Potyvirus

The virion is non-enveloped with a flexuous and filamentous nucleocapsid, 680 to 900 nanometers (nm) long and is 11–20 nm in diameter. The nucleocapsid contains around 2000 copies of the capsid protein. The symmetry of the nucleocapsid is helical with a pitch of 3.4-3.5 nm.

File:OPSR.Pot.Fig2.v3.png

The genome is a linear, positive-sense, single-stranded RNA ranging in size from 9,000 to 12,000 nucleotide bases. Most potyviruses have non-segmented genomes, though a number of species are bipartite. The typical base compositions of some of the most common, non-recombinant strains of the type species, PVY, range between ~23.4-23.8 % G; ~31-31.6 % A; ~18.2-18.8 % C; and ~26.5-26.8 % U.{{cite journal | vauthors = Gómez MM, de Mello Volotão E, Assandri IR, Peyrou M, Cristina J | title = Analysis of codon usage bias in potato virus Y non-recombinant strains | journal = Virus Research | volume = 286 | pages = 198077 | date = September 2020 | pmid = 32619560 | doi = 10.1016/j.virusres.2020.198077 | s2cid = 220335898 }}

In the species with a monopartite genome, a genome-linked VPg protein is covalently bound to the 5' end and the 3' end is polyadenylated. The genome encodes a single open reading frame (ORF) expressed as a 350 kDa polyprotein precursor. This polyprotein is processed into ten smaller proteins: protein 1 protease (P1-Pro), helper component protease (HC-Pro), protein 3 (P3), cylindrical inclusion (CI), viral protein genome-linked (Vpg), nuclear inclusion A (NIa), nuclear inclusion B (NIb), capsid protein (CP) and two small putative proteins known as 6K1 and 6K2. The P3 cistron also contains an overlapping reading frame called "Pretty interesting Potyviridae ORF" (PIPO).{{cite journal | vauthors = Chung BY, Miller WA, Atkins JF, Firth AE | title = An overlapping essential gene in the Potyviridae | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 105 | issue = 15 | pages = 5897–5902 | date = April 2008 | pmid = 18408156 | pmc = 2311343 | doi = 10.1073/pnas.0800468105 | doi-access = free | bibcode = 2008PNAS..105.5897C }} PIPO codes for an alternative C-terminus to the P3 protein, which is generated into a subset of transcripts by a +2 frameshift caused by a ribosome slippage mechanism at a conserved GA₆ repeat sequence.{{cite journal | vauthors = Rodamilans B, Valli A, Mingot A, San León D, Baulcombe D, López-Moya JJ, García JA | title = RNA polymerase slippage as a mechanism for the production of frameshift gene products in plant viruses of the potyviridae family | journal = Journal of Virology | volume = 89 | issue = 13 | pages = 6965–6967 | date = July 2015 | pmid = 25878117 | pmc = 4468506 | doi = 10.1128/JVI.00337-15 | veditors = Simon A }}{{cite journal | vauthors = Olspert A, Chung BY, Atkins JF, Carr JP, Firth AE | title = Transcriptional slippage in the positive-sense RNA virus family Potyviridae | journal = EMBO Reports | volume = 16 | issue = 8 | pages = 995–1004 | date = August 2015 | pmid = 26113364 | pmc = 4552492 | doi = 10.15252/embr.201540509 }} The resulting protein is called P3N-PIPO. A similar mechanism is thought to produce an alternative reading frame within the P1 cistron, named "pretty interesting sweet potato potyvirus ORF" (PISPO), in a number of sweet potato-infecting potyviruses including sweet potato feathery mottle virus (Potyvirus batataplumei).{{cite journal | vauthors = Untiveros M, Olspert A, Artola K, Firth AE, Kreuze JF, Valkonen JP | title = A novel sweet potato potyvirus open reading frame (ORF) is expressed via polymerase slippage and suppresses RNA silencing | journal = Molecular Plant Pathology | volume = 17 | issue = 7 | pages = 1111–1123 | date = September 2016 | pmid = 26757490 | pmc = 4979677 | doi = 10.1111/mpp.12366 }}

File:OPSR.Pot.Fig1.v1-potyvirus_(l)_shema.png

P1 (~33 kilodaltons (kDa) in molecular weight) is a serine protease which facilitates its own cleavage from the polyprotein at the P1-HC-Pro junction.{{cite journal | vauthors = Pasin F, Simón-Mateo C, García JA | title = The hypervariable amino-terminus of P1 protease modulates potyviral replication and host defense responses | journal = PLOS Pathogens | volume = 10 | issue = 3 | pages = e1003985 | date = March 2014 | pmid = 24603811 | pmc = 3946448 | doi = 10.1371/journal.ppat.1003985 | doi-access = free }} P1 consists of a conserved C-terminal protease domain and an N-terminal region which has a high level of variation in sequence and length between potyvirus species but exhibits conserved patterns of intrinsic disorder. P1 is also promotes viral RNA replication, though it is not required for it.{{cite journal | vauthors = Verchot J, Carrington JC | title = Evidence that the potyvirus P1 proteinase functions in trans as an accessory factor for genome amplification | journal = Journal of Virology | volume = 69 | issue = 6 | pages = 3668–3674 | date = June 1995 | pmid = 7745715 | pmc = 189082 | doi = 10.1128/jvi.69.6.3668-3674.1995 }}

