Genus: Rafivirus


Genus: Rafivirus

Distinguishing features

The genus is distinguished on the basis of genetic characters.

Virion

Morphology

No details are available on the morphology of the virions.

Nucleic acid

Genome (Ng et al., 2015b, Shi et al., 2018): 7,204-7,400 nt (5′–UTR: 435-487 nt; ORF: 6,699-6,861 nt; 3′–UTR: 52-70 nt). The location of the cre has not been identified. 

Genome organization and replication

Genome layout:

VPg+5′-UTR-[L-1AB-1C-1D/2A-2B-2C/3A-3B-3C-3D]-3′-UTR

The deduced polyprotein ranges from 2,233 to 2,287 aa. The function of the L and 2A proteins is unclear. 1AB remains uncleaved. The 1D/2A and 2A/2B cleavage sites are unclear.

Antigenicity

See discussion under family description.

Biology

Viral RNA has been detected in faecal samples and tissue specimens of Forsten's tortoises (Indotestudo forstenii), Chinese stripe-necked turtles and geckos (Gekko similignum). 

Species demarcation criteria

Members of a species of genus Rafivirus:

  • share a common genome organization,
  • are less than 30% divergent in the polyprotein aa sequence,
  • are less than 30% divergent in the P1 aa sequence,
  • are less than 30% divergent in the 2C + 3CD aa sequence.

Member species

SpeciesVirus name(s)Exemplar isolateExemplar accession numberExemplar RefSeq numberAvailable sequenceOther isolatesOther isolate accession numbersVirus abbreviationIsolate abbreviation
Rafivirus Atortoise rafivirusUF4KJ415177NC_023988Complete genomeRaV-A
Rafivirus BHainan gekko similignum picornavirusPXYC222841MG600090NC_043544Complete genomeRaV-B

Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.

Derivation of names

Rafi: refers phonetically to Raph(ael), a fictional comics character.

Related, unclassified viruses 

Virus name

Accession number

Virus abbreviation

rhimavirus [cane toad/AU1/Australia/2017]

MG967619

 

Virus names and virus abbreviations are not official ICTV designations.

Phylogenetic analysis indicates that this virus may be a member of a novel Rafivirus species.