Genus: Cyclovirus


Genus: Cyclovirus

Distinguishing features

Cyclovirus genomes contain two major ORFs encoding the replication-associated protein (Rep) and capsid protein (Cp). . In contrast to members of the genus Circovirus, cycloviruses have the putative ori on the Cp-encoding strand (Rosario et al., 2012). In addition, cyclovirus genomes have an intergenic region (IR) between the 5-end of major ORFs; however, the IR between the 3-ends of these ORFs is smaller than that of genomes representing the genus Circovirus or may be absent (Li et al., 2010, Delwart and Li 2012). Introns have been identified within the ORFs of several cyclovirus genomes, while none have been reported for circoviruses.

Virion

Morphology

Unknown.

Physicochemical and physical properties

Unknown.

Nucleic acid

Cycloviruses exhibit small, circular ssDNA genomes ranging from 1.7 to 1.9 kb.

Proteins

Unknown.

Lipids

Unknown.

Carbohydrates

Unknown.

Genome organization and replication

Cyclovirus genomes contain two major ORFs encoding the Rep and Cp (Figure 1.Cyclovirus) (Rosario et al., 2017). Although the virion strand has not be experimentally demonstrated for cycloviruses, knowledge from other eukaryotic Rep-encoding ssDNA viruses suggests that the strand containing the nonanucleotide motif is encapsidated (Rosario et al., 2012). Since the putative cyclovirus ori and predicted Rep share conserved features with members of the genus Circovirus, cycloviruses are also thought to replicate through rolling circle replication (RCR).  Similar to circoviruses, the putative cyclovirus ori contains the canonical nonanucleotide motif ‘NAGTATTAC’ located at the apex of a potential stem-loop structure found between the 5ʹ-ends of major ORFs. In addition, the Rep contains endonuclease and helicase domains with RCR and SF3 motifs similar to those identified in circovirus Reps. These conserved motifs include RCR motifs I [FT(L/W)NN], II [(P/x)HLQG] and III [Y(C/l)(S/x)K] and SF3 helicase motifs Walker-A [G(P/x)(P/t)(G/x)xGKS], Walker-B [uuDDF], and motif C [uTS(N/e)], where ‘‘x’’ represents any type of residue and ‘‘u’’ represents a hydrophobic amino acid (i.e., F, I, L, V, M). Moreover, putative Rep-binding domains characterized by iterative sequences near the stem-loop structure have been identified for some cyclovirus genomes (Dayaram et al., 2013).

Figure 1.Cyclovirus. Genome schematics illustrate the major open reading frames (ORFs) characteristic of members of the Circoviridae family. Members of the family Circoviridae, including the Circovirus and Cyclovirus genera, have two major ORFs encoding replication-associated (Rep) and capsid (Cp) proteins as well as a conserved nonanucleotide motif marking the origin of replication. The nonanucleotide motif sequence is depicted through sequence probability logos generated in Weblogo 3 (Crooks et al., 2004). Note that the orientation of major ORFs relative to the nonanucleotide motif differs between genomes representing the Circovirus and Cyclovirus genera. The rep of members of the Cyclovirus type species, Human associated cyclovirus 8  is interrupted by an intron. Although the presence of introns has been observed in various cyclovirus genomes, this has not been reported for circoviruses. Figure reprinted with permission of Springer from Archives of Virology, “Revisiting the taxonomy of the family Circoviridae: establishment of the genus Cyclovirus and removal of the genus Gyrovirus”, doi: 10.1007/s00705-017-3247, Rosario, K., Breitbart, M., Harrach, B., Segales, J., Dewart, E., Biagini, P., Varsani, A. © Springer-Verlag Wien 2017 (Rosario et al., 2017).

Antigenicity

Unknown.

