Virus Taxonomy The ICTV Report on Virus Classiﬁcation and …taxonomy.cvr.gla.ac.uk/PDF/Virgaviridae.pdf · 2020. 10. 4. · Plants (all genera); furoviruses, peculviruses and pomoviruses

Virus TaxonomyThe ICTV Report on Virus Classification and Taxon Nomenclature

Virgaviridae Chapter

Virgaviridae

Michael J. Adams, Scott Adkins, Claude Bragard, David Gilmer, Dawei Li, Stuart A. MacFarlane, Sek-Man Wong, Ulrich Melcher,Claudio Ratti and Ki Hyun Ryu

Edited by Hélène Sanfaçon and Stuart G. Siddell

Corresponding author: Michael J Adams ([email protected])

Posted August 2017

PDF created: October 2020

Citation

A summary of this ICTV Report chapter has been published as an ICTV Virus Taxonomy Profile article in the Journal of General Virology, andshould be cited when referencing this online chapter as follows:

Adams, M.J., Adkins, S., Bragard, C., Gilmer, D., Li, D., MacFarlane, S.A., Wong, S-M., Melcher, U., Ratti, C., Ryu, K.H., and ICTV ReportConsortium. 2017, ICTV Virus Taxonomy Profile: Virgaviridae. Journal of General Virology, 98: 1999–2000.

Summary

The Virgaviridae is a family of plant viruses with rod-shaped virions, a single-stranded RNA genome with a 3′-terminal tRNA-like structure anda replication protein similar to those of the alpha-like supergroup (Table 1.Virgaviridae). Differences in the numbers of genome components,genome organisation and the modes of transmission provide the basis for genus demarcation.

Table 1.Virgaviridae. Characteristics of members of the family Virgaviridae.

Characteristic Description

Typicalmember tobacco mosaic virus variant 1 (V01408), species Tobacco mosaic virus, genus Tobamovirus

Virion Non-enveloped, rod shaped particles about 20 nm in diameter and up to 300 nm long. Except in members of the genusTobamovirus, the particle length distribution is bi- or tri-modal

Genome Approximately 6.3 to 13 kb of positive-sense RNA; non-segmented in members of the genus Tobamovirus but multipartitein other genera with segments separately encapsidated in 2 or 3 components

Replication Cytoplasmic, probably associated with the endoplasmic reticulum

Translation From genomic or subgenomic RNAs

Host rangePlants (all genera); furoviruses, peculviruses and pomoviruses are transmitted by plasmodiophorids, tobraviruses aretransmitted by nematodes and goraviruses and hordeiviruses are transmitted by pollen and/or seed. Tobamoviruses haveno known vectors but are readily transmitted mechanically

Taxonomy 7 genera containing about 60 species

Viruses classified into the seven genera show distinct host ranges, genome organisation and modes of transmission:

Goravirus. Members of the type species (Gentian ovary ringspot virus, GORV) of this genus are transmitted through pollen, so resemblinghordeiviruses. Genomes are bipartite and encode "triple gene block" (TGB) movement proteins, thus resembling pecluviruses but there aredifferences between members of the two genera in the position of some other open reading frames (ORFs).

Furovirus. This genus contains viruses of graminaceous plants that are transmitted to plant roots by the plasmodiophorid Polymyxa graminis.Genomes are bipartite and encode a ‘30K’-type movement protein. Soil-borne wheat mosaic virus and similar viruses cause serious diseasesof winter cereals in North America, Europe and Asia.

InternationalCommitteeonTaxonomyofViruses(ICTV)-www.ictv.global

www.ictv.global/report/virgaviridae 1

http://www.ictv.global

http://www.ictv.global/report

https://www.ictv.global/report/virgaviridae

http://jgv.microbiologyresearch.org/content/journal/jgv/10.1099/jgv.0.000884

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Hordeivirus. This genus contains viruses of graminaceous plants that are transmitted through pollen and seed. The genomes are tripartite and(uniquely within the family), the RNA-dependent RNA polymerase is encoded on a separate RNA segment and not as a readthrough producttranslated together with the other viral-encoded replication proteins. Barley stripe mosaic virus has a worldwide distribution.

Pecluvirus. This genus contains soil-borne viruses of leguminous and graminaceous plants from India and Africa that are transmitted to plantroots by the plasmodiophorid Polymyxa graminis. Genomes are bipartite; they encode TGB movement proteins.

Pomovirus. This genus contains viruses of solanaceous and chenopodiaceous plants that are transmitted to plant roots by theplasmodiophorids Spongospora subterranea and Polymyxa betae. Genomes are tripartite; they encode TGB movement proteins and the coatprotein has a carobxyl (readthrough) extension associated with transmission.

Tobamovirus. This genus contains viruses with monopartite genomes that encode a ‘30K’-type movement protein. Tobacco mosaic virus wasthe first virus discovered (in 1886); it is present in high concentrations in infected plants, is extremely stable, and has been extensively studied(Harrison and Wilson 1999, Scholthof 2004).

Tobravirus. This genus contains viruses of solanaceous plants that are transmitted to plant roots by nematodes. Genomes are bipartite andthey encode a ‘30K’-type movement protein.

Virion

Morphology

The non-enveloped, rod-shaped particles are helically constructed with a pitch of 2.3 to 2.5 nm and an axial canal. They are about 20 nm indiameter, with predominant lengths that depend upon the genus.

Physicochemical and physical properties

The S values range from 194 to 306 for large particles that include RNA encoding the replication protein and 125 to 245 for smallerparticles. Particles are stable at higher temperatures (60–90 °C) with the exception of pomoviruses, which lose infectivity at room temperaturewithin a few hours.

Nucleic acid

The genome consists of positive sense ssRNA with 5′-cap (m GpppG) and a 3′-terminal tRNA-like structure. The number of genomecomponents depends upon the genus.

Proteins

The capsid comprises multiple copies of a single polypeptide of about 17–24 kDa, depending upon the genus. Some viruses encode anadditional capsid protein (CP) produced by suppression of the CP ORF stop codon to produce a larger readthrough (RT) protein of variablemass called the minor CP or CP-RT.

Genome organization and replication

The largest ORF encodes an alpha-like replication protein with conserved methyltransferase (Mtr) and helicase (Hel) domains. This protein istranslated directly from genomic RNA. In viruses of all genera except Hordeivirus, the RNA-dependent RNA polymerase (RdRP) is expressedas the C-terminal part of this protein by readthrough of a leaky stop codon. Other ORFs are expressed either directly from the smallergenomic RNAs or from subgenomic mRNAs, some of which may be bicistronic. In some genera, the viruses have a single cell-to-cellmovement protein (MP) of the “30K” superfamily (Melcher 2000), while in other genera there is a triple gene block (TGB). There aredifferences in the number of genomic RNAs (1, 2 or 3 depending on the genus). Replication is cytoplasmic.

Biology

Biologically, the viruses are fairly diverse. They have been reported from a wide range of herbaceous and mono- and dicotyledonous plantspecies but the host range of individual members is usually limited. All members can be transmitted experimentally by mechanical inoculation,and for those in the genus Tobamovirus, this is the only known means of transmission. In some genera, transmission is by soil-borne vectors,while members of the genus Hordeivirus and Goravirus are transmitted through pollen and seed.

Antigenicity

Virions are moderately to strongly antigenic.

Derivation of names

Virga: from the Latin for ‘rod’, referring to the morphology of virus particles.

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https://www.ncbi.nlm.nih.gov/pubmed/10336387



Genus demarcation criteria

Genera are distinguished by the number of genomic RNAs, various features of genome organization, the type of cell-to-cell movement proteinand the natural mode of transmission. These are summarized in Table 2.Virgaviridae. Genus distinctions are also supported by phylogeneticanalyses of homologous proteins.

Table 2.Virgaviridae. Distinguishing properties of genera in the family Virgaviridae.

Genus RNAs RdRP MP CP 3′ structure TransmissionGoravirus 2 RT TGB 22K t-RNA pollenFurovirus 2 RT “30K” 19K+RT t-RNA plasmodiophoridHordeivirus 3 Separate TGB 22K t-RNA seedPecluvirus 2 RT TGB 23K t-RNA plasmidophorid + seedPomovirus 3 RT TGB 20K+RT t-RNA plasmodiophoridTobamovirus 1 RT “30K” 17–18K t-RNA mechanicalTobravirus 2 RT “30K” 22–24K t-RNA nematode

Relation of the RdRP encoding ORF to the replication protein (methyltransferase, helicase) encoding ORF; RT, in a 3′-proximal regionexpressed by ribosomal readthrough.

MP, Movement protein either of the “30K” superfamily or a triple gene block (TGB).

CP, Coat protein size in kDa (with indication of a readthrough domain (RT) at the C-terminus if present).

t-RNA , t-RNA like structure accepting valine, tyrosine, histidine, unknown amino acid, or not aminoacylated respectively.

