Variability of a portion of RNA 3 containing the coat protein gene of Citrus variegation virus (CVV) using single-strand conformation polymorphism (SSCP)

A portion of RNA 3 of Citrus variegation virus (CVV), comprising part of the intergenic region and the coat protein (CP) gene from eight viral isolates, was amplified by RT-PCR and cloned. The clones were compared for intra and inter-isolate variations by single-strand conformation polymorphism analysis. Some of the results were compared with sequence data previously obtained. The test discriminated between clones differing in as little as 3.2% of the nucleotides. Most isolates included several variants, in some cases with a predominant pattern, which, however, could no longer be recognised in new RT-PCR products obtained 13 months later. This procedure can therefore be used to identify and detect variations between CVV isolates. It is rapid, inexpensive and may reduce the amount of sequencing needed for comparing viral isolates.