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

Abstract

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.

Host Range, Purification, and Genetic Variability in Sweet potato chlorotic fleck virus

“…A single protein band of about 33 kDa was observed in SDS-PAGE. This size is similar to previous estimates (4,15) and falls within the range (31 to 36 kDa) obtained for other carlaviruses (1,2). During SPCFV purification, the CsCl gradients formed one major and a minor band above and below the virus band.…”

“…However, SPCFV remained unclassified until complete sequencing of a Ugandan isolate of SPCFV revealed that it has a singlestranded, positive-sense RNA genome consisting of 9,104 nucleotides (nt) containing six putative open reading frames (ORFs) and sharing highest nucleotide and amino acid sequence similarities with viruses of the genus Carlavirus in the family Flexiviridae (4). The closest relative of SPCFV is Melon yellowing-associated virus (MYaV), a whitely-transmitted carlavirus from Brazil (25), with which it shares ORF5 and ORF6 amino acid sequence similarities of 61 and 46%, respectively.…”

Mixed Infections of Four Viruses, the Incidence and Phylogenetic Relationships of Sweet Potato Chlorotic Fleck Virus (Betaflexiviridae) Isolates in Wild Species and Sweetpotatoes in Uganda and Evidence of Distinct Isolates in East Africa

“…no. AY461421) is 9104 nucleotides (nt) long, excluding the 3′-terminal poly(A) tail, and contains six open reading frames (ORFs) [67]. ORF5 encodes the coat protein (CP).…”

Analysis of the triple gene block sequence in an important melon pathogen, Melon yellowing-associated virus

“…All three TGB sequences of MYaV formed a clade with SPCFV (Fig. 2), as did the CP sequence (as shown in Aritua et al 2007), and all trees exhibited a clear relationship between MYaV sequence and various carlavirus sequences. The amino acid sequences of MYaV and SPCFV shared 51% identity for TGBp1, 68% for TGBp2, and 30% for TGBp3.…”

“…It is more closely related to SPCFV and Narcissus symptomless virus (NSV), both unassigned species but ones that will most likely be accepted as definite carlavirus members. Although the biological characterization of these two species are not well elucidated (Aritua et al 2007;Chen et al 2006), the clustering of TGB1p of MYaV, SPCFV, NSV and CPMMV suggests that they share a common biological feature, for instance, the vector type. The complete genome sequence of MYaV is essential to establish its taxonomic position, however, because of difficulties in virus maintenance in greenhouse conditions and the low virus concentration in infected plants, the remaining 5 0 end genomic region is still undetermined.…”