Genus: Kobuvirus


Genus: Kobuvirus

Virion

Morphology

Unlike other picornaviruses, kobuvirus capsids show a distinctive surface morphology when observed by electron microscopy (Fig. 1E). The crystal structure of AiV-A was recently resolved (Sabin et al., 2016)

Physicochemical and physical properties

Virions are stable at pH 3.5.

Nucleic acid

Length of genome (Yamashita et al., 1998, Yamashita et al., 2003, Smits et al., 2013, Reuter et al., 2008, Reuter et al., 2009, Otomaru et al., 2016, Pankovics et al., 2016): up to 8,280 nt (5'-UTR: up to 744 nt; ORF: 7,299-7,467 nt; 3'-UTR: 136-240 nt). The genome of Aichi virus (AiV) has a high G+C base composition (59%). The 3′-UTR differs in the three species: members of Aichivirus A have the longest 3'-UTR at 240 nt, however, the 3′-UTRs of bovine kobuvirus (BKV, Kobuvirus B) and porcine kobuvirus (PKV, Kobuvirus C) are shorter at 177 and 170 nt, respectively. In AiV-1, there is a 5′-proximal stem-loop involved in RNA replication and encapsidation. The IRESs of members of the Aichivirus A and Aichivirus B species are of type V, however, those of Aichivirus C (PKV) possess a type IV IRES. The cre is located in the 2A gene region of rabbit kobuvirus but has not been identified in other kobuviruses.

Genome organization and replication

Genome layout:

VPg+5'UTRIRES[L/1AB-1C-1D/2AH-box/NC-2B-2C/3A-3B-3C-3D]3'UTR-poly(A)

The deduced polyprotein has a length of c. 2,432-2,488 amino acids. There is a leader polypeptide of unknown function, and distinctive length (170-195 aa). 1AB remains uncleaved; however, a myristoylation signal (GxxxT) is present at the amino terminus of the polypeptide. The 2A protein contains an H-Box/NC motif.

Antigenicity

Aichivirus and bovine kobuvirus have been distinguished by neutralization of infectivity and serological assays. 

Biology

AiV grows in cell cultures (BSC-1, Vero). AiV is thought to be a cause of human gastroenteritis. Kobuviruses have been isolated from humans, cattle, sheep and pigs. Kobuvirus genomes have been detected in faeces of dogs, cats, mice, ferrets, goats, rabbits, bats, birds and in sewage.

Species demarcation criteria

Members of a species of the genus Kobuvirus:

  • share greater than70% aa identity in the polyprotein,
  • share greater than 70% aa identity in P1,
  • share greater than 80% aa identity in 2C + 3CD,
  • share a common genome organization.

The divergence (number of differences per site between sequences) of known Kobuvirus species ranges from 0.37-0.60 for P1 and 0.21-0.48 for 3CD.

Sixteen types have been characterized genetically by phylogenetic clustering (Aichivirus A: 6 types, Aichivirus B: 3 types, Aichivirus C: 2 types, Aichivirus D: 2 types, Aichivirus E: 1 type, Aichivirus F: 2 types).

Member species

SpeciesVirus name(s)Exemplar isolateExemplar accession numberExemplar RefSeq numberAvailable sequenceOther isolatesOther isolate accession numbersVirus abbreviationIsolate abbreviation
Aichivirus AAichi virus AAB040749Complete genomeAiV-A
Aichivirus Bbovine kobuvirus U-1AB084788NC_004421Complete genomeBKV
Aichivirus Cporcine kobuvirusswine-S-1-HUN-2007EU787450NC_011829Complete genomePKV
Aichivirus Dkagovirus 1cattle/Kagoshima-1-22-KoV/2014/JPNLC055961NC_027919Complete genomeKV-1
Aichivirus Erabbit kobuvirusNy4H/2010/HUNKT325853Partial genomeRaPV
Aichivirus Fbat kobuvirus 1BtMr-PicoV/JX2010KJ641686Partial genomeBaPV-1

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

Derivation of names

Aichi: from the Aichi prefecture in Japan

Kobu: from Japanese kobu, 'knuckle, bump' (reference to surface structure of virus particle).

Related, unclassified viruses

Virus name

Accession number

Virus abbreviation

bat/TM001k/USA/2008

HM228881

 

Caprine kobuvirus [12Q108]

KF793927

 

Norway rat kobuvirus 2 [rat/NYC-D21a/USA/2013]

KJ950970

 

Virus names and virus abbreviations are not official ICTV designations.