HC-Pro (~52 KDa) is a cysteine protease which cleaves a glycine-glycine dipeptide at its own C-terminus. It also interacts with eukaryotic initiation factor 4 (eIF4). It acts as a viral RNA silencing suppressor through its interactions with host AGO proteins.{{cite journal | vauthors = Pollari M, De S, Wang A, Mäkinen K | title = The potyviral silencing suppressor HCPro recruits and employs host ARGONAUTE1 in pro-viral functions | journal = PLOS Pathogens | volume = 16 | issue = 10 | pages = e1008965 | date = October 2020 | pmid = 33031436 | pmc = 7575100 | doi = 10.1371/journal.ppat.1008965 | doi-access = free }} HC-Pro's activity is regulated by the adjacent P1 protein: before P1 cleaves itself off the P1-HC-Pro intermediate, the P1 terminus reduces HC-Pro's RNA silencing suppression activity. The rate of P1 cleavage therefore regulates the level of RNA interference suppression during infection. HC-Pro is also involved in aphid transmission.{{cite journal | vauthors = Pirone TP, Blanc S | title = Helper-dependent vector transmission of plant viruses | journal = Annual Review of Phytopathology | volume = 34 | issue = 1 | pages = 227–247 | date = September 1996 | pmid = 15012542 | doi = 10.1146/annurev.phyto.34.1.227 }} Though the exact mechanism is unknown, HC-Pro has been proposed to attach to host aphid mouth parts through its N-terminal zinc finger-like domain and anchor virions through its interactions with the capsid protein.{{cite journal | vauthors = Valli AA, Gallo A, Rodamilans B, López-Moya JJ, García JA | title = The HCPro from the Potyviridae family: an enviable multitasking Helper Component that every virus would like to have | journal = Molecular Plant Pathology | volume = 19 | issue = 3 | pages = 744–763 | date = March 2018 | pmid = 28371183 | pmc = 6638112 | doi = 10.1111/mpp.12553 }}

P3 (~41 kDa) is a membrane protein which is required for viral replication and accumulates in viral replication vesicles.{{cite journal | vauthors = Cui X, Yaghmaiean H, Wu G, Wu X, Chen X, Thorn G, Wang A | title = The C-terminal region of the Turnip mosaic virus P3 protein is essential for viral infection via targeting P3 to the viral replication complex | journal = Virology | volume = 510 | pages = 147–155 | date = October 2017 | pmid = 28735115 | doi = 10.1016/j.virol.2017.07.016 }} It mediates the interactions between replication vesicles and movement complex proteins which may allow replication vesicles to be recruited to the movement complex for efficient intercellular movement.{{cite journal | vauthors = Chai M, Wu X, Liu J, Fang Y, Luan Y, Cui X, Zhou X, Wang A, Cheng X | display-authors = 6 | title = P3N-PIPO Interacts with P3 via the Shared N-Terminal Domain To Recruit Viral Replication Vesicles for Cell-to-Cell Movement | journal = Journal of Virology | volume = 94 | issue = 8 | date = March 2020 | pmid = 31969439 | pmc = 7108826 | doi = 10.1128/JVI.01898-19 | veditors = Simon AE }} P3 also interacts with large subunit of the ribulose-1,5-bisphosphate carboxylase/oxygenase.{{Citation needed|date=August 2023}}

CI (~71 kDa) is an RNA helicase with ATPase activity.{{cite journal | vauthors = Sorel M, Garcia JA, German-Retana S | title = The Potyviridae cylindrical inclusion helicase: a key multipartner and multifunctional protein | journal = Molecular Plant-Microbe Interactions | volume = 27 | issue = 3 | pages = 215–226 | date = March 2014 | pmid = 24405034 | doi = 10.1094/MPMI-11-13-0333-CR | doi-access = free }} Its most unusual property is its ability to form large and highly symmetrical conical and cylindrical inclusions with a central hollow cylinder from which laminate sheets radiate outward and fold in on themselves in a pattern often described as "pinwheels". These inclusions are easily seen in transmission electron micrographs of infected tissues and were historically used as a diagnostic criterion for potyvirus infections. CI inclusions are a major component of the potyviral movement complex which is assembled at plasmodesmata. CI is also required for viral replication and is present on replication membranes. Its exact contributions to replication are not clear but, as an RNA helicase, CI is likely facilitating replication by dismantling the secondary structures of viral RNA.

NIa (~50 kDa) forms crystalline inclusions in the host nucleus. It is cleaved into NIa-Pro and VPg.

NIa-Pro (~27 kDa) is a cysteine protease which processes most of the cleavage sites of the polyprotein.{{cite journal | vauthors = Mann KS, Sanfaçon H | title = Expanding Repertoire of Plant Positive-Strand RNA Virus Proteases | journal = Viruses | volume = 11 | issue = 1 | pages = 66 | date = January 2019 | pmid = 30650571 | pmc = 6357015 | doi = 10.3390/v11010066 | doi-access = free }} The only exceptions are the self-cleavages of P1 and HC-Pro. The high degree of cleavage sequence specificity and conservation has made NIa-Pro (often that of Tobacco etch virus) a valuable tool in biotechnology, especially in applications which require removing affinity tags from recombinant proteins after affinity purification. NIa-Pro has also shown to exhibit sequence-independent DNase activity and to interfere with host DNA methylation suggesting that NIa and/or NIa-Pro are altering in host gene expression.{{cite journal | vauthors = Gong YN, Tang RQ, Zhang Y, Peng J, Xian O, Zhang ZH, Zhang SB, Zhang DY, Liu H, Luo XW, Liu Y | display-authors = 6 | title = The NIa-Protease Protein Encoded by the Pepper Mottle Virus Is a Pathogenicity Determinant and Releases DNA Methylation of Nicotiana benthamiana | journal = Frontiers in Microbiology | volume = 11 | pages = 102 | date = 2020-02-21 | pmid = 32153517 | pmc = 7047827 | doi = 10.3389/fmicb.2020.00102 | doi-access = free }} Potyviral NIa-Pro shares a high level of homology with the picornaviral 3C protease.{{cite journal | vauthors = Koonin EV, Wolf YI, Nagasaki K, Dolja VV | title = The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups | journal = Nature Reviews. Microbiology | volume = 6 | issue = 12 | pages = 925–939 | date = December 2008 | pmid = 18997823 | doi = 10.1038/nrmicro2030 | s2cid = 205497478 | doi-access = free | author-link = Eugene Koonin }}

