Sequence analysis of the entire RNA genome of a sweet potato chlorotic fleck virus isolate reveals that it belongs to a distinct carlavirus species.

Since the paucity of information on sweet potato chlorotic fleck virus (SPCFV) had precluded its classification, we have determined the complete nucleotide sequence of the single-stranded RNA genome of a Ugandan isolate of SPCFV. The genome is 9104 nucleotides long (excluding the poly(A) tail) and potentially includes six open reading frames (ORFs). Based on genomic organisation and sequence similarity, SPCFV appears to be a member of the genus Carlavirus (family Flexiviridae). However, SPCFV is distantly related to typical carlaviruses, as most of its putative gene products share amino acid sequence identities of <40% with those of typical carlaviruses. Its closest relative is melon yellowing-associated virus, a proposed carlavirus from Brazil, with which it shares ORF5 and ORF6 amino acid sequence identities of 61 and 46%, respectively.