239}}</ref> Nidoviruses are named for the Latin ''nidus'', meaning nest, as all viruses in this order produce a 3' co-terminal nested set of subgenomic mRNAs during infection.<ref>{{cite journal |author=Antoine A.F. de Vries |author2=Marian C. Horzinek |author3=Peter J. M. Rottier |author4=Raoul J. de Groot |title=The Genome Organization of the Nidovirales: Similarities and Differences between Arteri-, Toro-, and Coronaviruses |journal=Seminars in Virology |volume=8 |issue=1 |pages=33–47 |doi=10.1006/smvy.1997.0104 |year=1997 |pmid=32288441 |pmc=7128191 |citeseerx=10.1.1.462.1825 |s2cid=85383257 }}</ref>
== Virology ==
=== Structure === [[File:Journal.ppat.1003500.g003.tif|thumb|Comparison of genomes and proteomes of different families of nidoviruses]]
Nidoviruses have a viral envelope and a positive-sense, single-stranded RNA genome which is capped and polyadenylated.<ref name=":0" /> The group expresses structural proteins separately from the nonstructural ones. The structural proteins are encoded at the 3' region of the genome and are expressed from a set of subgenomic mRNAs.{{cn|date=October 2022}}
Member viruses encode one main proteinase and between one and three accessory proteinases which are mainly involved in expressing the replicase 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.{{cn|date=October 2022}}
=== 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 and the remaining four in ORF1b. TM2 and TM3 and transmembrane domains; RdRp is the RNA-dependent RNA polymerase; Zm is a Zn-cluster binding domain fused with a helicase (HEL1); 3CLpro is a 3C-like protease; and NendoU is an uridylate-specific endonuclease. The 3CLpro has a catalytic His-Cys dyad, and is related to the SARS coronavirus main proteinase (Mpro).{{cn|date=October 2022}}
Most, but not all, nidovirus subgenomic RNAs contain a 5′ leader sequence derived from the 5′ end of the genomic RNA. The frameshift that generates ORF1b frameshift occurs at a UUUAAAC heptanucleotide 'slippery' sequence located upstream of the ORF1a stop codon and a putative RNA pseudoknot structure.{{cn|date=October 2022}}
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-like proteases, ADP-ribose/poly(ADP-ribose)-binding or ADP-ribose 1''-phosphate phosphatase activities and cyclic nucleotide phosphodiesterase.{{cn|date=October 2022}}
== Phylogenetics == [[File:Nidovirus genome phylogeny.jpg|thumb|Phylogeny and pp1ab domain organization of selected nidoviruses.<ref name="gulyaeva_2021">{{cite journal |last1=Gulyaeva |first1=Anastasia A. |last2=Gorbalenya |first2=Alexander E. |title=A nidovirus perspective on SARS-CoV-2 |journal=Biochemical and Biophysical Research Communications |date=January 2021 |volume=538 |pages=24–34 |doi=10.1016/j.bbrc.2020.11.015|pmid=33413979 |pmc=7664520}}</ref>]] The order ''Nidovirales'' can be divided into two clades 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).{{cn|date=October 2022}}
The large nidoviruses encode both a 2'-O-methyltransferase and a 3'–5' exoribonuclease (ExoN)—the latter being very unusual for an RNA virus. They also encode a superfamily 1 helicase, uridylate-specific endonuclease (an enzyme unique to nidoviruses) and several proteases.{{cn|date=October 2022}}
