Four hundred and forty-eight symptomatic and 638 asymptomatic samples were collected from sweet potato fields throughout Kenya and analysed serologically using antibodies to Sweet potato feathery mottle virus (SPFMV), Sweet potato chlorotic stunt virus (SPCSV), Sweet potato mild mottle virus (SPMMV), Cucumber mosaic virus (CMV), Sweet potato chlorotic fleck virus (SPCFV), Sweet potato latent virus (SwPLV), Sweet potato caulimo-like virus (SPCaLV), Sweet potato mild speckling virus (SPMSV) and C-6 virus in enzyme-linked immunosorbent assays (ELISA). Only SPFMV, SPMMV, SPCSV, and SPCFV were detected. Ninety-two percent and 25% of the symptomatic and asymptomatic plants respectively tested positive for at least one of these viruses. Virus-infected plants were collected from 89% of the fields. SPFMV was the most common and the most widespread, detected in 74% of the symptomatic plants and 86% of fields surveyed. SPCSV was also very common, being detected in 38% of the symptomatic plants and in 50% of the fields surveyed. SPMMV and SPCFV were detected in only 11% and 3% of the symptomatic plant samples respectively. Eight different combinations of these four viruses were found in individual plants. The combination SPFMV and SPCSV was the most common, observed in 22% of symptomatic plants. Virus combinations were rare in the asymptomatic plants tested. Incidence of virus infection was highest (18%) in Kisii district of Nyanza province and lowest (1%) in Kilifi and Malindi districts of Coast province.
In a survey of most sweetpotato-growing areas of Uganda, virus-like diseases were observed in all districts surveyed. Out of 338 fields sampled in 35 of the then 42 districts, 219 (65%) had some plants with symptoms. The most common symptoms included vein clearing, mottling, leaf distortion, yellowing, stunting and leaf strapping. Particularly high viruslike disease incidences (means of 34-86%) were encountered in districts around Lake Victoria and in the Rift Valley in southern and western parts of Uganda; particularly low incidences were encountered in the east and north of Uganda. Using four formats of enzyme-linked immunosorbent assay in combination with immunoelectron microscopy and polymerase chain reaction assays, five viruses were identified. Sweet potato feathery mottle virus (SPFMV) and Sweet potato chlorotic stunt virus (SPCSV) were most commonly detected, being found in about 90% of samples. Sweet potato mild mottle virus at 10%, Sweet potato chlorotic fleck virus (SPCFV) at 8% and Sweet potato caulimo-like virus (SPCaLV) at 0·07% were more rarely detected. Most infections were multiple, SPCSV + SPFMV constituting > 90% of all double infections. Triple infections, involving mainly SPFMV, SPCSV and either SPMMV or SPCFV, and quadruple infections of SPFMV + SPCSV + SPMMV + SPCFV were observed in < 10% of the diseased samples. The identification of SPCaLV is the first evidence of its occurrence in Africa.
Reverse transcriptase (RT)-polymerase chain reaction (PCR) and immunocapture (IC)-RT-PCR protocols were developed and optimized for the sensitive detection of Onion yellow dwarf virus, Leek yellow stripe virus and allexiviruses infecting Allium species. Polyvalence of the designed primers was successfully demonstrated, using samples of dierent plant species and geographic origins. Dierent sample preparation procedures were evaluated for their suitability to provide appropriate PCR templates. IC-PCR, RT-PCR with plant tissue extracts, and RT-PCR with total RNA, proved to be 10 2 ±10 4 times more sensitive than double-antibody sandwich-enzymelinked immunosorbent assay (ELISA). Furthermore, à one step' IC-RT-PCR assay was developed using plant leaf extract as template source, which proved to be 102 times more sensitive than ELISA, and convenient for testing large numbers of leaf samples.
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.
Sweet potato virus 2 (SPV2) is a tentative member of the genus Potyvirus, family Potyviridae. In addition to the type isolate of SPV2 recently characterised in greater detail, twelve additional isolates of this virus were obtained from sweet potato clones originating from China, Portugal, South Africa and Zambia. Sequences of the coat protein (CP) gene and 3' non-translated region (NTR) were determined. Comparisons of the CP gene sequences of these isolates revealed nucleotide and amino acid sequence identities ranging from 81 to 99% and from 86 to 99%, respectively. Phylogenetic analysis of sequences distinguished several groups, which partially correlated with the geographic origin of the isolates, and indicated that some isolates from South Africa and a Zambian isolate are most distinct both in CP and 3'NTR sequences. Host range studies of a selected number of isolates revealed some differences in test plant reactions, which appeared to correlate to some extent with the geographic origin and molecular distinctness of the SPV2 isolates. The results strongly suggest the occurrence of biologically and genetically diverse strains of SPV2.
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