103.
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Type Species |
(SCSV) |
The genus includes plant infecting viruses with a genome consisting of multiple (at least 6) circular ssDNA molecules each of approximately 1 kb in size and encapsidated in an icosahedral (non-geminate) virion about 20 nm in diameter.
Virions are 17 to 20 nm in diameter and exhibit icosahedral symmetry. They are not enveloped. Capsomeres may be evident, producing an angular or hexagonal outline (Fig. 1).
Physicochemical and Physical Properties
The buoyant density of virions is 1.24 to 1.30 g/cm3 in Cs2SO4, and 1.34 g/cm3 in CsCl. Instability in CsCl has been reported for SCSV. An S20w of 46S has been reported for Banana bunchy top virus (BBTV). Particle morphology is not affected by freezing of tissue before virion extraction.
The genome is composed of several species of circular ssDNA ranging in size from 985 to 1111 nts. All of them seem to be structurally similar in being positive sense, transcribed in one direction, and containing a conserved stem-loop structure (and other conserved domains) in the non-coding region. Six to 10 DNA components, each of which appears to be encapsidated in a separate particle, have been isolated from virion preparations of different species and their isolates. The number and types of ssDNA components constituting the integral genome parts have not been determined yet for any of the nanoviruses.
Virions have a single capsid protein with a Mr of 19-20 103.
None reported.
None reported.
Genome Organization and Replication
The genomic information is distributed over at least 6 molecules of circular ssDNA. Since the the nanovirus DNAs are structurally similar to those of the geminiviruses and at least one of the DNA components of each species codes for a replication-associated protein (Rep), nanovirus DNAs are proposed to be replicated from transcriptionally and replicationally active dsDNA forms via a rolling circle type of replication mechanism. Nicking and joining activity of the BBTV Rep protein has been demonstrated in vitro. Complementary strand synthesis of BBTV genomic ssDNA is attributed to a population of endogenous primers derived from BBTV-DNA 5, which appears to encode a protein that is potentially involved into cell cycle regulation.
All ssDNAs found associated with the assigned species contain a major virion sense ORF and appear to be transcribed unidirectionally. Each coding region is preceded by a promoter sequence with a TATA box and followed by a poly(A) addition signal (Fig. 2). At least one of the genome components codes for a Rep protein (Rep; Mr 32.4-33.6 103). For some isolates of the four assigned species, two to four Rep components have been described but their significance is enigmatic, as some of the additional Rep components may actually be satellite components. A second virion-sense ORF, completely within the Rep ORF and encoding a putative 5 103 protein of unknown function, was also identified for the BBTV Rep component (DNA-1), which is present in all BBTV isolates studied.
Available information suggests that the genome of each virus has 5 to 6 components coding for protein other than Rep proteins, which are referred to as non-Rep proteins. Based on the amino-acid sequence identities among the nanovirus non-Rep proteins, the non-Rep components of the four assigned species code for:
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the capsid protein (18.7-19.3 | |
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a putative movement protein (12.7-13.7 | |
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a protein (19-19.7 | |
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a putative protein (12.7-13.7 | |
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a putative protein (16.9-18 | |
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a putative protein 15 | |
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a putative protein 10.4 |
Virions are immunogenic. Species are serologically distinct except that Milk vetch dwarf virus (MDV) reacts with Faba bean necrotic yellows virus (FBNYV) antiserum and the majority of monoclonal antibodies to FBNYV. SCSV antiserum binds weakly to FBNYV particles. BBTV seems to be serologically unrelated to any of the other assigned members.
Individual species have narrow host ranges. FBNYV, MDV and SCSV naturally infect a range of leguminous species, whereas BBTV has been reported only from Musa spp. All virus species are associated with stunting of infected plants, and infected hosts may also show leafroll, chlorosis and premature death. None of the viruses has been transmitted mechanically either in sap or after purification. Only SCSV has been shown to replicate in inoculated protoplasts. Under natural conditions, all viruses are transmitted by aphids in a persistent manner. Available information suggests that viruses do not replicate in their vectors. BBTV is widely distributed in banana growing countries in the Asia-Pacific region and Africa. SCSV occurs in Australia, FBNYV occurs in West Asia and North and East Africa, and MDV occurs in Japan.
