Distribution and genetic diversity of Coguvirus eburi in South African citrus and the development of a real-time RT-PCR assay for citrus-infecting coguviruses

Plant Disease ◽  
2022 ◽  
Author(s):  
Rochelle de Bruyn ◽  
Rachelle Bester ◽  
Glynnis Cook ◽  
Chanel Steyn ◽  
Johannes Hendrik Jacobus Breytenbach ◽  
...  
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
Real Time ◽  
South African ◽  
High Throughput Sequencing ◽  
Rna Virus ◽  
Citrus Paradisi ◽  
Virus Elimination ◽  
Shoot Tip Grafting ◽  
Citrus Production

Citrus virus A (CiVA), a novel negative-sense single-stranded RNA virus assigned to the species Coguvirus eburi in the genus Coguvirus, was detected in South Africa with the use of high-throughput sequencing (HTS) after its initial discovery in Italy. CiVA is closely related to citrus concave gum-associated virus (CCGaV), recently assigned to the species Citrus coguvirus. Disease association with CiVA is however incomplete. CiVA was detected in grapefruit (Citrus paradisi Macf.), sweet orange (C. sinensis (L.) Osb.) and clementine (C. reticulata Blanco) in South Africa and a survey to determine the distribution, symptom association and genetic diversity was conducted in three provinces and seven citrus production regions. The virus was detected in ‘Delta’ Valencia trees in six citrus production regions and a fruit rind symptom was often observed on CiVA-positive trees. Additionally, grapefruit showing symptoms of citrus impietratura disease were positive for CiVA. This virus was primarily detected in older orchards that were established prior to the application of shoot tip grafting for virus elimination in the South African Citrus Improvement Scheme. The three viral encoded genes of CiVA isolates from each cultivar and region were sequenced to investigate sequence diversity. Genetic differences were detected between the ‘Delta’ Valencia, grapefruit and clementine samples, with greater sequence variation observed with the nucleocapsid protein (NP) compared to the RNA-dependent RNA polymerase (RdRp) and the movement protein (MP). A real-time detection assay, targeting the RdRp, was developed to simultaneously detect citrus infecting coguviruses, CiVA and CCGaV, using a dual priming reverse primer to improve PCR specificity.

scholarly journals Privacy in wearable health devices: How does POPIA measure up?

10.29007/qsp7 ◽  
2019 ◽  
Author(s):  
Munyaradzi Katurura ◽  
Liezel Cilliers
Keyword(s):  
South Africa ◽  
Real Time ◽  
Health Information ◽  
South African ◽  
Health Monitoring ◽  
Personal Information ◽  
Wearable Devices ◽  
Health And Wellbeing ◽  
The Past ◽  
Social Disclosure

The market for wearable devices that is used for health monitoring has steadily increased over the past few years. South Africa has also seen an increase in the adoption of these wearable device. This is partly because these devices allow users to monitor their health and wellbeing in real time. However, to be efficient, the devices must collect a large amount of data. Some of the data that is collected include personally identifiable and health information which could be considered sensitive to the user. This study investigated if the Protection of Personal Information Act (POPIA) provides adequate protection to South African users of wearable health devices. The POPIA and the privacy policy of the 2 most popular wearable health devices in South Africa, the Apple watch and Fit- bit, were qualitatively compared making use of Hutton et al’s (2018) heuristic framework. The study found that POPIA protected the users’ privacy when it came to notice, users’ awareness, choice and consent, access and participation. The Act did not cover any privacy matters related to social disclosure of information by users. The study also found that Apple watch and Fitbit did well in protecting users’ privacy with regards to notice and awareness as well as access and participation. The two wearables performed poorest in regards to choice and consent as well as social disclosure controls to protect users’ privacy. The study recommend that users educate themselves in regard to how their data collected by wearable health devices are collected and protected.

scholarly journals Genetic diversity in selected stud and commercial herds of the Afrikaner cattle breed

2015 ◽  
Vol 44 (5) ◽  
pp. 80-84
Author(s):  
L Pienaar ◽  
JP Grobler ◽  
FWC Neser ◽  
MM Scholtz ◽  
H Swart ◽  
...  
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
Genetic Structure ◽  
South African ◽  
Bos Taurus ◽  
Cattle Breed ◽  
Significant Loss ◽  
Indigenous Cattle ◽  
Loss Of Genetic Diversity ◽  
High Degree

