366
September 1998
Family: Potyviridae
Genus:
Species:
Acronym:

This partially supercedes the Potyvirus Group description (245) which is mostly a Potyvirus genus description

Potyviridae family

D. D. Shukla
CSIRO, Division of Molecular Science, Parkville, Victoria, Australia

C. W. Ward
CSIRO, Division of Molecular Science, Parkville, Victoria, Australia

A. A. Brunt
Horticulture Research International, Wellesbourne, Warwickshire, UK

P. H. Berger
Department of Plant, Soil and Entomological Sciences, University of Idaho, Moscow, USA

Contents

Type Member
Main Characteristics
Members
Geographical Distribution etc
Association with Vectors
Ecology
Relations with Cells and Tissues
Particle Properties
Genome Properties
Replication
Satellites
Defective-Interfering RNA
Relationships within the Taxon
Notes on Tentative Members
Affinities with Other Groups
Notes
References
Acknowledgements
Figures

Type Member

Potyvirus: Potato virus Y
Macluravirus: Maclura mosaic virus
Ipomovirus: Sweet potato mild mottle virus
Tritimovirus: Wheat streak mosaic virus
Rymovirus: Ryegrass mosaic virus
Bymovirus: Barley yellow mosaic virus

Main Characteristics

Flexuous filamentous particles, 11-15 nm in diameter with a helical pitch of c. 3.4 nm; those of genera with monopartite genomes (Potyvirus, Macluravirus, Ipomovirus, Tritimovirus, Rymovirus) are 650-950 nm long and those of the genus with bipartite genome (Bymovirus) are 200-300 and 500-600 long. Particles of monopartite genera members have a sedimentation coefficient (s20,w) of 150-160 and a density in CsCl of 1.31 g cm-3; those of bipartite members have a density in CsCl of 1.29 g cm-3. The particles consist of 95% coat protein and 5% RNA. The genome is single-stranded, positive-sense RNA. The genome size of monopartite members is c. 8.0 to 11 kb (mol. wt 2.7 x 106 to 3.0 x 106); the sizes of the two genome parts of bipartite members are 7.5 kb (mol. wt 2.6 x 103) and 3.5 kb (mol. wt 1.5 x 103). The genomic RNAs, like those of the picorna-like supergroup of viruses, have a genome-linked protein (VPg) of mol. wt c. 24,000 covalently bound to the 5' terminus and a poly(A) tail at the 3' end. Most members of the family Potyviridae have a coat protein of 30-37 kDa; that of WSMV (Tritimovirus) and MacMV (Macluravirus) is c. 40 kDa. All members of the Potyviridae induce the formation of cytoplasmic cylindrical inclusions (‘pinwheels’) consisting of a protein of c. 70 kDa.Some members also induce the formation of nuclear inclusions which consist of two proteins (c. 49 and 58 kDa) and/or amorphous proteinaceous inclusions (c. 56 kDa). Monopartite members are transmitted by aphids (Potyvirus, Macluravirus), mites (Rymovirus, Tritimovirus) or whiteflies (Ipomovirus), and bipartite members (Bymovirus) by the fungus Polymyxa graminis. Except for some bymoviruses, the viruses are transmissible by inoculation of sap; some potyviruses are carried within or on the testae of a small proportion of the seeds of some host species.

Most members of the Potyviridae have restricted, or very restricted, host ranges, but a few occur naturally in a wide range of monocotyledonous and/or dicotyledonous species. However, members of the Potyviridae infect many important crop species. Some induce no conspicuous symptoms in infected plants, but most cause mosaic or mottle symptoms in leaves; many also induce colour-breaking in flowers, mottled and/or distorted fruits and seeds, and some cause considerable losses of crop yield and quality.

Members

Definitive and possible members of each of the six genera with their acronyms are listed below:

Table 1. Members and possible members of the six genera of the Potyviridae*

Virus or species*** Acronym**
  
Genus:       Potyvirus  
Definitive Species:  
Alstroemeria mosaic virus AlMV
Amaranthus leaf mottle virus AmLMV
Araujia mosaic virus ArjMV
artichoke latent virus ALV
asparagus virus 1 AV-1
bean common mosaic virus (73, 337) BCMV
        (Azuki bean mosaic virus)  
        (blackeye cowpea mosaic virus) (305)  
        (Dendrobium mosaic virus)  
        (guar green sterile virus)  
        (peanut stripe virus)  
        (peanut mild mottle virus)  
        (peanut chlorotic ring mottle virus)  
        (some cowpea aphid-borne mosaic virus strains)     
bean common mosaic necrosis virus BCMNV
        (serotype A of BCMV)  
bean yellow mosaic virus (40) BYMV
        (Crocus tomasinianus virus)  
        (white lupin mosaic virus)  
        (pea mosaic virus)  
beet mosaic virus (53) BtMV
bidens mottle virus (161) BiMoV
calanthe mild mosaic virus CalMMV
cardamom mosaic virus CdMV
carnation vein mottle virus (78) CVMoV
carrot thin leaf virus (218) CTLV
celery mosaic virus (50) CeMV
chilli veinal mottle virus ChiVMV
        (pepper vein banding mosaic virus)  
clover yellow vein virus (131) ClYVV
        (pea necrosis virus)  
        (statice virus Y)  
cocksfoot streak virus (59) CSV
Colombian datura virus CDV
Commelina mosaic virus ComMV
Cowpea aphid-borne mosaic virus (134) CABMV
        (South African passiflora virus)  
cowpea green vein banding virus CGVBV
dasheen mosaic virus (191) DsMV
datura shoestring virus DSTV
endive necrotic mosaic virus ENMV
freesia mosaic virus FreMV
Gloriosa stripe mosaic virus GSMV
groundnut eyespot virus GEV
guinea grass mosaic virus (190) GGMV
Helenium virus Y HVY
henbane mosaic virus (95) HMV
Hippeastrum mosaic virus (117) HiMV
hyacinth mosaic virus HyaMV
iris fulva mosaic virus (310) IFMV
iris mild mosaic virus (116, 324) IMMV
iris severe mosaic virus (338) ISMV
         (bearded iris mosaic virus) (147)  
Johnsongrass mosaic virus (340) JGMV
Kalanchoe mosaic virus (Husted et al., 1994) KMV
konjak mosaic virus KonMV
leek yellow stripe virus (240) LYSV
        (garlic potyvirus)  
        (garlic virus 2)  
lettuce mosaic virus (9) LMV
lily mottle virus LiMoV
maize dwarf mosaic virus (341) MDMV
Moroccan watermelon mosaic virus WMMV
narcissus degeneration virus NDV
narcissus late season yellows virus (367) NLSYV
        (jonquil mild mosaic virus)  
narcissus yellow stripe virus (76) NYSV
nerine yellow stripe virus NeYSV
Nothoscordum mosaic virus NoMV
onion yellow dwarf (158) OYDV
Ornithogalum mosaic virus OrMV
papaya ringspot virus (84, 292) PRSV
         (watermelon mosaic virus 1) (63)  
parsnip mosaic virus (91) ParMV
passionfruit woodiness virus (122) PWV
pea seed-borne mosaic virus (146) PSbMV
peanut mottle virus (141) PeMoV
pepper mottle virus (253) PepMoV
pepper severe mosaic virus PeSMV
pepper veinal mottle virus (104) PVMV
Peru tomato virus (255) PTV
petunia flower mottle virus PFMoV
plum pox virus (70) PPV
pokeweed mosaic virus (97) PkMV
potato virus A (54) PVA
potato virus V (316) PVV
potato virus Y (37, 242) PVY
Rembrandt tulip breaking virus RTBV
sesame mosaic virus SeMV
shallot yellow stripe virus SYSV
        (Welsh onion yellow stripe virus)  
sorghum mosaic virus (359) SrMV
soybean mosaic virus (93) SMV
sugarcane mosaic virus (88, 342) SCMV
sweet potato feathery mottle virus SPFMV
        (sweet potato russet crack)  
        (sweet potato A)  
        (sweet potato chlorotic leaf spot)  
        (sweet potato internal cork)  
sweet potato latent virus SwPLV
tamarillo mosaic virus TamMV
Telfairia mosaic virus TeMV
tobacco etch virus (55, 258) TEV
tobacco vein banding mosaic virus TVBMV
tobacco vein mottling virus (325) TVMV
tulip breaking virus (71) TBV
turnip mosaic virus (8) TuMV
        (tulip top breaking virus)  
        (tulip chlorotic blotch virus)  
Wakegi yellow dwarf virus (Tsuneyoshi et al., 1998) WYDV
watermelon mosaic virus 2 (63, 293) WMV-2
        (vanilla necrosis virus)  
Wisteria vein mosaic virus WVMV
yam mild mosaic virus (Mumford & Seal, 1997) YMMV
yam mosaic virus (314) YMV
        (Dioscorea green banding virus)  
zucchini yellow fleck virus ZYFV
zucchini yellow mosaic virus (282) ZYMV
   
