Genus: Kobuvirus


Genus: Kobuvirus

Distinguishing features

The genus is distinguished on the basis of genetic characters.

Virion

Morphology

Unlike other picornaviruses, kobuvirus capsids show a distinctive surface morphology when observed by electron microscopy (Figure 1E.Picronaviridae). The crystal structure of Aichi virus A (AiV-A1) was recently resolved (Sabin et al., 2016)

Physicochemical and physical properties

Virions are stable at pH 3.5.

Nucleic acid

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-A) 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 is 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-A grows in cell cultures (BSC-1, Vero). AiV-A 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:

  • are less than 30% divergent in polyprotein aa sequence,
  • are less than 30% divergent in P1 aa sequence,
  • are less than 20% divergent in 2C + 3CD aa sequence,
  • share a common genome organization.

The divergence (number of differences per site between sequences) of members of different 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: 7 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 A1; Aichi virus 1A846/88AB040749NC_001918Complete genomeAiV-A1
Aichivirus AAichi virus A2; canine kobuvirusdog-AN211D-USA-2009JN387133AiV-A2
Aichivirus AAichi virus A3; murine kobuvirusUSA/2010/M-5JF755427AiV-A3
Aichivirus AAichi virus A4; feline kobuvirusFK-13KF831027AiV-A4
Aichivirus AAichi virus A5; roller kobuvirusSZAL6-KoV/2011/HUNKJ934637AiV-A5
Aichivirus AAichi virus A6; Kathmandu sewage kobuvirusKoV-SewKTMJQ898342AiV-A6
Aichivirus AAichi virus A7RtMruf-PicoV/JL2014-2KY432931AiV-A7
Aichivirus Bbovine kobuvirusU-1AB084788NC_004421Complete genomeBKV
Aichivirus Baichivirus B2; ferret kobuvirusMpKoV38/Netherlands/2010KF006985AiV-B2
Aichivirus Baichivirus B3; ovine kobuvirussheep/TB3/HUN/2009GU245693AiV-B3
Aichivirus Cporcine kobuvirusswine/S-1-HUN/2007/HungaryEU787450NC_011829Complete genomePKV
Aichivirus Caichivirus C2; caprine kobuvirus12Q108/South Korea/2012KF793927AiV-C2
Aichivirus Dkagovirus 1cattle/Kagoshima-1-22-KoV/2014/JPNLC055961NC_027919Complete genomeKV-1
Aichivirus Daichivirus D1; kagovirus 2cattle/Kagoshima-1-24-KoV/2015/JPNLC055960AiV-D2; KV-2
Aichivirus Erabbit kobuvirusNy4H/2010/HUNKT325853NC_039211Partial genomeRaPV
Aichivirus Fbat kobuvirus 1BtMr-PicoV/JX2010KJ641686NC_043071Partial genomeBaPV-1
Aichivirus Faichivirus F2BtMf-PicoV-2/GD2012KJ641691AiV-F2

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

 

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

KJ950970

 

Virus names and virus abbreviations are not official ICTV designations.