scholarly journals Genetic diversity of ‘Candidatus Liberibacter africanus’ in South Africa based on microsatellite markers

2021 ◽  
Author(s):  
Ronel Roberts ◽  
Hong Lin ◽  
Gerhard Pietersen
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
Western Cape ◽  
African Continent ◽  
High Genetic Diversity ◽  
North West ◽  
Citrus Greening Disease ◽  
Genetic Groups ◽  
Candidatus Liberibacter ◽  
Fastidious Bacterium

AbstractCitrus Greening disease (CG) in South Africa (SA) is associated with the fastidious bacterium ‘Candidatus Liberibacter africanus’ (Laf). It has been observed that Laf isolates obtained from different geographic localities in SA differed in the rate of transmission during grafting experiments leading to the hypothesis that genetic variation of Laf may exist in this country. To determine this, 167 Laf isolates obtained from Limpopo, North West, Mpumalanga and the Western Cape were subjected to microsatellite analyses, using four polymorphic markers. From UPGMA and STRUCTURE analysis, it was shown that most sources belong to one of two major genetic groups of Laf and these comprise 25 distinct haplotypes. Four samples included within this study did not group with these two major groups, suggesting a potential third and fourth genetic group of Laf being present, which can be validated by further sampling. Results further indicate that Laf populations in SA are formed by geographic locality. The high genetic diversity observed for Laf within this study is consistent with the hypothesis that Laf originated on the African continent, warranting further genetic analysis of Laf populations from Africa. This is the first study to unveil the genetic diversity of Laf.

scholarly journals Progress towards the 2020 targets for HIV diagnosis and antiretroviral treatment in South Africa

2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Leigh F. Johnson ◽  
Rob E. Dorrington ◽  
Haroon Moolla
Keyword(s):  
South Africa ◽  
Antiretroviral Treatment ◽  
Routine Data ◽  
Hiv Positive ◽  
Western Cape ◽  
Hiv Diagnosis ◽  
Public And Private ◽  
North West ◽  
South Africans ◽  
Northern Cape

Background: The UNAIDS targets for 2020 are to achieve a 90% rate of diagnosis in HIVpositive individuals, to provide antiretroviral treatment (ART) to 90% of HIV-diagnosed individuals and to achieve virological suppression in 90% of ART patients.Objectives: To assess South Africa’s progress towards the 2020 targets and variations in performance by province.Methods: A mathematical model was fitted to HIV data for each of South Africa’s provinces, and for the country as a whole. Numbers of HIV tests performed in each province were estimated from routine data over the 2002–2015 period, and numbers of patients receiving ART in each province were estimated by fitting models to reported public and private ART enrolment statistics.Results: By the middle of 2015, 85.5% (95% CI: 84.5% – 86.5%) of HIV-positive South African adults had been diagnosed, with little variation between provinces. However, only 56.9% (95% CI: 55.3% – 58.7%) of HIV-diagnosed adults were on ART, with this proportion varying between 50.8% in North West and 72.7% in Northern Cape. In addition, 78.4% of adults on ART were virally suppressed, with rates ranging from 69.7% in Limpopo to 85.9% in Western Cape. Overall, 3.39 million (95% CI: 3.26–3.52 million) South Africans were on ART by mid- 2015, equivalent to 48.6% (95% CI: 46.0% – 51.2%) of the HIV-positive population. ART coverage varied between 43.0% in Gauteng and 63.0% in Northern Cape.Conclusion: Although South Africa is well on its way to reaching the 90% HIV diagnosis target, most provinces face challenges in reaching the remaining two 90% targets.

scholarly journals A Survey for ‘Candidatus Liberibacter’ Species in South Africa Confirms the Presence of Only ‘Ca. L. africanus’ in Commercial Citrus

Plant Disease ◽  
2010 ◽  
Vol 94 (2) ◽  
pp. 244-249 ◽  
Author(s):  
G. Pietersen ◽  
E. Arrebola ◽  
J. H. J. Breytenbach ◽  
L. Korsten ◽  
H. F. le Roux ◽  
...  
Keyword(s):  
South Africa ◽  
Western Cape ◽  
Chain Reaction ◽  
Citrus Production ◽  
Candidatus Liberibacter ◽  
Citrus Orchards ◽  
Polymerase Chain ◽  
Serious Disease ◽  
Production Areas ◽  
Representative Samples

