Distribution of grapevine leafroll associated virus-3 variants in South African vineyards

Three genetic variants of Grapevine leafroll-associated virus 3 (GLRaV-3) were identified from vineyards of the Western Cape, South Africa. In a previous study, three full genome sequences of isolates representing each of the variant groups were determined. The three variant groups were represented by accessions 621, 623 and PL-20, of variant groups I, II and III respectively. A specific single strand conformation polymorphism (SSCP) profile was assigned to each variant which was used as a quick, reliable detection and differentiation method. In this study we analysed the occurrence of these three GLRaV-3 variants in mother blocks in different cultivars and from different vine growing regions using SSCP. The majority of the plants studied, were infected with the group II variant, similar to isolates 623 and GP18. The distribution of three GLRaV-3 variants within a spatio-temporally recorded cluster of diseased plants was studied by means of SSCP profile analysis of ORF5 amplified PCR products. We showed that different GLRaV-3 variants are transmitted to adjacent plants in an infection cluster. Results showed that, in some leafroll disease clusters, the variant that was present in the original GLRaV-3 infected plant of a cluster was transmitted to adjacent plants in a row and across rows.     

Genotypic diversity of Citrus tristeza virus within red grapefruit,in a field trial site in South Africa

European Journal of Plant Pathology - Grapefruit cultivars (Citrus paradisi Macfad.) are extremely sensitive to Citrus tristeza virus (CTV) infections and are pre-immunized with mild-strain...     

Survey of <Emphasis Type="Italic">Citrus tristeza virus</Emphasis> (CTV) diversity in pigmented <Emphasis Type="Italic">Citrus x paradisi</Emphasis> (Macfad.) (Grapefruit) trees in north-western Argentina

Citrus tristeza virus (CTV) is the most severe viral pathogen of citrus and elicits a wide range of devastating disease symptoms. Grapefruit cultivars (Citrus x paradisi) are the most sensitive among citrus to the effects of CTV infections. Grapefruit is an important crop within the north-western Argentine citrus industry; however, production has been affected by CTV stem-pitting. In general, CTV diversity within South America is poorly studied, with data on grapefruit CTV populations being particularly limited. In this study, 50 samples were collected from Star Ruby, Henninger’s Ruby and Ruben Pink cultivars, within the provinces of Tucumán, Salta and Jujuy in north-western Argentina. The CTV p33 gene was PCR amplified and the resulting amplicons sequenced with Sanger sequencing. A subset of these amplicons was sequenced with Illumina MiSeq sequencing. AT-1-like sequences were dominant within the majority of populations, as determined by Sanger sequencing, followed by sequences clustering within the unresolved Kpg3/SP/T3 and RB clades. Sequencing by Illumina MiSeq confirmed this, as well as detecting minor sequence types within the HA 16–5, VT, B165 and A18 clades.     

Survey for viruses affecting maize along the major grain transport route between Gauteng and KwaZulu-Natal in South Africa

European Journal of Plant Pathology - The recent introduction of maize chlorotic mottle virus (MCMV) and spread of the resulting maize lethal necrosis disease (MLN) in East Africa presents a threat...     

Alternative hosts and seed transmissibility of soybean blotchy mosaic virus

Soybean blotchy mosaic virus (SbBMV) is an important virus of soybean in the warmer regions of South Africa. The presence of the virus is associated with blotchy mosaic symptoms on soybean leaves and significant annual yield losses. The virus is a member of the genus Cytorhabdovirus and persists between soybean growing seasons. In this study, multiple specimens of indigenous tree species, other crops and herbaceous weeds surrounding soybean fields with high disease incidences of SbBMV were tested for the presence of SbBMV by RT-PCR in order to determine whether the presence of alternative hosts facilitates the seasonal carry-over of the virus. Commercial soybean cultivars commonly grown in the region were also evaluated for seed transmissibility of the virus. A total of 487 accessions representing 27 different species were screened and one accession each of Flaveria bidentis, Lamium amplexicaule and Gymnosporia buxifolia tested positive for the presence of SbBMV and may serve as possible alternative hosts of SbBMV, allowing over-wintering of the virus when soybean is absent. Symptoms associated with SbBMV infection were not present in any of the 2, 829 seedlings collected from naturally infected SbBMV plants, and none of the 21 seedlings showing various abnormalities and tested by RT-PCR were positive. SbBMV does not appear to be seed transmissible in soybean at an incidence above that which numbers screened would have detected the virus. It was concluded that the presence of alternative plant hosts, functioning as viral reservoirs during the soybean off-season might allow for the re-emergence of the disease early in the soybean production season each year. Future work will investigate the role of Peragallia caboverdensis, the leafhopper vector of SbBMV, and specifically the possible propagative transmission of the virus in the persistence of the disease.     

