Polymorphism of the 5 ' terminal region of Citrus tristeza virus (CTV) RNA: Incidence of three sequence types in isolates of different origin and pathogenicity

Sequences of the 5' terminal region of the genomic RNA from eight isolates of Cirrus tristeza virus (CTV) were previously classified into three types (I, II and III), with intragroup sequence identity higher than 88% and inte rgroup sequence identity as low as 44%. Sequencing of an additional 58 cDNA clones from 15 virus isolates showed that all sequences could be unequivoc ally assigned to one of the three types previously established. The relativ e frequency of each sequence type was assessed in 57 CTV isolates of differ ent geographic origin and pathogenic characteristics by RT-PCR with sets of type-specific primers using CTV dsRNA as template. None of the isolates yi elded amplification of the type I or II sequences alone, but in 19 of them type III sequences were the only amplification product detected. Within iso lates containing more than one sequence type, eight had type II and III seq uences, ii had type I and III sequences, and 19 had sequences of the three types. Isolates containing only type III sequences caused only mild to mode rate symptoms in Mexican lime, an indicator species for most CTV isolates, whereas isolates causing stem pitting in sweet orange an/or grapefruit, gen erally contained sequences type II. None of the sequence types could be tra ced to a precise geographic area, as all types were detected in isolates fr om at least nine of the 12 countries from which samples were taken.