Relationships within the family

Phylogenetic trees obtained using the entire replication protein including the RdRP (or the conserved Mtr, Hel and RdRP domains) correlatewell with genome organisation to support the existence of the different genera. However, these genera are usually reliably delineated,regardless of the protein used (Figures 1.Virgaviridae - 5.Virgaviridae). Using both the replication protein and the coat protein, the genusTobamovirus separates substantially from the remaining genera. Furovirus and Pomovirus occur together on the same branch in all trees asdo Pecluvirus, Goravirus and Hordeivirus.

a b c d

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Val

Tyr

Val

Val

His

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Figure 1.Virgaviridae. Phylogenetic tree based on the codon-aligned nucleotide sequences of the replication proteins (including Mtr andHel domains) of viruses in the family Virgaviridae. The analyses were conducted in MEGA7 using the Maximum Likelihood method basedon the Tamura-Nei model and 1000 bootstrap replicates. The tree with the highest log likelihood (-135263.7399) is shown. The percentageof trees in which the associated taxa clustered together is shown next to the branches (where >60%). The scale indicates the number ofsubstitutions per site. All positions containing gaps and missing data were eliminated. Virus abbreviations are explained in the tables ofmember species and other viruses. This phylogenetic tree and corresponding sequence alignment are available to download fromthe Resources page.



https://talk.ictvonline.org/ictv-reports/ictv_online_report/positive-sense-rna-viruses/w/virgaviridae/665/resources-virgaviridae

Figure 2.Virgaviridae. Phylogenetic tree based on the codon-aligned nucleotide sequences of the RdRP domain of viruses in the familyVirgaviridae. The analyses were conducted in MEGA7 using the Maximum Likelihood method based on the Tamura-Nei model and 1000bootstrap replicates. The tree with the highest log likelihood (-57431.3254) is shown. The percentage of trees in which the associated taxaclustered together is shown next to the branches (where >60%). The scale indicates the number of substitutions per site. All positionscontaining gaps and missing data were eliminated. Virus abbreviations are explained in the tables of member species and otherviruses. This phylogenetic tree and corresponding sequence alignment are available to download from the Resources page.




Figure 3.Virgaviridae. Phylogenetic tree based on the codon-aligned nucleotide sequences of the coat proteins of viruses in the familyVirgaviridae. The analyses were conducted in MEGA7 using the Maximum Likelihood method based on the Tamura-Nei model and 1000bootstrap replicates. The tree with the highest log likelihood (-19333.2064) is shown. The percentage of trees in which the associated taxaclustered together is shown next to the branches (where >60%). The scale indicates the number of substitutions per site. All positionscontaining gaps and missing data were eliminated. Virus abbreviations are explained in the tables of member species and otherviruses. This phylogenetic tree and corresponding sequence alignment are available to download from the Resources page.




Figure 4.Virgaviridae. Phylogenetic tree based on the codon-aligned nucleotide sequences of the movement proteins of viruses in thefamily Virgaviridae. Only viruses with a 30K-like movement protein were included in the analyses. The analyses were conducted in MEGA7using the Maximum Likelihood method based on the Tamura-Nei model and 1000 bootstrap replicates. The tree with the highest loglikelihood (-24269.0075) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches(where >60%). The scale indicates the number of substitutions per site. All positions containing gaps and missing data were eliminated.Virus abbreviations are explained in the tables of member species and other viruses. This phylogenetic tree and corresponding sequencealignment are available to download from the Resources page.




Figure 5.Virgaviridae. Phylogenetic tree based on the codon-aligned nucleotide sequences of the first triple gene block protein (TGB1) ofviruses in the family Virgaviridae. The analyses were conducted in MEGA7 using the Maximum Likelihood method based on the Tamura-Neimodel and 1000 bootstrap replicates. The tree with the highest log likelihood (-13286.8458) is shown. The percentage of trees in which theassociated taxa clustered together is shown next to the branches (where >60%). The scale indicates the number of substitutions per site. Allpositions containing gaps and missing data were eliminated. Virus abbreviations are explained in the tables of member species and otherviruses. This phylogenetic tree and corresponding sequence alignment are available to download from the Resources page.

Within genera, only members of the genus Tobamovirus have enough diversity for particular subgroupings to be distinguished. Here, there areclearly groupings of closely-related viruses infecting similar hosts. The most obvious are those infecting cucurbits (cucumber fruit mottlemosaic virus, cucumber green mottle mosaic virus, cucumber mottle virus, kyuri green mottle mosaic virus, zucchini green mottle mosaicvirus), cruciferous plants (ribgrass mosaic virus, turnip vein-clearing virus, wasabi mottle virus, youcai mosaic virus) and solanaceous plants(brugmansia mild mottle virus, obuda pepper virus, paprika mild mottle virus, pepper mild mottle virus, rehmannia mosaic virus, tobacco mildgreen mosaic virus, tobacco mosaic virus, tomato brown rugose fruit virus, tomato mosaic virus, tropical soda apple mosaic virus, yellowtailflower mild mottle virus).

Relationships with other taxa

The replication proteins are related to those of other viruses with alpha-like replicases, and more particularly to those in the familiesClosteroviridae and Bromoviridae and the unassigned genera Idaeovirus, Blunervirus, Cilevirus and Higrevirus (Figure 6.Virgaviridae). Theonly other viruses with rod-shaped virions are those classified in the genus Benyvirus (family Benyviridae) and they are distinguishedbecause they are distantly related in phylogenetic analyses and because (unlike the members of the Virgaviridae) they have a polyadenylatedgenome and a polymerase that is processed by autocatalytic protease activity.




Figure 6.Virgaviridae. Phylogenetic tree based on the codon-aligned nucleotide sequences of the RdRP proteins of viruses in the familyVirgaviridae and some other viruses. The analyses were conducted in MEGA7 using the Maximum Likelihood method based on theTamura-Nei model and 1000 bootstrap replicates. The tree with the highest log likelihood (-42095.8020) is shown. The percentage of treesin which the associated taxa clustered together is shown next to the branches (where >60%). The scale indicates the number ofsubstitutions per site. All positions containing gaps and missing data were eliminated. Representative isolates of the type species of thegenera Benyvirus, Blunervirus, Cilevirus, Higrevirus, Idaeovirus, Orthohepevirus and Rubivirus and of each of the genera in the familiesBromoviridae, Closteroviridae and Virgaviridae and the order Tymovirales were used in the analysis. This phylogenetic tree andcorresponding sequence alignment are available to download from the Resources page.

Related, unclassified viruses

Virus name Accession number Virus abbreviationNicotiana velutina mosaic virus D00906* NVMV

Virus names and virus abbreviations are not official ICTV designations.

* partial genome




https://www.ncbi.nlm.nih.gov/nuccore/D00906

Genus: Furovirus

Distinguishing features

Furoviruses have a bipartite genome, a “30K”-like cell-to-cell movement protein and are transmitted by root-infecting vectors in the familyPlasmodiphorales, once described as fungi but now classified as Cercozoa.

Virion

Morphology

Virions are non-enveloped hollow rods, which have helical symmetry. Virions are about 20 nm in diameter, with predominant lengths of 140–160 nm and 260–300 nm. The length distribution of the soil-borne wheat mosaic virus (SBWMV) short particles is broad, 80–160 nm, due tothe presence of deletion mutants in some cultures (Figure 1.Furovirus).

Figure 1.Furovirus. Negative contrast electron micrograph of stained (ammonium molybdate pH 7.0) particles of soil-borne wheat mosaicvirus (SBWMV). The bar represents 200 nm. Inset: Negative contrast electron micrograph of particles SBWMV stained with 1% uranylacetate. The bar represents 100 nm.


Virions sediment as two (or three) components; for SBWMV the S values are 220–230S (long particles) and 170–225S (short particles),and 126–177S (deletion mutants). SBWMV loses infectivity in extracts of wheat kept at 60–65 °C for 10 min.

Nucleic acid

Complete or almost complete sequences are available for isolates representing all species in the genus (Shirako and Wilson 1993, Diao etal., 1999a, Shirako et al., 2000, Diao et al., 1999b). The genome is bipartite, linear, positive sense ssRNA. RNA 1 is about 6–7 kb and RNA 2about 3.5–3.6 kb. The RNA molecules of SBWMV have a 5′ cap (m GpppG) and in all of the species where the complete sequences havebeen determined there is a 3′-terminal tRNA-like structure with a putative anti-codon for valine. The 3′ terminus of SBWMV RNA was shownexperimentally to accept valine (Goodwin and Dreher 1998).

Proteins

The capsid comprises (or mostly comprises) multiple copies of a polypeptide of about 19–20.5 kDa. The CPs of SBWMV, Chinese wheatmosaic virus (CWMV), soil-borne cereal mosaic virus (SBCMV) and oat golden stripe virus (OGSV) comprise 176 aa with 76–82% aa identity;they share only 46% identity with that of sorghum chlorotic spot virus (SrCSV). The CP ORF terminates in a leaky (UGA) stop codon that canbe suppressed to produce a read-through minor capsid protein (ca. 85 kDa), which is thought to be involved in natural transmission by theplasmodiophorid vector. In SBWMV and CWMV, it has been experimentally shown that a further minor coat protein of 25 kDa is initiated froma CUG codon upstream of the canonical CP AUG but in SBWMV neither minor capsid protein was essential for particle formation or systemicinfection (Shirako 1998, Yamamiya and Shirako 2000, Yang et al., 2016).


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Genome organization and structure are conserved between members of the species but there are substantial differences in the genomicsequences. SBWMV RNA 1 encodes a 150 kDa protein, a 209 kDa readthrough product and a 37 kDa protein (Figure 2.Furovirus). The 150kDa protein contains Mtr and NTP-binding Hel motifs. The readthrough protein, in addition, contains RNA polymerase motifs, indicating thatthese proteins are involved in replication. The 37 kDa protein belongs to the “30K”-like cell-to-cell movement protein superfamily and isthought to be involved in virus movement as it shares some sequence similarity to the MPs of dianthoviruses (An et al., 2003). RNA 2encodes the CP (19 kDa), the sequence of which terminates in a UGA codon that can be suppressed to give a readthrough product of 84 kDa.Also, a 25 kDa polypeptide is initiated from a CUG codon upstream of the CP AUG. A 3′ proximal ORF of RNA 2 encodes a 19 kDa proteinthat contains seven conserved cysteine residues. This protein is a suppressor of gene silencing (Te et al., 2005, Sun et al., 2013). Productscorresponding to the 37 kDa protein and the cysteine-rich 19 kDa protein were not found in in vitro transcription/translation experiments, andthese proteins are thought to be expressed from subgenomic mRNAs. Spontaneous deletions in RNA2 occur on successive passage bymanual inoculation, and in field isolates in older infected plants, resulting in a shorter CP readthrough product (Chen et al., 1994, Chen et al.,1995).