Possible Species:  
Amazon lily mosaic virus AliMV
Aneilema virusb AneV
Anthoxanthum mosaic virusa AntMV
Aquilegia virusa,b AqV
Arracacha virus Y AVY
Asystasia gangetica mottle virusa AGMoV
bidens mosaic virus BiMV
bramble yellow mosaic virus BrmYMV
Bryonia mottle virus BryMoV
Calanthe mosaic virus CalMV
canary reed mosaic virus CRMV
Canavalia maritima mosaic virus CnMMV
carrot mosaic virus CtMV
Cassia yellow spot virus CasYSP
celery yellow mosaic virus CeYMV
chickpea bushy dwarf virus CpBDV
chickpea filiform virus CpFV
clitoria yellow mosaic virus CtYMV
cowpea rugose mosaic virus CPRMV
Crinum mosaic virusa CriMV
Croatian clover virusb CroCV
Cypripedium calceolus virusa CypCV
daphne virus Y DVY
datura virus 437 DV-437
datura distortion mosaic virus DDMV
datura mosaic virusa DTMV
datura necrosis virus DNV
Desmodium mosaic virus DesMV
Dioscorea trifida virusb DTV
Dipladenia mosaic virus DipMV
dock mottling mosaic virus DMMV
eggplant green mosaic virus EGMV
eggplant severe mottle virus ESMoV
Euphorbia ringspot virusa EuRV
Ficus carica virusb FicCV
guar symptomless virusa GSLV
Habenaria mosaic virus HaMV
Holcus streak virusa HSV
Hungarian Datura innoxia virusa HDIV
Indian pepper mottle virus IPMoV
isachne mosaic virusa IsaMV
Kennedya virus Y KVY
lily mild mottle virus LiMMoV
Malva vein clearing virus MVCV
marigold mottle virus MaMoV
Melilotus mosaic virus MeMV
Melon vein-banding mosaic virus MVBMV
mungbean mosaic virusa MbMV
mungbean mottle virus MbMoV
Nasturtium mosaic virus NasMV
nerine virus Y NVY
palm mosaic virusa PalMV
papaya leaf distortion mosaic virus PLDMV
passionfruit mottle virus PFMoV
passionfruit ringspot virus PFRSV
patchouli mottle virus PatMoV
peanut green mottle virus PeGMoV
Pecteilis mosaic virus PcMV
pepper mild mosaic virus PMMV
pepper vein banding virus PVBV
perilla mottle virus PerMoV
plantain virus 7 PlV-7
Pleioblastus mosaic virus PleMV
Populus virusa PV
primula mosaic virus PrMV
primula mottle virus PrMoV
ranunculus mottle virus RanMoV
rudbeckia mosaic virus RuMV
Sri Lankan passionfruit mottle virus SLPMoV
sunflower mosaic virusa SuMV
sweet potato vein mosaic virus SPVMV
sweet potato mild speckling virus SPMSV
sword bean distortion mosaic virus SBDMV
teasel mosaic virus TeaMV
tobacco wilt virus TWV
Tongan vanilla virus TVV
Tradescantia/Zebrina virusb TZV
Trichosanthes mottle virus TrMoV
Tropaeolum virus 1 TV-1
Tropaeolum virus 2 TV-2
tulip band breaking virus TBBV
Ullucus mosaic virus UMV
Vallota mosaic virus ValMV
vanilla mosaic virus VanMV
white bryony virus WBV
wild potato mosaic virus WPMV
Zoysia mosaic virus ZMV
   
   
Genus:       Macluravirus  
Definitive Species:  
Maclura mosaic virus (239) MacMV
Narcissus latent virus (170) NLV
   
Possible Species:  
None reported  
   
   
Genus:      Ipomovirus  
Definitive Species:  
sweet potato mild mottle virus (162) SPMMV
   
Possible Species:  
sweet potato yellow dwarf virus SPYDV
   
   
Genus:      Tritimovirus  
Definitive Species:  
wheat streak mosaic virus (48) WSMV
brome streak mosaic virus BrSMV
   
Possible species:  
Sugarcane streak mosaic virus SCSMV
   
   
Genus:      Rymovirus  
Definitive Species:  
Agropyron mosaic virus (118) AgMV
Hordeum mosaic virus HoMV
oat necrotic mottle virus (169) ONMV
ryegrass mosaic virus (86) RGMV
   
Possible species:  
Spartina mottle virus SpMV
   
   
Genus:      Bymovirus  
Definitive species:  
barley yellow mosaic virus (143) BaYMV
barley mild mosaic virus (356) BaMMV
oat mosaic virus (145) OMV
rice necrosis mosaic virus (172) RNMV
wheat spindle streak mosaic virus (167) WSSMV
wheat yellow mosaic virus (Namba et al., 1998) WYMV
   
Possible species:  
None reported  

*As listed in Francki et al. (1991), and with amendments suggested by the ICTV Potyvirus Study Group (Berger et al., 1998).
**Acronyms of members as suggested by Hull et al. (1991) and Berger et al. (1998).
***   Key References for each virus are listed in Shukla et al. (1994) and Berger et al. (1997). Numbers in parentheses are those of the relevant Description, if available.
  
aAphid transmission not confirmed.
bName inadequate, but denotes the species in which the virus was first found.

Geographical Distribution etc

Potyviruses occur world-wide but are especially prevalent in tropical and subtropical countries. Rymoviruses have been reported in temperate regions of North America and Europe. Bymoviruses and tritimoviruses occur in temperate regions of North America, Europe and Japan. By contrast, ipomoviruses occur naturally only in tropical East Africa or Asia and macluraviruses have been reported only from Europe, USA and Australia (NLV) and the former Yugoslavia (MacMV).

