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.



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 40-50 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 1.9-2.0 and 1.7-1.9 kbp.


There is a single major CP with predicted Mr of 51-57 kDa. The Mr of the 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.


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 Abbreviation(s)
Beet cryptic virus 1beet cryptic virus 1Hungary RNA1: EU489061; RNA2: EU489062RNA1: NC_011556; RNA2: NC_011557Complete genomeBCV1-Hungary
Carrot cryptic viruscarrot cryptic virusGermany RNA1: FJ550604; RNA2: FJ550605Complete genomeCCV-Germany
Cherry chlorotic rusty spot associated partitiviruscherry chlorotic rusty spot associated partitivirusTurkeyRNA1: AJ781168; RNA2: AJ781167RNA1: NC_006441; RNA2: NC_006440Complete genomeCCRSaPV-Turkey
Cherry chlorotic rusty spot associated partitiviruscherry chlorotic rusty spot associated partitivirusCampaniaRNA1: AJ781401; RNA2: AJ781402CCRSaPV-Campania
Chondrostereum purpureum cryptic virus 1Chondrostereum purpureum cryptic virus 1Mesachie Lake RNA1: AM999771; RNA2: AM999772Complete genomeCpCV1-Mesachie Lake
Flammulina velutipes browning virusFlammulina velutipes browning virusMagaeRNA1: AB465308; RNA2: AB465309Complete genomeFvBV-Magae
Helicobasidium mompa partitivirus V70Helicobasidium mompa partitivirus V70OsakiRNA1: AB025903Partial genomeHmPVV70-Osaki
Heterobasidion partitivirus 1Heterobasidion partitivirus 1ab1 RNA1: HQ541323; RNA2: HQ541324Complete genomeHetPV1-ab1
Heterobasidion partitivirus 12Heterobasidion partitivirus 12an1RNA1: KF963175; RNA2: KF963176Complete genomeHetPV12-an1
Heterobasidion partitivirus 13Heterobasidion partitivirus 13an1RNA1: KF963177; RNA2: KF963178Complete genomeHetPV13-an1
Heterobasidion partitivirus 13Heterobasidion partitivirus 13an2RNA1: KF963179; RNA2: KF963180HetPV13-an2
Heterobasidion partitivirus 13Heterobasidion partitivirus 13an3RNA1: KF963181; RNA2: KF963182HetPV13-an3
Heterobasidion partitivirus 13Heterobasidion partitivirus 13pa1RNA1: KF963183; RNA2: KF963184HetPV13-pa1
Heterobasidion partitivirus 15Heterobasidion partitivirus 15pa1RNA1: KF963186; RNA2: KF963187Complete genomeHetPV15-pa1
Heterobasidion partitivirus 3Heterobasidion partitivirus 3ec1RNA1: FJ816271; RNA2: FJ816272Complete genomeHetRV3-ec1
Rosellinia necatrix partitivirus 2Rosellinia necatrix partitivirus 2W57 RNA1: AB569997; RNA2: AB569998RNA1: NC_020234; RNA2: NC_020235Complete genomeRnPV2-W57
Vicia cryptic virusVicia cryptic virusGermanyRNA1: AY751737; RNA2: AY751738RNA1: NC_007241; RNA2: NC_007242Complete genomeVCV-Germany
Vicia cryptic virusVicia cryptic virusFA061102RNA1: EU605883; RNA2: EU605884VCV-FA061102
Vicia cryptic virusVicia cryptic virusDreifach WeisseRNA1: EF173392; RNA2: EF173391VCV-Dreifach Weisse
Vicia cryptic virusVicia cryptic virusHangdown GruenkernRNA1: EF173396; RNA2: EF173395VCV-Hangdown Gruenkern
Vicia cryptic virusVicia cryptic virusFruehe WeisskeimigeRNA1: EF173394; RNA2: EF173393VCV-Fruehe Weisskeimige
Vicia cryptic virusVicia cryptic virusThe SuttonRNA1: EF173389VCV-The Sutton
Vicia cryptic virusVicia cryptic virusDivineRNA2: EF173390VCV-Divine
White clover cryptic virus 1white clover cryptic virus 1BoccardoRNA1: AY705784; RNA2: AY705785RNA1: NC_006275; RNA2: NC_006276Complete genomeWCCV1-Boccardo

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




Raphanus sativus cryptic virus 1




Diuris pendunculata cryptic virus isolate SW3.3



Dill clover cryptic virus 1 isolate IPP_hortorum



Red clover cryptic virus 1 isolate IPP_Nemaro




Rhizoctonia solani partitivirus 2




Arabidopsis halleri partitivirus 1



Rose partitivirus isolate PB




Rosellinia necatrix partitivirus 7



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