Genus: Alphapartitivirus


Genus: Alphapartitivirus

Distinguishing features

Members of the genus Alphapartitivirus infect plants, ascomycetous or basidiomycetous fungi. All members have two dsRNA segments of similar sizes that are individually encapsidated in separate particles. Alphapatitivirus genomes typically range from 3.6 to 3.9 kbp in total.

Virion

Morphology

Based on negative-contrast electron microscopy, the virions of white clover cryptic virus 1 (WCCV1) are isometric and ~34 nm in diameter (Boccardo et al., 1985). The particles appear rounded and are usually penetrated by stain to give a ring-like appearance (Figure 1.Alphapartitivirus). Other reported alphapartitivirus particle sizes range from 25 to 4050 nm in diameter (Chiba et al., 2013, Abou-Elnasr et al., 1985, Magae and Hayashi 1999, Osaki et al., 2002).

Figure 1.Alphapartitivirus. Negative-contrast electron micrograph of particles of an isolate of White clover cryptic virus 1, the type species of the genus Alphapartitivirus. The bar represents 50 nm. (Ghabrial et al., 2000).

Physicochemical and physical properties

The buoyant density of WCCV1 virions in CsCl is 1.392 g cm−3 (Boccardo et al., 1985) and that of Vicia cryptic virus is 1.37 g cm−3 (Abou-Elnasr et al., 1985).

Nucleic acid

The viral genome comprises two dsRNA segments which are individually 1.92.0 and 1.71.9 kbp.

Proteins

There is a single major coat protein (CP) with predicted Mr of 5157 kDa. The Mr of the RNA-dependent RNA polymerase (RdRP), as deduced from nucleotide sequence analysis, ranges from 68 to 73 kDa. Virion-associated RNA polymerase activity is present.

Genome organization and replication

Each genome segment is monocistronic: the larger dsRNA segment typically encodes the RdRP and the smaller one encodes the CP. The alphapartitivirus Rosellinia necatrix partitivirus 2 has a third genome segment, which is a truncated version of the RdRP that may function as defective-interfering RNA (see GenBank record AB569999) (Chiba et al., 2013). A second version of dsRNA2, encoding seemingly full-length capsid protein has been reported for the related, unclassified Raphanus sativus cryptic virus 1. Cherry chlorotic rusty spot associated partitivirus has dsRNA satellites appearing not to encode any proteins (GenBank records AM749118–20). Alphapartitivirus dsRNA typically possess a poly(A) stretch which may be interrupted by other nucleotides at the 3′-end of the coding-strand of one or both genome segments.

Biology

Members of the genus Alphapartitivirus infect ascomycetous, basidiomycetous fungi (ten species) or plants (four species). They are transmitted intracellularly during cell division (plants, fungi) or cell fusion and sporogenesis (fungi). Plant alphapartitiviruses include former members of the defunct genus Alphacryptovirus, which cause persistent infections. Various host effects have been described for fungal alphapartitiviruses: the related, unclassified Rhizoctonia solani partitivirus 2 causes hypovirulence in Rhizoctonia solani, a soil-borne basidiomycete fungus (Zheng et al., 2014), and Heterobasidion partitivirus 3 seems to reduce the growth rate of the basidiomycete fungus Heterobasidion abietinum at low temperatures (Vainio et al., 2010). The presence of Flammulina velutipes browning virus correlates with brown discoloration of the host fungus (Magae and Sunagawa 2010).

Species demarcation criteria

The criteria to differentiate species in genus Alphapartitivirus are:

  • ≤ 90% aa sequence identity in the RdRP, and
  • ≤ 80% aa sequence identity in the CP