Biology

Cyclovirus genomes were originally discovered in primate stool samples and meat products from a diverse range of animals (camels, chickens, cows, goats, sheep) (Li et al., 2010, Delwart and Li 2012). However, cyclovirus genomes have now been reported from various types of human samples other than faeces, including cerebrospinal fluid, blood serum, and respiratory secretions (Smits et al., 2013, Tan le et al., 2013, Phan et al., 2014, Phan et al., 2015). Additionally, cycloviruses have been detected in samples from a wide range of mammalian and insect species (Rosario et al., 2017). Since genomes belonging to the genus Cyclovirus have only been identified through sequence-based analyses (i.e., degenerate PCR and metagenomic sequencing), definitive hosts and biology are largely unknown.

Species demarcation criteria

The species demarcation threshold is 80% genome-wide nucleotide sequence identity based on pairwise identity distribution analysis (Figure 2.Cyclovirus) (Rosario et al., 2017).

Figure 2.Cyclovirus. Distribution of pairwise identities among members of the genus Cyclovirus (purple bars; left) and the genus Circovirus (blue bars; right). Plots reflect pairwise identities based on calculations for the complete genome sequences (top) as well as the replication-associated (rep; middle) and capsid (cp; bottom) genes. All pairwise identities were calculated using the Sequence Demarcation Tool version 1.2 (Muhire et al., 2014) with the MUSCLE alignment algorithm (Edgar 2004). Figure reprinted with permission of Springer from Archives of Virology, “Revisiting the taxonomy of the family Circoviridae: establishment of the genus Cyclovirus and removal of the genus Gyrovirus”, doi: 10.1007/s00705-017-3247, Rosario, K., Breitbart, M., Harrach, B., Segales, J., Dewart, E., Biagini, P., Varsani, A. © Springer-Verlag Wien 2017 (Rosario et al., 2017).