Figure 2.Furovirus. Genome organization of soil-borne wheat mosaic virus (SBWMV). The tRNA structure motifs at the 3′-ends of theRNAs are represented by a dark square, the methyl transferase (Met), Helicase (Hel) and RNA-dependent RNA polymerase (RdRP) motifsby asterisks and the readthrough of the polymerase and coat protein ORFs by RT and an arrow. The major CP (19K) is shown in orange. Aminor 25K CP is initiated from an upstream CUG codon. CRP, cysteine-rich protein.

Biology

Furoviruses are found in temperate regions worldwide including the United States of America, Europe, China and Japan. The natural hostranges of furoviruses are narrow and confined to species within the Graminae. SBWMV induces green or yellow mosaic and stunting in winterwheat (Triticum aestivum) causing up to 80% yield loss in severely infected crops. It also may infect barley and rye. SBCMV infects mainlywheat and triticale in Western and Southern Europe and mainly rye in Central and North-Eastern Europe. Both viruses are (not readily)mechanically transmissible to Chenopodium quinoa. OGSV infects oats (Avena sativa) but failed to infect wheat when plants were grown inviruliferous soil. Mechanically OGSV can be transmitted to some Nicotiana and Chenopodium species. SrCSV infects Sorghum bicolor andcan be mechanically transmitted to a range of species including Chenopodium quinoa, C. amaranticolor, Nicotiana clevelandii, Arachishypogaea, Zea mays and T. aestivum.

The furoviruses are soil-borne; Polymyxa graminis has been identified as a vector for SBWMV ( Estes and Brakke 1966) and is probably thevector of the other viruses in the genus. Virions are thought to be carried within the motile zoospores. Soil containing the resting sporesremains infectious for many years.

Virions are found scattered, or in aggregates and inclusion bodies in the cytoplasm and vacuole. Inclusion bodies can be crystalline inclusionsor comprise loose clusters of virus particles in association with masses of microtubules. Amorphous inclusion bodies can be seen in tissuesections by light microscopy (Peterson 1970, Hibino et al., 1974a, Hibino et al., 1974b).

Antigenicity

Virions are immunogenic and members of the different species can be distinguished serologically.

Derivation of names

Furo: from fungus-borne, rod-shaped virus.

Species demarcation criteria












Isolates of different species have less than 75% nt identity for RNA 1 and less than 80% nt identity for RNA 2. SBWMV, SBCMV, CWMV andOGSV can be discriminated also by reactivity with selected monoclonal and polyclonal antibodies. OGSV and SrCSV differ in host range toSBWMV, SBCMV and CWMV. The latter three viruses have similar biological properties and experimental re-assortants of SBWMV(Nebraska), SBWMV (Japan) and SBCMV were infectious (Miyanishi et al., 2002). With the other viruses this possibility has not yet beenchecked.

Member species

★ Exemplar isolate of the speciesSpecies Virus name Isolate Accession number RefSeq number Available

sequenceVirus

Abbrev.★ Chinese wheat mosaic virus Chinese wheat mosaic virus Yantai China RNA1: AJ012005; RNA2:

AJ012006RNA1: NC_002359; RNA2:NC_002356

Completegenome CWMV

★ Japanese soil-borne wheatmosaic virus Japanese soil-borne wheat mosaic virus JT RNA1: AB033689; RNA2:

AB033690RNA1: NC_038850; RNA2:NC_038851

Completegenome JSBWMV

Japanese soil-borne wheatmosaic virus French barley mosaic virus AJ749657; AJ749658 Partial genome FBMV

★ Oat golden stripe virus oat golden stripe virus United Kingdom RNA1: AJ132578; RNA2:AJ132579

RNA1: NC_002358; RNA2:NC_002357

Completegenome OGSV

★ Soil-borne cereal mosaicvirus

European wheat mosaic virus; Soil-bornerye mosaic virus France RNA1: AJ132576; RNA2:

AJ132577RNA1: NC_002351; RNA2:NC_002330

Completegenome SBCMV

★ Soil-borne wheat mosaicvirus soil-borne wheat mosaic virus US_Nebraska 1981

wild typeRNA1: L07937; RNA2:L07938

RNA1: NC_002041; RNA2:NC_002042

Completegenome SBWMV

★ Sorghum chlorotic spot virus Sorghum chlorotic spot virus Shirako RNA1: AB033691; RNA2:AB033692

RNA1: NC_004014; RNA2:NC_004015

Completegenome SrCSV

Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.




https://www.ncbi.nlm.nih.gov/nuccore/AJ012005,AJ012006

https://www.ncbi.nlm.nih.gov/nuccore/NC_002359,NC_002356

https://www.ncbi.nlm.nih.gov/nuccore/AB033689,AB033690







https://www.ncbi.nlm.nih.gov/nuccore/L07937,L07938




Genus: Goravirus


Viruses in the genus are distinctive in genome organisation and phylogeny. Like pecluviruses, they have 2 genomic RNAs and encode a ‘triplegene block’ but (a) the small cysteine-rich protein ORF is located near the 3′-end of RNA 2 (RNA 1 in pecluviruses) and (b) there is noequivalent of the second (39 kDa) ORF on RNA 2 that is characteristic of pecluviruses (Atsumi et al., 2015, Ong et al., 2016).

Virion

Morphology

Virions are rod-shaped and about 20nm in width, but it is difficult to determine their length because of disintegration during purification.

Nucleic acid

Complete or almost complete sequences are available for isolates of both species in the genus. RNA 1 is about 4.5-5.5 kb and RNA 2 about3.0–3.9 kb. There is a 3′-terminal tRNA-like structure on both genomic RNAs.

Proteins

The capsid comprises multiple copies of a single polypeptide of about 22 kDa.


RNA 1 has one predicted ORF. The 5'-proximal region encodes a replication protein containing methyltransferase and helicase domains. The3'-proximal region, which is probably expressed as a readthrough product, encodes the RdRP. The 5'-proximal ORF of RNA 2 encodes a coatprotein of about 22 kDa and downstream ORFs encode the triple gene block proteins (involved in virus cell-to-cell movement) and a cysteine-rich protein (CRP) that was shown to act as a suppressor of gene silencing (Figure 1.Goravirus).

Figure 1.Goravirus. Genomic organization of gentian ovary ringspot virus (GORV). The tRNA structure motifs at the 3′-ends of the RNAsare represented by a dark square. ORFs are indicated by rectangles and the presumed suppressible termination codon by an arrow(RT=readthrough). CRP, cysteine-rich protein.

Biology

GORV is transmitted through pollen and causes ringspot symptoms on the ovaries of infected plants. The viruses can be transmittedexperimentally by sap inoculation but the natural host range and any vectors are unknown (Atsumi et al., 2015).




https://talk.ictvonline.org/ictv-reports/ictv_online_report/positive-sense-rna-viruses/w/virgaviridae/663/references-virgaviridae


Derivation of names

Gora: from gentian ovary ringspot virus.


There are only two species recognised in the genus and only single isolates of each have been characterized. The two viruses are onlydistantly related (<50% aa identity between homologous proteins) and clearly belong to different species. More rigorous demarcation criteriawill be developed if further members of the genus are reported.

Member species


sequence Virus Abbrev.

★ Drakaea virus A Drakaea virus A CanningMills

RNA1: KP760461; RNA2:KP760462

RNA1: NC_043398; RNA2:NC_043399 Partial genome DrVA

★ Gentian ovary ringspotvirus

gentian ovary ringspotvirus S RNA1: AB976029; RNA2:

AB976030RNA1: NC_024501; RNA2:NC_024502 Complete genome GORV




https://www.ncbi.nlm.nih.gov/nuccore/KP760461,KP760462




Genus: Hordeivirus


Hordeiviruses have three genomic RNAs and encode a “triple gene block” set of cell-to-cell movement proteins. They differ from viruses of allother genera because the RdRP is encoded on a separate RNA (rather than by readthrough of a stop codon from an upstream replicationprotein encoding ORF).

Virion

Morphology

Virions are non-enveloped, elongated and rigid, about 20×110–150 nm in size; they are helically symmetrical with a pitch of 2.5 nm (Figure1.Hordeivirus). The high-resolution structure of barley stripe mosaic virus (BSMV) obtained by cryo-electron microscopy shows that there aretwo types of virion that differ in the number of coat protein (CP) subunits per turn, and in the interactions between the CP subunits (Clare etal., 2015).

Figure 1.Hordeivirus. Electron micrograph of purified barley stripe mosaic virus (BSMV) particles stained with 2% uranyl acetate. Theparticles are approximately 20 nm wide and have a length that varies depending on the size of the encapsidated RNA. The field wasselected to represent monomers, but often a range of heterodisperse end-to-end aggregates up to 1000 nm in length predominate inpurified preparations. The particles in the top left, bottom center, and upper left side of the micrograph are end-to-end aggregates. The barrepresents 150 nm.


BSMV virions occur as heterodisperse sedimenting species with an S of about 182–193S; members of other species in the genus have anS of about 165–200S, depending on the virus. The BSMV isoelectric point is pH 4.5. Thermal inactivation of infectivity occurs at 63–70 °C.Virions are stable and their survival in plant sap ranges from a few days to several weeks.

Nucleic acid

Virions normally contain three positive sense ssRNAs. The RNAs are designated α (RNA 1), β (RNA 2) and γ (RNA 3), and their respectivesizes are 3.8, 3.2 and 2.8 kb (BSMV-ND18 strain), 3.8, 3.0 and 2.7 kb (Lychnis ringspot virus, LRSV), and 3.8, 3.6 and 3.1 kb (Poa semilatentvirus, PSLV). The sizes of the α and β RNAs are similar between different strains of BSMV, whilst RNAγ varies in size because of internalduplications of unknown significance.

