Population structure and genetic diversity within California Citrus tristeza virus (CTV) isolates

The Closterovirus, Citrus tristeza virus (CTV) is an aphid-borne RNA virus that is the causal agent of important worldwide economic losses in citrus. Biological and molecular variation has been observed for many CTV isolates. In this work we detected and analyzed sequence variants (haplotypes) withi n individual CTV isolates. We studied the population structure of five Cali fornia CTV isolates by single strand conformation polymorphism (SSCP) analy sis of four CTV genomic regions. Also, we estimated the genetic diversity w ithin and between isolates by analysis of haplotype nucleotide sequences. M ost CTV isolates were composed of a population of genetically related varia nts (haplotypes), one being predominant. However in one case, we found a hi gh nucleotide divergence between haplotypes of the same isolate. Comparison of these haplotypes with those from other isolates suggests that some CTV isolates could have arisen as result of a mixed infection of two divergent isolates.