Nidoviruses as a group have the largest RNA genomes of viruses. The largest reported genomes for RNA viruses are Crassostrea gigas nidovirus (CGNV)<ref>{{Cite journal |last=Neuman |first=Benjamin W. |last2=Smart |first2=Alexandria |last3=Gilmer |first3=Orian |last4=Smyth |first4=Redmond P. |last5=Vaas |first5=Josef |last6=Böker |first6=Nicolai |last7=Samborskiy |first7=Dmitry V. |last8=Bartenschlager |first8=Ralf |last9=Seitz |first9=Stefan |last10=Gorbalenya |first10=Alexander E. |last11=Caliskan |first11=Neva |last12=Lauber |first12=Chris |date=2025-02-18 |title=Giant RNA genomes: Roles of host, translation elongation, genome architecture, and proteome in nidoviruses |url=https://www.pnas.org/doi/10.1073/pnas.2413675122 |journal=Proceedings of the National Academy of Sciences |volume=122 |issue=7 |article-number=e2413675122 |doi=10.1073/pnas.2413675122 |pmc=11848433 |pmid=39928875}}</ref> and Pacific oyster nidoviirus 1 (PONV 1);<ref name=":1">{{Cite journal |last=Zhong |first=Kevin Xu |last2=Chan |first2=Amy M. |last3=Miller |first3=Kristina M. |last4=Saunders |first4=Rob |last5=Suttle |first5=Curtis A. |date=2025-08-19 |title=Evolutionarily divergent nidovirus with an exceptionally large genome identified in Pacific oysters undergoing mass mortality |url=https://www.pnas.org/doi/10.1073/pnas.2426923122 |journal=Proceedings of the National Academy of Sciences |volume=122 |issue=33 |article-number=e2426923122 |doi=10.1073/pnas.2426923122|doi-access=free |pmc=12377751 }}</ref> they are biseqmented, ~64kb in size, and infect Pacific oysters. They are members of a widely distributed group of viruses that belong to the proposed family Megarnaviridae.<ref name=":1" /> Previously, the largest reported genome was the 41.1kb, nonsegmented genome of planarian secretory cell nidovirus (PSCNV)<ref>{{Cite web|title=Taxonomy browser (Planidovirus 1)|url=https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2508226&lvl=3&lin=f&keep=1&srchmode=1&unlock|access-date=2020-06-08|website=www.ncbi.nlm.nih.gov}}</ref> that infect a planarian flatworm.<ref>{{Cite journal|last1=Saberi|first1=Amir|last2=Gulyaeva|first2=Anastasia A.|last3=Brubacher|first3=John L.|last4=Newmark|first4=Phillip A.|last5=Gorbalenya|first5=Alexander E.|date=2018-11-01|title=A planarian nidovirus expands the limits of RNA genome size|journal=PLOS Pathogens|language=en|volume=14|issue=11|article-number=e1007314|doi=10.1371/journal.ppat.1007314|issn=1553-7374|pmc=6211748|pmid=30383829 |doi-access=free }}</ref>
== Taxonomy == The following suborders and families are recognized (-''virineae'' denotes suborders and -''viridae'' denotes families):<ref>{{cite web|title=Virus Taxonomy: 2019 Release|url=https://ictv.global/taxonomy|access-date=30 April 2020|website=talk.ictvonline.org|publisher=International Committee on Taxonomy of Viruses}}</ref> thumb|Taxonomy tree of the order ''Nidovirales'' {{Div col|colwidth=15em}} * ''Abnidovirineae'' ** ''Abyssoviridae'' * ''Arnidovirineae'' ** ''Arteriviridae'' ** ''Cremegaviridae'' ** ''Gresnaviridae'' ** ''Olifoviridae'' * ''Cornidovirineae'' ** ''Coronaviridae'' * ''Mesnidovirineae'' ** ''Medioniviridae'' ** ''Mesoniviridae'' * ''Monidovirineae'' ** ''Mononiviridae'' * ''Nanidovirineae'' ** ''Nanghoshaviridae'' ** ''Nanhypoviridae'' * ''Ronidovirineae'' ** ''Euroniviridae'' ** ''Roniviridae'' * ''Tornidovirineae'' ** ''Tobaniviridae''
{{div col end}}
== See also == * Animal viruses * Coronaviruses * Serpentoviruses
==References== {{Reflist|2}} * {{cite journal|last1=Ziebuhr|first1=J|last2=Snijder|first2=EJ|last3=Gorbalenya|first3=AE|title=Virus-encoded proteinases and proteolytic processing in the Nidovirales.|journal=The Journal of General Virology|date=April 2000|volume=81|issue=Pt 4|pages=853–79|doi=10.1099/0022-1317-81-4-853|pmid=10725411|doi-access=free}}
==External links== * [https://web.archive.org/web/20000818075429/http://www.ncbi.nlm.nih.gov/ICTVdb/ICTVdB/index.htm Nidovirales]—ICTVdB—The Universal Virus Database, version 4. * {{MeshName|Nidovirales}} * [https://www.ncbi.nlm.nih.gov/mesh?cmd=search&term=nidovirales NIH/MeSH] * "The Nidoviruses" {{ISBN|0306466341}}
{{Taxonbar|from=Q963408}} {{Authority control}}
Category:Nidovirales Category:Animal virology Category:Virus orders Category:Riboviria