Each RNA has m7GpppGUA at its 5′ end, and a highly conserved 238 nt (BSMV), 184 nt (LRSV), or 268 nt (PSLV) tRNA-like structure at the3′ end. In the case of BSMV, this structure can be charged with tyrosine. In the BSMV and LRSV genomes, a poly(A) sequence that is variablein length (~20 nt in BSMV, ~30-50 nt in LRSV) separates the coding region from the tRNA-like structure; however, this sequence is notpresent in the PSLV genome. A close sequence similarity between the first 70 nt of RNAα and RNAγ of the CV17 strain of BSMV suggeststhat a natural recombination event has occurred. A similar recombination event appears to have occurred between the 5′-untranslated leadersof RNAα and RNAβ of LRSV. These findings, plus sequence duplications in RNAγ, provide persuasive evidence that RNA recombination hashad a substantial role in the evolution of hordeiviruses (Edwards et al., 1992).

Proteins

The virion capsid is constructed from subunits of a single protein. The CP of all species is 22 kDa in size, yet the proteins differ in

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electrophoretic mobility.


All three BSMV genomic RNAs are required for systemic infection of plants, but RNAs α and γ alone can infect protoplasts. The 5′- and 3′-non-coding regions (NCR) of each BSMV RNA are required for replication (Jackson et al., 2009). The hordeivirus genome encodes sevenproteins as illustrated for BSMV in Figure 2.Hordeivirus.

Figure 2.Hordeivirus. Genome organization of barley stripe mosaic virus (BSMV). The colored rectangles and smaller solid blackrectangles represent the ORFs, and the 3′-terminal tRNA-like structure, respectively. The 3′-proximal ORFs on each RNA terminate with anUAA that initiates the short poly (A) tract directly preceding the 238 nt tRNA-like terminus. See text for explanation.

RNAα is monocistronic and encodes the αa protein (130 kDa in BSMV, 129 kDa in LRSV and 127 kDa in PSLV) that functions as the helicasesubunit of the viral replicase. The αa protein has two conserved sequence domains, an amino-terminal Mtr and a carboxy-terminalNTPase/Hel.

The 5′-terminal ORFs of RNAβ (βa) of BSMV, LRSV and PSLV encode a 22 kDa CP. The BSMV CP, which is dispensable for systemicmovement of the virus, is more closely related to the PSLV CP (53.2% aa identity) than to the LRSV CP (33.7% aa identity). An intergenicregion separates a “triple gene block” (TGB) that encodes three nonstructural proteins, TGB1, TGB2 and TGB3. In BSMV, The TGB1 proteinis expressed from a 2,450 nt subgenomic RNA (sgRNAß1) , and the TGB2 and TGB3 proteins are expressed from a second bicistronic 960 ntsubgenomic RNA (sgRNA ß2) with TGB3 being expressed via a leaky scanning mechanism. In BSMV, a minor 23 kDa translationalreadthrough extension of the TGB2 protein, designated TGB2′, is present in plants. However, genetic experiments have not identified afunction for TGB2′, so it appears to be dispensable for infection in all local lesion and systemic hosts tested. The BSMV sgRNAβ1 andsgRNAβ2 promoters reside between positions −29 to −2 and −32 to −17 relative to the transcription initiation sites, respectively, and the ntsequences preceding the transcription initiation sites of these sgRNAs are conserved in LRSV and PSLV. The TGB1 protein (58 kDa inBSMV, 50 kDa in LRSV, and 63 kDa in PSLV) contains a conserved NTPase/Hel domain. The BSMV TGB1 protein binds RNA, NTPs andexhibits ATPase and helicase activity in vitro (Donald et al., 1997). It also elicits resistance to BSMV strains that are unable to infectBrachypodium distachyon inbred lines containing the Bsr1 resistance gene. Protein kinase CK2 phosphorylation of the TGB1 protein plays acritical role in promoting viral movement in monocots and dicots by affecting the interactions between the TGB1 and TGB3 proteins (Lee et al.,2012, Hu et al., 2015). The TGB2 (17 kDa in BSMV, 14 kDa in LRSV and 15 kDa in PSLV) and TGB3 (14 kDa in BSMV, 18 kDa in LRSV, andPSLV) proteins are hydrophobic and membrane-associated. Each of the BSMV TGB proteins is required for virus cell-to-cell movement inplants.

RNAγ is bicistronic and encodes the γa polymerase subunit of the viral replicase (74 kDa in the BSMV-ND18 strain, 72 kDa in LRSV, and 81kDa in PSLV), and the cysteine-rich γb protein (17 kDa in BSMV, 16 kDa in LRSV, and 20 kDa in PSLV). The γa protein is variable in sizebecause of a repeated sequence of 351-363 nt present in some strains of BSMV (Kozlov Iu et al., 1989). The BSMV γb protein is expressedfrom a 737 nt subgenomic RNA (sgRNAγ) and is a pathogenicity determinant involved in regulating expression of ORFs encoded by RNAβ.The sgRNAγ promoter is between nt −21 to +2 relative to its transcription start site, and this sequence has similarity to sequences upstream ofthe γb proteins in PSLV and LRSV. The BSMV γb protein has both RNA binding and zinc binding ability, participates in homologousinteractions, and may act as a suppressor of post-transcriptional gene silencing.

Translation of a functional αa protein is required for replication of RNAα in cis, whilst replication of RNAβ is dependent on the presence of theCP and TGB1 intergenic region, and replication of RNAγ depends upon approximately 600 nt of the 5′-terminal region. The TGB proteins








encoded on RNAβ are required for cell-to-cell and systemic movement in plants, but the CP and TGB2′ are dispensable. The γb protein isalso dispensable in some genetic backgrounds. A mutation in the 5′-NCR sequence of the γa ORF interfered with systemic infection ofNicotiana benthamiana, suggesting that modulation of γa expression can affect movement. Full-length dsRNAs corresponding to all viralgenomic ssRNAs can be isolated from infected plants. Virus particles accumulate predominantly in the cytoplasm and also in nuclei. Infectedbarley plants develop pronounced enlargements of the plasmodesmata that contain the TGB1 protein (Gorshkova et al., 2003), andprominent peripheral vesicles appear in proplastids and chloroplasts. These vesicles are the sites of replication (Torrance et al., 2006, Zhanget al., 2017).

Biology

The native hosts of three viruses (ALBV, BSMV, PSLV) are grasses (family Gramineae); strains of LRSV occur naturally in dicotyledonousplants of the families Caryophyllaceae and Labiatae. Various strains of these viruses elicit local lesions in Chenopodium species and are ableto establish systemic infections in a common host, Nicotiana benthamiana. BSMV and LRSV are efficiently seed-transmitted and aretransmitted less efficiently by pollen. Field spread from primary infection foci occurs efficiently by direct leaf contact. There are no knownvectors for any members of the genus. Anthoxanthum latent blanching virus (ALBV) has been reported only from Great Britain; BSMV occursworld-wide wherever barley is grown and has recently been isolated from 750-year-old barley grains found near the Nile River (Smith et al.,2014); LRSV (mentha strain) has been isolated in Hungary ( Beczner et al., 1992), and the type strain which is highly seed-transmissible in thefamily Caryophyllaceae, was initially discovered in California from seed of Lychnis divaricata introduced from Europe. PSLV has beenrecovered from Poa palustris isolated from two locations in Western Canada (Slykhuis 1972).

Antigenicity

Hordeivirus particles are strong immunogens. Member species are distantly related serologically with BSMV being more closely related toPSLV than to LRSV, which is in agreement with sequence analyses.

Derivation of names

Hordei: from hordeus, Latin name of the primary host of the type species virus of the genus Hordeivirus.


Species differ in host range and are phylogenetically distinct. Precise molecular discrimination criteria have not been established because,except for isolates of the type species, few sequences have been determined.

Member species


sequenceVirus

Abbrev.★ Anthoxanthum latent

blanching virusAnthoxanthum latentblanching virus

UK/Aberystwyth

No entry inGenbank ALBV

★ Barley stripe mosaic virus barley stripe mosaic virus Type strain RNA1: J04342; RNA2: X03854;RNA3: M16576

RNA1: NC_003469; RNA2: NC_003481;RNA3: NC_003478

Completegenome BSMV

★ Lychnis ringspot virus Lychnis ringspot virus USA/California RNA2: Z46351; RNA3: Z46353 RNA2: NC_038932; RNA3: NC_038933 Partial genome LRSV

★ Poa semilatent virus Poa semilatent virus Canadian RNA2: M81486; RNA3: M81487 RNA2: NC_043400; RNA3: NC_043401 Partial genome PSLV










https://www.ncbi.nlm.nih.gov/nuccore/J04342,X03854,M16576

https://www.ncbi.nlm.nih.gov/nuccore/NC_003469,NC_003481,NC_003478

https://www.ncbi.nlm.nih.gov/nuccore/Z46351,Z46353


https://www.ncbi.nlm.nih.gov/nuccore/M81486,M81487


Genus: Pecluvirus


Pecluviruses have a bipartite genome, a “triple gene block” set of cell-to-cell movement proteins and are transmitted by root-infecting vectorsin the family Plasmodiphorales, once described as fungi but now classified as Cercozoa.

Virion

Morphology

Virions are rod-shaped, about 21 nm in diameter and of two predominant lengths, 190 and 245 nm (Figure 1.Pecluvirus). The lengthdistribution of the short particles is broad and in some preparations an additional class of 160 nm particles is recognizable. Virions havehelical symmetry with a pitch of 2.6 nm.

Figure 1.Pecluvirus. Negative contrast electron micrograph of virions of Indian peanut clump virus (L serotype) negatively stained with 2%phosphotungstic acid, pH 6. The bar represents 150 nm.


Virions sediment as two major components with S of 183S and 224S. Buoyant density in CsCl is 1.32 g cm . Virion isoelectric point is pH6.45. Thermal inactivation of infectivity occurs at 64 °C. Virions are stable in frozen leaves.

