Two paths of sequence divergence in the citrus tristeza virus complex

Comparison of a sampling of complementary DNA (cDNA) sequences from the Flo rida citrus tristeza virus (CTV) isolates T3 and T30 to the sequence of the genome of the Israeli isolate VT showed a relatively consistent or symmetr ical distribution of nucleotide sequence identity in both the 5' and 3' reg ions of the 19.2-kb genome. In contrast, comparison of these sequences to t he sequence of isolate T36 showed a dramatic decrease in sequence identity in the 5' proximal 11 kb of the genome. A cDNA probe derived from this regi on of the T36 genome hybridized to double-stranded RNA (dsRNA) of only 3 of 10 different Florida CTV isolates. In contrast, analogous probes from T3 a nd T30 hybridized differentially to the seven isolates not selected by the T36 probe. Primers designed from cDNA sequence for polymerase chain reactio n (PCR) selectively amplified these 10 isolates, allowing them to be classi fied as similar to T3, T30, or T36. In contrast, individual cDNA probes der ived from the 3' terminal open reading frames of the T3, T30, and T36 genom es all hybridized to dsRNA from all Florida CTV isolates tested, and PCR pr imers designed from the T36 capsid protein gene sequence amplified successf ully from all isolates. Based on these data, we propose the creation of two groups of CTV, exemplified by the VT and T36 isolates, respectively. Isola tes in the VT group, which include isolates VT, T3, and T30, have genomic s equence divergence that is relatively constant in proportion and distributi on throughout the genome, and candidate isolates for that group could be co nsidered strains of the same virus. The T36 group is differentiated from th e VT group by the highly divergent 5' genomic sequence. This 5' region of t he CTV genome, thus, can serve as a measure of the extent of sequence diver gence and can be used to define new groups and group members in the CTV com plex.