Sequence variability within the 3′-proximal part of the Sweet potato mild mottle virus genome

Summary.

 Sweet potato mild mottle virus (SPMMV) is the type member of the genus Ipomovirus (family Potyviridae) and is only known to occur in East Africa. In Uganda, SPMMV is the third most prevalent virus infecting sweet potato. The sequence variability of SPMMV was studied by cloning and sequencing a 1.8-kb fragment representing the 3′-end of the genome of eight SPMMV isolates collected from different districts of Uganda. Sequence comparisons indicated 85.9–99.9% nucleotide sequence identity and 92.8–100% amino acid sequence similarity for the coat protein (CP) encoding region. The nucleotide sequence identity within the 3′-untranslated region (3′ UTR) was 84.7–100%, and the region was variable in length (303–308 nucleotides) due to some deletions within the 5′-proximal part of the 3′ UTR. Phylogenetic analysis of the CP amino acid sequences revealed significant clustering, indicating the existence of distinguishable sequence variants or strains. The low CP amino acid sequence similarity of SPMMV isolates with other characterised viruses of the family Potyviridae and the unusual putative proteolytic cleavage site at the NIb/CP junction further demonstrate SPMMV as a very distinct virus in the family Potyviridae.