Family Pospiviroidae

Chapter Version: ICTV Ninth Report; 2009 Taxonomy Release

Distinguishing features

Presence of a central conserved region (CCR) and lack of RNA self-cleavage mediated by hammerhead ribozymes. According to the conserved residues there are basically three types of CCRs exemplified by those of PSTVd, apple scar skin viroid (ASSVd) and coleus blumei viroid 1 (CbVd-1). Genera Pospiviroid, Hostuviroid and Cocadviroid share an identical subset of nucleotides within their CCRs, which are, therefore, more closely related between themselves than with the CCRs of members of the genera Apscaviroid and Coleviroid (Figure 2). Replication studies have been done mostly with PSTVd, and the inferred mechanism (see below) is presumed to operate in the other members of the family as well.

Genus Pospiviroid

Type species Potato spindle tuber viroid

Distinguishing features

Circular ssRNAs between 356 and 375 nt (excluding duplications) depending on species and sequence variants. The most stable secondary structure is a rod-like or quasi-rod-like conformation with five domains, a central conserved region (CCR) and a terminal conserved region (TCR) (Figure 2 and Figure 6). Replication, which takes place in the nucleus where the viroid also accumulates, occurs by an asymmetric rolling-circle mechanism since longer-than-unit minus strands have been found in infected tissue (see Figure 3).

Biological properties

Pospiviroids are found world-wide and in a wide range of plants, mostly solanaceous species, but also in other hosts including citrus, avocado and some ornamentals. They can be experimentally transmitted to many other hosts in which symptom expression differs from symptomless to almost lethal. Some members, particularly TPMVd, can be transmitted by aphids under specific ecological conditions. PSTVd is also aphid-transmissible when encapsidated in particles of potato leafroll virus.

List of species in the genus Pospiviroid

Species names are in italic script; names of isolates are in roman script; names of synonyms are in roman script and parentheses. Sequence accession numbers [ ] length in nucleotides { } and assigned abbreviations ( ) are also listed.

List of other related viroids which may be members of the genus Pospiviroid but have not been approved as species

None.

Genus Hostuviroid

Type species Hop stunt viroid

Distinguishing features

A circular ssRNA of 295–303 nt depending on isolates and sequence variants. The most stable secondary structure is a rod-like or quasi-rod-like conformation with five domains, a central conserved region (CCR) similar to that of pospiviroids and cocadviroids, and a terminal conserved hairpin (TCH) (Figure 2). Replication occurs through an asymmetric rolling-circle model since longer-than-unit minus strands have been found in infected tissue (see Figure 3).

Biological properties

HpSVd infects a very broad range of natural hosts and has been reported to be the causal agent of five different diseases. It is distributed worldwide.

List of species in the genus Hostuviroid

Species names are in italic script; names of isolates are in roman script; names of synonyms are in roman script and parentheses. Sequence accession numbers [ ], length in nucleotides { } and assigned abbreviations ( ) are also listed.

List of other related viroids which may be members of the genus Hostuviroid but have not been approved as species

None.

Genus Cocadviroid

Type species Coconut cadang-cadang viroid

Distinguishing features

Circular ssRNAs of 246–301 nt depending on species and sequence variants. The most stable secondary structure is a rod-like or quasi-rod-like conformation with five domains, a central conserved region (CCR) similar to that of pospiviroids and hostuviroids, and a terminal conserved hairpin (TCH) (Figure 2). Single or double cytosine residues occur at a specific locus. The T_R domain is variable as a result of 41, 50 or 55 nt duplications that generate large variants between 287 and 301 nt. As the disease progresses from the early to the medium stages the small forms are modified to the large forms. Dimeric forms of CCCVd occur with their corresponding monomeric forms. Replication most probably occurs through an asymmetric rolling-circle model by analogy with PSTVd (Figure 3). At the subnuclear level, CCCVd is concentrated in the nucleolus with the remainder distributed throughout the nucleoplasm.

Biological properties

CCCVd and CTiVd are lethal to coconut palm, and have a host range restricted to members of the family Arecaceae. CCCVd has a geographic distribution that includes the Philippines, Malaysia and Sri Lanka. CTiVd is found in Guam. HpLVd and CBCVd have broader geographic distributions.

List of species in the genus Cocadviroid

Species names are in italic script; names of isolates are in roman script; names of synonyms are in roman script and parentheses. Sequence accession numbers [ ], length in nucleotides { } and assigned abbreviations ( ) are also listed.

List of other related viroids which may be members of the genus Cocadviroid but have not been approved as species

None.

Genus Apscaviroid

Type species Apple scar skin viroid

Distinguishing features

Circular ssRNAs between 306 and 369 nt depending on species and sequence variants. The most stable secondary structure is a rod-like or quasi-rod-like conformation with five domains, a central conserved region (CCR) and a terminal conserved region (TCR) (see Figure 2). Replication most probably occurs through an asymmetric rolling-circle model by analogy with PSTVd (see Figure 3).

