Family Avsunviroidae

Chapter Version: ICTV Ninth Report; 2009 Taxonomy Release

Distinguishing features

Lack of a central conserved region (CCR). RNA self-cleavage is mediated by hammerhead ribozymes in strands of either polarity. Replication studies have been carried out with ASBVd and PLMVd, and the inferred mechanism (see below) is presumed to operate in the other members of the family.

Genus Avsunviroid

Type species Avocado sunblotch viroid

Distinguishing features

A circular ssRNA between 246 and 250 nt depending on isolates and sequence variants. It is unique in having a base composition rich in A+U (62%) in contrast to the other viroids, which are rich in G+C (53–60%). The most stable secondary structure is a rod-like or quasi-rod-like conformation in which neither five domains nor a central conserved region (CCR) can be distinguished. It is soluble in 2 M LiCl as are typical viroids like PSTVd, ASSVd and CbVd-1 which also have most stable secondary structures that are rod-like or quasi-rod-like. Plus and minus strands of ASBVd can form hammerhead structures. Because both single hammerhead structures of ASBVd are thermodynamically unstable, double hammerhead structures have been proposed to operate in the self-cleavage reactions, especially in that of the plus polarity RNA (see Figure 3). Replication occurs through a symmetric rolling-circle model since the minus circular monomer has been found in infected tissue (see Figure 3). ASBVd replicates and accumulates in chloroplasts.

Biological properties

Found naturally only in avocado but it can be experimentally transmitted into other members of the family Lauraceae. Reported in USA, Mexico, Australia, Israel, Spain, South Africa and South America.

List of species in the genus Avsunviroid

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

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

None.

Genus Pelamoviroid

Type species Peach latent mosaic viroid

Distinguishing features

Circular ssRNAs between 337 and 401 nt depending on isolates and sequence variants. The most stable secondary structure is a branched conformation, stabilized by a kissing-loop interaction, in which neither five domains nor a central conserved region (CCR) can be distinguished (Figure 5). RNAs are insoluble in 2 M LiCl. Thermodynamically stable single hammerhead structures can be formed in both strands, and plus and minus monomeric RNAs self-cleave in vitro as predicted by these structures (see Figure 3). Replication most probably occurs by a symmetric rolling-circle mechanism since the PLMVd minus circular monomers have been found in infected tissue (see Figure 3). PLMVd and, most likely, CChMVd, replicate and accumulate in the chloroplast.

Biological properties

PLMVd and CChMVd appear to be restricted to their natural hosts and very closely related species, but some reports indicate that PLMVd naturally infects additional species within and outside the genus Prunus. Recorded in many peach and chrysanthemum-growing areas. Most isolates of PLMVd are non-symptomatic or incite a mosaic, but others, with a specific hairpin insertion of 12 nt, incite an extreme albinism (peach calico). Symptomatic and non-symptomatic isolates of CChMVd differ in the sequence of a hairpin tetraloop.

List of species in the genus Pelamoviroid

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 Pelamoviroid but have not been approved as species

None.

Genus Elaviroid

Type species Eggplant latent viroid

Distinguishing features

A circular ssRNA between 332 and 335 nt depending on isolates and sequence variants. Like most other viroids, ELVd is rich in G+C (57–59%). The most stable secondary structure is a quasi rod-like conformation with bifurcations at both termini. Neither five domains nor a central conserved region (CCR) can be distinguished. Like other viroids having a rod-like or quasi-rod-like conformation, ELVd is soluble in 2 M LiCl. Plus and minus strands of ELVd can form thermodynamically stable hammerhead structures. Because infected tissue contains circular forms of both plus and minus ELVd, replication appears to proceed through a symmetric rolling circle model – presumably in the chloroplast (see Figure 3).

Biological properties

Found naturally in eggplant growing in eastern Spain. No symptoms observed under greenhouse conditions, and host range appears to be restricted. Seed-transmitted at relatively high rates (16–26%), but attempts to transmit ELVd to tomato, chrysanthemum, cucumber and citron were unsuccessful.

List of species in the genus Elaviroid

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

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

None.

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.