Nucleic acid

The genome consists of two molecules of linear positive sense ssRNA: RNA 1 of about 5,900 nt and RNA 2 of about 4,500 nt. RNAs arethought to have a 5′-cap structure but this has not been confirmed. The 3′ ends of the RNAs can fold into a tRNA-like structures and are notpolyadenylated.

Proteins

The virion CP proteins are 23 kDa.


RNA 1 contains two ORFs (Figure 2.P ecluvirus). The 5′-proximal ORF encodes a 131 kDa protein and suppression of a termination codoncan result in the synthesis of a readthrough protein of 191 kDa. The 3′ proximal ORF encodes a 15 kDa protein. The proteins of 131 and 191kDa contain NTP-binding, Hel and RNA polymerase motifs and are involved in the putative replication complex (Miller et al., 1996, Herzog etal., 1994). The 15 kDa protein is translated from a subgenomic RNA. It is a suppressor of post-transcriptional gene silencing ( Dunoyer et al.,2002a) and is targeted to peroxisomes or related punctate bodies during infection. RNA 2 contains five ORFs ( Manohar et al., 1993): the 5′proximal ORF encodes the CP, the adjacent ORF which, in PCV RNA 1, overlaps the first ORF by 2 nts encodes a 39 kDa protein. Thisprotein is expressed by leaky scanning (Herzog et al., 1995) and is thought to be involved in the transmission of PCV by its fungus vector.Further downstream, and separated by a 135 nt intergenic region, is a triple gene block sequence that codes for proteins of 51, 14 and 17 kDa

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that are thought to be involved in the movement of virus from cell to cell. These proteins are probably expressed via one or more sgRNAs butthese have not been clearly identified. The 3′-NCRs for PCV are 298 nt for RNA 1 and 275 nt for RNA 2; the 3' terminal 96 nt are identical inboth RNAs. The NCRs differ in size among isolates from the different serotypes of IPCV.

Both genomic RNAs are required for systemic invasion of plants but RNA 1 is able to replicate in absence of RNA 2 in protoplasts ( Dunoyer etal., 2002b). The virus is found in the cells of roots, stems and leaves of systemically infected plants.

Figure 2.Pecluvirus. Genomic organization of peanut clump virus (PCV). The tRNA structure motifs at the 3′-ends of the RNAs arerepresented by a dark square. ORFs are indicated by rectangles and a suppressible termination codon by an arrow (RT, readthrough). CRP,cysteine-rich protein.

Biology

The first reported natural host of pecluvirus was Arachis hypogea (groundnut, Leguminosae). Disease symptoms are stunting – mottle –mosaic – chlorotic ringspot. PCV infects Sorghum arundinaceum, usually symptomlessly. IPCV infects a number of cereal crops andgraminaceous weeds, some symptomlessly and others to induce stunting. The experimental host range is wide and includes species ofAizoaceae, Amaranthaceae, Chenopodiaceae, Cucurbitaceae, Graminae, Leguminosae, Scrophulariaceae and Solanaceae. Nicotianabenthamiana and Phaseolus vulgaris are experimental propagation hosts. Chenopodium amaranticolor and Chenopodium quinoa are locallesions hosts (Thouvenel and Fauquet 1981).

The virus is transmitted naturally by Polymyxa graminis or by seed (in groundnuts) (Dieryck et al., 2011, Dieryck et al., 2009). It ismechanically transmissible.

PCV exists in West Africa (Bénin, Burkina Faso, Congo, Côte d’Ivoire, Mali, Niger, Senegal and Pakistan). IPCV is widely distributed in Indiaand Pakistan. A soil type favourable to the vector is a prerequisite for the virus to cause disease.

Antigenicity

The viruses are highly immunogenic. There is a serological variability among isolates of PCV. IPCV isolates fall into one of three very distinctserotypes: IPCV-H, IPCV-L, IPCV-T (Huguenot et al., 1989). All are serologically distinct from PCV.

Derivation of names

Peclu: from peanut clump virus.


There are two species in the genus. Isolates of both species are serologically distinct (heterologous reactions are weak or undetectable) anddiffer by geographical distribution (PCV only in Africa; IPCV in the Indian subcontinent). There are also serologically distinct strains withineach species and better demarcation criteria may need to be re-examined when more isolates have been studied or other members of thegenus are discovered.








Member species


sequence Virus Abbrev.

★ Indian peanut clumpvirus

Indian peanut clumpvirus

Hyderabadserotype

RNA1: X99149; RNA2:AF447397

RNA1: NC_004729; RNA2:NC_004730 Complete genome IPCV

★ Peanut clump virus peanut clump virus 87/TGTA2 RNA1: X78602; RNA2: L07269 RNA1: NC_003672; RNA2:NC_003668 Complete genome PCV




https://www.ncbi.nlm.nih.gov/nuccore/X99149,AF447397


https://www.ncbi.nlm.nih.gov/nuccore/X78602,L07269


Genus: Pomovirus


Pomoviruses have three genomic RNAs, a “triple gene block” set of cell-to-cell movement proteins and are transmitted by root-infectingvectors in the family Plasmodiophorales, once described as fungi but now classified as Cercozoa.

Virion

Morphology

The non-enveloped, rod-shaped particles are helically constructed with a pitch of 2.4 to 2.5 nm and an axial canal (Figure 1.Pomovirus). Theyhave predominant lengths of about 65–80, 150–160 and 290–310 nm and diameters of 18–20 nm. Crude extracts of plants infected with beetsoil-borne virus (BSBV), beet virus Q (BVQ) and potato mop-top virus (PMTV) contain characteristic small bundles of side-by-side aggregatedparticles in addition to singly dispersed particles.

Figure 1.Pomovirus. Negative contrast electron micrograph of particles of potato mop-top virus. The gold-labeling shows the binding ofmonoclonal antibody SCR 68, which detects the CP readthrough protein, to one extremity of the particles. The bar represents 100 nm(Courtesy I.M. Roberts).


Virions sediment as three components with S of about 125S, 170S and 230S, respectively. In plant sap at room temperature, most virusinfectivity is lost within a few hours.

Nucleic acid

Virions contain three molecules of linear positive sense ssRNA of about 6, 3–3.5 and 2.5–3 kb, respectively. The sequence of the threegenomic RNAs has been determined for at least one isolate of each species in the genus (Gil et al., 2016, Lu et al., 1998, Koenig et al., 1996,Koenig et al., 1997, Koenig and Loss 1997, Koenig et al., 1998, Sandgren et al., 2001, Savenkov et al., 1999). The RNAs are probably cappedat the 5′ end; their 3′ ends can be folded into tRNA-like structures that are preceded by a long hairpin-like structure and an upstreampseudoknot domain. The tRNA-like structures of pomoviruses like those of tymoviruses contain an anticodon for valine and are capable ofhigh-efficiency valylation (Savenkov et al., 1999).

Proteins

The major capsid protein (CP) species is 20 kDa in size. It is not needed for systemic infection. The CP readthrough protein may be detectedin some PMTV particles near one extremity by means of immunogold labeling (Cowan et al., 1997). Sequences in the CP readthrough proteinare necessary for the transmission of PMTV by Spongospora subterranean (Reavy et al., 1998). Yeast two-hybrid experiments reveal that theCP readthrough protein interacts in vitro with the triple gene block protein movement protein TGB1. In this system, TGB proteins show selfinteractions and TGB2 and TGB3 interact with each other. TGB2 and TGB3 are membrane-associated and TGB2 binds ssRNA in a sequencenonspecific manner. It has been suggested that they may form a complex with PMTV RNA that is translocated and localized to theplasmodesmata by TGB3 thus facilitating cell-to-cell movement (Tilsner et al., 2010).


RNA 1 of PMTV has an ORF encoding a 148 kDa protein and a 206 kDa readthrough protein that are presumably involved in replication. TheORF encoding the 148 kDa protein is terminated by an apparently suppressible UGA stop codon (Figure 2.Pomovirus). Proteins of similar

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sizes are encoded on RNA 1 of BVQ, BBNV and BSBV. The smaller protein contains a Mtr motif in its N-terminal part and a Hel motif in its C-terminal part; the motifs for RdRP are found in the C-terminal part of the readthrough protein (Figure 2.Pomovirus). The two proteins containother highly conserved domains of unknown function in their N- and C-terminal parts, but their central regions (designated as “variable” inFigure 2.Pomovirus) are specific for each virus. RNA-CP in PMTV (RNA 2 in other viruses), contains the CP ORF, which terminates with asuppressible UAG stop codon and then continues in frame to form a CP readthrough protein that varies in size between differentpomoviruses; possibly because it readily undergoes internal deletions. [Note: large deletions have been found in both natural and laboratoryisolates of PMTV and PMTV RNA-CP was therefore originally designated as RNA 3]. RNA 3 encodes a triple gene block (TGB) of proteinsinvolved in viral movement; in PMTV there is also a unique 3’-proximal ORF encoding a cysteine-rich protein and in BBNV a predicted 6 kDaglycine-rich protein. TGB1 also contains Hel motifs. The sequences of the C-terminal part of TGB1, of the entire TGB2 and of the N-terminalpart of TGB3 are highly conserved among pomoviruses. The replication mechanisms are unknown but both RNA 1 and RNA 3 are essentialfor BSBV replication and symptom production in Chenopodium quinoa. However, RNA 2 was not essential ( Crutzen et al., 2009).

Figure 2.Pomovirus. Genome organization typical of potato mop-top virus. Arrows indicate respectively the UGA and UAG stop codonsthat are thought to be suppressible, and solid squares indicate a 3′-terminal tRNA-like structure. Hel, helicase; Mt, methyltransferase;RdRP, RNA dependent RNA polymerase; RT, readthrough.

Biology

The natural host range of pomoviruses is very narrow; only dicotyledonous hosts have been described. Pomoviruses are transmitted by soil.Spongospora subterranea and Polymyxa betae have been identified as vectors for PMTV (Arif et al., 1995) and BSBV, respectively. Theviruses are also transmissible mechanically.

