Carlavirus biodiversity in horticultural host plants: Efficient virus detection and identification combining electron microscopy and molecular biology tools

Biodiversity within virosphere comprising virus-host, virus-vector, virusvirus and virus-viroid interactions is illustrated by the genus Carlavirus. They belong to the family of Betaflexiviridae with the type member Carnation latent virus (CLV). 43 members are listed by the latest ICTV taxonomy report (Adams et al., 2012). Samples obtained in Germany in 2006 to 2012 included monocot host plants comprising the families Alliaceae and Convallariaceae as well as dicot host plants of the families of Cactaceae, Ericaceae, Passifloraceae, Ranunculaceae, Scrophulariaceae and Solanaceae. Twelve different carlaviruses have been identified, for two of which no published record for Germany existed so far. In Alliaceae, Cactaceae, Ranunculaceae and Solanaceae mixed infections were frequent. Those consisted of two different carlaviruses or of Carlavirus accompanied by Poty- or Allexi-, or Potex- or Tobamo-, or Cucumovirus infection. Thus, symptom expression was variable and visual diagnosis was limited. Additional methods were employed to increase reproducibility and to generate reliable results. Synergy of electron microscopy and molecular biology tools were used to improve virus detection. Doing so we obtained evidence for the presence of three different isolates of Shallot latent virus in Allium sativum and for at least three Potato virus M isolates in Solanaceae. In addition, we identified the presence of Helleborus net necrosis virus and Blueberry scorch virus in Germany.