The family contains viruses with flexuous filamentous virions that infect plants and a few viruses discovered in plant-infecting fungi. They share a distinct lineage of alphavirus-like replication proteins that is unusual in lacking any recognized protease domain.
Virions are flexuous filaments, usually 12–13 nm in diameter (range 10–15 nm) and from 470 to about 800 nm in length, depending on the genus. They have helical symmetry with a pitch of about 3.4 nm (range 3.3–3.7 nm) and in some genera there is clearly visible cross-banding.
Virions sediment as a single band (or occasionally two very close bands) with an S20,w of 92–176S, depending on the genus.
Virions contain a single molecule of linear ssRNA of about 5.9–9.0 kb which is 5–6% by weight of the virion. The RNA is capped (or probably capped) at the 5′ terminus with m7G and has a polyadenylated tract at the 3′ terminus. Smaller 3′-co-terminal sgRNAs are encapsidated in some, but not all, members of the genus Potexvirus.
The viral capsid of all members of the family (except in the genus Lolavirus) is composed of a single polypeptide ranging in size from 18 to 43 kDa. In allexiviruses, a 42 kDa polypeptide was also detected as a minor component of virions. In lolaviruses a shorter (ca. 28 kDa) carboxy co-terminal polypeptide forms an equimolar fraction of the virion with the polypeptide originating from the first AUG (ca. 32 kDa).
Usually none, but the coat protein of some strains of the species Potato virus X (genus Potexvirus) and both forms of the lolavirus coat protein are reported to be glycosylated.
There are five or six genes depending upon the genus (except in the genus Sclerodarnavirus). The ORF1-encoded product, which follows a short 5’-UTR sequence, has homologies with polymerase proteins of the “alphavirus-like” supergroup of RNA viruses. This protein (150–195 kDa) contains conserved methyltransferase, helicase and RNA-dependent RNA polymerase (RdRp) motifs; some also include an AlkB domain (alkylated DNA repair protein). In all plant-infecting members, ORFs 2–4 encode the “triple gene block” (TGB) proteins involved in cell-to-cell movement and ORF5 is the viral coat protein. In some genera (Allexivirus, Lolavirus and Mandarivirus) a final ORF encodes a protein with a zinc binding finger motif and the ability to bind nucleic acids. ORFs downstream of the polymerase are translated from 3’-terminal sgRNAs that can often be found in infected tissue. Replication is (or is presumed to be) cytoplasmic and the product of ORF1 is the only virus-encoded protein known to be involved.
Virions are usually highly immunogenic. Within (but not usually between) genera, some viruses are serologically related.
Members have been reported from a wide range of mono- and dicotyledonous plant species but the host range of individual members is usually limited. Many of the viruses have relatively mild effects on their host. All species can be transmitted by mechanical inoculation, often readily. Many of the viruses have no known invertebrate or fungus vectors; however, allexiviruses are thought to be mite-borne. Aggregates of virus particles accumulate in the cytoplasm but there are usually no specific cytopathic structures.
Genera are distinguished by various features of genome organization and host. These are summar-ized in Table 1. Throughout the family, isolates of different species should have less than about 72% nt identity (or 80% aa identity) between their respective CP or polymerase genes. Viruses from different genera usually have less than about 45% nt identity in these genes.
Table 1 Distinguishing properties of genera in the family Alphaflexiviridae
Virion length (nm)
a Rep, replication protein size (kDa).
b CP, coat protein size (kDa).
c No virions found.
Type species Shallot virus X
Allexiviruses are distinguished by mite transmission and by the presence of a large ORF4 in the position where the third, and smallest, of the TGB proteins is found in the other plant-infecting members of the family.
Virions are highly flexible filamentous particles, about 800 nm in length and 12 nm in diameter. They resemble potyviruses in their length, but closteroviruses in their flexibility and cross-banded substructure (Figure 1).