Member Species

SpeciesVirus name(s)Exemplar isolateExemplar accession numberExemplar RefSeq numberAvailable sequenceOther isolatesOther isolate accession numbersVirus Abbreviation(s)Isolate Abbreviation
Bat associated cyclovirus 1bat faeces associated cyclovirus 1GF/4cHM228874NC_034547Complete genomeBatACyV1
Bat associated cyclovirus 10bat associated cyclovirus 10POA/2012/6KM382270NC_025792Complete genomeBatACyV10
Bat associated cyclovirus 11bat associated cyclovirus 11BtMspp/CV/GD2012KJ641717Complete genomeBatACyV11
Bat associated cyclovirus 12bat associated cyclovirus 12POA/2012/IIKM382269NC_025791Complete genomeBatACyV12
Bat associated cyclovirus 13bat associated cyclovirus 13BtPa/CV/2/NX2013KJ641728Complete genomeBatACyV13
Bat associated cyclovirus 14bat associated cyclovirus 14Tbat7H/103699KT732785Complete genomeBatACyV14
Bat associated cyclovirus 15bat associated cyclovirus 15Tbat/H/88317KT732786Complete genomeBatACyV15
Bat associated cyclovirus 16bat associated cyclovirus 16Tbat/K/103923KT732787Complete genomeBatACyV16
Bat associated cyclovirus 2bat faeces associated cyclovirus 2YN/BtCV/2JF938079Complete genomeBatACyV2
Bat associated cyclovirus 3bat faeces associated cyclovirus 3YN/BtCV/4JF938081Complete genomeBatACyV3
Bat associated cyclovirus 4bat faeces associated cyclovirus 4YN/BtCV/5JF938082Complete genomeBatACyV4
Bat associated cyclovirus 5bat associated cyclovirus 5CyCV/TBHQ738637NC_014929Complete genomeBatACyV5
Bat associated cyclovirus 6bat associated cyclovirus 6BtRp/CV/3/GD2012KJ641712Complete genomeBatACyV6
Bat associated cyclovirus 7bat associated cyclovirus 7BtRf/CV/24/YN2010KJ641740Complete genomeBatACyV7
Bat associated cyclovirus 8bat associated cyclovirus 8BtRp/CV/52/GD2012KJ641715Complete genomeBatACyV8
Bat associated cyclovirus 9bat associated cyclovirus 9BtTp/CV/2/GX2012KJ641720Complete genomeBatACyV9
Bovine associated cyclovirus 1bovine cyclovirusPKbeef23HQ738634Complete genomeBoACyV1
Chicken associated cyclovirus 1chicken associated cyclovirus 1NGchicken8HQ738643Complete genomeChickACyV1
Chimpanzee associated cyclovirus 1chimpanzee faeces associated cyclovirusChimp11GQ404849Complete genomeChimpACyV1
Cockroach associated cyclovirus 1Florida wood cockroach cyclovirusGS140JX569794NC_020206Complete genomeCroACyV1
Dragonfly associated cyclovirus 1dragonfly cyclovirus 1TO/DFpB1/2010JX185419Complete genomeDfACyV1
Dragonfly associated cyclovirus 2dragonfly cyclovirus 2FL1/NZ38/2010JX185422NC_023869Complete genomeDfACyV2
Dragonfly associated cyclovirus 3dragonfly cyclovirus 3FL2/5E/2010JX185424NC_023868Complete genomeDfACyV3
Dragonfly associated cyclovirus 4dragonfly cyclovirus 4US/DFKWGX/2012KC512916Complete genomeDfACyV4
Dragonfly associated cyclovirus 5dragonfly cyclovirus 5PR/6E/2010JX185426NC_023866Complete genomeDfACyV5
Dragonfly associated cyclovirus 6dragonfly cyclovirus 6US/DFKWGX/2012KC512918Complete genomeDfACyV6
Dragonfly associated cyclovirus 7dragonfly cyclovirus 7NZ/DFNZ3/2011KC512919Complete genomeDfACyV7
Dragonfly associated cyclovirus 8dragonfly cyclovirus 8AU/DFB007B/2012KC512920Complete genomeDfACyV8
Feline associated cyclovirus 1feline cyclovirusKM017740NC_024700Complete genomeFeACyV1
Goat associated cyclovirus 1goat cyclovirusPKgoat11HQ738636NC_014928Complete genomeGoACyV1
Horse associated cyclovirus 1horse cyclovirusEqu1KR902499Complete genomeHoACyV1
Human associated cyclovirus 1human associated cyclovirus 1PK5510GQ404847Complete genomeHuACyV1
Human associated cyclovirus 10human associated cyclovirus 107078AKF726984NC_023874Complete genomeHuACyV10
Human associated cyclovirus 11human associated cyclovirus 11SL/108277KJ831064Complete genomeHuACyV11
Human associated cyclovirus 12human associated cyclovirus 12IECSF08KU053483Complete genomeHuCyC12
Human associated cyclovirus 2human associated cyclovirus 2PK5006GQ404844Complete genomeHuACyV2
Human associated cyclovirus 3human associated cyclovirus 3PK5222GQ404846Complete genomeHuACyV3
Human associated cyclovirus 4human associated cyclovirus 4TN25GQ404857Complete genomeHuACyV4
Human associated cyclovirus 5human associated cyclovirus 5PK5034GQ404845Complete genomeHuACyV5
Human associated cyclovirus 6human associated cyclovirus 6NG12GQ404854Complete genomeHuACyV6
Human associated cyclovirus 7human associated cyclovirus 7NG14GQ404855Complete genomeHuACyV7
Human associated cyclovirus 8human associated cyclovirus 8hcf2KF031466Complete genomeHuACyV8
Human associated cyclovirus 9human associated cyclovirus 9VS5700009KC771281NC_021568Complete genomeHuACyV9
Mouse associated cyclovirus 1mouse associated cyclovirus 1Cyclo-sf1KT878836NC_031755Complete genomeMoACyV1
Squirrel associated cyclovirus 1squirrel cyclovirusP/NUBS/2014LC018134NC_027530Complete genomeSqACyV1

Virus names, the choice of exemplar isolates, and virus abbreviations, are not official ICTV designations.
Download GenBank/EMBL query for sequences listed in the table here.

Derivation of names

Cyclo: from cyclo, latinised form of kyklos in Greek, meaning a circle, wheel or ring