VPg (~22 kDa) is covalently attached to the 5' end of the viral genomic RNA through uridylation and is thought to act as a primer for viral genome replication similarly to the VPg proteins of picornaviridae.{{cite journal | vauthors = Walter J, Barra A, Doublet B, Céré N, Charon J, Michon T | title = Hydrodynamic Behavior of the Intrinsically Disordered Potyvirus Protein VPg, of the Translation Initiation Factor eIF4E and of their Binary Complex | journal = International Journal of Molecular Sciences | volume = 20 | issue = 7 | pages = 1794 | date = April 2019 | pmid = 30978975 | pmc = 6479716 | doi = 10.3390/ijms20071794 | doi-access = free }} It is a highly disordered protein and its flexibility has been suggested to allow it to interact with many other viral proteins. VPg also interacts with various host proteins including eukaryotic initiation factor 4E (eIF4E), eukaryotic elongation factor 1A (eEF1A), and poly(A)-binding protein (PABP).{{cite journal | vauthors = Léonard S, Plante D, Wittmann S, Daigneault N, Fortin MG, Laliberté JF | title = Complex formation between potyvirus VPg and translation eukaryotic initiation factor 4E correlates with virus infectivity | journal = Journal of Virology | volume = 74 | issue = 17 | pages = 7730–7737 | date = September 2000 | pmid = 10933678 | pmc = 112301 | doi = 10.1128/jvi.74.17.7730-7737.2000 }}{{cite journal | vauthors = Wang A | title = Dissecting the molecular network of virus-plant interactions: the complex roles of host factors | journal = Annual Review of Phytopathology | volume = 53 | issue = 1 | pages = 45–66 | date = 2015-08-04 | pmid = 25938276 | doi = 10.1146/annurev-phyto-080614-120001 | doi-access = free }}

NIb (~59 kDa) is a superfamily II RNA-dependent RNA polymerase (RdRp) which polymerises viral RNA during replication.{{cite journal | vauthors = Shen W, Shi Y, Dai Z, Wang A | title = The RNA-Dependent RNA Polymerase NIb of Potyviruses Plays Multifunctional, Contrasting Roles during Viral Infection | journal = Viruses | volume = 12 | issue = 1 | pages = 77 | date = January 2020 | pmid = 31936267 | pmc = 7019339 | doi = 10.3390/v12010077 | doi-access = free }} Like NIa, NIb forms inclusions in the host nucleus where it is transported due to its two nuclear localisation sequences. NIb has the three-domain "palm, thumb, and fingers" structure typical of RdRps.

6K1 (~6 kDa) the function is not known, but because it accumulates in replication vesicles and has a transmembrane domain, 6K1 is thought to contribute to virus-induced vesicle formation.{{cite journal | vauthors = Cui H, Wang A | title = Plum Pox Virus 6K1 Protein Is Required for Viral Replication and Targets the Viral Replication Complex at the Early Stage of Infection | journal = Journal of Virology | volume = 90 | issue = 10 | pages = 5119–5131 | date = May 2016 | pmid = 26962227 | pmc = 4859702 | doi = 10.1128/JVI.00024-16 | veditors = Simon A }}

6K2 (~6 kDa) is a transmembrane protein which rearranges host membranes into virus-induced membrane structures.{{cite journal | vauthors = Laliberté JF, Sanfaçon H | title = Cellular remodeling during plant virus infection | journal = Annual Review of Phytopathology | volume = 48 | issue = 1 | pages = 69–91 | date = 2010-07-01 | pmid = 20337516 | doi = 10.1146/annurev-phyto-073009-114239 }} It interacts with various ER exit site proteins to produce vesicular and tubular extensions which eventually mature into replication vesicles.{{cite journal | vauthors = Wei T, Wang A | title = Biogenesis of cytoplasmic membranous vesicles for plant potyvirus replication occurs at endoplasmic reticulum exit sites in a COPI- and COPII-dependent manner | journal = Journal of Virology | volume = 82 | issue = 24 | pages = 12252–12264 | date = December 2008 | pmid = 18842721 | doi = 10.1128/JVI.01329-08 | pmc = 2593340 }} 6K2 has three main domains: the N-terminal domain which is required for cell-to-cell movement, the central hydrophobic transmembrane alpha helix, and the C terminal domain which is required for viral replication.{{cite journal | vauthors = González R, Wu B, Li X, Martínez F, Elena SF | title = Mutagenesis Scanning Uncovers Evolutionary Constraints on Tobacco Etch Potyvirus Membrane-Associated 6K2 Protein | journal = Genome Biology and Evolution | volume = 11 | issue = 4 | pages = 1207–1222 | date = April 2019 | pmid = 30918938 | pmc = 6482416 | doi = 10.1093/gbe/evz069 | veditors = Wayne M }}

P3N-PIPO (~25 kDa) is a dedicated movement protein which anchors the movement complex to the plasmodesma.{{cite journal | vauthors = Wei T, Zhang C, Hong J, Xiong R, Kasschau KD, Zhou X, Carrington JC, Wang A | display-authors = 6 | title = Formation of complexes at plasmodesmata for potyvirus intercellular movement is mediated by the viral protein P3N-PIPO | journal = PLOS Pathogens | volume = 6 | issue = 6 | pages = e1000962 | date = June 2010 | pmid = 20585568 | pmc = 2891837 | doi = 10.1371/journal.ppat.1000962 | veditors = Manchester M | doi-access = free }} It may also modulate the plasmodesmatal size exclusion limit by interacting with host proteins which sever plasmodesmatal actin filaments and reduce callose deposition.{{cite journal | vauthors = Cheng G, Yang Z, Zhang H, Zhang J, Xu J | title = Remorin interacting with PCaP1 impairs Turnip mosaic virus intercellular movement but is antagonised by VPg | journal = The New Phytologist | volume = 225 | issue = 5 | pages = 2122–2139 | date = March 2020 | pmid = 31657467 | doi = 10.1111/nph.16285 | s2cid = 204948140 | doi-access = free | bibcode = 2020NewPh.225.2122C }}{{cite journal | vauthors = Rocher M, Simon V, Jolivet MD, Sofer L, Deroubaix AF, Germain V, Mongrand S, German-Retana S | display-authors = 6 | title = StREM1.3 REMORIN Protein Plays an Agonistic Role in Potyvirus Cell-to-Cell Movement in N. benthamiana | journal = Viruses | volume = 14 | issue = 3 | pages = 574 | date = March 2022 | pmid = 35336981 | pmc = 8951588 | doi = 10.3390/v14030574 | doi-access = free }} It interacts with both the large and small subunits of the ribulose-1,5-bisphosphate carboxylase/oxygenase.{{Citation needed|date=August 2023}}