Greening disease of citrus is a serious disease known in South Africa since the late 1920s. In South Africa, it is associated with infection by ‘Candidatus Liberibacter africanus’, a heat sensitive, phloem-limited, noncultured alpha-proteobacterium. Huanglongbing (HLB), a similar, but more devastating disease that was described initially from China but which now occurs in several citrus producing countries, is associated with a different Liberibacter species, ‘Ca. L. asiaticus’. A ‘Ca. L. africanus’ subspecies, ‘Ca. L. africanus subsp. capensis’, has been found only in South Africa infecting an indigenous Rutaceous species, Calodendrum capense (Cape Chestnut), in the Western Cape in 1995. The discovery of a new Liberibacter species in Brazil, ‘Ca. L. americanus’, and the spread of ‘Ca. L. asiaticus’ to a number of additional countries over the last few years prompted us to assess whether only ‘Ca. L. africanus’ is present in commercial citrus orchards in South Africa. Samples displaying greening or similar symptoms were collected from 249 citrus trees from 57 orchards distributed throughout the greening affected citrus production areas of South Africa. Multiplex polymerase chain reaction (PCR) was performed on DNA extracts to detect the known citrus Liberibacters. Amplicons were obtained from 197 samples. None of the samples yielded a 1,027-bp amplicon indicative of ‘Ca. L. americanus’ infection. The amplicons of 84 samples were sequenced, and all were identical to the cognate ‘Ca. L. africanus’ Nelspruit sequence in GenBank. No instance of ‘Ca. L. asiaticus’ or ‘Ca. L. africanus subsp. capensis’ sequence was found. Geographically representative samples that tested negative for Liberibacter also tested negative for phytoplasmas based on real-time PCR results. Based on the results of this survey, it is concluded that to date only ‘Ca. L. africanus’ is associated with citrus greening in commercial citrus in South Africa.

Genetic Diversity of Rice vampireweed (Rhamphicarpa fistulosa) Populations in Rainfed Lowland Rice in West Africa

Weed Science ◽  
2016 ◽  
Vol 64 (3) ◽  
pp. 430-440
Author(s):  
Norliette Zossou ◽  
Hubert Adoukonèou-Sagbadja ◽  
Daniel Fonceka ◽  
Lamine Baba-Moussa ◽  
Mbaye Sall ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Lowland Rice ◽  
Rice Grain ◽  
High Genetic Diversity ◽  
Genetic Groups ◽  
Rainfed Lowland ◽  
Rice Genotypes ◽  
The Relationship ◽  
Aflp Technique

Rice vampireweed belongs to the Orobanchaceae and is found in Africa and Australia. It is a hemiparasitic weed of lowland rice genotypes and causes losses of 40 to 100% of rice grain yield. Our study addressed the genetic diversity of rice vampireweed in Benin and Senegal. The specific objectives of this research were to study the genetic diversity of rice vampireweed accessions in Benin and Senegal and the relationship between the different genotypes of rice vampireweed through agroecological areas. To achieve these objectives, the genetic diversity of rice vampireweed accessions using the AFLP technique was studied. Based on our results, dendrogram classification has distinguished four different genetic groups. The populations of Benin and Senegal are genetically diverse. Substantial genetic differentiation (GST) exists among agroecological areas within Benin and Senegal (GST = 0.17). The high genetic diversity of rice vampireweed in Benin and Senegal presents a challenge for the development of resistant rice germplasm.

Population genetic analyses of Phytophthora cinnamomi reveals three lineages and movement between natural vegetation and avocado orchards in South Africa

2022 ◽  
Author(s):  
Juanita Engelbrecht ◽  
Tuan A. Duong ◽  
Trudy Paap ◽  
Joseph Michael Hulbert ◽  
Juanita Joyce Hanneman ◽  
...  
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
Phytophthora Cinnamomi ◽  
Resistance Breeding ◽  
Natural Vegetation ◽  
Economic Losses ◽  
Western Cape ◽  
Natural Ecosystems ◽  
Agricultural Industries ◽  
Production Areas

Phytophthora cinnamomi is the causal agent of root rot, canker and dieback of thousands of plant species around the globe. This oomycete not only causes severe economic losses to forestry and agricultural industries, but also threatens the health of various plants in natural ecosystems. In this study, 380 isolates of P. cinnamomi from four avocado production areas and two regions of natural vegetation in South Africa were investigated using 15 microsatellite markers. These populations were found to have a low level of genetic diversity and consisted of isolates from three lineages. Shared genotypes were detected between isolates from avocado orchards and natural vegetation, indicating the movement of isolates between these areas. The population from the Western Cape natural vegetation had the highest genotypic diversity and unique alleles, indicating this could be the point of introduction of P. cinnamomi to South Africa. Index of association analysis suggested that five out of six populations were under linkage disequilibrium suggesting a clonal mode of reproduction whereas genotypes sampled from a recently established avocado orchard in the Western Cape were derived from a randomly recombined population. This study provided novel insights on the genetic diversity and spread of P. cinnamomi in South Africa. It also reported on the predominance of triploidy in natural occurring populations and provided evidence for recombination of P. cinnamomi for the first time. The presence of two dominant genotypes in all avocado production areas in South Africa highlight the importance of considering them in disease management and resistance breeding programmes.

