Variability and evolution of the plant RNA virus pepper mild mottle virus

The RNA genomes of 26 isolates of pepper mild mottle virus were compared by their RNase T1 fingerprints. Twenty-three isolates came from epidemic outbreaks in greenhouse-grown peppers in Almería (southeastern Spain) from 1983 to 1987; three other isolates, from 1980, came from Sicily (Italy) and Zaragoza (central Spain). The 26 fingerprints can be classified into 10 different types; nucleotide substitution rates show them to be very similar. Cluster and cladistic analyses group types corresponding to the Almería isolates separate from those of 1980. Intraannual and interannual nucleotide differences were estimated. An evolutionary model for pepper mild mottle virus built on these data indicates a highly stable population, maintaining its diversity through time, with a main prevailing haplotype from which closely related variants arise that do not replace it. This high stability could be due to strong functional constraints on variation, as suggested by the high proportion of invariant versus polymorphic sites in fingerprints.