The Afrikaner is one of three indigenous cattle breeds found in South Africa. Afrikaner cattle were originally extensively used for crossbreeding purposes and breed development. The objective of this study was to determine the genetic diversity of selected stud and commercial herds from the whole South African Afrikaner population, as well as to determine the genetic structure among these herds. Assignment methods (based on STRUCTURE software) revealed a real structure consisting of four genetic populations (K = 4). Estimates of genetic diversity did not support the hypothesis of significant loss of genetic diversity in any individual Afrikaner herd. Heterozygosity estimates ranged from 0.456 - 0.737 within individual populations, with an overall heterozygosity estimate of 0.568 for the Afrikaner breed. The average number of alleles per locus was regarded as being 2.67 - 7.78, with an average of 5.18 alleles per locus. It could be concluded that a moderate to high degree of variation is still present within the Afrikaner cattle breed, despite the recent decline in numbers of this indigenous breed.Keywords: Bos taurus africanus, heterozygosity, inbreeding, microsatellite markers

scholarly journals South African Buffalo-Derived Theileria parva Is Distinct From Other Buffalo and Cattle-Derived T. parva

2021 ◽  
Vol 12 ◽  
Author(s):  
Boitumelo B. Maboko ◽  
Kgomotso P. Sibeko-Matjila ◽  
Rian Pierneef ◽  
Wai Y. Chan ◽  
Antoinette Josemans ◽  
...  
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
South African ◽  
Variant Calling ◽  
Protozoan Parasite ◽  
Rhipicephalus Appendiculatus ◽  
Theileria Parva ◽  
African Buffalo ◽  
Illumina Hiseq

Theileria parva is a protozoan parasite transmitted by the brown-eared ticks, Rhipicephalus appendiculatus and Rhipicephalus zambeziensis. Buffaloes are the parasite’s ancestral host, with cattle being the most recent host. The parasite has two transmission modes namely, cattle–cattle and buffalo–cattle transmission. Cattle–cattle T. parva transmission causes East Coast fever (ECF) and January disease syndromes. Buffalo to cattle transmission causes Corridor disease. Knowledge on the genetic diversity of South African T. parva populations will assist in determining its origin, evolution and identify any cattle–cattle transmitted strains. To achieve this, genomic DNA of blood and in vitro culture material infected with South African isolates (8160, 8301, 8200, 9620, 9656, 9679, Johnston, KNP2, HL3, KNP102, 9574, and 9581) were extracted and paired-end whole genome sequencing using Illumina HiSeq 2500 was performed. East and southern African sample data (Chitongo Z2, Katete B2, Kiambu Z464/C12, Mandali Z22H10, Entebbe, Nyakizu, Katumba, Buffalo LAWR, and Buffalo Z5E5) was also added for comparative purposes. Data was analyzed using BWA and SAMtools variant calling with the T. parva Muguga genome sequence used as a reference. Buffalo-derived strains had higher genetic diversity, with twice the number of variants compared to cattle-derived strains, confirming that buffaloes are ancestral reservoir hosts of T. parva. Host specific SNPs, however, could not be identified among the selected 74 gene sequences. Phylogenetically, strains tended to cluster by host with South African buffalo-derived strains clustering with buffalo-derived strains. Among the buffalo-derived strains, South African strains were genetically divergent from other buffalo-derived strains indicating possible geographic sub-structuring. Geographic sub- structuring was also observed within South Africa strains. The knowledge generated from this study indicates that to date, ECF is not circulating in buffalo from South Africa. It also shows that T. parva has historically been present in buffalo from South Africa before the introduction of ECF and was not introduced into buffalo during the ECF epidemic.

scholarly journals DNA-based identification of aquatic invertebrates useful in the South African context?