New species and new collection records of aquatic beetles in the genus Ochthebius Leach from southern Africa (Coleoptera: Hydraenidae)

Zootaxa ◽  
2011 ◽  
Vol 3093 (1) ◽  
pp. 1 ◽  
Author(s):  
PHILIP D. PERKINS
Keyword(s):  
South Africa ◽  
New Species ◽  
Southern Africa ◽  
Western Cape ◽  
Western Cape Province ◽  
African Species ◽  
North West ◽  
Distribution Maps ◽  
Water Beetle ◽  
Kwazulu Natal

The southern African species of the water beetle genus Ochthebius Leach, 1815, are reviewed. Eight new species are described, and new collection records are given for eight previously described species, based on the examination and databasing of 8,919 specimens from 253 localities/events. Male genitalia of the new species are illustrated, and high resolution habitus images of the holotypes of new species are provided. Distribution maps are given for the 18 species of Ochthebius now known from southern Africa, including Namibia, South Africa, Lesotho, Zimbabwe, the extreme southern part of Angola, and the southern part of Mozambique. New species of Ochthebius are: O. anchorus (South Africa, KwaZulu-Natal Province, Oribi Gorge); O. bicomicus (South Africa, Western Cape Province, 22 mi. N. Nelspoort); O. bupunctus (Namibia, Kaokoveld, Kunene River, Swartbooisdrift); O. endroedyi (South Africa, North West Province, Barberspan); O. granulinus (South Africa, Western Cape Province, Elandsdrift); O. involatus (South Africa, Western Cape Province, near Kommetje); O. sitiensis (Namibia, Okau Fountain, 12.5 km inland); and O. zulu (South Africa, KwaZulu-Natal Province, Nqutu).

scholarly journals Mitochondrial genetic variation reveals phylogeographic structure and cryptic diversity in Trioza erytreae

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Inusa Ajene ◽  
Fathiya M. Khamis ◽  
Gerhard Pietersen ◽  
Barbara van Asch
Keyword(s):  
South Africa ◽  
Citrus Greening ◽  
Phylogeographic Structure ◽  
Citrus Greening Disease ◽  
Trioza Erytreae ◽  
Baseline Information ◽  
Candidatus Liberibacter ◽  
Mitochondrial Sequences ◽  
Greening Disease ◽  
Genetic Clustering

AbstractTrioza erytreae is the main vector for ‘Candidatus Liberibacter africanus’, the causative agent of African Citrus Greening disease. The insect is widespread in Africa, and has recently disseminated to Southwestern Europe. This study aimed at generating reference mitogenome sequences for T. erytreae, as a background for future genetic diversity surveys. Complete mitochondrial sequences of three specimens collected in Ethiopia, Uganda and South Africa were recovered using Ion Torrent technology. The mitogenomes of T. erytreae from Uganda and Ethiopia were highly similar, and distinct from that found in South Africa. The phylogeographic structure of T. erytreae was assessed using genetic clustering and pairwise distances, based on a dataset of public COI sequences recorded as T. erytreae. The dataset revealed ten haplotypes with strong phylogeographic structure in Africa and Europe. Three haplotypes found in Kenya on Clausena anisata belonged to pairs separated by distances as high as 11.2%, and were basal to all other sequences. These results indicate that not all sequences identified as T. erytreae belong to the same species, and that some degree of specificity with different plant hosts is likely to exist. This study provides new baseline information on the diversity of T. erytreae, with potential implications for the epidemiology of African Citrus Greening disease.

scholarly journals Isolation and high genetic diversity in dwarf mountain toads (Capensibufo) from South Africa

2010 ◽  
Vol 100 (4) ◽  
pp. 822-834 ◽  
Author(s):  
KRYSTAL A. TOLLEY ◽  
ATHERTON L. DE VILLIERS ◽  
MICHAEL I. CHERRY ◽  
G. JOHN MEASEY
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
High Genetic Diversity

scholarly journals Parasite genetic diversity reflects continued residual malaria transmission in Vhembe District, a hotspot in the Limpopo Province of South Africa

