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, Reuter et al., 2008, Reuter et al., 2009Smits et al., 2013Otomaru 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-A1, 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.

Biology

AiV-A1 grows in cell cultures (BSC-1, Vero). AiV-A1 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, marmots, rats, ferrets, goats, rabbits, bats, birds and in sewage.

Twenty genetic types are distinguished by means of phylogenetic analysis (Aichivirus A: 10 types, Aichivirus B: 3 types, Aichivirus C: 2 types, Aichivirus D: 2 types, Aichivirus E: 1 type, Aichivirus F: 3 types).

Antigenicity

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

Derivation of names

Aichivirus: from the Aichi prefecture in Japan

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

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.

Member species

Exemplar isolate of the species
SpeciesVirus nameIsolateAccession numberRefSeq numberAvailable sequenceVirus Abbrev.
Aichivirus Aaichivirus A1; Aichi virus 1A846/88AB040749NC_001918Complete genomeAiV-A1
Aichivirus Aaichivirus A2; canine kobuvirusdog-AN211D-USA-2009JN387133Complete genomeAiV-A2
Aichivirus Aaichivirus A3; murine kobuvirusUSA/2010/M-5JF755427Complete genomeAiV-A3
Aichivirus Aaichivirus A4; feline kobuvirusFK-13KF831027Complete genomeAiV-A4
Aichivirus Aaichivirus A5; roller kobuvirusSZAL6-KoV/2011/HUNKJ934637Complete genomeAiV-A5
Aichivirus Aaichivirus A6; rat kobuvirus20724x33MF947444Complete genomeAiV-A6
Aichivirus Aaichivirus A7RtMruf-PicoV/JL2014-2KY432931Complete genomeAiV-A7
Aichivirus Aaichivirus A8; murine kobuvirusMKV1/NYC/2014MF175074Complete genomeAiV-A8
Aichivirus Aaichivirus A9; rat kobuvirusWencheng-Rt386-2MF352432Complete genomeAiV-A9
Aichivirus Aaichivirus A10; rat kobuvirus16715x14MF947429Partial genomeAiV-A10
Aichivirus Baichivirus B1; bovine kobuvirusU-1AB084788NC_004421Complete genomeAiV-B1; BKV
Aichivirus Baichivirus B2; ferret kobuvirusMpKoV38/Netherlands/2010KF006985Complete genomeAiV-B2
Aichivirus Baichivirus B3; ovine kobuvirussheep/TB3/HUN/2009GU245693Complete genomeAiV-B3
Aichivirus Caichivirus C1; porcine kobuvirusswine/S-1-HUN/2007/HungaryEU787450NC_011829Complete genomeAiV-C1; PKV
Aichivirus Caichivirus C2; caprine kobuvirus12Q108/South Korea/2012KF793927Complete genomeAiV-C2
Aichivirus Daichivirus D1; kagovirus 1cattle/Kagoshima-1-22-KoV/2014/JPNLC055961NC_027919Complete genomeAiV-D1
Aichivirus Daichivirus D2; kagovirus 2cattle/Kagoshima-1-24-KoV/2015/JPNLC055960Complete genomeAiV-D2
Aichivirus Eaichivirus E1; rabbit kobuvirusNy4H/2010/HUNKT325853NC_039211Partial genomeAiV-E1
Aichivirus Faichivirus F1; bat kobuvirus 1BtMr-PicoV/JX2010KJ641686NC_043071Partial genomeAiV-F1
Aichivirus Faichivirus F2BtMf-PicoV-2/GD2012KJ641691Partial genomeAiV-F2

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

Related, unclassified viruses

Virus name

Accession number

Virus abbreviation

bat/TM001k/USA/2008

HM228881*

 

grey squirrel kobuvirus [grey squirrel/UK/2010]

GQ179640

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

KJ950970*

 

Virus names and virus abbreviations are not official ICTV designations.
* partial genome