Virions of shallot virus X sediment with an S20,w of about 170S in 0.1 M tris-HC1, pH 7.5 at 20 °C and have a buoyant density in CsCl of 1.33 g cm−3.
Virions contain a single molecule of linear ssRNA, about 9.0 kb in size, with a 3’-poly(A) tract.
Virions are composed of a 28–36 kDa polypeptide as a major CP. A 42 kDa polypeptide is a minor component of virions.
The genomic RNA contains six large ORFs and short UTRs at the 5′ and 3′ termini (Figure 2). The ORFs code for polypeptides of about 195, 26, 11, 42, 28 and 15 kDa, respectively from 5′ end to 3′ end. The 195 kDa polypeptide is the polymerase. The 26 and 11 kDa proteins are similar to the first two proteins encoded by the TGB of related plant viruses and are probably involved in cell-to-cell movement of the virus. There is a coding sequence for a third small (7–8 kDa) TGB protein but it lacks the initiation AUG-codon. The 42 kDa polypeptide (ORF4) has no significant homology with any known proteins but, in plants infected with an isolate of the type species, it was expressed in relatively large amounts and was shown to be involved in virion assembly. The 28 kDa polypeptide is the CP. In SDS-polyacrylamide gel electrophoresis it migrates as an apparently 32–36 kDa protein, which could be due to its high hydrophilicity. The 15 kDa protein has a zinc binding finger motif and an ability to bind nucleic acids. The function of this polypeptide is not known.
Allexivirus particles are good immunogens. Some members of the genus are serologically inter-related. Specific antisera and monoclonal antibodies against pure virus particles as well as antisera against recombinant CPs have been used for differentiation purposes.
Host range is extremely restricted. Some isolates from shallot, onion, garlic and sand leek have been experimentally transmitted to Chenopodium murale, in which they induced local lesions.
Allexiviruses are thought to be mite-borne. Garlic viruses C and D have been shown to be transmitted by the eriophyd mite, Aceria tulipae. All are manually transmissible by sap inoculation to healthy host plants. None could be transmitted by aphids.
Allexiviruses are widely distributed and probably occur wherever the host plants are grown.
Most induce no visible or only very mild symptoms in many species, although certain isolates can cause severe damage to crops. In infected tissue allexiviruses can induce formation of granular inclusion bodies and small bundles of flexible particles.
The criteria demarcating species in the genus are:
The available information about the identity of the members in the genus Allexivirus is still fragmentary. They are almost always found in mixed infections of vegetatively propagated species and it is difficult or impossible to isolate and/or separate the viruses.
Garlic mite-borne filamentous virus
Garlic mite-borne filamentous virus-South Korea
Garlic virus A
Garlic virus A-Japan
[AB010300 = NC_003375]
Garlic virus B
Garlic virus B-Japan
Garlic virus C
Garlic virus C-Japan
[AB010302 = NC_003376]
Garlic virus D
Garlic virus D-Japan
Garlic virus E
Garlic virus E-China:Yuhang
[AJ292230 = NC_004012]
Garlic virus X
Garlic virus X-Korea
[U89243 = NC_001800]
Shallot virus X
Shallot virus X-Russia
[M97264 = NC_003795]
Species names are in italic script; names of isolates are in roman script. Sequence accession numbers [ ] and assigned abbreviations ( ) are also listed.
* Sequences do not comprise the complete genome.
Type species Botrytis virus X
The single member of the genus infects a filamentous fungus. The genome lacks the TGB characteristic of plant-infecting members of the family.
Virions are flexuous filaments of 720 nm modal length and about 13 nm in diameter.
Virions contain a single molecule of linear ssRNA, 6966 nt in length, excluding the 3’-poly(A) tail.
The only structural protein is the coat protein composed of 400 aa (43 kDa).
The genomic RNA comprises five putative ORFs on the positive strand, a 5′-UTR of 95 nt and a 3’-UTR of 149 nt, followed by a poly(A) tail (Figure 3). ORF1 is the 158 kDa polymerase, ORF3 encodes the 44 kDa coat protein and the functions of the other predicted proteins (ORF2, 30 kDa; ORFs 4 and 5 both 14 kDa) are unknown.