Association with Vectors

The natural mode of vector transmission of members of the six genera is as follows:

Potyvirus
Usually transmitted by aphids in a non-persistent, non-circulative manner. Virus is acquired and transmitted most efficiently after brief feeding probes (a few min); acquisition is enhanced if the aphids are previously starved for 1 to 3 h. Aphids usually remain viruliferous for less than 1 h with continued feeding, or 4 h if starved, although retention is much longer (up to 24 h) under some conditions. There is no latent period between acquisition and transmission, and no virus multiplication within the vector. Although some members are transmissible by several or many aphid species, considerable virus-vector specificity occurs; there are also marked differences in efficiency of transmission between different clones and colonies of one aphid species, or between different virus strains.

Potyvirus species tested so far require a ‘helper factor’ for their transmission by aphids (Govier & Kassanis, 1974); this factor, designated HC-Pro, is a labile protein of c. 56 kDa which is encoded in the viral genome (Fig.1) and possibly facilitates the attachment of virus particles to the mouth parts of the vector aphids (Govier et al., 1977; Pirone & Thornbury, 1983; Thornbury et al., 1990). A conserved three amino acid motif, Asp-Ala-Gly (DAG), located in the surface-exposed, amino-terminal domain of the coat protein also is involved in aphid transmission of Potyvirus species (Atreya et al., 1990, 1991; Gal-On et al., 1992). HC-Pro and virions have been shown to co-localize in the maxillary food canal and foregut of aphids (Berger & Pirone, 1986; Ammar et al., 1994; Wang et al., 1996), and a direct interaction between HC-Pro and coat protein of TVMV was demonstrated recently (Blanc et al., 1997). A seven amino acid residue region (DTVDAGK), located in the N-terminus of the coat protein and which includes the DAG motif, was shown to mediate HC-Pro binding (Blanc et al., 1997). Thus, it appears that the long-standing hypothesis (Govier & Kassanis, 1974), termed recently as the ‘bridge’ hypothesis by Pirone & Blanc (1996), to explain the aphid transmission mechanism for potyviruses has been supported. According to this hypothesis HC-Pro acts as a bifunctional molecule, one domain of which binds to the coat protein and the other to putative receptor in the vector mouth parts.

Members of a few other invertebrate taxa have been reported to transmit Potyvirus species: PRSV-W and CeMV were reported to be inefficiently transmitted by the leaf miner Liriomyza sativae (Diptera: Agromyzidae) (Zitter & Tsai, 1977); and PSbMV and PVY by red spider mites (Tetranychus urticae) (Khetarpal et al., 1989). Apparent soil transmission of SCMV in the absence of root contact suggested the involvement of a soil-living vector (Bond & Pirone, 1970). SCMV-MDB was reported to be transmitted in South Africa by the uredospores of Puccinia sp. (Von Wechmar et al., 1992).

Macluravirus
Like species of the genus Potyvirus, are transmitted by aphids in a non-persistent, stylet-borne manner (Brunt, 1976, 1977; Plese & Stefanac, 1976; Koenig & Plese, 1981).

Ipomovirus
Transmitted by the whitefly Bemisia tabaci, possibly in a non-persistent manner (Hollings et al., 1976; Liao et al., 1979).

Tritimovirus
Transmitted in a persistent manner by eriophyid mites (Abacarus hystrix and Aceria tulipae) (Shepard & Carroll, 1967; Slykhuis, 1973; Plumb & Jones, 1973; Paliwal, 1980).

Rymovirus
Transmitted in a persistent-circulative manner by eriophyid mites (Abacarus hystrix and Aceria tulipae) (Shepard & Carroll, 1967; Slykhuis, 1973; Plumb & Jones, 1973; Paliwal, 1980).

Bymovirus
Transmitted within zoospores of the chytrid fungus Polymyxa graminis (Saito et al., 1968; Inouye & Fujii, 1977; Inouye & Saito, 1975), and survives for many years within resting spores.

Ecology

Potyvirus species, transmitted by aphids, are very successful pathogens in a wide range of crops and environmental conditions; they are most prevalent in tropical or subtropical countries, where continuous or successive cropping is usually practised. Of the many different factors that affect their rate of spread and severity in crops, the most important are the proximity and prevalence of virus sources, and the number, activity and occurrence of vector species. Early infection of the crop often results in extensive spread and thus a high incidence and severe disease. In temperate climates, potyviruses survive in perennial or vegetatively propagated crops but, because most have narrow, often extremely restricted, host ranges, comparatively few naturally infect alternative host species; even where this does occur, it is often of only minor importance. The most important virus sources are infected seed, planting material, or infected volunteer plants from previous crops (Hollings & Brunt, 1981a, 1981b).

Host-specialization of different members has resulted in the occurrence of numerous strains, or pathotypes, which may have survived through the absence of inter-strain competition in common hosts (Hollings & Brunt, 1981a, 1981b); nevertheless, complexes of two or more different potyviruses are often found in individual plants of some species.

The ecology of Macluravirus species has yet to be investigated, but is probably similar to that of potyviruses (Brunt, 1977; Koenig & Plese, 1981).

Ipomovirus species are disseminated in infected propagation stock of sweet potato and spread locally by their whitefly vector (Hollings et al., 1976, Liao et al., 1979).

Tritimovirus and Rymovirus species and their vectors persist in wheat, maize, millets and susceptible grasses. Spread is facilitated by overlapping summer and autumn-sown crops (Slykhuis et al., 1957; Atkinson & Slykhuis, 1963) and by wind dispersal of viruliferous mites.

Bymovirus species are disseminated within fungal resting spores by wind, water and farm equipment and the movement of soil during cultivation (Toler & Hebert, 1964; Slykhuis, 1970; Kusaba et al., 1971). Local spread by viruliferous zoospores is most rapid when soil moisture content is high.

Relations with Cells and Tissues

Virus particles are sometimes found scattered randomly throughout the cytoplasm of infected cells, within plasmodesmata, in uniseriate arrays parallel to the tonoplast or cytoplasmic lamellae, and/or in cytoplasmic strands projecting into or bridging the cell vacuole (e.g. Lawson & Hearon, 1971; Weintraub et al., 1974). Membrane-associated particle aggregates present in negatively stained tissue extracts are possibly either fragments of the virus-containing cytoplasmic strands or tonoplast-associated particles entrapped during cellular disruption by pieces of the adjacent membrane (Brunt & Atkey, 1974). Infected cells sometimes contain unusual aggregates of mitochondria or chloroplasts (Kitajima & Lovisolo, 1972; Kitajima & Costa, 1973; Weintraub et al., 1973).

