Reassessment of the Columnea latent viroid (CLVd) Taxonomic Classification

Columnea latent viroid (CLVd) is one of the Pospiviroid family members and its naked circular RNA genome typically forms native “rod-like” secondary structures. In this work, the CLVd taxonomy was re-evaluated based on sequence similarity and phylogenetic analysis, and symptom development and disease severity evaluation of four selected CLVd isolates, on a range of host species. The phylogenetic analysis showed that all CLVd isolates were clustered into five distinct clades: (I) severe isolates originally found in tomato crops in Thailand, (II) ornamental isolates, (III) mild isolates originally found in tomato crops in Thailand, and two clades (IV and V) containing mild isolates mainly originating from tomato crops in European countries, with different virulence levels on several hosts. The sequence analysis demonstrated that some CLVd isolates have a sequence similarity of less than 90% within the species taxon, as well as distinct biological characteristics (symptom development and virulence), both important ICTV criteria for viroid classification. For these reasons, we propose that CLVd should be re-classified in at least three main taxonomic lineages: a “CLVd-tomato Asian lineage” (I), a “CLVd-tomato European lineage” (IV) and a “CLVd-ornamental European lineage” (II), plus two minor lineages (III and V), fitting the ICTV criteria.