A database to support plant pest diagnostic activities

Nature of Plant Viruses and Viroids

Viruses are infectious particles that consist of a DNA or RNA genome surrounded by a protein coat and in some cases a phospolipid membrane. The viral genome encodes for the viral coat protein(s) and proteins involved in replication, movement and transmission. Viroids consist of a circular RNA molecule. This molecule directs its own replication but does not encode for any protein. For gene expression and replication, both viruses and viroids are dependent on the metabolism of their host cells.


For viruses and viroids, the term species means in fact quasispecies. A quasispecies consists of a collection of sequence variants around a consensus sequence. Thus, sequence micro heterogeneity is always present in natural populations (Domingo et al., 1985, Gene 40, 1-8). Moreover, a high mutation rate, especially in the case of single-stranded RNA viruses (the majority of plant viruses), coupled with a very high rate of replication, can potentially lead to rapid change in virus populations. For virus collections, this implies that isolates may change each time they are renewed for maintenance, even in the case of type material.


  • Type isolate: original isolate used to describe a virus or viroid species or strain
  • Reference material: well-defined isolate that represent a virus or viroid species, for which the identity has to be verified again after transmission and propagation
  • Strain: group of isolates belonging to the same lineage, distinct from those of other isolates of the same species bases on molecular and/or biological properties
  • Isolate: population of sequence variants identified to the species level and maintained in its original host or on experimental host(s)

Because of the quasispecies nature of viruses and viroids, it should be kept in mind that these definitions cannot be interpreted as strict as for other organisms.


Domingo E, Martínez-Salas E, Sobrino F, de la Torre JC, Portela A, Ortín J, López-Galindez C, Pérez-Breña P, Villanueva N, Nàjera R, VandePol S, Steinhauer D, DePolo N & Holland J (1985) The quasispecies (extremely heterogeneous) nature of viral RNA genome populations: biological relevance - a review. Gene 40, 1-8