Cytoplasmic inclusions
Members of the family Potyviridae characteristically induce the formation of cytoplasmic inclusions (CI), which are detectable by light microscopy in suitably stained epidermal leaf cells (Christie & Edwardson, 1977). Their structure has been elucidated from ultrastructural studies of infected plants (Edwardson, 1966; Rubio-Huertos & Lopez-Abella, 1966) and freeze-etch electron microscopy (McDonald & Hiebert, 1974). Inclusions each have a central core from which radiate 10-20 thin striated rectangular or triangular curved plates or ‘lamellae’, which have a surface lattice of 5 nm. In transverse sections, CI are seen as ‘pinwheels’ and in longitudinal sections as ‘bundles’. Sections of ‘lamellae’, when not obviously associated with the ‘pinwheel’ core, are described as ‘laminated inclusions’ if straight or unfolded, as ‘scrolls’ or ‘tubes’ if rolled inwardly, and as ‘laminated aggregates’ if two or more are closely associated or partially fused. Morphologically, CI are generally considered to be either cylindrical (Edwardson, 1966) or conical (Andrews & Shalla, 1974). Members have been subdivided into four sub-divisions on the basis of morphology of their CI (Edwardson, 1974; Edwardson et al., 1984). Viruses in the genera Macluravirus, Ipomovirus, Tritimovirus, Rymovirus and Bymovirus, induce the formation of CI which are usually indistinguishable from those of Potyvirus species (Langenberg & Schroeder, 1973, 1974; Plumb & Jones, 1973; Hollings et al., 1976; Plese & Stefanac, 1976; Chamberlain & Catherall, 1977). The CI of WSMV are elliptic hyperboloids (Mernaugh et al., 1980). Viruses in the genus Bymovirus induce massive accumulation of membranes and CI with laminated aggregates but no scrolls (Saito et al., 1966). The WSMV infected cells also contain hypertrophied endoplasmic reticulum, small vesicles and abnormally numerous ribosomes (Huth et al., 1984).

The lamellae and/or their fragments can be extracted and purified from infected plants with yields (16-18 A280 units/kg leaf tissue) sometimes considerably greater than those of virus particles (Hiebert & McDonald, 1973). Cytoplasmic inclusions contain a single virus-specific protein of 67-70 kDa, identified as an RNA helicase (Lain et al., 1990, 1991) (see Fig.1).

Nuclear inclusions
A few Potyvirus species, notably TEV, also induce the formation of virus-encoded crystalline nuclear inclusions (NI) which, like CI, are readily detectable by light microscopy in suitably stained epidermal cells (Kassanis, 1939; Christie & Edwardson, 1977). The NI are flat crystals 6 to 8 µm square when viewed from above, but are slightly curved plates in side view.

The NI of TEV can be extracted and purified, yields of 2 x 108 to 8 x 108 inclusions/kg leaf tissue being readily obtained (Knuhtsen et al., 1974). NI consist of thin rectangular plates which may be present in regular stacks but are often offset at 45° to each other. The plates have a clearly discernible lattice with striations 10.2 nm apart and having primary axes intersecting at 90° (McDonald & Hiebert, 1974). In transverse section, the NI appear to be multilayered pyramids.

The NI of TEV contain two proteins designated NIa and NIb (49.8 and 54.5 kDa, respectively) which are serologically unrelated to the capsid protein of the associated virus particles, or to the CI protein or to healthy plant protein (Knuhtsen et al., 1974). The NIa codes for VPg-proteinase, while NIb is the RNA-dependent RNA polymerase (Fig.1). NI of various shapes and sizes induced by other potyviruses have yet to be similarly characterized (Christie & Edwardson, 1977).

Amorphous inclusions
Some members of the Potyviridae also induce the formation of amorphous inclusions (AI), which are aggregates of a single protein species (53-58 kDa), the virus-encoded aphid transmission helper factor (De Mejia et al., 1985a, 1985b; Hellmann et al., 1988; Baunoch et al., 1990).

Particle Properties

Most members of the Potyviridae have flexuous filamentous particles 11 to 12 nm wide, made up of 1700-2000 copies of a single coat protein subunit arranged in a helical manner around a single molecule of viral RNA.

The particles of monopartite genera have modal length of 650-675 nm (Macluravirus), 680 to 750 nm (Tritimovirus), 690 to 720 nm (Rymovirus), 720 to 850 nm (Potyvirus) or 750 to 950 nm (Ipomovirus) (Hollings & Brunt, 1981a, 1981b; Koenig & Plese, 1981), and those of the bipartite genus (Bymovirus) have biomodal lengths of 200 to 300 nm and 500 to 600 nm (Usugi et al., 1989). Particles of some Potyvirus species (such as HMV and PVMV) are straight and c. 850 nm long in the presence of Mg++ ions, but otherwise flexuous and c. 750 nm long (Govier & Woods, 1971).

Particles of members of the Potyviridae show very little substructure, although some have a discernible central canal 2 to 3 nm diameter in negatively stained preparations. The protein subunits have a helical pitch of c. 3 to 4 nm (Varma et al., 1968). A particle weight of 60 x 106 - 70 x 106 daltons, estimated from nucleic acid and protein contents, indicates that each particle contains 1700-2000 protein subunits, possibly arranged 7-8 per turn of the helix and with c. 6 nucleotides per protein subunit (Veerisetty, 1979). Dissembled PVY coat protein readily forms long (up to several µm) flexuous particles of non-helical stacked discs (repeat distance 4 nm) in the absence of RNA (Goodman et al., 1976; McDonald et al., 1976; McDonald & Bancroft, 1977). A schematic diagram illustrating the tertiary structure of a virus particle of a typical member of the Potyviridae is shown in Fig.2. It is based on the demonstrated surface location of the N- and C-termini of the coat protein and the predictions of secondary structure that suggest four major antiparallel alpha-helical segments (Shukla et al., 1988; Shukla & Ward, 1989a).

Members have U.V. absorbance spectra typical of nucleoproteins, with a maximum at 260 to 262 nm and a minimum at 240 to 246 nm. The A260/A280 ratios of 1.14-1.25, and Amax/Amin ratios of 1.11-1.27 are typical of nucleoproteins containing 5-6% nucleic acid (Layne, 1957). The extinction coefficient (A0.1%, 1cm, 260nm), which has been determined for only a few members, ranges from 2.4 to 2.9. Several members are stable in CsCl at 20 to 25°C, and have buoyant densities of 1.318 to 1.336 g cm-3 (Huttinga & Mosch, 1974; Damirdagh & Shepherd, 1970).

Coat protein weights have been estimated by sodium dodecyl sulphate- polyacrylamide gel electrophoresis (SDS-PAGE), amino acid analysis, and protein and gene sequencing. The values obtained by SDS-PAGE and amino acid analysis have varied from the definitive values calculated from the coat protein amino acid sequences (see Shukla et al., 1994). The coat protein sequences of members of the Potyviridae show that the coat proteins range in size from 253 to 332 amino acids (Ward & Shukla, 1991; Shukla et al., 1994; Berger et al., 1997).

The coat proteins of members of the Potyviridae are often reported to be heterogeneous with two (Hiebert & McDonald, 1973; Huttinga & Mosch, 1974; Moghal & Francki, 1976), three (Choi & Wakimoto, 1979) or more components (Brakke et al., 1990; Niblett et al., 1991). Multiple bands (Huttinga & Mosch, 1974; Moghal & Francki, 1976) are attributed to partial degradation of the polypeptide by proteolytic enzymes of host or microbial origin, probably by removal of the N and C termini of the coat proteins (Shukla et al., 1988). A second explanation, at least for PRSV, is differential polyprotein processing at two or more sites in the junction between NIb and coat protein (Yeh et al., 1992).