PMTV-infected cells contain virions aggregated in sheaves in the cytoplasm. Infections with BSBV and BVQ induce voluminous cytoplasmicinclusions which consist of hypertrophied endoplasmic reticulum, convoluted membrane accumulations, numerous small virion bundles andrarely compact virus aggregates.

Antigenicity

Virions are moderately antigenic. Distant serological relationships have been found between the particles of BSBV and BVQ but not betweenthose of the two beet viruses and PMTV. This is probably due to the fact that PMTV CP has an extra ten amino acids on its immunodominantN-terminus that are missing in the CP proteins of the two beet viruses. A conserved sequence EDSALNVAHQL is found in the CPs of PMTV,BSBV and BVQ (Koenig et al., 1998). An epitope within this sequence recognised by the monoclonal antibody SCR 70 is only detectable byWestern blotting after disruption of the particles. Other epitopes are either exposed along the entire particle length, e.g. the immunodominantN-terminus, or are accessible only on one extremity (Figure 1.Pomovirus). PMTV and BBNV show distant serological relationships totobamoviruses.

Derivation of names

Pomo: from potato mop-top virus.







The criteria demarcating species in the genus are:

Differences in host rangeEffects in infected tissue: different inclusion body morphologyTransmission: different vector speciesSerology: virions are distantly related serologicallyGenome: different numbers of genome components (presence or absence of an ORF encoding a cysteine-rich protein)Sequence: less than about 80% nt identity over whole genomeSequence: less than about 90% identical in CP amino acid sequence

Member species


sequenceVirus

Abbrev.★ Beet soil-borne virus beet soil-borne virus Ahlum RNA1: Z97873; RNA2: U64512; RNA3:

Z66493RNA1: NC_003520; RNA2: NC_003518;RNA3: NC_003519

Completegenome BSBV

★ Beet virus Q beet virus Q Koenig RNA1: AJ223596; RNA2: AJ223597;RNA3: AJ223598


Completegenome BVQ

★ Broad bean necrosis virus broad bean necrosis virus Namba RNA1: D86636; RNA2: D86637; RNA3:D86638


Completegenome BBNV

★ Colombian potato soil-borne virus

Colombian potato soil-borne virus IS9 RNA1: KT225271; RNA2: KT225272;

RNA3: KT225273RNA1: NC_029034; RNA2: NC_029035;RNA3: NC_029037

Completegenome CPSBV

★ Potato mop-top virus potato mop-top virus Swedish

RNA1: AJ238607; RNA2: AJ243719;RNA3: AJ277556


Completegenome PMTV



Virus name Accession number Virusabbreviation

Soil-borne virus2

RNA1: KT225277*; RNA3:KT225278* SBV2


* partial genome



https://www.ncbi.nlm.nih.gov/nuccore/Z97873,U64512,Z66493


https://www.ncbi.nlm.nih.gov/nuccore/AJ223596,AJ223597,AJ223598


https://www.ncbi.nlm.nih.gov/nuccore/D86636,D86637,D86638


https://www.ncbi.nlm.nih.gov/nuccore/KT225271,KT225272,KT225273


https://www.ncbi.nlm.nih.gov/nuccore/AJ238607,AJ243719,AJ277556


https://www.ncbi.nlm.nih.gov/nuccore/KT225277


Genus: Tobamovirus


Tobamoviruses are the only members of the family to have a non-segmented genome. They have a “30K”-like cell-to-cell movement protein,are not vector-transmissible and when seed transmitted, the embryo is not affected. It is the largest genus in the family and the literature isextensive. For reviews of diversity and evolution within the genus see (Gibbs et al., 2015, Lartey et al., 1996, Stobbe et al., 2012).

Virion

Morphology

Virions are 18 nm in diameter and have a predominant length of 300–310 nm (Figure 1.Tobamovirus). Structure and assembly of the particleshave been reviewed by (Klug 1999). Shorter virions produced by the encapsidation of subgenome-sized RNA are usually a minor componentof the virion population, although virions of two species produce an abundant short virion of 32–34 nm. Virions often form large crystallinearrays visible by light microscopy.

Figure 1.Tobamovirus. (Left) Model of particle of tobacco mosaic virus (TMV). Also shown is the RNA as it is thought to participate in theassembly process. (Right) Negative contrast electron micrograph of TMV particle stained with uranyl acetate. The bar represents 100 nm.


Virion Mr is 40×10 . Buoyant density in CsCl is 1.325 g cm . S is 194S. Tobamoviruses have thermal inactivation points (10 min) of 90 °Cand survive in plant sap for many years.

Nucleic acid

The genome is 6.3–6.6 kb in size. An approximately 70 nt long 5′-NTR contains many AAC repeats and few or no G nucleotides. The 0.2–0.4kb 3′-NTR contains sequences that can be folded into pseudoknots followed by 3′-terminal sequences that can be folded into a tRNA-like,amino acid-accepting structure. The subgenomic mRNAs transcribed in infected cells also have a 5′-terminal cap and 3′-tRNA-like structure.The encapsidation signal is usually located within the ORF encoding the MP (Wilson and McNicol 1995) or within the ORF encoding the CP inthe studied isolates of Cucumber green mottle mosaic virus and Sunn hemp mosaic virus.

Proteins

Virions contain a single structural protein (17–18 kDa). Two nonstructural proteins are expressed directly from the genomic RNA: a 124–132kDa protein terminated by an amber (UAG) stop codon and a 181–189 kDa protein produced by readthrough of this stop codon, both of whichare required for efficient replication. A third nonstructural protein (28–31 kDa) is required for cell-to-cell and long-distance movement andbelongs to the “30K”-like cell-to-cell movement proteins. The MP is associated with plasmodesmata and has single-stranded nucleic acidbinding activity in vitro. The CP is not required for cell-to-cell movement, but has a role in vascular tissue dependent virus accumulation. Thereplication proteins have also been implicated in virus movement. The MP and CP are expressed from individual 3′-co-terminal subgenomicmRNAs. The MP is expressed early during infection, whereas the CP is expressed later, and at higher levels. The MP and CP are not requiredfor replication in single cells. The N-terminal one-third of the 124–132 kDa protein has similarity with methyltransferase/guanylyl transferaseswhereas the C-terminal one-third of the 124–132 kDa protein has similarity with RNA helicases (including an NTP-binding motif). Thereadthrough domain of the 181–189 kDa protein has motifs common to RdRPs.


The single genomic RNA encodes at least four proteins. The 124–132 kDa and 181–189 kDa replication proteins are translated directly fromthe 5' proximal ORF of the genomic RNA. The 124–132 kDa replication protein contains the Mtr and Hel domains. The 181–189 kDareplication protein additionally contains the polymerase domain, synthesized by occasional readthrough of the leaky termination codon of the

6 −3 20,w








124–132 kDa protein encoding ORF. The 181–189 kDa replication protein is the only protein required for replication in single cells, althoughthe 124–132 kDa replication protein is also required for efficient replication. The downstream ORFs encode the 28–31 kDa MP and 17–18kDa CP, which are translated from their respective 3′ co-terminal sgRNAs, both of which contain a 5′ cap (Figure 2.Tobamovirus). In themembers of some species, the MP ORF overlaps both the 181–189 kDa protein and the CP ORFs, whereas in other species it does notoverlap either ORF or overlaps one of the ORFs. An ORF that encodes a cysteine-rich protein is located between the 181-189 kDa and MPORFs in passion fruit mosaic virus. a tobamovirus isolated from maypop, a plant classified in the order Malpighiales (Stobbe et al., 2012).

Figure 2.Tobamovirus. Genome organization of tobacco mosaic virus (TMV). Genomic RNA is capped and is template for expression ofthe 126 and 183 kDa proteins. The 3′ distal movement protein (MP) and capsid protein (CP) ORFs are expressed from separate 3′ co-terminal sgRNAs. The tRNA structure motif at the 3′-end of the RNA is represented by a dark square.

RNA replication occurs via several steps: (a) synthesis of viral replication proteins by translation of the genomic RNA; (b) translation-coupledbinding of the replication proteins to a 5'-terminal region of the genomic RNA; (c) recruitment of the genomic RNA by replication proteins ontomembranes and formation of a complex with host proteins TOM1 and ARL8; (d) synthesis of complementary (negative-strand) RNA in thecomplex; and (e) synthesis of progeny genomic RNA (Ishibashi and Ishikawa 2016).

Biology

Most species have moderate to wide host ranges under experimental conditions, although in nature host ranges are usually quite narrow. Theviruses are found in all parts of host plants. Transmission occurs without the help of vectors by contact between plants and sometimes byseed, although this occurs in the absence of infection of the embryo.

Antigenicity

The virions act as strong immunogens and members of different species are serologically distinct.

Derivation of names

Tobamo: from tobacco mosaic virus.


Many tobamoviruses that were historically designated as strains of tobacco mosaic virus are now defined as separate species based onnucleotide sequence data.


Sequence similarity: more than 90% whole genome nt sequence identity is considered to characterize strains of the same species. Mostof the sequenced tobamoviruses of different species have considerably less than 90% sequence identityHost range: however many of these viruses have wider and more overlapping host ranges in experimental rather than natural situationsAntigenic relationships between the CPs

Member species

★ Exemplar isolate of the species





Species Virus name IsolateAccession

number RefSeq numberAvailablesequence

VirusAbbrev.