Biological properties

Known natural hosts are confined to genera Malus, Pyrus, Citrus and Vitis. Reported worldwide, particularly those affecting the genera Citrus and Vitis.

List of species in the genus Apscaviroid

Species names are in italic script; names of isolates are in roman script; names of synonyms are in roman script and parentheses. Sequence accession numbers [ ], length in nucleotides { } and assigned abbreviations ( ) are also listed.

List of other related viroids which may be members of the genus Apscaviroid but have not been approved as species

Genus Coleviroid

Type species Coleus blumei viroid 1

Distinguishing features

Circular ssRNAs between 248 and 364 nt depending on species and sequence variants. The most stable secondary structure is a rod-like or quasi-rod-like conformation with five domains and a central conserved region (CCR) different from that of other viroid genera, and a terminal conserved region (TCR) in the two largest members of the genus (see Figure 2). Replication most probably occurs through an asymmetric rolling-circle model by analogy with PSTVd (see Figure 3).

Biological properties

Known hosts are confined to the genus Coleus. Identified in Brazil, Canada and Germany. Seed transmission of CbVd-1 (and presumably CbVd-2 and CbVd-3) is particularly efficient.

Species demarcation criteria in the genus

Recombination events appear to be especially frequent in this genus. In the future, recognition of new species will be based on the standard criteria for all viroids.

List of species in the genus Coleviroid

Species names are in italic script; names of isolates are in roman script. Sequence accessions [ ], length in nucleotides { } and assigned abbreviations ( ) are also listed.

List of other related viroids which may be members of the genus Coleviroid but have not been approved as species

Derivation of names

Viroid: from the name given to the subviral agent of potato spindle tuber disease.

Apsca: from apple scar skin viroid.

Avsun: avocado sunblotch viroid.

Cocad: from coconut cadang-cadang viroid.

Cole: from Coleus blumei viroid 1.

Ela: from eggplant latent viroid.

Hostu: from hop stunt viroid.

Pelamo: from peach latent mosaic viroid.

Pospi: from potato spindle tuber viroid.

Further reading

Journals and books

[1] F. Bussière, J. Ouellet, F. Coté, D. Lévesque, J.P. Perreault., Mapping in solution shows the peach latent mosaic viroid to possess a new pseudoknot in a complex, branched secondary structure. J. Virol. 74 (2000) 2647–2654.

Diener, 1971 T.O. Diener, Potato spindle tuber “virus” IV. A replicating low molecular weight RNA. Virology. 45 (1971) 411–428.

Ding, 2009 B. Ding, The biology of viroid–host interactions. Annu. Rev. Phytopathol. 47 (2009) 105–131.

Elena et al., 2001 S.F. Elena, J. Dopazo, M. De la Peña, R. Flores, T.O. Diener, A. Moya, Phylogenetic analysis of viroid and viroid-like satellite RNAs from plants: a reassessment. J. Mol. Evol. 53 (2001) 155–159.

Flores et al., 2005 R. Flores, C. Hernández, A.E. Martínez de Alba, J.A. Daròs, F. Di Serio, Viroids and viroid–host interactions. Annu. Rev. Phytopathol. 43 (2005) 117–139.

Gas et al., 2007 M.E. Gas, C. Hernández, R. Flores, J.A. Daròs, Processing of nuclear viroids in vivo: An interplay between RNA conformations. PLoS Pathog. 3 (2007) 1813–1826.

Gross et al., 1978 H.J. Gross, H. Domdey, C. Lossow, P. Jank, M. Raba, H. Alberty, H.L. Sänger, Nucleotide sequence and secondary stucture of potato spindle tuber viroid. Nature. 273 (1978) 203–208.

Hadidi et al., 2003 A. Hadidi, R. Flores, J.W. Randles, J.S. Semancik, Viroids. In: A. Hadidi, R. Flores, J.W. Randles, J.S. Semancik, Viroids. CSIRO Publishing, Collingwood, Australia2003.

Keese and Symons, 1985 P. Keese, R.H. Symons, Domains in viroids: evidence of intermolecular RNA rearrangements and their contribution to viroid evolution. Proc. Natl Acad. Sci., U S A. 82 (1985) 4582–4586.

Owens, 2007 R.A. Owens, Potato spindle tuber viroid: The simplicity paradox resolved?. Mol. Plant Pathol. 8 (2007) 549–560.

Zhong et al., 2008 X. Zhong, A.J. Archual, A.A. Amin, B. Ding, A genomic map of viroid RNA motifs critical for replication and systemic trafficking. Plant Cell. 20 (2008) 35–47.

Websites

Subviral RNA Database: http://subviral.med.uottawa.ca.

NCBI Entrez Viral Genomes (includes viroids): http://www.ncbi.nlm.nih.gov/genomes/GenomesHome.cgi?taxid=10239.

Contributed by

Owens, R.A., Flores, R., Di Serio, F., Li, S-F., Pallás, V., Randles, J.W., Sano, T. and Vidalakis, G.