Genome Properties

Members of the Potyviridae have particles containing 5 to 6% single-stranded positive-sense RNA (Matthews, 1979). The genomes of the genera Potyvirus, Macluravirus, Ipomovirus , Rymovirus and Tritimovirus consist of one RNA molecule, estimated by PAGE for some Potyvirus species to have Mr (x 10-6) of 3.5 (TuMV), 3.2 (PVY) and 3.15 (TEV) (Hill & Shepherd, 1972; Hinostroza-Orihuela, 1975; Hari et al., 1979). By density gradient centrifugation, the mol. wt of RNA of SCMV-MDB was estimated to be 2.7 x 106 and that of PVY-RNA to be 3.1 x 106 (Pring & Langenberg, 1972; Makkouk & Gumpf, 1974, 1975). Complete genome sequences are now available for at least 20 species of the genus Potyvirus, one species of the genus Ipomovirus and two species each of the genera Tritimovirus and Bymovirus.

The Potyvirus species for which the complete nucleotide sequences presently available are: TEV (Allison et al., 1986; Chu et al., 1995), TVMV (Domier et al., 1986; Nicolas et al., 1996), PPV (Lain et al., 1989; Maiss et al., 1989; Teycheney et al., 1989; Palcovics et al., 1993), PVY (Robaglia et al., 1989; Thole et al., 1993; Singh & Singh, 1996; Jakab et al., 1997), PSbMV (Johansen et al., 1991, 1996), SMV (Jayaram et al., 1992), TuMV (Nicolas & Laliberte, 1992; Oshima et al., 1996), PepMoV (Vance et al., 1992), PRSV (Yeh et al., 1992), JGMV (Gough & Shukla, 1993), PStV (Gunasinghe et al., 1994), PVA (Puurand et al., 1994), BCMNV (Fang et al., 1995), ZYMV (Wisler et al., 1995), YMV (Aleman et al., 1996), BYMV (Guyatt et al., 1996; Nakamura et al., 1996), ClYVV (Takahashi et al., 1997), LMV (Revers et al., 1997) and SPFMV (Sakai et al., 1997). The genome sizes of species of the genus Potyvirus sequenced to date range from 9496 (TEV) to 10,326 (PRSV) nucleotides excluding the poly(A) tail (see Shukla et al., 1994). The length of the 5' non-coding region in different species of this genus ranges from 85 to 205 nucleotides. Alignment of sequences of this region revealed two conserved blocks which are referred to as box ‘a’ and ‘b’ (Nicolas and Laliberte, 1992). The 3' non-coding regions are much more heterogeneous in size (161 to 473 nucleotides) and sequence (Frenkel et al., 1989; Berger et al., 1997). They can be predicted to fold into stable secondary structures (Turpen, 1989).

Infectious RNA preparations have been obtained from some Potyvirus species such as SCMV-MDB, PVY, TuMV and TEV (Pring & Langenberg, 1972; Makkouk & Gumpf, 1974, 1975; Hill & Benner, 1976); TEV-RNA is reported to contain strands with or without poly(A) which are equally infective (Hari et al., 1979). Infectious RNA transcripts have been produced from full-length cDNA clones to several species of the genus Potyvirus, e.g. TVMV (Domier et al., 1989; Nicolas et al., 1996), PPV (Riechmann et al., 1990; Maiss et al., 1992), ZYMV (Gal-On et al., 1991), PSbMV (Johansen et al., 1992), TEV (Dolja et al., 1992), PStV (Flasinski et al., 1996), PVA (Puurand et al., 1996), PVY (Fakhfakh et al., 1996; Jakab et al., 1997) and ClYVV (Takahashi et al., 1997).

The polyprotein precursor of Potyvirus species is cleaved by proteinases into 10 different polypeptides (Dougherty & Carrington, 1988; Shukla et al., 1991; Riechmann et al., 1992), these products being (Fig.1): first protein (P1-Pro), helper component (HC-Pro), third protein (P3), cylindrical inclusion protein (CI), small nuclear inclusion protein (NIa) which includes VPg at its N-terminus and the major proteinase (Pro) at its C-terminus, large nuclear inclusion protein (NIb) and coat protein (CP). VPg and CP are the only gene products present in virus particles, but P1-Pro, HC-Pro, P3, CI, NIa and NIb have been detected in infected plants (Dougherty & Carrington, 1988; Rodriguez-Cerezo & Shaw, 1991). Two small putative protein products (6 kDa each) also occur between P3 and CI and between CI and NIa, as indicated by the presence of potential cleavage site motifs and the analysis of in vitro cleavage products, but the former has not been detected in infected tissue (Riechmann et al., 1992), although the latter has (Restrepo-Hartwig & Carrington, 1994).

Macluravirus species probably have a genomic organization similar to that of Potyvirus species (Fig.1) as, like potyviruses, they are also transmitted by aphids. The genome of Macluravirus species consists of a single species of RNA of approximately 8 kb (Badge et al., 1997). The sequences of the C-terminal one-third of the polyproteins of two species, MacMV and NLV, of this genus presently available show that the coat protein coding region of the viruses is at the 3'-end of their RNA and a motif similar to DAG, found in the coat protein N-terminus of Potyvirus species, is also found in macluraviruses. In MacMV this motif is DAE whereas in NLV it is DVG (Badge et al., 1997). In the Potyvirus species TVMV, a mutation from DAG to DAE gave a non-transmissible product whereas a mutation to DVG left only minimal transmission function (Atreya et al., 1990, 1995). The aphid transmissibility of the sequenced MacMV and NLV isolates has not been determined experimentally (Badge et al., 1997).

The genomic RNA of the Ipomovirus species SPMMV consists of 10,818 nucleotides (Colinet et al., 1998) and is slightly longer than that of the longest RNA of the Potyvirus species PRSV (10,326 nucleotides). However, the 5' and 3' non-coding regions of SPMMV are 139 and 308 nucleotides long, which are similar to those found in Potyvirus species. The genome organization and predicted polyprotein cleavage sites of SPPMV (Colinet et al., 1998) are very similar to those of Potyvirus species (see Fig.1).

The genomic RNA of the Tritimovirus species BrSMV consists of 9672 nucleotides and of WSMV consists of 9384 nucleotides, excluding the poly(A) tail (Gotz & Maiss, 1995; Stenger et al., 1998). The 5' and 3' non- coding regions are 145 and 245 nucleotides and 130 and 149 nucleotides long for BrSMV and WSMV, respectively. Thus, the genome size and length of the 5' and 3' non-coding regions of Tritimovirus species are very similar to those of the Potyvirus species. Also, the genome organization and the predicted cleavage sites of the polyprotein of tritimoviruses are very similar to those of Potyvirus species (Gotz & Maiss, 1995; Stenger et al., 1998). Specific motifs, described for Potyvirus species polyproteins, are also almost all present in the polyprotein of tritimoviruses (see Fig.1).

The genomic RNA of Rymovirus species is expected to have similar organization to that of the Potyvirus species. Partial sequence data shows the NIb and CP coding regions are at the 3' end of the genome.

However, the aphid transmissibility motif found in the N-terminal part of coat protein of almost all Potyvirus species is not found in the coat protein of Tritimovirus, Rymovirus or Ipomovirus species. This is not surprising as species of these latter genera are transmitted by mites or whiteflies.

