Genetic variation of Citrus tristeza virus isolates from California and Spain: Evidence for mixed infections and recombination

mWe examined the population structure and genetic variation of four genomic regions within and between 30 Citrus tristeza virus (CTV) isolates from Sp ain and California. Our analyses showed that most isolates contained a popu lation of sequence variants, with one being predominant. Four isolates show ed two major sequence variants in some genomic regions. The two major varia nts of three of these isolates showed very low nucleotide identity to each other but were very similar to those of other isolates, suggesting the poss ibility of mixed infections with two divergent isolates. Incongruencies of phylogenetic relationships in the different genomic regions and statistical analyses suggested that the genomes of some CTV sequence variants originat ed by recombination events between diverged sequence variants. No correlati on was observed between geographic origin and nucleotide distance, and thus from a genetic view, the Spanish and Californian isolates analyzed here co uld be considered members of the same population.