Member Species

SpeciesVirus name(s)Exemplar isolateExemplar accession numberExemplar RefSeq numberAvailable sequenceOther isolatesOther isolate accession numbersVirus abbreviationIsolate abbreviation
Beet cryptic virus 1beet cryptic virus 1HungaryRNA1: EU489061; RNA2: EU489062RNA1: NC_011556; RNA2: NC_011557Complete genomeBCV1
Carrot cryptic viruscarrot cryptic virusGermanyRNA1: FJ550604; RNA2: FJ550605Complete genomeCCV
Cherry chlorotic rusty spot associated partitiviruscherry chlorotic rusty spot associated partitivirusTurkeyRNA1: AJ781168; RNA2: AJ781167RNA1: NC_006441; RNA2: NC_006440Complete genomeCCRSaPV
Cherry chlorotic rusty spot associated partitiviruscherry chlorotic rusty spot associated partitivirusCampaniaRNA1: AJ781401; RNA2: AJ781402CCRSaPV
Chondrostereum purpureum cryptic virus 1Chondrostereum purpureum cryptic virus 1Mesachie LakeRNA1: AM999771; RNA2: AM999772Complete genomeCpCV1
Flammulina velutipes browning virusFlammulina velutipes browning virusMagaeRNA1: AB465308; RNA2: AB465309Complete genomeFvBV
Helicobasidium mompa partitivirus V70Helicobasidium mompa partitivirus V70OsakiRNA1: AB025903Partial genomeHmPVV70
Heterobasidion partitivirus 1Heterobasidion partitivirus 1ab1 RNA1: HQ541323; RNA2: HQ541324Complete genomeHetPV1
Heterobasidion partitivirus 3Heterobasidion partitivirus 3ec1RNA1: FJ816271; RNA2: FJ816272Complete genomeHetRV3
Heterobasidion partitivirus 12Heterobasidion partitivirus 12an1RNA1: KF963175; RNA2: KF963176Complete genomeHetPV12
Heterobasidion partitivirus 13Heterobasidion partitivirus 13an1RNA1: KF963177; RNA2: KF963178Complete genomeHetPV13
Heterobasidion partitivirus 13Heterobasidion partitivirus 13an2RNA1: KF963179; RNA2: KF963180HetPV13
Heterobasidion partitivirus 13Heterobasidion partitivirus 13an3RNA1: KF963181; RNA2: KF963182HetPV13
Heterobasidion partitivirus 13Heterobasidion partitivirus 13pa1RNA1: KF963183; RNA2: KF963184HetPV13
Heterobasidion partitivirus 15Heterobasidion partitivirus 15pa1RNA1: KF963186; RNA2: KF963187Complete genomeHetPV15
Rosellinia necatrix partitivirus 2Rosellinia necatrix partitivirus 2W57RNA1: AB569997; RNA2: AB569998RNA1: NC_020234; RNA2: NC_020235Complete genomeRnPV2
Vicia cryptic virusVicia cryptic virusGermanyRNA1: AY751737; RNA2: AY751738RNA1: NC_007241; RNA2: NC_007242Complete genomeVCV
Vicia cryptic virusVicia cryptic virusFA061102RNA1: EU605883; RNA2: EU605884VCV
Vicia cryptic virusVicia cryptic virusDreifach WeisseRNA1: EF173392; RNA2: EF173391VCV
Vicia cryptic virusVicia cryptic virusHangdown GruenkernRNA1: EF173396; RNA2: EF173395VCV
Vicia cryptic virusVicia cryptic virusFruehe WeisskeimigeRNA1: EF173394; RNA2: EF173393VCV
Vicia cryptic virusVicia cryptic virusThe SuttonRNA1: EF173389VCV
Vicia cryptic virusVicia cryptic virusDivineRNA2: EF173390VCV
White clover cryptic virus 1white clover cryptic virus 1BoccardoRNA1: AY705784; RNA2: AY705785RNA1: NC_006275; RNA2: NC_006276Complete genomeWCCV1

Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.
Download GenBank/EMBL query for sequences listed in the table here.

Related, Unclassified Viruses 

 

 

Virus name*

Accession number

dsRNA1/RdRP

dsRNA2/CP

dsRNA3

Raphanus sativus cryptic virus 1

AY949985

DQ181926

DQ181927

Diuris pendunculata cryptic virus isolate SW3.3

JX156424

JX891460

 
dill clover cryptic virus 1 isolate IPP_hortorum

KF484726

KF484727

 
red clover cryptic virus 1 isolate IPP_Nemaro

KF484724

KF484725

 

Rhizoctonia solani partitivirus 2

KF372436

KF372437

 

Arabidopsis halleri partitivirus 1

LC151461

LC151462

 
rose partitivirus isolate PB

KU896858

KU896859

 

Rosellinia necatrix partitivirus 7

LC076694

LC076695

 
* Representative isolate of a virus with a complete published genome sequence
Segment encoding the larger version of CP