The complete nucleotide sequences of two Bymovirus species, namely BaYMV (Kashiwazaki et al., 1990, 1991; Davidson et al., 1991; Peerenboom et al., 1992) and BaMMV (Timpe & Kuehne, 1994; Jacobi et al., 1995; Dessens & Meyer, 1996; Kashiwazaki, 1996; Meyer & Dessens, 1996; Peerenboom et al., 1996) are known. The genomes of these viruses consist of two RNA molecules, RNA-1 and RNA-2 (Fig.1). The RNA-1 (7632-7648 bases in BaYMV and 7263 bases in BaMMV) in both viruses corresponds to the 3' two-thirds of the Potyvirus genome, and codes for proteins analogous to P3, 6K1, CI, 6K2, VPg/NIa, NIb and CP (Kashiwazaki et al., 1990; Peerenboom et al., 1992; Kashiwazaki, 1996; Meyer & Dessens, 1996). The RNA-2 (3585 bases in BaYMV and 3516 bases in BaMMV) codes for a polyprotein which is processed into two mature proteins which have been designated as P1 and P2 (Dessens et al., 1995; Dessens & Meyer, 1996; Kashiwazaki, 1996). The first (P1) shares extensive sequence similarities with HC-Pro of potyviruses (Kashiwazaki et al., 1991; Davidson et al., 1991) and should be called HC-ProLP (helper component-proteinase like protein) to avoid confusion with the unrelated P1 protein of genera with a monopartite genome. The second (P2) is related to the capsid readthrough protein of furoviruses and is believed to play a role in virus transmission by Polymyxa graminis (Dessens et al., 1995; Jacobi et al., 1995; Dessens and Meyer, 1996). The total length of the two BaYMV RNA molecules (11,217 nucleotides) is greater than that of the single Potyvirus genomic RNA due to the presence of 5' and 3' non- coding regions on both RNA molecules (Kashiwazaki et al., 1990, 1991). The 5' non-coding regions of RNA-1 and RNA-2 are very similar in size (171 and 154 nucleotides, respectively) and in sequence (87% identity in the first 154 nucleotides). By contrast, the 3' non-coding regions of RNA-1 and RNA-2 differ in size (231 and 761 nucleotides long, respectively) and show no significant sequence identity (Kashiwazaki et al., 1991). Infectious RNA transcripts have been produced from full-length cDNA clones to BaMMV (Meyer & Dessens, 1997)

Replication

Members of the Potyviridae probably replicate in the cytoplasm. The replication cycle involves infection, uncoating, translation, polyprotein processing to yield functional viral-coded products, genome replication via a negative strand RNA template, progeny virus particle assembly, cell-to-cell movement and vector transmission from infected to healthy plants. The functions of the gene products are incompletely known; some gene products, however, have multiple functions.

The functions of some gene products have been determined by direct evidence, while those of others have been predicted from sequence similarities with non-structural proteins of other plant and animal viruses (Domier et al., 1987; Dougherty and Carrington, 1988; Shukla et al., 1991; Riechmann et al., 1992).

There is little information on the early events in infection. With other plant viruses it appears that there is usually no virus-host cell receptor recognition system and that the initial infection process results from virus already present in the seed or introduced into the potential host by physical damage (insect or fungal vectors or experimentally by mechanical inoculation). Viral proteins play little, if any, role in cell entry and viral uncoating is not host-specific (Matthews, 1991).

The genomic RNA of members of the Potyviridae apparently has no associated polymerase molecules. Thus, following uncoating, the viral RNA is translated to generate sufficient virus-coded proteins for subsequent replication, assembly and spread of progeny virus particles. Although little is known about the translation process, cap-independent internal initiation of translation has been proposed for several species of the genus Potyvirus (Carrington & Freed, 1990; Nicolaisen et al., 1992; Levis & Astier-Manifecier, 1993; Basso et al., 1994). However, the genomic RNA of PPV seems to have a leaky scanning mechanism for translation (Riechmann et al., 1991; Simon-Buela et al., 1997).

RNA of Potyvirus species is translated as a single polyprotein that is subsequently cleaved by three distinct proteinases to yield functional viral products. The C-terminal half (Dougherty & Carrington, 1988) of the small nuclear inclusion protein (NIa) is the major proteinase of potyviruses and is involved in processing the P3/CI, CI/6kDa, CI/NIa, NIa/NIb and NIb/CP junctions in the C-terminal two-thirds of the polyprotein (Carrington & Dougherty 1987; Carrington et al., 1988; Hellmann et al., 1988; Dougherty et al., 1989; Garcia et al., 1989; Ghabrial et al., 1990). The two 6 kDa products between P3/CI and CI/NIa are also bounded by the NIa cleavage motifs (Riechmann et al., 1992). These primary cleavages usually occur at susceptible QS, QG or QA bonds (Shukla et al., 1991), although occasionally at QV (Dinant et al., 1991) or QE bonds (Johansen et al., 1991; Gough & Shukla, 1993). In some cases the Q residue in the above dipeptide sequences is replaced by E (Shukla et al., 1994). Thus, there appears to be a simple cleavage motif, V-x-x-Q(E)-(A,S,G, E or V), that is common to all members of the Potyviridae (Shukla et al., 1994). The NIa proteinase is a cysteine-type proteinase that is probably structurally related to trypsin-like serine proteinases (Bazan & Fletterick, 1988). Its active site is Cys2188 in the TEV polyprotein (Dougherty & Carrington, 1988).

The processing of the N-terminal third of the Potyvirus polyprotein (P1- Pro/HC-Pro/P3) does not involve the QG, QA or QS type recognition sequences that are cleaved by the NIa proteinase in the C-terminal two-thirds of the precursor. The HC-Pro/P3 cleavage site is G763-G764 in TEV (Carrington et al., 1989); equivalent sites exist in other genomic sequences (Riechmann et al., 1992; Shukla et al., 1994). The cleavage is effected by a second potyvirus-encoded proteinase similar to papain-like cysteine proteinases (Kamphuis et al., 1985) which is in a 20 kDa domain of the carboxyl-terminal half of the aphid transmission HC-Pro protein (Carrington et al., 1989). The active site cysteine and histidine residues are residues 649 and 722 in the TEV polyprotein (Oh & Carrington, 1989).

The third proteinase involved in polyprotein processing is the P1-Pro protein, a serine protease with the active site serine at position 256 in TEV (Verchot et al., 1991), which cleaves the P1-Pro/HC-Pro junction at a conserved YS (304-305 in TEV) or FS bond (Mavankal & Rhoads, 1991; Carrington & Herndon, 1992).

The subcellular site(s) of potyviral RNA synthesis has yet to be identified but, as found with other positive-strand RNA viruses (Verchot et al., 1991), is probably in the cytoplasm. Potyviruses produce no sub-genomic RNA molecules and the entire RNA genome is copied. Replication thus requires a polymerase, a primer and an unwinding protein to separate the dsRNA products and enable multiple copies of progeny strands to be transcribed. The viral proteins involved are CI, VPg(NIa) and NIb, which form a multicomponent, membrane-associated, replication complex, similar to that found in picorna-, como- and nepoviruses in which proteins are coded for by a similarly ordered gene set (Domier et al., 1987; Goldbach & Wellink, 1988). CI is an RNA helicase that, in the presence of NTP, can unwind RNA duplexes with 3'-overhangs in the 3' to 5' direction (Lain et al., 1990, 1991; Fernandez et al., 1995, 1997). The VPg (Shahabuddin et al., 1988) is the N-terminal half of NIa (Murphy et al., 1990) and is attached to the 5' end of the RNA via a phosphate ester linkage to Y60 (Y1860 in the TVMV polyprotein) in the conserved sequence motif MNY (Murphy et al., 1991). NIb is the RNA-dependent RNA polymerase of members of the Potyviridae (Domier et al., 1987; Martin et al., 1995; Hong & Hunt, 1996); it contains the consensus sequence motif (GDD) of viral RNA-dependent RNA polymerases and is the most conserved of the Potyviridae gene products.