The tentative member of the genus, Coconut foliar decay virus (CFDV) is transmitted by a cixiid plant hopper and occurs in Vanuatu.
List of Species Demarcation Criteria in the Genus
The criteria demarcating species in the genus are:
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Different reactions to antibodies to individual species, | |
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Differences in the capsid protein amino acid sequences more than 15%, | |
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Different host ranges, and | |
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Some species have different vectors. |
The genus includes species with multiple genomic DNAs that are unidirectionally transcribed, Coconut foliar decay virus (CFDV), a tentative species within the genus has similar morphology but differs from the assigned members by containing a single circular ssDNA of 1291 nts which is proposed to be transcribed bidirectionally by having a capsid protein of Mr approximately 24 103 and by being transmitted by a plant hopper.
Official virus species names are in italics. Tentative virus species names, alternative names ( ), strains or serotypes are not italicized. Virus names, genome sequence accession numbers [ ], and assigned abbreviations ( ) are:
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Banana bunchy top virus |
[S56276 (DNA1), U18077 to U18079 (DNA H1, H3, H4) L32166, L32167, U02312 (Y1)] |
(BBTV) |
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Faba bean necrotic yellows virus |
[X80879 (C1), Y11405 to Y11409 (C2 to C6) AJ005964 to AJ005968 (C1, C7 to C10)] |
(FBNYV) |
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Milk vetch dwarf virus |
[AB000920 to 000927, 0009046, 0009047] |
(MDV) |
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Subterranean clover stunt virus |
[U16730 to U16736] |
(SCSV) |
Tentative Species in the Genus
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Coconut foliar decay virus |
[M29963] |
(CFDV) |
Phylogenetic Relationships within the Genus
Comparison of the 15 potential Rep proteins identified from assigned and tentative members of the genus revealed amino acid identities ranging from about 28% to 90%. In addition, there is a high variability among Rep proteins, not only from different nanovirus species but also from a given virus. Since some of the Rep components appear to be associated only with some isolates of a given species and thus may not be integral genome parts, a phylogenetic tree based on nanovirus Rep protein sequences is currently unsuitable for illustrating the interrelationships among the species.
Analysis of four non-Rep proteins identified from all four assigned species (Fig. 3) suggests that the most conserved (46-91% identity) non-Rep protein is the putative protein of 17.3 to 17.7 103, followed by the capsid protein (20-84%), the putative movement protein (14-77%), and the putative Rb-binding protein (19-71%). All six non-Rep proteins of FBNYV are most closely related to those of MDV (52-91%), and the FBNYV and MDV non-Rep proteins are intermediately (44-67%) and distantly (14-48%) related to the known non-Rep proteins of SCSV and BBTV, respectively. The distant relationships of the BBTV non-Rep [and Rep] proteins to those of the legume-infecting nanoviruses may warrant a later subdivision of the nanoviruses into dicot- and monocot-infecting species.
All Rep proteins of the assigned and tentative species have most of the amino acid domains characteristic of Rep proteins. The nanovirus Rep proteins differ form those of members of the family Geminiviridae in being smaller (about 33 kDa) having a slightly distinct dNTP-binding motif (GP/SXGG/NEGKS/T), lacking the Rb-binding motif, and in sharing amino acid sequence identities of only 17 to 22% with them. Moreover, the assigned species are clearly distinct from the geminiviruses in particle morphology, genome size, number and size of DNA components, mode of transcription, as well as in vector species. The putative Rep protein of Porcine circovirus (family Circoviridae) has only insignificant identity (18 to 23%) with nanovirus Rep proteins, and has a bidirectionally transcribed ssDNA genome resembling that of CFDV. All of these viruses have a conserved nonanucleotide motif at the apex of the stem-loop sequence which is consistent with operation of a rolling circle model for DNA replication.
Nano: from the Greek “nanos”, meaning dwarf, fact referring to the observations that these plant viruses have the smallest known virions and genome segment sizes, and dwarf their hosts.
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