CP (~30 - 35 kDa) is the capsid protein. It has two terminal domains which are disordered and exposed at the surface of the virion.{{cite journal | vauthors = Cuesta R, Yuste-Calvo C, Gil-Cartón D, Sánchez F, Ponz F, Valle M | title = Structure of Turnip mosaic virus and its viral-like particles | journal = Scientific Reports | volume = 9 | issue = 1 | pages = 15396 | date = October 2019 | pmid = 31659175 | pmc = 6817885 | doi = 10.1038/s41598-019-51823-4 | bibcode = 2019NatSR...915396C }}{{cite journal | vauthors = Kežar A, Kavčič L, Polák M, Nováček J, Gutiérrez-Aguirre I, Žnidarič MT, Coll A, Stare K, Gruden K, Ravnikar M, Pahovnik D, Žagar E, Merzel F, Anderluh G, Podobnik M | display-authors = 6 | title = Structural basis for the multitasking nature of the potato virus Y coat protein | journal = Science Advances | volume = 5 | issue = 7 | pages = eaaw3808 | date = July 2019 | pmid = 31328164 | pmc = 6636993 | doi = 10.1126/sciadv.aaw3808 | bibcode = 2019SciA....5.3808K }} The central core domain contains an RNA-binding pocket which binds to viral RNA. The structure of the capsid protein is highly conserved in potyviruses, though there is a relatively high degree of sequence variability. In addition to encapsidating the virion, CP core domain is required for intercellular movement and contributes to seed transmission.{{cite book | vauthors = Martínez-Turiño S, García JA | title = Virus Assembly and Exit Pathways | chapter = Potyviral coat protein and genomic RNA: A striking partnership leading virion assembly and more | series = Advances in Virus Research |date= January 2020 |volume=108 |pages=165–211 | veditors = Kielian M, Mettenleiter TC, Roossinck MJ |publisher=Academic Press |doi=10.1016/bs.aivir.2020.09.001 | pmid = 33837716 | isbn = 9780128207611 | s2cid = 224990458 }}

Certain atypical potyviruses code for additional proteins or protein domains, such as P1-PISPO, Alkylation B (AlkB), and inosine triphosphate pyrophosphatase (known as ITPase or HAM1).{{cite journal | vauthors = Pasin F, Daròs JA, Tzanetakis IE | title = Proteome expansion in the Potyviridae evolutionary radiation | journal = FEMS Microbiology Reviews | volume = 46 | issue = 4 | pages = fuac011 | date = July 2022 | pmid = 35195244 | pmc = 9249622 | doi = 10.1093/femsre/fuac011 }} Such anomalies are often situated in the hypervariable P1-HC-Pro region.

File:Plants-09-00219-g001.png (SMV) within cell]]

Most potyviruses are transmitted by aphids as they probe plant tissues with their stylet during feeding.{{Cite journal |last1=Gadhave |first1=K R |last2=Gautam |first2=S |last3=Rasmussen |first3=D A |last4=Srinivasan |first4=R |date=2020-07-17 |title=Aphid Transmission of Potyvirus: The Largest Plant-Infecting RNA Virus Genus |journal=Viruses |language=en |volume=12 |issue=7 |pages=773 |doi=10.3390/v12070773 |issn=1999-4915 |pmc=7411817 |pmid=32708998 |doi-access=free }} They do not circulate or multiply within the aphid and typically only persist in the aphid for a few minutes. Certain potyviruses have been shown to alter the feeding patterns of their aphid vectors, which may manifest as longer periods of time spent on infected plants, reduced non-probing feeding time, and increased phloem sap ingestion.

Seed and pollen transmission has been documented in certain potyvirus species, for instance in PVY and Turnip mosaic virus (Potyvirus rapae, TUMV).{{Citation |last1=Simmons |first1=H E |title=Seed Transmission in the Potyviridae |date=2014 |url=https://link.springer.com/10.1007/978-94-017-9389-6_1 |work=Global Perspectives on the Health of Seeds and Plant Propagation Material |pages=3–15 |editor-last=Gullino |editor-first=M L |access-date=2023-08-16 |place=Dordrecht |publisher=Springer Netherlands |language=en |doi=10.1007/978-94-017-9389-6_1 |isbn=978-94-017-9388-9 |last2=Munkvold |first2=G P |editor2-last=Munkvold |editor2-first=Gary|url-access=subscription }} Vegetative transmission by infected tubers or grafting material are of particular concern for certain agricultural crops, such as potato and fruit trees, respectively.

Transmission can also occur by physical contact with infected plants or with contaminated tools, clothes, or even water.{{Cite journal |last1=Mehle |first1=N. |last2=Gutiérrez-Aguirre |first2=I. |last3=Prezelj |first3=N. |last4=Delić |first4=D. |last5=Vidic |first5=U. |last6=Ravnikar |first6=M. |date=2014-02-15 |title=Survival and Transmission of Potato Virus Y, Pepino Mosaic Virus, and Potato Spindle Tuber Viroid in Water |journal=Applied and Environmental Microbiology |language=en |volume=80 |issue=4 |pages=1455–1462 |doi=10.1128/AEM.03349-13 |issn=0099-2240 |pmc=3911042 |pmid=24334672|bibcode=2014ApEnM..80.1455M }}

After entry, potyvirus particles are uncoated and genomic RNA is released into host cytoplasm. Potyviral RNA mimicks host mRNA: the 5' VPg protein shares functional similarities with the 5' cap and the 3' end is polyadenylated.{{Cite journal |last1=Jaramillo-Mesa |first1=Helena |last2=Rakotondrafara |first2=Aurélie M. |date=2023-10-01 |title=All eggs in one basket: How potyvirus infection is controlled at a single cap-independent translation event |journal=Seminars in Cell & Developmental Biology |series=Special Issue: Plant pathogens and disease susceptibility |volume=148-149 |pages=51–61 |doi=10.1016/j.semcdb.2022.12.011 |pmid=36608998 |s2cid=255728197 |issn=1084-9521|doi-access=free }} VPg and its interactions with eIF4E and eIF4(iso)E allow the virus to utilise host cap-dependent translation machinery for its translation. Similarly to eukaryotic translation, the VPg-eIF4E interaction assembles the eIF4F complex around viral RNA.