★ Bell pepper mottle virus bell pepper mottle virus Netherlands DQ355023 NC_009642 Complete genome BPMV★ Brugmansia mild mottle virus Brugmansia mild mottle virus 2373 AM398436 NC_010944 Complete genome BrMMV★ Cactus mild mottle virus cactus mild mottle virus Kr EU043335 NC_011803 Complete genome CMMoV★ Clitoria yellow mottle virus Clitoria yellow mottle virus Larrimah JN566124 NC_016519 Complete genome CliYMV★ Cucumber fruit mottle mosaic virus cucumber fruit mottle mosaic virus Wang AF321057 NC_002633 Complete genome CFMMV★ Cucumber green mottle mosaic virus cucumber green mottle mosaic virus SH D12505 NC_001801 Complete genome CGMMV★ Cucumber mottle virus cucumber mottle virus Kubota AB261167 NC_008614 Complete genome CMoV★ Frangipani mosaic virus Frangipani mosaic virus P HM026454 NC_014546 Complete genome FrMV★ Hibiscus latent Fort Pierce virus Hibiscus latent Fort Pierce virus J AB917427 NC_025381 Complete genome HLFPV★ Hibiscus latent Singapore virus Hibiscus latent Singapore virus Singapore AF395898 NC_008310 Complete genome HLSV★ Kyuri green mottle mosaic virus Kyuri green mottle mosaic virus C1 AJ295948 NC_003610 Complete genome KGMMV★ Maracuja mosaic virus maracuja mosaic virus Peru DQ356949 NC_008716 Complete genome MarMV★ Obuda pepper virus Obuda pepper virus Ob D13438 NC_003852 Complete genome ObPV★ Odontoglossum ringspot virus Odontoglossum ringspot virus 18KDa coat

protein X82130 NC_001728 Complete genome ORSV

★ Opuntia chlorotic ringspot virus Sammons's Opuntia virus SOV No entry inGenbank SOV

★ Paprika mild mottle virus paprika mild mottle virus Japanese AB089381 NC_004106 Complete genome PaMMV★ Passion fruit mosaic virus passion fruit mosaic virus USA HQ389540 NC_015552 Complete genome PFMV★ Pepper mild mottle virus pepper mild mottle virus S M81413 NC_003630 Complete genome PMMoV★ Plumeria mosaic virus Plumeria mosaic virus Plu-Ind-1 KJ395757 NC_026816 Complete genome PluMV★ Rattail cactus necrosis-associated

virus rattail cactus necrosis-associated virus South Korea JF729471 NC_016442 Complete genome RCNaV

★ Rehmannia mosaic virus Rehmannia mosaic virus Henan EF375551 NC_009041 Complete genome RheMV★ Ribgrass mosaic virus ribgrass mosaic virus Kons.1105-R14 HQ667979 NC_002792 Complete genome RMV★ Streptocarpus flower break virus Streptocarpus flower break virus Willingmann AM040955 NC_008365 Complete genome SFBV★ Sunn-hemp mosaic virus sunn-hemp mosaic virus SHMV U47034; J02413 NC_043383;

NC_043384 Partial genome SHMV

★ Tobacco latent virus tobacco latent virus; Nigerian tobacco latentvirus TLV1 AY137775 NC_038703 Partial genome TLV1

★ Tobacco mild green mosaic virus tobacco mild green mosaic virus Solis M34077 NC_001556 Complete genome TMGMV★ Tobacco mosaic virus tobacco mosaic virus variant 1 V01408 NC_001367 Complete genome TMV★ Tomato brown rugose fruit virus tomato brown rugose fruit virus Tom1-Jo KT383474 NC_028478 Complete genome TBRFV★ Tomato mosaic virus tomato mosaic virus Queensland AF332868 NC_002692 Complete genome ToMV★ Tomato mottle mosaic virus tomato mottle mosaic virus MX5 KF477193 NC_022230 Complete genome ToMMV★ Tropical soda apple mosaic virus tropical soda apple mosaic virus Okeechobee KU659022 NC_030229 Complete genome TSAMV★ Turnip vein-clearing virus turnip vein-clearing virus OSU U03387 NC_001873 Complete genome TVCV★ Ullucus mild mottle virus Ullucus mild mottle virus UMMV No entry in

Genbank UMMV

★Wasabi mottle virus wasabi mottle virus Shizuoka AB017503 NC_003355 Complete genome WMoV★ Yellow tailflower mild mottle virus yellow tailflower mild mottle virus Cervantes KF495564 NC_022801 Complete genome YTMMV★ Youcai mosaic virus youcai mosaic virus; oil-seed rape mosaic

virus U30944 NC_004422 Complete genome YoMV

★ Zucchini green mottle mosaic virus zucchini green mottle mosaic virus K AJ295949 NC_003878 Complete genome ZGMMV



Virus name Accession number Virus abbreviationAbutilon yellow mosaic virus EU559678* AbYMVHoya chlorotic spot virus KX434725 HCSV


* partial genome



https://www.ncbi.nlm.nih.gov/nuccore/DQ355023

https://www.ncbi.nlm.nih.gov/nuccore/NC_009642

https://www.ncbi.nlm.nih.gov/nuccore/AM398436


https://www.ncbi.nlm.nih.gov/nuccore/EU043335


https://www.ncbi.nlm.nih.gov/nuccore/JN566124


https://www.ncbi.nlm.nih.gov/nuccore/AF321057




https://www.ncbi.nlm.nih.gov/nuccore/AB261167


https://www.ncbi.nlm.nih.gov/nuccore/HM026454






https://www.ncbi.nlm.nih.gov/nuccore/AJ295948


https://www.ncbi.nlm.nih.gov/nuccore/DQ356949




https://www.ncbi.nlm.nih.gov/nuccore/X82130




https://www.ncbi.nlm.nih.gov/nuccore/HQ389540


https://www.ncbi.nlm.nih.gov/nuccore/M81413


https://www.ncbi.nlm.nih.gov/nuccore/KJ395757


https://www.ncbi.nlm.nih.gov/nuccore/JF729471


https://www.ncbi.nlm.nih.gov/nuccore/EF375551


https://www.ncbi.nlm.nih.gov/nuccore/HQ667979


https://www.ncbi.nlm.nih.gov/nuccore/AM040955


https://www.ncbi.nlm.nih.gov/nuccore/U47034,J02413


https://www.ncbi.nlm.nih.gov/nuccore/AY137775


https://www.ncbi.nlm.nih.gov/nuccore/M34077


https://www.ncbi.nlm.nih.gov/nuccore/V01408






https://www.ncbi.nlm.nih.gov/nuccore/KF477193


https://www.ncbi.nlm.nih.gov/nuccore/KU659022


https://www.ncbi.nlm.nih.gov/nuccore/U03387




https://www.ncbi.nlm.nih.gov/nuccore/KF495564


https://www.ncbi.nlm.nih.gov/nuccore/U30944


https://www.ncbi.nlm.nih.gov/nuccore/AJ295949


https://www.ncbi.nlm.nih.gov/nuccore/EU559678

https://www.ncbi.nlm.nih.gov/nuccore/KX434725

Genus: Tobravirus


Tobraviruses have a bipartite genome, a “30K”-like cell-to-cell movement protein and are transmitted by trichodorid nematodes.

Virion

Morphology

Virions are tubular particles with no envelope (Figure 1. Tobravirus). They are of two predominant lengths, (L) 180–215 nm and (S) rangingfrom 46 to 115 nm, depending on the isolate. Many strains produce in addition small amounts of shorter particles (Harrison and Robinson1978, Blanch et al., 2001). The particle diameter is 21.3–23.1 nm by electron microscopy or 20.5–22.5 nm by X-ray diffraction, and there is acentral canal 4–5 nm in diameter. Virions have helical symmetry with a pitch of 2.5 nm; the number of subunits per turn has been variouslyestimated as 25 or 32.

Figure 1.Tobravirus. (Left) Diagram of a virion of tobacco rattle virus (TRV), in section. (Right) Negative contrast electron micrograph ofparticles of TRV. The bar represents 100 nm.


Virion Mr is 48–50×10 (L particles) and 11–29×10 (S particles). Buoyant density in CsCl is 1.306–1.324 g cm . S is 286–306S (Lparticles) and 155–245S (S particles). Virions are stable over a wide range of pH and ionic conditions and are resistant to many organicsolvents, but are sensitive to treatment with EDTA. In N. clevelandii sap, the thermal inactivation point (10 min) of M-type isolates is 80–85 °C.

Nucleic acid

The genome consists of two molecules of linear positive sense ssRNA; RNA 1 is about 6.8 kb and RNA 2 ranges from 1.8 kb to about 4.5 kbin size (varying in different isolates). The 5′ terminus is capped with the structure m G ppp Ap. The 3′ terminus can adopt a tRNA-likestructure that can be adenylated but not aminoacylated (MacFarlane 1999).

Proteins

Virions contain a single structural protein of 22–24 kDa.


RNA 1 codes for four non-structural proteins: a 134-141 kDa protein terminated by an opal stop codon and a 194-201 kDa protein producedby readthrough of this stop codon, both of which are probably involved in RNA replication; a 29-30 kDa protein (P1a) involved in intercellulartransport of the virus; and a 12-16 kDa protein (P1b), which is a suppressor of RNA silencing (Martin-Hernandez and Baulcombe 2008) anddeterminant of seed transmission, as shown for Pea early-browning virus (PEBV) in pea(Wang et al., 1997). In addition to the virion structuralprotein, RNA 2 codes for two non-structural proteins, P2b and P2c. The size of P2b ranges from 27 to 40 kDa in different isolates, and that ofP2c from 18 to 33 kDa. P2b is absolutely required for transmission by nematodes, whereas mutation of the P2c ORF affects nematodetransmission in some strains but not in others (MacFarlane et al., 1996, Vassilakos et al., 2001). The ORFs for P2b and P2c are missing fromsome laboratory strains that have been maintained by mechanical transmission. RNA 2 of some tobravirus isolates contains an additionalsmall ORF between the CP and P2b ORFs, which codes for a potential 9 kDa protein. RNA2 of TRV isolate SYM has an unusual genomicorganisation, with additional, novel ORFs being located upstream of the CP ORF.