Nevertheless, it is still unclear (Riechmann et al., 1992) (i) how the parental RNA establishes and organizes the specific replication site within the cytoplasm; (ii) how the polymerase primes parental RNA to transcribe the negative sense RNA copies that are used as templates for subsequent viral RNA synthesis; (iii) what the precise nature of the potyvirus replicative intermediate is; or (iv) what the significance of the nuclear targeting signals and nuclear accumulation of VPg(NIa), NIb and the NIa-NIb complex are. NIa and NIb aggregate as equimolar nuclear inclusions in many, but not all, Potyvirus infections and both contain nuclear targeting signals (Restrepo et al., 1990; Carrington et al., 1991).

The low sequence identity between the P1-Pro proteins of biologically distinct potyviruses suggest that P1-Pro, particularly its N-terminal, non-proteinase domain, may be involved in some specific virus-host interaction. The weak sequence identity between the cell movement protein (P30) of tobacco mosaic tobamovirus and P1-Pro of some potyviruses suggests that the latter may control cell-to-cell movement (Domier et al., 1987), although the precise role of P1-Pro has yet to be resolved.

Proteins encoded by the genome of members of the Potyviridae appear to have multiple functions with different functions associated with different protein domains. For example, the central domain of coat protein is required for virus assembly (Jagadish et al., 1991) and cell-to-cell transport (Dolja et al., 1994), the surface-exposed N-terminal domain is involved in aphid transmission (Atreya et al., 1990, 1991) whereas the N- and C- terminal domains mediate long-distance transport (Dolja et al., 1994, 1995). Furthermore, cis-active RNA elements within the CP cistron have been associated with genome amplification (Mahajan et al., 1996; Haldeman-Cahill et al., 1998). Similarly, the N-terminal domain of HC-Pro is involved in aphid-mediated transmission (Atreya et al., 1992), the central region is necessary for efficient genome amplification (Klein et al., 1994; Cronin et al., 1995; Kasschau et al., 1997) and long- distance movement (Cronin et al., 1995; Kasschau et al., 1997) and the C-terminal domain mediates polyprotein processing (Carrington et al., 1989) and possibly cell-to-cell movement (Rojas et al., 1997). The N-terminal domain of NIa acts as VPg (Murphy et al., 1990) and interacts either directly or indirectly with host components to facilitate long-distance movement (Schaad et al., 1997) whereas its C-terminal domain is the major proteinase of members of the Potyviridae (Carrington & Dougherty, 1987). Besides being an RNA helicase (Lain et al., 1990, 1991), the CI protein is also involved in cell-to-cell movement (Andrews & Shalla, 1974; Forster et al., 1988; Carrington et al., 1998) as CI are associated with plasmodesmata (Lawson et al., 1971; Murant & Roberts 1971; Andrews & Shalla, 1974; Rodriquez-Cerezo et al., 1997); moreover, the CI protein is a major component of the replication complex, and ribonucleoprotein complexes probably also facilitate cell transport.

Relationships within the Taxon

Serology
Serological relationships among members of the Potyviridae are complex. Most definitive potyviruses are serologically related to at least one and, in many instances, to several other potyviruses. Serological relationships between many pairs of potyviruses have not been detected, and other relationships may be only indirect. Thus, unexpected paired relationships were found between LMV and BYMV, and between BYMV and BCMV, but not between BCMV and LMV (Alba & Oliveira, 1976). Also, strains of one potyvirus may differ considerably in their serological affinities. Although a few potyviruses react adequately in agar-gel immunodiffusion tests, the particles of many must first be fragmented, e.g. by sonication (Tomlinson et al., 1965), or the coat protein chemically dissociated into subunits (e.g. with SDS and/or pyrrolidine) (Shepard et al., 1974). However, dissociated proteins are very poor immunogens, and may not react with antisera to intact particles (Moghal & Francki, 1976), and/or fail to detect the relationships observed between the dissociated particle proteins of related members of the Potyviridae.

Biochemical and immunochemical investigations of coat proteins have established the molecular basis for serology in the family Potyviridae and provided explanations for the occurrence of variable cross-reactivity of polyclonal antisera, unexpected paired relationships between distinct viruses, and lack of cross-reactions between some strains (Shukla et al., 1992b). Thus it is now known that the N- and C- terminal regions of the coat protein are on the particle surface (Fig.2) and can be removed without affecting particle assembly (Allison et al., 1985; Shukla et al., 1988); that the exposed N termini of the coat proteins are highly variable in length and sequence (Shukla & Ward, 1988, 1989a, 1989b), are immunodominant, and that antibodies to this region are usually virus-specific (Dougherty et al., 1985; Shukla et al., 1988, 1989b); that most cross-reactions between distinct viruses are attributable to the presence of differing proportions of antibodies against the conserved core region of the coat protein (Shukla et al., 1989b; 1989d); that these cross-reacting antibodies are increased if degraded virus particles or prolonged injection protocols are employed; such antibodies are valuable family- or genus-specific probes capable of detecting species of the genera Potyvirus, Tritimovirus and Ipomovirus (Shukla et al., 1989a: Jordan & Hammond, 1991; Mishra et al., 1997). The location, size and sequence of the virus- specific and group-specific epitopes have been identified by immunochemical analysis of overlapping synthetic octatapeptides (Shukla et al., 1989d).

The CI proteins induced by members of the Potyviridae are distinct gene products which have an RNA helicase function (Lain et al., 1990, 1991) and are antigenically unrelated to the coat protein; the CI of unrelated viruses are also serologically unrelated even when the viruses are propagated in the same plant species; however, CI proteins of serologically closely related Potyvirus strains appear to be immunochemically indistinguishable (Hiebert et al., 1971; Purcifull et al., 1973).

Cross-protection
Cross-protection occurs between some Potyvirus species (e.g. TEV, PVY and HMV; Bawden & Kassanis, 1941) but not between different strains of the same Potyvirus species, such as PVY (Horvath, 1969) or MDMV (Shepherd, 1965; Paulson & Sill, 1970; Gillaspie & Koike, 1973; Tosic, 1981). Two or more potyviruses can occur, and have synergistic effects, in naturally infected plants (Hollings & Brunt, 1981b). Conflicting reports on failed cross-protection may sometimes be attributed to the incorrect identification of the viruses and strains used. For example, the SCMV/MDMV group is now know to consist of four distinct viruses (SCMV, MDMV, JGMV and SrMV) (Shukla et al., 1989c, 1992a); similarly, viruses previously referred to as BCMV (McKern et al., 1992; Vetten et al., 1992) and SMV (Jain et al., 1992) have also been shown to consist of more than one distinct virus (also see Shukla et al., 1994).

Coat protein and genome sequences
Several attempts have been made to differentiate individual potyviruses, to define virus strains, and to separate potyviruses into sub-groups by using host range, cross-protection, particle length and serology (Bos, 1970: Lindsten et al., 1976), host range and serology (Jones & Diachun, 1977), serology and amino acid analyses of the particle protein (Moghal & Francki, 1976), and morphology of CI (Edwardson, 1974). Sub-groupings suggested by using these criteria show various anomalies and inconsistencies, and none has been generally accepted (Francki et al., 1985).