A number of weak internal ribosome entry sites (IRES) have been identified in many potyvirus species but it is not known whether cap-independent translation is an important translation mechanism for potyviruses.

Like many other positive strand RNA viruses, potyvirus replication is heavily associated with host membranes.{{Cite journal |last1=Wei |first1=Taiyun |last2=Huang |first2=Tyng-Shyan |last3=McNeil |first3=Jamie |last4=Laliberté |first4=Jean-François |last5=Hong |first5=Jian |last6=Nelson |first6=Richard S. |last7=Wang |first7=Aiming |date=2010-01-15 |title=Sequential Recruitment of the Endoplasmic Reticulum and Chloroplasts for Plant Potyvirus Replication |journal=Journal of Virology |language=en |volume=84 |issue=2 |pages=799–809 |doi=10.1128/JVI.01824-09 |pmid=19906931 |issn=0022-538X|pmc=2798358 }} The viral 6K2 protein coordinates the rearrangement of host membranes into various infection-associated structures which, depending on the potyvirus species, can include anything from small round viral vesicles to complex globular structures with many cisternae or lobes. These structures are dotted with viral replication complexes and are often called "replication vesicles", "viroplasm" or "viral factories". Replication vesicle membranes are derived from a variety of host organelles and the sources differ between potyvirus species. Some membrane sources include the ER, chloroplasts, Golgi apparatus, and vacuoles.

The exact replication mechanism is not known but it involves a negative sense RNA intermediate and requires both viral and host proteins. Viral proteins detected in replication complexes include HC-Pro, P3, 6K1, 6K2, CI, VPg, NIa-Pro, and NIb.{{Cite journal |last1=Lõhmus |first1=Andres |last2=Varjosalo |first2=Markku |last3=Mäkinen |first3=Kristiina |date=August 2016 |title=Protein composition of 6K2-induced membrane structures formed during Potato virus A infection: PVA replication complex proteome |journal=Molecular Plant Pathology |language=en |volume=17 |issue=6 |pages=943–958 |doi=10.1111/mpp.12341|pmid=26574906 |pmc=6638329 }} Host factors present in replication vesicles include eIF4A and several heat shock proteins.

Like most plant viruses, potyviruses have evolved to move from one plant cell to another through plasmodesmata. However, unlike some well-studied plant viruses, such as the Tobacco mosaic virus, potyviruses do not have a single movement protein but instead assemble a movement complex around the plasmodesma.{{Cite journal |last=Wang |first=Aiming |date=June 2021 |title=Cell-to-cell movement of plant viruses via plasmodesmata: a current perspective on potyviruses |url=https://linkinghub.elsevier.com/retrieve/pii/S1879625721000183 |journal=Current Opinion in Virology |language=en |volume=48 |pages=10–16 |doi=10.1016/j.coviro.2021.03.002|pmid=33784579 |s2cid=232431891 |url-access=subscription }} This complex is primarily composed of three viral proteins: CI, CP, P3N-PIPO. Conical CI inclusions are anchored to plasmodesmata by P3N-PIPO during the early stages of potyvirus infection. This allows the inclusion to funnel either viral particles or viral RNA-CP complexes through the plasmodesma. Replication vesicles are also recruited to the movement complex, suggesting that replication and movement are coupled. Replication vesicles are recruited by P3N-PIPO, which interacts with both CI and P3 through the shared P3N-domain. P3's interaction with 6K2 allows replication vesicles to be tethered to the movement complex.

Potyviruses evolved between 6,600 and 7,250 years ago.{{cite journal | vauthors = Gibbs AJ, Ohshima K, Phillips MJ, Gibbs MJ | title = The prehistory of potyviruses: their initial radiation was during the dawn of agriculture | journal = PLOS ONE | volume = 3 | issue = 6 | pages = e2523 | date = June 2008 | pmid = 18575612 | pmc = 2429970 | doi = 10.1371/journal.pone.0002523 | bibcode = 2008PLoSO...3.2523G | doi-access = free }}{{cite journal | vauthors = Gibbs A, Ohshima K | title = Potyviruses and the digital revolution | journal = Annual Review of Phytopathology | volume = 48 | issue = 1 | pages = 205–223 | year = 2010 | pmid = 20438367 | doi = 10.1146/annurev-phyto-073009-114404 | publisher = Annual Reviews | s2cid = 10599654 }} They appear to have evolved in southwest Eurasia or north Africa. The estimated mutation rate is about 1.15{{e|−4}} nucleotide substitutions/site/year.{{Citation needed|date=January 2021|reason=Same source as before?}}

Agriculture was introduced into Australia in the 18th century. This introduction also included plant pathogens. Thirty eight potyvirus species have been isolated in Australia. Eighteen potyviruses have been found only in Australia and are presumed to be endemic there. The remaining twenty appear to have been introduced with agriculture.{{Citation needed|date=January 2021|reason=refernce date also missing}}