RNA 1 is capable of independent replication and systemic spread in plants. The 134–141 kDa and 194–201 kDa replication proteins are

6 6 −3 20,W

7 5′ 5′










translated directly from it, whereas P1a and P1b are translated from sgRNA species 1a and 1b, respectively. RNA 2 does not itself havemessenger activity; the CP is translated from sgRNA 2a (Harrison and Robinson 1978, MacFarlane 1999). The means by which the otherRNA 2 encoded proteins are expressed is not known but probably also involves sgRNAs (Figure 2.Tobravirus). There is sequence similaritybetween RNA 1 and RNA 2 at both ends, but the extent of the similarity varies between strains. In some strains, the similar region at the 3′end is large enough to include some or all of the P1a and P1b ORFs of RNA 1, but it is not known if these ORFs are expressed from RNA 2.Accumulation of virus particles is sensitive to cycloheximide but not to chloramphenicol, suggesting that only cytoplasmic ribosomes areinvolved in viral protein synthesis. Virions accumulate in the cytoplasm. L particles of pepper ringspot virus (PepRSV) become radiallyarranged around mitochondria, which are often distorted, and in cells infected with some TRV isolates, “X-bodies” largely composed ofabnormal mitochondria and containing small aggregates of virus particles may be produced.

Figure 2.Tobravirus. Genome organization and strategy of expression of tobacco rattle virus (TRV). The tRNA structure motifs at the 3′-ends of the RNAs are represented by a dark square. The arrow shows translational readthrough (RT) to produce the larger replicationprotein. P1a and P1b are translated from separate 3’-terminal subgenomic (sg) mRNAs, sgRNA1a and sgRNA1b. The CP is translatedfrom sgRNA2a; the mechanism by which the P2b and P2c proteins are expressed is unknown.

Biology

The host ranges are wide, including members of more than 50 monocotyledonous and dicotyledonous plant families. The natural vectors arenematodes in the genera Trichodorus and Paratrichodorus (Trichodoridae); different species being specific for particular virus strains (Ploeg etal., 1991). Adults and juvenile nematodes can transmit, but virus is probably not retained through the molt. Ingested virus particles becomeattached to the esophageal wall of the nematodes, and are thought to be released by salivary gland secretions and introduced into susceptibleroot cells during exploratory feeding probes (Macfarlane 2003). Virus can be retained for many months by non-feeding nematodes. There isno evidence for multiplication of virus in the vector and it is probably not transmitted through nematode eggs. The viruses are transmittedthrough seed of many host species. TRV occurs in Europe (including Russia), Japan, New Zealand and North America; PEBV occurs inEurope and North Africa, and PepRSV occurs in South America. TRV causes diseases in a wide variety of crop plants as well as weeds andother wild plants, including spraing (corky ringspot) and stem mottle in potato, rattle in tobacco, streaky mottle in narcissus and tulip, ringspotin aster, notched leaf in gladiolus, malaria in hyacinth and yellow blotch in sugar beet. PEBV is the cause of diseases in several legumes,including broad bean yellow band, distorting mosaic of bean and pea early-browning. PepRSV causes diseases in artichoke, pepper andtomato.

Most tissues of systemically invaded plants can become infected but in many species virus remains localized at the initial infection site in theroots. In some virus–host combinations, notably TRV in some potato cultivars, limited systemic invasion occurs, and virus may not be passedon to all the vegetative progeny of infected mother plants.

Normal particle-producing isolates (called M-type) are readily transmitted by inoculation with sap and by nematodes (Harrison and Robinson1978). Other isolates (called nm-type) have only RNA 1, do not produce particles, are transmitted with difficulty by inoculation with sap, andare probably not transmitted by nematodes. nm-type isolates are obtained from M-type isolates by using inocula containing only L particles,and are also found in naturally infected potato plants. They often cause more necrosis in plants than do their parent M-type cultures.

Antigenicity

Tobravirus particles are moderately immunogenic. There is little or no serological relationship between members of the genus, andconsiderable antigenic heterogeneity among different isolates of the same virus species (Robinson and Harrison 1985).









Derivation of names

Tobra: tobacco rattle virus.



Nucleotide sequences of RNA 1 show <75% identityInterspecific pseudo-recombinant isolates cannot be madeHost ranges differ in specific hosts (e.g. legumes)RNA 2 sequences and serological relationships are of limited value

Member species

★ Exemplar isolate of the speciesSpecies Virus name Isolate Accession number RefSeq number Available sequence Virus Abbrev.

★ Pea early-browningvirus

pea early-browningvirus SP5 RNA1: X14006; RNA2: X51828 RNA1: NC_002036; RNA2: NC_001368 Complete genome PEBV

★ Pepper ringspot virus pepper ringspot virus CAM RNA1: L23972; RNA2: X03241 RNA1: NC_003669; RNA2: NC_003670 Complete genome PepRSV★ Tobacco rattle virus tobacco rattle virus PpK20 RNA1: AF166084; RNA2: Z36974 RNA1: NC_003805; RNA2: NC_003811 Complete genome TRV




https://www.ncbi.nlm.nih.gov/nuccore/X14006,X51828


https://www.ncbi.nlm.nih.gov/nuccore/L23972,X03241


https://www.ncbi.nlm.nih.gov/nuccore/AF166084,Z36974


Authors: Virgaviridae

Michael J Adams*Virgaviridae Study Group ChairMineheadSomersetTA24 5DY E-mail: [email protected]

Scott Adkins USDA ARS USHRL 2001 South Rock Road Fort Pierce, FL 34945, USA Tel: +001 772-462-5885 E-mail: [email protected]

Claude Bragard, Université catholique de Louvain, ELIM - Croix du Sud 2 bte L7.05.25 à 1348 Louvain-la-Neuve, Belgium Tel: +32 10 47 40 23 E-mail: [email protected]

David Gilmer Institut de biologie moléculaire des plantes, 12 rue du Général Zimmer, 67084 Strasbourg cedex, France. Tel: +33 388 417259 E-mail: [email protected]

Dawei Li, State Key Laboratory for Agro-biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, P.R. China Tel: +86 10 6273 6336 extn 2673 E-mail: [email protected]

Stuart A MacFarlane, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK Tel: +44 344 928 5428 E-mail: [email protected]

Sek-Man Wong, Department of Biological Sciences National University of Singapore 14 Science Drive 4 Singapore 117543 Tel: +65 6516 5696 E-mail: [email protected]

Ulrich Melcher, Oklahoma State University Department of Biochemistry and Molecular Biology 246 Noble Research Center, OSU, Stillwater, OK 74078 USA Tel: +001-405-7446210 E-mail: [email protected]

Claudio Ratti, Università di Bologna, Dipartimento di Scienze e Tecnologie Agroambientali, Area Patologia Vegetale, Viale G. Fanin, 40 - II piano, 40127, Bologna, Italy Tel: +39 051 2096733 E-mail: [email protected]

Ki Hyun Ryu



Department of Horticultural Science, College of Natural Science, Seoul Women's University, Korea E-mail: [email protected]

* to whom correspondence should be addressed

The chapter in the Ninth ICTV Report, which served as the template for this chapter, was contributed by Adams, M.J., Heinze, C., Jackson, A.O.,Kreuze, J.F., Macfarlane, S.A. and Torrance, L.



Resources: Virgaviridae

Sequence alignments and tree files:

Figure 1.Virgaviridae

Alignment file (FASTA format)

Tree file (newick format)


















https://talk.ictvonline.org/cfs-file/__key/communityserver-wikis-components-files/00-00-00-00-84/OPSR.Virga.Alignment.Fig1.v1.fst

https://talk.ictvonline.org/cfs-file/__key/communityserver-wikis-components-files/00-00-00-00-84/OPSR.Virga.Tree_5F00_file.Fig1.v1.nwk











Further reading: Virgaviridae

Adams, M. J., Antoniw, J. F. & Kreuze, J. (2009). Virgaviridae: a new family of rod-shaped plant viruses. Arch Virol 154, 1967-1972. [PubMed]

Beuch, U., Berlin, S., Åkerblom, J., Nicolaisen, M., Nielsen, S. L., Crosslin, J. M., Hamm, P. B., Santala, J., Valkonen, J. P. & Kvarnheden,A. (2015). Diversity and evolution of potato mop-top virus. Arch Virol 160, 1345-1351. [PubMed]

Gibbs, A. (1999). Evolution and origins of tobamoviruses. Philos Trans R Soc Lond B Biol Sci 354, 593-602. [PubMed]

Kendall, A., Williams, D., Bian, W., Stewart, P. L. & Stubbs, G. (2013). Barley stripe mosaic virus: structure and relationship to thetobamoviruses. Virology 443, 265-270. [PubMed]

Verchot-Lubicz, J., Torrance, L., Solovyev, A. G., Morozov, S. Y., Jackson, A. O. & Gilmer, D. (2010). Varied movement strategies employedby triple gene block-encoding viruses. Mol Plant-Microbe Interact 23, 1231-1247. [PubMed]








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Citation: Virgaviridae

A summary of this ICTV Report chapter has been published as an ICTV Virus Taxonomy Profile article in the Journal of General Virology, andshould be cited when referencing this online chapter as follows:

Adams, M.J., Adkins, S., Bragard, C., Gilmer, D., Li, D., MacFarlane, S.A., Wong, S-M., Melcher, U., Ratti, C., Ryu, K.H., and ICTV ReportConsortium. 2017, ICTV Virus Taxonomy Profile: Virgaviridae. Journal of General Virology, 98: 1999–2000.

Funding support

Support for the preparation of this ICTV Report chapter and associated Journal of General Virology taxonomy profile, was funded by a grant fromthe Wellcome Trust (WT108418AIA).



http://jgv.microbiologyresearch.org/content/journal/jgv/10.1099/jgv.0.000884

Virus Taxonomy The ICTV Report on Virus Classiﬁcation and …taxonomy.cvr.gla.ac.uk/PDF/Virgaviridae.pdf · 2020. 10. 4. · Plants (all genera); furoviruses, peculviruses and pomoviruses

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