2016 ◽  
Vol Volume 112 (Number 5/6) ◽  
Author(s):  
Hermoine J. Venter ◽  
Cornelius C. Bezuidenhout ◽  
◽  
Keyword(s):  
South Africa ◽  
Dna Barcoding ◽  
South African ◽  
High Throughput Sequencing ◽  
Environmental Dna ◽  
Bulk Sample ◽  
Aquatic Macroinvertebrates ◽  
South African Context ◽  
The South ◽  
African Context

Abstract The concept of using specific regions of DNA to identify organisms – processes such as DNA barcoding – is not new to South African biologists. The African Centre for DNA Barcoding reports that 12 548 plant species and 1493 animal species had been barcoded in South Africa by July 2013, while the Barcode of Life Database (BOLD) contains 62 926 records for South Africa, 11 392 of which had species names (representing 4541 species). In light of this, it is surprising that aquatic macroinvertebrates of South Africa have not received much attention as potential barcoding projects thus far – barcoding of aquatic species has tended to focus on invasive species and fishes. Perusal of the BOLD records for South Africa indicates a noticeable absence of aquatic macroinvertebrates, including families used for biomonitoring strategies such as the South African Scoring System. Meanwhile, the approach of collecting specimens and isolating their DNA individually in order to identify them (as in the case of DNA barcoding), has been shifting towards making use of the DNA which organisms naturally shed into their environments (eDNA). Coupling environmental and bulk sample DNA with high-throughput sequencing technology has given rise to metabarcoding, which has the potential to characterise the whole community of organisms present in an environment. Harnessing barcoding and metabarcoding approaches with environmental DNA (eDNA) potentially offers a non-invasive means of measuring the biodiversity in an environment and has great potential for biomonitoring. Aquatic ecosystems are well suited to these approaches – but could they be useful in a South African context?

scholarly journals Real time optimal water allocation in the Orange River catchment in South Africa

2015 ◽  
Author(s):  
◽  
Oluwatosin Onaopemipo Olofintoye ◽  
◽  
Josiah Adeyemo ◽  
Fredrick Alfred O. Otieno ◽  
...  
Keyword(s):  
South Africa ◽  
Water Resources ◽  
Real Time ◽  
South African ◽  
Water Allocation ◽  
Pareto Optimal ◽  
Multi Objective ◽  
Real Time Analysis ◽  
Allocation Problems ◽  
Pareto Optimal Fronts

The planning and management of water resources systems often involve formulation and establishment of optimal operating policies and the study of trade-off between different objectives. Due to the intricate nature of water resources management tasks, several models with varying degrees of complexities have been developed and applied for resolving water resources optimisation and allocation problems. Nevertheless, there still exist uncertainties about finding a generally consistent and trustworthy method that can find solutions which are very close to the global optimum in all scenarios. This study presents the development and application of a new evolutionary multi-objective optimisation algorithm, combined Pareto multi-objective differential evolution (CPMDE). The algorithm combines methods of Pareto ranking and Pareto dominance selections to implement a novel generational selection scheme. The new scheme provides a systematic approach for controlling elitism of the population which results in the simultaneous creation of short solution vectors that are suitable for local search and long vectors suitable for global search. By incorporating combined Pareto procedures, CPMDE is able to adaptively balance exploitation of non-dominated solutions found with exploration of the search space. Thus, it is able to escape all local optima and converge to the global Pareto-optimal front. The performance of CPMDE was compared with 14 state-of-the-art evolutionary multi-objective optimisation algorithms. A total of ten test problems and three real world problems were considered in the benchmark of the algorithm. Findings suggest that the new algorithm presents an improvement in convergence to global Pareto-optimal fronts especially on deceptive multi-modal functions where CPMDE clearly outperformed all other algorithms in convergence and diversity. The convergence metric on this problem was several orders of magnitude better than those of the other algorithms. Competitive results obtained from the benchmark of CPMDE suggest that it is a good alternative for solving real multi-objective optimisation problems. Also, values of a variance statistics further indicate that CPMDE is reliable and stable in finding solutions and converging to Pareto-optimal fronts in multi-objective optimisation problems. CPMDE was applied to resolve water allocation problems in the Orange River catchment in South Africa. Results obtained from the applications of CPMDE suggest it represents an improvement over some existing methods. CPMDE was applied to resolve water allocation problems in the agricultural and power sectors in South Africa. These sectors are strategic in forging economic growth, sustaining technological developments and contributing further to the overall development of the nation. They are also germane in capacitating the South African government’s commitment towards equity and poverty eradication and ensuring food security. Harnessing more hydropower from existing water sources within the frontier of the country is germane in capacitating the South African Government’s commitment to reduction of the countries’ greenhouse gas emissions and transition to a low-carbon economy while meeting a national target of 3 725 megawatts by 2030. Application of CPMDE algorithm in the behavioural analysis of the Vanderkloof reservoir showed an increase of 20 310 MWH in energy generation corresponding to a 3.2 percent increase. On analysis of storage trajectories over the operating period, it was found that the real time analysis incorporating a hybrid between CPMDE and ANN offers a procedure with a high ability to minimize deviation from target storage under the prevailing water stress condition. Overall, the real time analysis provides an improvement of 49.32 percent over the current practice. Further analysis involving starting the simulation with a proposed higher storage volume suggests that 728.53 GWH of annual energy may be generated from the reservoir under medium flow condition without system failure as opposed to 629 GWH produced from current practice. This corresponds to a 13.66 percent increase in energy generation. It was however noted that the water resources of the dam is not in excess. The water in the dam is just enough to meet all current demands. This calls for proper management policies for future operation of the reservoir to guard against excessive storage depletions. The study herein also involved the development of a decision support system for the daily operation of the Vanderkloof reservoir. This provides a low cost solution methodology suitable for the sustainable operation of the Vanderkloof dam in South Africa. Adopting real time optimisation strategies may be beneficial to the operation of reservoirs. Findings from the study herein indicate that the new algorithm represents an improvement over existing methods. Therefore, CPMDE presents a new tool that nations can adapt for the proper management of water resources towards the overall prosperity of their populace.