Historically, potyvirus diagnostics relied on the detection of various proteinaceous inclusions in infected plant cells. These may appear as crystals in either the cytoplasm or in the nucleus, as amorphous X-bodies, membranous bodies, viroplasms or pinwheels.[http://www.freshfromflorida.com/Divisions-Offices/Plant-Industry/Science/Florida-Plant-Viruses-And-Their-Inclusions/Florida-Plant-Viruses-And-Their-Inclusions/Potyvirus Florida Department of Agriculture and Consumer Services: Florida plant viruses and their inclusions—Potyvirus] The inclusions may or may not (depending on the species) contain virions.{{Citation needed|date=August 2023}} These inclusions can be seen by light microscopy in leaf strips of infected plant tissue stained with Orange-Green (protein stain) but not Azure A (nucleic acid stain).{{cite web |title=Materials and Methods for the Detection of Viral Inclusions |url=http://www.doacs.state.fl.us/pi/enpp/pathology/florida_viruses/Howto.html |url-status=dead |archive-url=https://web.archive.org/web/20120219032419/http://plantpath.ifas.ufl.edu/pdc/Inclusionpage/Howto.html |archive-date=19 February 2012 |publisher=University of Florida - Institute of Food and Agricultural Sciences}}Christie, R.G. and Edwardson, J.R. (1977). Fla Agric. Exp. Stn Monog. No. 9, 150 pp.[http://www.doacs.state.fl.us/pi/enpp/pathology/florida_viruses/Diag/What%20is%20it.html How do you diagnose a virus infection in a plant?] {{webarchive|url=https://archive.today/20120804095220/http://www.doacs.state.fl.us/pi/enpp/pathology/florida_viruses/Diag/What%20is%20it.html|date=4 August 2012}}

Modern detection methods rely primarily on reverse transcription PCR.{{Cite journal |last1=Thomson |first1=Darelle |last2=Dietzgen |first2=Ralf G. |date=August 1995 |title=Detection of DNA and RNA plant viruses by PCR and RT-PCR using a rapid virus release protocol without tissue homogenization |url=https://linkinghub.elsevier.com/retrieve/pii/016609349500022M |journal=Journal of Virological Methods |language=en |volume=54 |issue=2–3 |pages=85–95 |doi=10.1016/0166-0934(95)00022-M|pmid=8530569 |url-access=subscription }}

Potyvirus contains the following species:

