Citrus variegation virus:: Molecular variability of a portion of the RNA 3 containing the coat protein gene and design of primers for RT-PCR detection

The coat protein gene and part of the intergenic region of the RNA 3 of several isolates of Citrus variegation virus (CVV) producing either infectious variegation or crinkly leaf symptoms were amplified by RT-PCR, cloned and sequenced. Some isolates were composed of a mixture of sequence variants. The coat protein gene appeared to be highly conserved (lowest similarity among all CVV sequences 93%), especially at the N-terminal, indicating at the molecular level that both types of symptoms are indeed produced by the same virus species. No relationship could be found with the geographic origin. Sequences obtained from isolates producing infectious variegation clustered in a different branch of a dendrogram than those originating from crinkly leaf symptoms. Both clusters could further be distinguished by two parsimonious sites in the coat protein gene. In the short stretch of the intergenic RNA 3 region analysed, a stable hairpin exists in addition to the previously reported hairpin that constitutes the core promoter for the RNA 4 transcription. This second hairpin could also be recognised in the other subgroup 2 Ilarviruses. Surprisingly, at the nucleotide and amino acid levels and in the secondary features of the intergenic region, CVV appeared closer to the other subgroup 2 Ilarviruses than to Citrus leaf rugose virus to which it is serologically related and has been considered to be evolutionary related. Using primers designed for the conserved regions, the virus was detected with a prevalence of 25% and 13% in Portuguese and Moroccan citrus collections. A group of RT-PCR positives was further confirmed by ELISA and biological indexing.