Genetic diversity of the Fusarium oxysporum complex isolated from the grassland biome of South Africa.

2020 ◽  
Author(s):  
Mudzuli Mavhunga ◽  
Thiambi Grace Kwinda ◽  
Brett Anthony Summerell ◽  
Eduard Venter ◽  
Adriaana Jacobs
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
Fusarium Oxysporum ◽  
South African ◽  
Anthropogenic Disturbance ◽  
Elongation Factor ◽  
Sub Saharan Africa ◽  
Anthropogenic Activity ◽  
The South ◽  
Grassland Biome

The genetic diversity of pathogenic members of the Fusarium oxysporum species complex (FOSC) has been intensively studied worldwide, yet strains occurring from native soils with low anthropogenic disturbance remain poorly understood. This study focused on 355 F. oxysporum isolates from soils with low anthropogenic activity obtained from the grassland biome of South Africa. Analysis of the translation elongation factor 1-alpha (tef-1α) gene revealed high levels of sequence type (ST) diversity within the soil population in comparison to the global dataset. Phylogenetic relationships of the South African isolates revealed that only four nested within FOSC Clade 1. This is the first report of members of the basal clade recovered from ecosystems with low anthropogenic disturbance from Sub-Saharan Africa. The remaining strains nested within Clades 2 to 5. This study contributes significantly to our understanding of the distribution of the FOSC in natural systems as we show that FOSC populations in the South African grassland biome are genetically diverse. This fills in our knowledge gap as previous studies reported only on the occurrence and diversity of the FOSC isolated from plant debris in South Africa. This is the first comprehensive survey of fusaria from grassland soils with low anthropogenic disturbance in South Africa.

Post-recession share repurchase behaviour by JSE-listed companies: transparent or not?

2020 ◽  
Vol 10 (3) ◽  
pp. 465-486
Author(s):  
Gretha Steenkamp ◽  
Nicolene Wesson
Keyword(s):  
South Africa ◽  
Real Time ◽  
South African ◽  
Stock Exchange ◽  
Listed Companies ◽  
Annual Reports ◽  
Share Repurchases ◽  
Share Repurchase ◽  
Content Type ◽  
Johannesburg Stock Exchange

PurposeShare repurchases are increasingly employed in South Africa. Disclosure on share repurchases in annual reports is poor, and a high percentage of share repurchases are not announced in real time on the Johannesburg Stock Exchange (JSE). A comprehensive database of share repurchases by JSE-listed companies has been created up to 2009, but post-recession repurchase behaviour is not known. This study aims to examine South African share repurchase behaviour (activity, repurchase entity, repurchase type and transparency) in the post-recession period and compare this to the 2000–2009 period.Design/methodology/approachComprehensive share repurchase data for all JSE-listed companies (excluding those in the basic materials and financial industries) were obtained by scrutinising annual reports and JSE announcements.FindingsThe repurchasing of shares reached a peak during the financial recession of 2008/2009, with share repurchases stabilising at a lower level post-recession. Repurchases executed by subsidiaries have decreased post-recession, probably owing to the introduction of dividends tax. However, 45% of the share repurchase value was not announced via the JSE (compared to 22% in 2000–2009).Practical implicationsReal-time JSE announcements of all share repurchases are required to improve transparency.Originality/valueOwing to low announcement rates, a lack of transparency relating to share repurchases was observed in South Africa post-recession. Enhanced corporate governance requirements could improve transparency.