{{div col|colwidth=25em}}

{{Linked species list |abbreviated=yes

| Potyvirus achyranthis | Achyranthes virus A

| Potyvirus adiuris | Donkey orchid virus A

| Potyvirus algeriaense | Algerian watermelon mosaic virus

| Potyvirus alliumagrestis | Wild onion symptomless virus

| Potyvirus almeidi | Alternanthera mild mosaic virus

| Potyvirus alstromeriae | Alstroemeria mosaic virus

| Potyvirus amaranthi | Amaranthus leaf mottle virus

| Potyvirus ampeloprasi | Leek yellow stripe virus

| Potyvirus anemones | Anemone mosaic virus

| Potyvirus angelicae | Angelica virus Y

| Potyvirus apii | Apium virus Y

| Potyvirus apiumtessellati | Celery mosaic virus

| Potyvirus arachidis | Peanut mottle virus

| Potyvirus araujiae | Araujia mosaic virus

| Potyvirus arracachae | Arracacha mottle virus

| Potyvirus artichokis | Chinese artichoke mosaic virus

| Potyvirus ascaloniae | Shallot yellow stripe virus

| Potyvirus ascaloniavirgae | Scallion mosaic virus

| Potyvirus ashitabae | Ashitaba mosaic virus

| Potyvirus asparagi | Asparagus virus 1

| Potyvirus atuberosi | Potato virus A & Tamarillo mosaic virus

| Potyvirus barbacenense | Barbacena virus Y

| Potyvirus basellae | Basella rugose mosaic virus & peace lily mosaic virus

| Potyvirus batatalatentis | Sweet potato latent virus

| Potyvirus batatamaculae | Sweet potato mild speckling virus

| Potyvirus batataplumei | Sweet potato feathery mottle virus

| Potyvirus begoniae | Begonia flower breaking virus

| Potyvirus betaceum | Beet mosaic virus

| Potyvirus betaci | Tamarillo leaf malformation virus

| Potyvirus bidensia | Bidens mosaic virus

| Potyvirus bidenstessellati | Bidens mottle virus

| Potyvirus brugmansiae | Brugmansia mosaic virus

| Potyvirus calistephi | Callistephus mottle virus

| Potyvirus callanthis | Calanthe mild mosaic virus

| Potyvirus cannae | Canna yellow streak virus

| Potyvirus capsianuli | Chilli ringspot virus

| Potyvirus capsiflavi | Pepper yellow mosaic virus

| Potyvirus capsimaculae | Pepper mottle virus

| Potyvirus capsiseverum | Pepper severe mosaic virus

| Potyvirus capsivenae | Pepper veinal mottle virus

| Potyvirus capsivenamaculae | Chilli veinal mottle virus

| Potyvirus caricae | Papaya leaf distortion mosaic virus

| Potyvirus carotae | Carrot virus Y

| Potyvirus carotatenuifoli | Carrot thin leaf virus

| Potyvirus caryae | Pecan mosaic-associated virus

| Potyvirus catharantessellati | Catharanthus mosaic virus

| Potyvirus cebatatae | Sweet potato virus C

| Potyvirus cepae | Onion yellow dwarf virus

| Potyvirus ceratobii | Ceratobium mosaic virus

| Potyvirus chamaescillae | Blue squill virus A

| Potyvirus chichorii | Endive necrotic mosaic virus

| Potyvirus citrulli | Watermelon mosaic virus

| Potyvirus citrullimoroccense | Moroccan watermelon mosaic virus

| Potyvirus citrullufolimaculae | Watermelon leaf mottle virus

| Potyvirus clitoriae | Clitoria virus Y

| Potyvirus cliviaflavilineae | Clivia yellow stripe virus

| Potyvirus colchici | Meadow saffron breaking virus

| Potyvirus commelinae | Commelina mosaic virus

| Potyvirus cordophani | Sudan watermelon mosaic virus

| Potyvirus costus | Costus stripe mosaic virus

| Potyvirus croci | Saffron latent virus

| Potyvirus cucurbitae | Cucurbit vein banding virus

| Potyvirus cucurbitaflavitesselati | Zucchini yellow mosaic virus

| Potyvirus cynanchi | Keunjorong mosaic virus

| Potyvirus cypripedii | Cypripedium virus Y

| Potyvirus cyrtanthi | Cyrtanthus elatus virus A

| Potyvirus dactylis | Cocksfoot streak virus

| Potyvirus daphnis | Daphne mosaic virus

| Potyvirus dasheenis | Dasheen mosaic virus & Vanilla mosaic virus

| Potyvirus daturae | Datura shoestring virus

| Potyvirus dendrobii | Dendrobium chlorotic mosaic virus

| Potyvirus dianthi | Carnation vein mottle virus

| Potyvirus dioscoreae | Dioscorea mosaic virus

| Potyvirus duobatatae | Sweet potato virus 2

| Potyvirus esculentinecrosis | Tomato necrotic stunt virus

| Potyvirus eucharae | Amazon lily mosaic virus

| Potyvirus euphorbiae | Euphorbia ringspot virus

| Potyvirus fountaingrassi | Pennisetum alopecuroides mosaic virus

| Potyvirus freesiae | Freesia mosaic virus

| Potyvirus fritillariae | Fritillary virus Y

| Potyvirus gebatatae | Sweet potato virus G

| Potyvirus gladioli | Gladiolus mosaic virus

| Potyvirus gloriosae | Gloriosa stripe mosaic virus

| Potyvirus glycitessellati | Soybean mosaic virus

| Potyvirus gomphocarphi | Gomphocarpus mosaic virus

| Potyvirus habenariae | Habenaria mosaic virus

| Potyvirus halapensis | Johnsongrass mosaic virus

| Potyvirus hardenbergiae | Hardenbergia mosaic virus

| Potyvirus heliannulabis | Sunflower ring blotch virus

| Potyvirus helichloromaculae | Sunflower chlorotic mottle virus

| Potyvirus helitenuitessellati | Sunflower mild mosaic virus

| Potyvirus helitessellati | Sunflower mosaic virus

| Potyvirus henbanis | Henbane mosaic virus

| Potyvirus hibbertiae | Hibbertia virus Y

| Potyvirus hiemalisdaphnis | Daphne virus Y

| Potyvirus hippeastri | Hippeastrum mosaic virus

| Potyvirus hyacinthi | Hyacinth mosaic virus

| Potyvirus impatiensis | Impatiens flower break virus

| Potyvirus iris | Iris fulva mosaic virus

| Potyvirus iriseverum | Iris severe mosaic virus

| Potyvirus iristenuis | Iris mild mosaic virus

| Potyvirus jasmini | Jasmine virus T

| Potyvirus kalanchoes | Kalanchoë mosaic virus

| Potyvirus konjac | Konjac mosaic virus

| Potyvirus lactucae | Lettuce mosaic virus

| Potyvirus lactucaitalicense | Lettuce Italian necrotic virus

| Potyvirus lilimaculae | Lily mottle virus

| Potyvirus lupinus | Lupine mosaic virus

| Potyvirus lycorsis | Lycoris mild mottle virus

| Potyvirus malvae | Malva vein clearing virus

| Potyvirus melongenae | African eggplant mosaic virus

| Potyvirus melozonati | Wild melon banding virus

| Potyvirus mirabilis | Mirabilis crinkle mosaic virus

| Potyvirus miscanthi | Miscanthus sinensis mosaic virus

| Potyvirus morindatessellati | Noni mosaic virus

| Potyvirus muricati | Wild potato mosaic virus

| Potyvirus musae | Banana bract mosaic virus

| Potyvirus narcissus | Narcissus yellow stripe virus

| Potyvirus narcissusdegeneris | Narcissus degeneration virus

| Potyvirus narcissuslineae | Narcissus late season yellows virus

| Potyvirus nerinis | Nerine yellow stripe virus

| Potyvirus nicotianainsculpentis | Tobacco etch virus

| Potyvirus nicotianamaculae | Tobacco mosqueado virus

