Evidence of multiple recombination events between two RNA sequence variants within a Citrus tristeza virus isolate

Analysis of sequence variants of a natural Citrus tristeza virus (CTV) isolate (SY568) revealed that its population was composed of three sequence types: (I) the most frequent type had ≥97.9% nucleotide identity with the sequence predominant in severe CTV isolates from different origins; (II) a second variant, genetically close to the major component of several mild isolates, had ≤85% identity with the first; and (III) several variants (less than 4%) resulted from homologous recombination at one or more sites between sequences I and II. Recombination sites had an AU-rich stretch of 8-89 nucleotides shared by both parental sequences, flanked by GC- and AU-rich regions upstream and downstream, respectively. This context has been suggested as a hot-spot for homologous recombination in other RNA viruses.