Genus: Parechovirus


Genus: Parechovirus

Distinguishing features

The genus is distinguished on the basis of genetic characters.

Virion

Morphology

No surface morphology is visible by EM. The crystal structures of human parechovirus 1 and 3 and Ljungan virus 1 have been resolved (Zhu et al., 2015, Shakeel et al., 2016).

Physicochemical and physical properties

Virions are acid stable. The buoyant density in CsCl is 1.36 g cm-3.

Nucleic acid

Genome (Smits et al., 2013, Hyypia et al., 1992, Ghazi et al., 1998, Niklasson et al., 1999, Joffret et al., 2013): 7,339–7,608 nt (5′-UTR: 710–730 nt; ORF: 6,543–6,753; 3′-UTR: 87–111 nt). The 5′-UTR contains a typical type II IRES. The cre has been identified in the 1AB region for human parechoviruses and is thought to lie within the 3B region of Ljungan viruses.

Genome organization and replication

Genome layout

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

The deduced polyprotein ranges from 2,180–2,250 aa. The polyprotein contains only a single protease (3Cpro). Members of Parechovirus B, C, D possess a 2A protein with NPG↓P motif. all parechoviruses have 2A protein with a H-box/NC motif.

Biology

Human parechoviruses replicate in the respiratory and gastrointestinal tract. Infection is particularly prevalent in infants and young children but it is probably often asymptomatic apart from infections with human parechovirus (HPeV) type 3 which can present with severe neonatal sepsis and central nervous system damage. In addition to respiratory infections and diarrhoea, infections of the central nervous system (encephalitis, meningitis, ataxia) have been reported. HPeV types 1 and 6 have been found in monkeys with diarrhoea, although disease association was not proven. The cytopathology may be unusual in including changes in granularity and chromatin distribution in the nucleus, when viewed in the electron microscope. Ljungan viruses appear to infect predominantly rodents (voles) and have been proposed to infect humans, however, conclusive data is awaited. Some human parechoviruses (types 1, 2, 4, 5 and 6) possess an RGD tri-peptide (towards the carboxy-terminus of 1D) which is involved in integrin receptor-binding. The integrins αvβ3 and αvβ6 have been shown to be the primary receptors for HPeV-1 in A549 cells. Receptor usage for the remaining human parechoviruses and Ljungan viruses is not known. Sebokele virus was detected in mice (Hylomyscus spec.) in the Central African Republic. Ferret parechovirus was detected in rectal swabs of ferrets (Mustela putorius furo).

Antigenicity

Human parechoviruses are divided into 18 genetic types and there is no cross-neutralization between types 1, 2 and 3. There may be a cross-reaction between types 2 and 5, however, the remaining types have not been tested. Ljungan viruses are divided into five genetic types, but antigenic relationships have not been studied. Parechovirus C and D each contain one type.

Derivation of names

Parecho-: from par(a)echo from pará Greek for beside, and echo, the former name of the type species, an acronym for "enteric, cytopathic, human, orphan"

Species demarcation criteria

At least 25 types have been characterized genetically by phylogenetic clustering: Parechovirus A (18 types), Parechovirus B (5 types), Parechovirus C (1 type), Parechovirus D (1 type).

Members of a species of the genus Parechovirus:

  • 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) between members of different Parechovirus species ranges from 0.44–0.63 for P1 and 0.34–0.59 for 3CD.

Member species

Exemplar isolate of the species
SpeciesVirus nameIsolateAccession numberRefSeq numberAvailable sequenceVirus Abbrev.
Parechovirus Ahuman parechovirus 1HarrisS45208NC_038319Complete genomeHPeV-1
Parechovirus Ahuman parechovirus 2Williamson (Ohio/56)AJ005695Complete genomeHPeV-2
Parechovirus Ahuman parechovirus 3A308/99AB084913Complete genomeHPeV-3
Parechovirus Ahuman parechovirus 4K251176-02DQ315670Complete genomeHPeV-4
Parechovirus Ahuman parechovirus 5CT86-6760 (Connecticut/86)AF055846Complete genomeHPeV-5
Parechovirus Ahuman parechovirus 6NII561-2000 (Japan)AB252582Complete genomeHPeV-6
Parechovirus Ahuman parechovirus 7PAK5045EU556224Complete genomeHPeV-7
Parechovirus Ahuman parechovirus 8BR/217/2006EU716175Complete genomeHPeV-8
Parechovirus Ahuman parechovirus 9BAN2004-10902JX219575Partial genomeHPeV-9
Parechovirus Ahuman parechovirus 10BAN2004-10903JX219568Partial genomeHPeV-10
Parechovirus Ahuman parechovirus 11BAN2004-10905JX219574Partial genomeHPeV-11
Parechovirus Ahuman parechovirus 12BAN2004-10904JX219567Partial genomeHPeV-12
Parechovirus Ahuman parechovirus 13BAN2005-10901JX219579Partial genomeHPeV-13
Parechovirus Ahuman parechovirus 14451564/NL/2004FJ373179Partial genomeHPeV-14
Parechovirus Ahuman parechovirus 15BAN-11614JX219573Partial genomeHPeV-15
Parechovirus Ahuman parechovirus 16BAN-11615JX219580Partial genomeHPeV-16
Parechovirus Ahuman parechovirus 17M36/CI/2014KT319121Complete coding genomeHPeV-17
Parechovirus Ahuman parechovirus 18GhanaA29KY931659Partial genomeHPeV-18
Parechovirus BLjunganvirus 187-012AF327920NC_003976Complete genomeLV-1
Parechovirus BLjunganvirus 2145SLAF020541Complete genomeLV-2
Parechovirus BLjunganvirus 3M1146AF538689Complete genomeLV-3
Parechovirus BLjunganvirus 464-7855EU854568Complete genomeLV-4
Parechovirus BLjunganvirus 5Fuz1/Japan/2014LC133331Complete genomeLV-5
Parechovirus CSebokele virusAn/B/1227/dHF677705NC_021482Complete genomeSEBV
Parechovirus Dferret parechovirusferret/MpPeV1/NLKF006989NC_034453Complete genomeFPeV
Parechovirus Eparechovirus E1; falcon parechovirusfalcon/HA18-080/2014/HUNKY645497NC_035779Complete genome
Parechovirus Fparechovirus F1; gecko parechovirusLPWC210215MG600084Complete genome

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

Related, unclassified viruses

Virus name

Accession number

Virus abbreviation

Manhatten parechovirus [rat/NYC-A11/USA/2013]

KJ950935, KJ950936, KJ950913

MPeV

parechovirus-like picornavirus [falcon/HA18_080/2014/HUN]

KY645497

 

Yili teratoscincus roborowskii picornavirus 2 [LPWC210215]

MG600084

 

Virus names and virus abbreviations are not official ICTV designations.

Phylogenetic analysis indicates that these viruses may be members of novel Parechovirus species.