The Three-dimensional structure of frozen-hydrated nudaurelia capensis β virus

1987 ◽  
Vol 45 ◽  
pp. 650-651
Author(s):  
N. H. Olson ◽  
T. S. Baker ◽  
Wu Bo Mu ◽  
J. E. Johnson ◽  
D. A. Hendry
Keyword(s):  
South African ◽  
Rna Virus ◽  
Carbon Film ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Electron Dose ◽  
Total Electron ◽  
Three Dimensional Structure ◽  
Negative Stain ◽  
Dimensional Reconstruction

Nudaurelia capensis β virus (NβV) is an RNA virus of the South African Pine Emperor moth, Nudaurelia cytherea capensis (Lepidoptera: Saturniidae). The NβV capsid is a T = 4 icosahedron that contains 60T = 240 subunits of the coat protein (Mr = 61,000). A three-dimensional reconstruction of the NβV capsid was previously computed from visions embedded in negative stain suspended over holes in a carbon film. We have re-examined the three-dimensional structure of NβV, using cryo-microscopy to examine the native, unstained structure of the virion and to provide a initial phasing model for high-resolution x-ray crystallographic studiesNβV was purified and prepared for cryo-microscopy as described. Micrographs were recorded ∼1 - 2 μm underfocus at a magnification of 49,000X with a total electron dose of about 1800 e-/nm2.

Reframing Xenophobia in South Africa as Colour-Blind: The Limits of the Afro Phobia Thesis

2020 ◽  
Vol 17 (3) ◽  
pp. 433-444
Author(s):  
Amanuel Isak Tewolde
Keyword(s):  
South Africa ◽  
South African ◽  
Analytical Framework ◽  
Conflict Theory ◽  
Black African ◽  
South Africans ◽  
Theoretical Perspectives ◽  
Online Newspaper ◽  
Close Proximity ◽  
Realistic Conflict Theory

Many scholars and South African politicians characterize the widespread anti-foreigner sentiment and violence in South Africa as dislike against migrants and refugees of African origin which they named ‘Afro-phobia’. Drawing on online newspaper reports and academic sources, this paper rejects the Afro-phobia thesis and argues that other non-African migrants such as Asians (Pakistanis, Indians, Bangladeshis and Chinese) are also on the receiving end of xenophobia in post-apartheid South Africa. I contend that any ‘outsider’ (White, Asian or Black African) who lives and trades in South African townships and informal settlements is scapegoated and attacked. I term this phenomenon ‘colour-blind xenophobia’. By proposing this analytical framework and integrating two theoretical perspectives — proximity-based ‘Realistic Conflict Theory (RCT)’ and Neocosmos’ exclusivist citizenship model — I contend that xenophobia in South Africa targets those who are in close proximity to disadvantaged Black South Africans and who are deemed outsiders (e.g., Asian, African even White residents and traders) and reject arguments that describe xenophobia in South Africa as targeting Black African refugees and migrants.

Region of Birth and Child Mortality among Black Migrants to South Africa: Is there a foreign-born advantage?

2016 ◽  
Vol 13 (3) ◽  
pp. 359-376 ◽  
Author(s):  
Tiffany L Green ◽  
Amos C Peters
Keyword(s):  
South Africa ◽  
South African ◽  
Child Mortality ◽  
Southern Africa ◽  
Strong Relationship ◽  
Developed Countries ◽  
Black Immigrants ◽  
Foreign Born ◽  
Region Of Origin ◽  
Child Deaths

Much of the existing evidence for the healthy immigrant advantage comes from developed countries. We investigate whether an immigrant health advantage exists in South Africa, an important emerging economy.  Using the 2001 South African Census, this study examines differences in child mortality between native-born South African and immigrant blacks.  We find that accounting for region of origin is critical: immigrants from southern Africa are more likely to experience higher lifetime child mortality compared to the native-born population.  Further, immigrants from outside of southern Africa are less likely than both groups to experience child deaths.  Finally, in contrast to patterns observed in developed countries, we detect a strong relationship between schooling and child mortality among black immigrants.

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