Genetic diversity of a natural population of Cucurbit yellow stunting disorder virus

An analysis of nucleotide sequences in five coding and one non-coding genomic regions of 35 Cucurbit yellow stunting disorder virus (CYSDV) isolates collected on a local scale over an 8 year period is reported here. In total, 2277 nt were sequenced for each isolate, representing about 13% of the complete virus genome. Mean nucleotide diversity for the whole population in synonymous positions in the coding regions was 0.00068, whilst in the 5' untranslated region (5' UTR) of genomic RNA2, it was 0.00074; both of these values are very small, compared with estimates of nucleotide diversity for populations of other plant viruses. Nucleotide diversity was also determined independently for each of the ORFs and for the 5' UTR of RNA2; the data showed that variability is not distributed evenly among the different regions of the viral genome, with the coat protein gene showing more diversity than the other four coding regions that were analysed. However, the low variability found precluded any inference of selection differences among gene regions. On the other hand, no evidence of selection associated with host adaptation was found. In contrast, at least a single amino acid change in the coat protein appears to have been selected with time.