The virus was discovered infecting an isolate of the plant pathogenic fungus Botrytis cinerea. Its mode of transmission is unknown. The same fungal isolate was also infected with a virus now classified as Botrytis virus F (genus Mycoflexivirus, family Gammaflexiviridae).
Botrytis virus X
Botrytis virus X-New Zealand:Auckland
[AY055762 = NC_005132]
Type species Lolium latent virus
This genus consists of a single species. There are probably 6 ORFs (although the putative ORF6 is smaller than in other genera). The coat protein is larger and the virions are longer than the potex-viruses, which it otherwise resembles. Notably two carboxy co-terminal forms of the coat protein are found in essentially equimolar amounts in both extracts of infected plants and in purified virions.
Virions are slightly flexuous filaments of 640 nm modal length and about 13 nm diameter (Figure 4).
Virions have a buoyant density in CsCl of about 1.33 g cm−3.
Virions contain a single molecule of linear ssRNA, 7674 nt in length, excluding the poly(A) tail. Infectious clones have been produced.
The only structural proteins are two carboxy co-terminal forms of the coat protein, composed of 293 amino acids (32 kDa) and about 28 kDa. The two protein forms occur in virions in equimolar amounts. Both forms are glycosylated at one or more of several potential sites.
The genomic RNA is comprised of six putative ORFs on the positive strand, a 5′-UTR of 87 nt and a 3′-UTR of 97 nt, followed by a poly(A) tail (Figure 5). ORF 1 (196 kDa) contains conserved methyl transferase, AlkB, helicase and RdRp motifs. ORFs 2–4 encode the TGB proteins of 30.5, 13 and 7.5 kDa respectively. ORF 5 encodes the viral coat protein of 31.6 kDa; the smaller carboxy co-terminal coat protein is potentially derived by internal initiation at a second AUG 141 nt downstream from the first (and in a stronger context) but might also arise from proteolytic removal of a non-canonical chloroplast transit peptide. ORF 6 partially overlaps ORF 5, and encodes a predicted 45 amino acid, 5.1 kDa highly basic protein (pI 9.56), which may act as a nucleic acid binding protein (NABP); three Cys and two His residues differ in spacing from those of characterized NABPs (10–23 kDa), and no significant homology is observed to other proteins in the database.
The virus is a good immunogen and its antiserum reacts with both forms of the coat protein. In indirect ELISA, the antiserum reacted to an isolate of Alternanthera mosaic virus (genus Potexvirus) in infected Nicotiana benthamiana. However, the virus was not detected with antiserum specific to this or other viruses in the genera Potexvirus and Carlavirus.
The natural host range of the virus is restricted to gramineaceous species including ryegrass (Lolium). It also readily infects N. benthamiana and a few other dicotyledonous species. In N. benthamiana, it induces local lesions and systemic mosaic that varies from mildly chlorotic to white.
Readily transmitted to healthy host plants by sap inoculation.
Reported from Europe (Germany, the Netherlands, France and the United Kingdom), and from the United States.
The virus induces insignificant symptoms or mild chlorotic flecking in its natural hosts. More severe chlorotic to necrotic streaking may occur in mixed infectious with other viruses. In infected tissue masses of flexuous virions may be observed in association with the chloroplasts.
Lolium latent virus
Lolium latent virus-US1
[EU489641 = NC_010434]
Type species Indian citrus ringspot virus
This genus contains a single virus species infecting a tree host. There are six ORFs in the genome and the coat protein is the largest of any plant-infecting member of the family.
Virions are flexuous filaments of 650 nm modal length, 13 nm in diameter, with clearly visible cross-banding (Figure 6).
The virus forms a single band in caesium sulphate density gradients. Purified preparations show maximum absorption at 260 nm with a A260/280 ratio of 1.1 (corrected for light scattering).