Diversity of <Emphasis Type="Italic">Citrus tristeza virus</Emphasis> populations in commercial grapefruit orchards in Southern Africa,determined using Illumina MiSeq technology

Grapefruit cultivars are highly sensitive to CTV infections and in order to increase their productive lifespan, the Southern African citrus industry makes use of cross-protection. However, the breakdown of cross-protection is commonly observed in commercial grapefruit plantings. In order to determine which genotypes of CTV are associated with commercial Citrus x paradisi (Macfad.) cv. ‘Star Ruby’ in Southern Africa, 192 samples, pre-immunised with the GFMS 12 population, were collected from the grapefruit production areas of Hoedspruit, Malelane, Swaziland, Northern Cape, Sundays River Valley and Nkwalini Valley and six samples from non-pre-immunised plants in Letsitele as well as three samples from greenhouse maintained plants harbouring populations derived from the original GFMS 12 source. The p33 gene was amplified with direct Sanger sequencing performed on the resulting amplicons. A subset of 92 samples randomly selected and p33 gene amplicons subjected to Illumina MiSeq amplicon sequencing. High levels of CTV diversity were observed between and within orchards. Most populations were made up of a dominant component with several minor sequence types. Resistance Breaking (RB) sequences were most numerous, especially in recently planted orchards and present within all of the populations. The Kpg3/SP/T3 group appeared to be the second most prevalent, with increased prevalence in older orchards. Sequences mapping to HA 16–5, VT, AT-1, T36, Taiwan-Pum/M/T5 and T30, were represented sporadically within numerous collection sites.     

Widespread occurrence of “Candidatus liberibacter africanus subspecies capensis” in Calodendrum capense in South Africa

Recent studies in citrus orchards confirmed that Citrus Greening, a heat sensitive citrus disease, similar to Huanglongbing (HLB), is associated with the presence of ??Candidatus Liberibacter africanus?? (Laf) in South Africa. Neither ??Candidatus Liberibacter asiaticus?? (Las), associated with HLB, ??Candidatus Liberibacter americanus??, nor ??Candidatus Liberibacter africanus ssp. capensis?? (LafC), previously detected in the Western Cape, South Africa on an indigenous Rutaceous species, Calodendrum capense (L. f.) Thunb. (Cape Chestnut), were detected in citrus. The current study aims to determine the potential role of C. capense in the epidemiology of Citrus Greening in South Africa and whether LafC poses a risk to citriculture. A total of 278?C. capense samples were collected throughout South Africa and tested for Liberibacters using real-time PCR. While LafC was found in 100 samples, distributed from all areas where collected, no evidence of Laf infection in any sample was found . The identity of the LafC present was confirmed by sequencing the amplicon derived from conventional PCR of the ?-operon of the ribosomal protein gene region of the first 17 infected trees found and of a representative sample from each district. The Liberibacter status of 44?C. capense and 272 citrus (Midnight Valencia) trees growing in close proximity to each other for over 15?years was determined. Out of 44?C. capense specimens, 43 were infected with LafC, but none of the citrus trees were infected with LafC. Based on the results of this it appears that natural spread of LafC to citrus does not occur.     

Characterization of a new potyvirus isolated from peanut (Arachis hypogaea)

During a survey of viruses of peanuts in South Africa a mechanically transmissible virus was isolated from a plant exhibiting chlorotic ringspots and blotches on the leaves. Typical potyvirus-like flexuous particles were detected by electron microscope examination. Pinwheel-shaped and laminated inclusions in ultrathin sections, reaction with a monoclonal antibody directed to a potyvirus common epitope, a single 33 kDa coat protein and aphid transmission using Myzus persicae all confirmed that the virus was a subdivision II member of the Potyviridae. Host range studies suggested that the virus was none of the previously reported potyviruses of peanuts or of subdivision II potyviruses. The serological relationships of the virus were studied using a range of 17 antisera to potyviruses in ELISA and immunosorbent electron microscopy (ISEM). The isolate reacted weakly with antisera to plum pox virus and bean yellow mosaic virus in ISEM only. Nucleotide sequence of a 624 bp DNA product was obtained following immuno-capture with a potyvirus common epitope antiserum, cDNA synthesis and PCR amplification with potyvirus specific primers which amplify the 3' untranslated region and a part of the coat protein gene. The sequence was only distantly related to a number of potyviruses, whether amino acid or nucleotide sequences were used for comparisons. It is proposed that the virus be named peanut chlorotic blotch virus and be accepted as a new member of the genus Potyvirus in the family Potyviridae.     

Detection and diversity of grapevine virus L from a Vitis cultivar collection in Stellenbosch,South Africa

European Journal of Plant Pathology - A total of 229 Vitis cultivars were sampled from a collection in Stellenbosch, Western Cape, South Africa and subjected to an RNAtag-seq workflow and Illumina...     

Characterization of Tomato curly stunt virus: a new tomato‐infecting begomovirus from South Africa

The biological and molecular characterization of a virus recognized as a distinct begomovirus species, Tomato curly stunt virus (ToCSV), first observed in South Africa in 1997, is reported here. Whitefly‐transmission and host‐range studies were carried out using a Bemisia tabaci colony identified as the B‐biotype. The experimental host range of ToCSV spanned primarily species in the Solanaceae and Fabaceae. The complete ToCSV genome (2·766 kb) was amplified by PCR, cloned, and the DNA sequence determined. Phylogenetic analysis revealed that ToCSV was most closely related to Tobacco leaf curl Zimbabwe virus (TbLCZV), at 84% nucleotide identity, indicating that ToCSV is a new species in the genus Begomovirus that is probably endemic to southern Africa. The ToCSV genome sequence contained all of the hallmark coding and non‐coding features characteristic of other previously recognized monopartite begomoviruses. ToCSV is only the second begomovirus described from southern Africa that infects solanaceous species. Neither a begomoviral DNA‐B component nor a satellite‐like DNA molecule was detected by PCR in extracts of ToCSV‐infected plants.