| Potyvirus nicotianavenamaculae | Tobacco vein mottling virus

| Potyvirus nicotianavenaobscurum | Tobacco vein banding mosaic virus

| Potyvirus nippodioscoreae | Japanese yam mosaic virus

| Potyvirus nothoscordi | Nothoscordum mosaic virus

| Potyvirus orionspassiflorae | East Asian Passiflora virus

| Potyvirus ornithogali | Ornithogalum virus 2

| Potyvirus ornithogalitessellati | Ornithogalum stripe mosaic virus

| Potyvirus pachyrhizus | Yambean mosaic virus

| Potyvirus panax | Panax virus Y

| Potyvirus papayanuli | Papaya ringspot virus

| Potyvirus paris | Paris virus 1

| Potyvirus parisnecrosis | Paris mosaic necrosis virus

| Potyvirus passifloradistorti | East Asian Passiflora distortion virus

| Potyvirus passiflorae | Passion fruit woodiness virus

| Potyvirus passifloraflavi | Passiflora chlorosis virus

| Potyvirus passiflorafricanse | Ugandan Passiflora virus

| Potyvirus passifloramaculae | Passionfruit Vietnam virus

| Potyvirus passiflory | Passiflora virus Y

| Potyvirus pastinacae | Parsnip mosaic virus

| Potyvirus pennisseti | Pennisetum mosaic virus

| Potyvirus pepo | Zucchini yellow fleck virus

| Potyvirus peporesticulae | Zucchini shoestring virus

| Potyvirus pepotigris | Zucchini tigre mosaic virus

| Potyvirus perulycopersici | Peru tomato mosaic virus

| Potyvirus pfaffiae | Pfaffia mosaic virus

| Potyvirus phaseoli | Bean common mosaic necrosis virus

| Potyvirus phaseoluteum | Bean yellow mosaic virus & White lupin mosaic virus

| Potyvirus phaseovulgaris | Bean common mosaic virus & Peanut stripe virus

| Potyvirus phytolaccae | Pokeweed mosaic virus

| Potyvirus pisumsemenportati | Pea seed-borne mosaic virus

| Potyvirus platycodonis | Platycodon mild mottle virus

| Potyvirus pleioblasti | Pleioblastus mosaic virus

| Potyvirus pleionis | Pleione flower breaking virus

| Potyvirus plumpoxi | Plum pox virus

| Potyvirus polianthis | Tuberose mild mosaic virus

| Potyvirus polianthismaculae | Tuberose mild mottle virus

| Potyvirus polygonati | Polygonatum mosaic-associated virus 1

| Potyvirus ranunculi | Ranunculus mosaic virus

| Potyvirus ranunculideformationis | Ranunculus leaf distortion virus

| Potyvirus ranunculitenuis | Ranunculus mild mosaic virus

| Potyvirus rapae | Turnip mosaic virus

| Potyvirus rhopalanthi | Rhopalanthe virus Y

| Potyvirus rutae | Mediterranean ruda virus

| Potyvirus sacchari | Sugarcane mosaic virus

| Potyvirus sarcochili | Sarcochilus virus Y

| Potyvirus schizanthi | Butterfly flower mosaic virus

| Potyvirus scorzaureum | Scorzonera virus A

| Potyvirus sorghitessellati | Sorghum mosaic virus

| Potyvirus spiranthesis | Spiranthes mosaic virus 3

| Potyvirus streptopi | Twisted-stalk chlorotic streak virus

| Potyvirus suaveolens | Brugmansia suaveolens mottle virus

| Potyvirus tagetis | Marigold mosaic virus

| Potyvirus telfairiae | Telfairia mosaic virus

| Potyvirus telosmae | Telosma mosaic virus

| Potyvirus tetraparis | Paris potyvirus 4

| Potyvirus thevetiae | Thevetia white spot virus

| Potyvirus thladiatessellati | Thladiantha dubia mosaic virus

| Potyvirus thurnbergii | Thunberg fritillary mosaic virus

| Potyvirus torvi | Wild tomato mosaic virus

| Potyvirus tradescantiae | Tradescantia mild mosaic virus

| Potyvirus trifolii | Clover yellow vein virus

| Potyvirus trompetae | Colombian datura virus

| Potyvirus tropaeoli | Mashua virus Y

| Potyvirus tuberosiflavi | Potato yellow blotch virus

| Potyvirus tulipadefractum | Tulip breaking virus

| Potyvirus tulipatessellati | Tulip mosaic virus

| Potyvirus vallotae | Vallota mosaic virus

| Potyvirus vanillae | Vanilla distortion mosaic virus

| Potyvirus verbenae | Verbena virus Y

| Potyvirus vetuberosi | Potato virus V

| Potyvirus vignae | Cowpea aphid-borne mosaic virus

| Potyvirus wisteriae | Wisteria vein mosaic virus

| Potyvirus yamplacidum | Yam mild mosaic virus

| Potyvirus yamtesselati | Yam mosaic virus

| Potyvirus yidiuris | Diuris virus Y

| Potyvirus yililii | lily yellow mosaic virus

| Potyvirus yiornithogali | Ornithogalum virus 3

| Potyvirus yipleionis | Pleione virus Y

| Potyvirus yituberosi | Potato virus Y

| Potyvirus zantedeschiae | Calla lily latent virus

| Potyvirus zantedeschiatenuis | Zantedeschia mild mosaic virus

| Potyvirus zeananus | Maize dwarf mosaic virus

| Potyvirus zeatessellati | Zea mosaic virus & Iranian johnsongrass mosaic virus

}}

{{Div col end}}

A further four viruses were previously classified as species in this genus but were abolished due to lack of genetic sequence information:{{cite web |vauthors=Wylie S, Adams MJ, Chalam C, Kreuze JF, Lopez-Moya JJ, Ohshima K, Praveen S, Rabenstein F, Stenger DC, Wang A, Zerbini FM |title=Create three species in genus Potyvirus and abolish five species in genus Potyvirus |url=https://ictv.global/ictv/proposals/2016.008a,bP.A.v3.Potyvirus_3sprem.pdf |year=2016 |access-date=26 July 2021}}

• Cowpea green vein banding virus
• Groundnut eyespot virus
• Helenium virus Y
• Tropaeolum mosaic virus

Potyviruses were further divided into the PVY, SCMV, BYMV, BCMV species groups in 1992. Gibbs and Ohshima 2010 produced a more extensive molecular phylogeny with the same four, but also several new groups: the BtMV, ChVMV, DaMV, OYDV, PRSV, TEV, and TuMV.

Contains 16 species including the type species of the genus (potato virus Y). The primary hosts are: Nine Solanaceae, three Amaranthus, three Asteraceae, one Lilium, and one Amaryllis.

{{Reflist|2}}

• {{cite journal | vauthors = Ward CW, Shukla DD | title = Taxonomy of potyviruses: current problems and some solutions | journal = Intervirology | volume = 32 | issue = 5 | pages = 269–296 | year = 1991 | pmid = 1657820 | doi = 10.1159/000150211 }}
• {{Cite book| veditors = King AM |title=Virus taxonomy : classification and nomenclature of viruses : ninth report of the International Committee on Taxonomy of Viruses|date=2012|publisher=Academic Press|location=London|isbn=978-0123846846|chapter-url=https://books.google.com/books?id=KXRCYay3pH4C&pg=PA1072|access-date=9 December 2014|chapter=Potyvirus|pages=926–1072|display-editors=etal}}

• [https://www.uniprot.org/taxonomy/12195 UniProt taxonomy: Potyvirus]
• [http://viralzone.expasy.org/all_by_species/50.html Viralzone: Potyvirus]
• [http://ictvonline.org/virusTaxonomy.asp ICTV]

{{Baltimore classification}}

{{Taxonbar|from=Q3400142}}

{{Authority control}}

Category:Virus genera

Category:Potyviruses

Category:Viral plant pathogens and diseases