Virions contain a single molecule of linear ssRNA, 7560 nt in length, excluding the 3′-poly(A) tail.
The only structural protein is the CP, composed of 325 aa (34 kDa).
The genomic RNA comprises six ORFs on the positive strand, a 5′-UTR of 78 nt and a 3′-UTR of 40 nt, followed by a poly(A) tail (Figure 7). No significant ORFs are in the negative strand. ORF1 encodes the viral polymerase. ORFs 2, 3 and 4 form the TGB. ORF5 encodes the CP. ORF6 encodes a putative protein of unknown function that shows limited similarity with nucleic acid-binding proteins encoded by ORF6 of allexi- and carlaviruses.
Particles are good immunogens, rabbit antisera can have titers of 1/128 and 1/2048 in gel diffusion and EM decoration, respectively.
The virus causes a serious disease of citrus, especially Kinnow mandarin, in India, with bright yellow ringspots on mature leaves, followed by rapid decline of the tree. Experimentally the virus can be mechanically inoculated to leaves of Chenopodium quinoa, C. amaranticolor, Glycine max, Vigna unguiculata and Phaseolus vulgaris, giving local lesions, but systemic infection only in P. vulgaris. No natural vector is known, but it is transmitted by grafting and persists in the host.
Indian citrus ringspot virus
Indian citrus ringspot virus-K1
[AF406744 = NC_003093]
Type species Potato virus X
Compared to other genera in the family, potexviruses have short virions (<700 nm) and only five ORFs. They infect herbaceous hosts and have no known vectors.
Virions are flexuous filaments, 470–580 nm in length and 13 nm in diameter, with helical symmetry and a pitch of 3.3–3.7 nm (Figure 8). A central axial canal, about 3 nm in diameter, is discernible only in best preparations. The number of protein subunits per turn of the primary helix is slightly less than 9.0. The RNA backbone is at a radial position of 3.3 nm.
Virion Mr is about. 3.5×106; S20,w is 115–130S; buoyant density in CsCl is 1.31 g cm−3.
Virions contain a single linear molecule of positive sense ssRNA of about. 5.9–7.0 kb which is approximately 6% by weight of the virion. The RNA is capped at the 5′ terminus with m7G and has a polyadenylated tract at the 3′ terminus.
The virus capsid consists of 1000–1500 protein subunits of a single 18–27 kDa polypeptide. Partial proteolytic cleavage of the CP subunits can occur during storage of purified virus.
Virions of the type member contain only genomic RNA, but other potexviruses also encapsidate the sgRNA for the CP. Genomic RNA is translated as a functionally monocistronic message; only the 5′-proximal RNA-polymerase gene is translated directly by ribosomes, producing the RNA polymerase (150–181 kDa). The 5′-UTR leader sequence of PVX RNA consists of 83 nt (excluding the cap-structure) and efficiently enhances translation. In infected plants, some potexviruses produce sgRNAs including one that acts as messenger RNA for the CP (Figure 9).
The genomic RNA of potexviruses typically has five ORFs. ORF1, at the 5′ terminus, is the polymerase gene and ORF5, located at the 3′ terminus, is the CP gene. Between ORF1 and ORF5 is the TGB of three overlapping ORFs, the products of which (25, 12 and 8 kDa) are involved in cell-to-cell movement of viral RNA. The 25 kDa protein (as well as the 166 kDa replicase) contains an NTPase-helicase domain, but is not involved in RNA replication. It has been shown to have RNA silencing suppressor activity which is necessary for virus movement. The 12 and 8 kDa proteins contain large blocks of uncharged aa and are associated with membrane vesicles derived from the endoplasmic reticulum. TGB3 of AltMV (but not that of PVX) is targeted to the chloroplast and is required for movement from the epidermis to the mesophyll layer. The CP is also involved in cell-to-cell movement. ORFs 2 to 5 are expressed via the production (and subsequent translation) of appropriate sgRNAs. Two or three 3′-co-terminal sgRNAs can be isolated from plants infected with potexviruses (2.1, 1.2 and 1.0 kb); the double stranded counterparts of these sgRNAs have also been detected. The medium-size sgRNA (1.2 kb) is probably functionally bicistronic, its translation yielding the 12 and 8 kDa proteins.