It has been shown that (i) coat protein and gene sequence data are the definitive criteria for establishing relationships between members of the Potyviridae (Ward et al., 1992); (ii) the N-terminal region of coat protein is highly variable whereas the C-terminal two-thirds of the protein (core region and C- terminus) is conserved and shows significant sequence identity (>65%) with other distinct potyviruses (Shukla & Ward, 1988, 1989a, 1989b; Ward & Shukla, 1991); (iii) variation in the coat protein core region is similar to that of other parts of the genome of Potyvirus species and is a good index of genetic relatedness (Shukla et al., 1991); (iv) coat protein sequence data can be used to discriminate among members of the Potyviridae and strains, the bimodal distribution of sequence identities being inconsistent with the ‘continuum’ hypothesis (Bos, 1970; Hollings & Brunt, 1981a, 1981b) which previously attempted to explain the inability to develop a satisfactory taxonomy of the family Potyviridae (Shukla & Ward, 1988; Ward & Shukla, 1991); (v) coat protein sequence data can be used to construct a phylogenetic tree in which the potyvirus ‘group’ is considered to be a family (Ward & Shukla, 1991; Barnett, 1991) divided into five genera, in which distinct viruses correspond to species and isolates with the highest levels of sequence identity (>90%) to strains (Ward & Shukla, 1991); (vi) strains of some Potyvirus species, such as those of SCMV and BCMV are now recognized as distinct viruses (Shukla et al., 1989c, 1992a; McKern et al., 1992; Vetten et al., 1992); (vii) some members of the genus Potyvirus previously believed to be distinct species are strains of the same virus, e.g. PStV, PMMV, BlCMV, AzMV, three soybean isolates from Taiwan, some strains of CABMV and the serogroup B strains of BCMV are strains of BCMV (McKern et al., 1992); PMV and WLMV are strains of BYMV (McKern et al., 1993); VNV is a strain of WMV 2 (Wang et al., 1993); and WMV 2 may appear to be a strain of SMV (Frenkel et al., 1989; Jain et al., 1992); (viii) the coat protein sequence data can also reveal previously unrecognized sub-sets of distinct viruses that are closely related, for example, ZYMV, SbMV, WMV 2, PWV, BCMV, BCMNV (formerly the serotype A strains of BCMV) form one sub-set (Ward & Shukla, 1991; Ward et al., 1992); BYMV and ClYVV form another; (ix) the 3' non-coding region of the potyviral genome is a good marker of genetic relatedness (Frenkel et al., 1989, 1992); (x) although any part of the viral genome can be used to establish phylogenetic relationships, the coat protein or 3' non-coding regions are the most convenient (Shukla et al., 1991; Ward & Shukla, 1991).

The coat protein and genome sequences have provided an hierarchical classification of members of the Potyviridae. Initially the family Potyviridae was divided into four genera, Potyvirus, Rymovirus, Bymovirus and tentatively Ipomovirus (Barnett, 1991) on the basis of sequence diversity (Ward & Shukla, 1991), and by coincidence these four genera corresponded to the four modes of vector transmission, aphid, mite, fungus and whitefly, respectively. At the time the only sequence available for the mite-transmitted viruses was that of WSMV, but since RGMV had been described first, the name Rymovirus was selected for this genus. Recent sequence data (Niblett et al., 1991; Gotz & Maiss, 1995; Schubert & Rabenstein, 1995; Salm et al., 1996a) has revealed that the mite-transmitted potyviruses fall into two groups and a new genus Tritimovirus was approved to accommodate WSMV, BrSMV and the possible species SCSMV. The remaining species (AgMV, HoMV, ONMV, RGMV and SpMV) have been retained as a distinct sixth genus (Rymovirus) by the ICTV Potyviridae Study Group. As shown in Fig.3, sequence analyses divide the Potyviridae into only five groupings not six, with the rymoviruses sharing strong sequence identity with members of the Potyvirus genus. Thus sequence identities no longer correlate with the current ICTV classification of the Potyviridae into six genera. It is our view that this classification is in error and that AgMV, RGMV, ONMV, HoMV and SpMV should be transferred from the Rymovirus genus to the Potyvirus genus and the Rymovirus genus be removed and made redundant from the family Potyviridae. Such a proposal is currently being discussed by the Potyviridae Study Group.

Affinities with Other Groups

Members of the Potyviridae are readily differentiated from other filamentous viruses of the genera Allexivirus, Capillovirus, Carlavirus, Closterovirus, Crinivirus, Foveavirus, Potexvirus, Trichovirus and Vitivirus. Their particles are more flexuous than those of allexiviruses, carlaviruses, foveaviruses and potexviruses but less so than those of capilloviruses, closteroviruses, criniviruses, trichoviruses and vitiviruses. Their genome organization indicates that they belong to the picorna-like supergroup of viruses whose RNAs have a VPg covalently bound to the 5' end, a poly(A) tail at the 3' end, and are expressed as a single polyprotein which is subsequently cleaved by proteinases to yield several functional proteins, including a conserved ordered gene set of non-structural proteins that are involved in RNA replication (Goldbach & Wellink, 1988).

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Figure 1

Genome organization of the Potyvirus (TEV) and Bymovirus (BaYMV) genera of the Potyviridae family. AI, amorphous inclusion; CI, cylindrical inclusion; NIa and NIb, small and large nuclear inclusion proteins which aggregate in the nucleus to form a nuclear inclusion body; CP, coat protein. P1-Pro and HC-Pro cleave the bonds between P1 and HC-Pro (helper component proteinase) and HC-Pro and P3 proteins, respectively while the NIa- Pro cleaves the rest of the polyprotein bonds (filled diamonds); VPg, genome- linked protein covalently attached to the 5' terminal nucleotide (represented by filled circle); HC-ProLP, HC-Pro-like protein. Modified from Berger et al. (1998).

Figure 2

Schematic drawing showing the linear sequence of the coat protein subunit, the subunit folding pattern, the surface location of the N- and C-termini and the assembly of PVY particle (based on Shukla & Ward, 1989a).

Figure 3

Phylogenetic analysis of coat protein amino acid sequences of members of the family Potyviridae using the FM method (modified from Berger et al., 1997). The family is divided currently into six genera, namely Potyvirus, Macluravirus, Ipomovirus, Tritimovirus, Rymovirus and Bymovirus. As shown here the mite-transmitted Rymovirus species, AgMV, HoMV and RGMV (enclosed in a box), cluster with the aphid-transmitted species of the genus Potyvirus. On the basis of this and other information we believe their inclusion in a separate genus Rymovirus is no longer justified. The Potyviridae Study Group are looking at this proposal to remove the Rymovirus genus and place these mite transmitted viruses in the genus Potyvirus. Other mite-transmitted viruses now form the new Tritimovirus genus. The ‘BCMV +’ represents the bean common mosaic virus subgroup consisting of BCMV (of which AzMV, BlCMV, DeMV, PStV are strains), BCMNV, CABMV (includes SAPV), WMV-2 (includes VNV), PWV and ZYMV, and the ‘BYMV +’ refers to the bean yellow mosaic virus subgroup consisting of BYMV (includes pea mosaic virus) and ClYVV.