DIFFERENTIATION OF ALLIUM CARLAVIRUSES ISOLATED FROM DIFFERENT PARTS OF THE WORLD BASED ON THE VIRAL COAT PROTEIN-SEQUENCE

Common primers which amplify the 3' terminal genomic RNAs of Allium ca rlaviruses were designed based on the nucleotide sequence of shallot l atent virus (SLV), garlic latent virus (GLV) and garlic common latent virus (GCLV). A total of fifteen cDNAs encoding the coat protein (CP) of the carlaviruses, including the biologically identified isolates SL V, GLV and GCLV as well as viruses from infected Allium plants cultiva ted in different parts of the world, were amplified by RT-PCR with the common primers. The cDNAs were then cloned and sequenced. The predict ed viral CP amino acid sequence as well as the nucleotide sequence rev ealed that SLV and GLV, previously considered as separate viruses on t he basis of their biological and physical properties, belong to the sa me species of the genus Carlavirus. Both viruses are clearly different iated from GCLV. In addition, every SLV and GLV isolate from the Alliu m plants in Taiwan showed characteristic and common variations in thei r CP sequences, suggesting the possible presence of geographical varia nts. However, no apparent sequence variations of SLV and GLV related t o their host plant species, including A. sativum, A. wakegi, A. chinen se, A. fistulosum, A. cepa and A. ampeloprasum, were observed. These f indings suggested that the sequence variations observed in the respect ive virus isolates do not correlate with the specificity of their infe ctivities for Allium species.