Virions are highly immunogenic; some species are antigenically related, but others are serologically distinct.
Some of the viruses are moderately pathogenic, causing mosaic or ringspot symptoms in a wide range of mono- and dicotyledonous plant species, but others alone cause little damage to infected plants. The host range of individual members is limited.
The viruses are transmitted in nature by mechanical contact. Potato aucuba mosaic virus can be vectored by aphids when assisted by a potyvirus providing a helper protein.
As a group, potexviruses occur world-wide. The distribution of some species is very wide but others are apparently more restricted.
The cytoplasm of infected cells contains fibrous, banded or irregular aggregates of virus particles, and often membrane accumulations. There is no cytopathology specific to potexviruses, although some viruses induce unique structures such as the beaded sheets found in cells infected by the type member.
The list of species demarcation criteria in the genus is:
Alstroemeria virus X
Alstroemeria virus X-Japan
[AB206396 = NC_007408]
Alternanthera mosaic virus
Alternanthera mosaic virus-USA:Pennsylvania
[AY863024 = NC_007731]
Asparagus virus 3
Asparagus virus 3-Japan
[AB304848 = NC_010416]
Scallion virus X-China: Hangzhou
[AJ316085 = NC_003400]
Bamboo mosaic virus
Bamboo mosaic virus-O
[D26017 = NC_001642]
Cactus virus X
Cactus virus X-Taiwan
[AF308158 = NC_002815]
Cassava common mosaic virus
Cassava common mosaic virus-Brazil
[U23414 = NC_001658]
Cassava virus X
Cassava virus X-Colombia
Clover yellow mosaic virus
Clover yellow mosaic virus-USA
[D29630 = NC_001753]
Commelina virus X
Commelina virus X-United Kingdom
Cymbidium mosaic virus
Cymbidium mosaic virus-Singapore
[U62963 = NC_001812]
Daphne virus X
Daphne virus X-New Zealand
Foxtail mosaic virus
Foxtail mosaic virus-USA
[M62730 = NC_001483]
Hosta virus X
Hosta virus X-type strain: HVX-Kr
[AJ620114 = NC_011544]
Hydrangea ringspot virus
Hydrangea ringspot virus-PD 109
[AY707100 = NC_006943]
Lettuce virus X
Lettuce virus X-Iran:Karaj
[AM745758 = NC_010832]
Lily virus X
Lily virus X-Netherlands
[AJ633822 = NC_007192]
Malva mosaic virus
Malva mosaic virus-Chenopodium mosaic virus X
[DQ660333 = NC_008251]
Mint virus X
Mint virus X-USA
[AY789138 = NC_006948]
Narcissus mosaic virus
Narcissus mosaic virus-Netherlands
[D13747 = NC_001441]
Nerine virus X
Nerine virus X-Japan
[AB219105 = NC_007679]
Opuntia virus X
Opuntia virus X-CC10
[AY366209 = NC_006060]
Papaya mosaic virus
Papaya mosaic virus-USA:Florida
[D13957 = NC_001748]
Pepino mosaic virus
Pepino mosaic virus-Sp-13
[AF484251 = NC_004067]
Phaius virus X
Phaius virus X-Japan
[AB353071 = NC_010295]
Plantago asiatica mosaic virus
Plantago asiatica mosaic virus-Russia
[Z21647 = NC_003849]
Nandina mosaic virus-USA
Plantago severe mottle virus
Plantago severe mottle virus-Canada
Plantain virus X
Plantain virus X-United Kingdom
Potato aucuba mosaic virus
Potato aucuba mosaic virus-Netherlands
[S73580 = NC_003632]
Potato virus X
Potato virus X-X3
[D00344 = NC_011620]
Schlumbergera virus X
Schlumbergera virus X-K11
[AY366207 = NC_011659]
Strawberry mild yellow edge virus
Strawberry mild yellow edge virus-MY-18
[D12517 = NC_003794]
Tamus red mosaic virus
Tamus red mosaic virus-Italy
Tulip virus X
Tulip virus X-J
[AB066288 = NC_004322]
White clover mosaic virus
White clover mosaic virus-USA
[X06728 = NC_003820]
Zygocactus virus X
Zygocactus virus X-B1
[AY366208 = NC_006059]
Species names are in italic script; names of strains and isolates are in roman script. Sequence accession numbers [ ] and assigned abbreviations ( ) are also listed.
Allium virus X
[FJ670570 = NC_012211]
Caladium virus X
Dioscorea latent virus
Paris polyphylla virus X
Parsnip virus 3
Viola mottle virus
Wineberry latent virus
Type species Sclerotinia sclerotiorum debilitation-associated RNA virus
The genus consists of a single member, a capsid-less mycovirus. Despite the lack of capsid, phylogenetic analysis of the polymerase places it within this family.
There are no virions.
A single linear molecule of positive sense ssRNA of 5470 nt with a polyadenylated tract at the 3′ terminus.
There is a single ORF encoding a replication protein of 193 kDa.
The single member was discovered in the plant pathogenic fungus Sclerotinia sclerotiorum and appears to cause debilitation (hypovirulence).
Sclerotinia sclerotiorum debilitation-associated RNA virus
Sclerotinia sclerotiorum debilitation-associated RNA virus-China
[AY147260 = NC_007415]
Ambrosia asymptomatic virus 1
Blackberry virus X
In a phylogenetic analysis of the replication protein, most genera fall on well-supported branches but the single member of the genus Mandarivirus groups with Potexvirus (Figure 10, p. 917). Similar results are obtained in analyses of the first (and largest) TGB protein (Figure 11) although members of the genus Potexvirus do not form such a coherent group.
The polymerase proteins are members of the “alphavirus-like” supergroup of RNA viruses and are most closely related to those of the other families in the order, namely Betaflexiviridae, Gammaflexiviridae and Tymoviridae. The TGB proteins are related to those of some genera in the family Betaflexiviridae and, more distantly, to those of rod-shaped viruses in the family Virgaviridae (genera Hordeivirus, Pecluvirus and Pomovirus).
Allexi: from Allium (the genus name for the principal host, shallot) + X.
Botrex: from Botrytis virus X.
Flexi: from Latin flexus, “bent”.
Lola: from Lolium latent virus.
Mandari: from mandarin (Citrus reticulata), the host of the type species, Indian citrus ringspot virus.
Potex: from Potato virus X.
Sclerodarna: from Sclerotinia sclerotiorum debilitation-associated RNA virus.
Adams et al., 2004 M.J. Adams, J.F. Antoniw, M. Bar-Joseph, A.A. Brunt, T. Candresse, G.D. Foster, G.P. Martelli, R.G. Milne, S.K. Zavriev, C.M. Fauquet, The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation. Arch. Virol. 149 (2004) 1045–1060.
Martelli et al., 2007 G. Martelli, M.J. Adams, J.F. Kreuze, V.V. Dolja, Family Flexiviridae: a case study in virion and genome plasticity. Annu. Rev. Phytopathol. 45 (2007) 73–100.
Verchot-Lubicz et al., 2007 J. Verchot-Lubicz, C.-M. Ye, D. Bamunusinghe, Molecular biology of potexviruses: Recent advances. J. Gen. Virol. 88 (2007) 1643–1655.
Adams, M.J., Candresse, T., Hammond, J., Kreuze, J.F., Martelli, G.P., Namba, S., Pearson, M.N., Ryu, K.H. and Vaira, A.M.