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Hazel B. Gwarinda ◽  
Sofonias K. Tessema ◽  
Jaishree Raman ◽  
Bryan Greenhouse ◽  
Lyn-Marié Birkholtz
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
Malaria Transmission ◽  
Limpopo Province ◽  
Parasite Population ◽  
High Genetic Diversity ◽  
Management Interventions ◽  
Imported Cases ◽  
Study Sites ◽  
Vhembe District

Abstract Background South Africa aims to eliminate malaria transmission by 2023. However, despite sustained vector control efforts and case management interventions, the Vhembe District remains a malaria transmission hotspot. To better understand Plasmodium falciparum transmission dynamics in the area, this study characterized the genetic diversity of parasites circulating within the Vhembe District. Methods A total of 1153 falciparum-positive rapid diagnostic tests (RDTs) were randomly collected from seven clinics within the district, over three consecutive years (2016, 2017 and 2018) during the wet and dry malaria transmission seasons. Using 26 neutral microsatellite markers, differences in genetic diversity were described using a multiparameter scale of multiplicity of infection (MOI), inbreeding metric (Fws), number of unique alleles (A), expected heterozygosity (He), multilocus linkage disequilibrium (LD) and genetic differentiation, and were associated with temporal and geospatial variances. Results A total of 747 (65%) samples were successfully genotyped. Moderate to high genetic diversity (mean He = 0.74 ± 0.03) was observed in the parasite population. This was ascribed to high allelic richness (mean A = 12.2 ± 1.2). The majority of samples (99%) had unique multi-locus genotypes, indicating high genetic diversity in the sample set. Complex infections were observed in 66% of samples (mean MOI = 2.13 ± 0.04), with 33% of infections showing high within-host diversity as described by the Fws metric. Low, but significant LD (standardised index of association, ISA = 0.08, P < 0.001) was observed that indicates recombination of distinct clones. Limited impact of temporal (FST range − 0.00005 to 0.0003) and spatial (FST = − 0.028 to 0.023) variation on genetic diversity existed during the sampling timeframe and study sites respectively. Conclusions Consistent with the Vhembe District’s classification as a ‘high’ transmission setting within South Africa, P. falciparum diversity in the area was moderate to high and complex. This study showed that genetic diversity within the parasite population reflects the continued residual transmission observed in the Vhembe District. This data can be used as a reference point for the assessment of the effectiveness of on-going interventions over time, the identification of imported cases and/or outbreaks, as well as monitoring for the potential spread of anti-malarial drug resistance.

scholarly journals Prevalence of Antibiotic Resistance in Salmonella Serotypes Concurrently Isolated from the Environment, Animals, and Humans in South Africa: A Systematic Review and Meta-Analysis

Antibiotics ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1435
Author(s):  
Tsepo Ramatla ◽  
Mpho Tawana ◽  
ThankGod E. Onyiche ◽  
Kgaugelo E. Lekota ◽  
Oriel Thekisoe
Keyword(s):  
South Africa ◽  
Systematic Review ◽  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
Environmental Samples ◽  
Meta Analysis ◽  
Western Cape ◽  
Eastern Cape ◽  
North West ◽  
Salmonella Serotypes

One of the main global concerns is the usage and spread of antibiotic resistant Salmonella serovars. The animals, humans, and environmental components interact and contribute to the rapid emergence and spread of antimicrobial resistance, directly or indirectly. Therefore, this study aimed to determine antibiotic resistance (AR) profiles of Salmonella serotypes isolated from the environment, animals, and humans in South Africa by a systematic review and meta-analysis. The preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines were followed to search four databases for studies published from 1980 to 2021, that reported the antibiotic resistance profiles of Salmonella serotypes isolated in South Africa. The AR was screened from 2930 Salmonella serotypes which were isolated from 6842 samples. The Western Cape province had high pooled prevalence estimates (PPE) of Salmonella isolates with AR profiles followed by North West, Gauteng, and Eastern Cape with 94.3%, 75.4%, 59.4%, and 46.2%, respectively. The high PPE and heterogeneity were observed from environmental samples [69.6 (95% CI: 41.7−88.3), Q = 303.643, I2 = 98.353, Q-P = 0.045], animals [41.9 (95% CI: 18.5–69.5), Q = 637.355, I2 = 98.745, Q-P = 0.577], as well as animals/environment [95.9 (95% CI: 5.4−100), Q = 55.253, I2 = 96.380, Q-P = 0.300]. The majority of the salmonella isolates were resistant to sulphonamides (92.0%), enrofloxacin and erythromycin (89.3%), oxytetracycline (77.4%), imipenem (72.6%), tetracycline (67.4%), as well as trimethoprim (52.2%), among the environment, animals, and humans. The level of multidrug-resistance recorded for Salmonella isolates was 28.5% in this review. This study has highlighted the occurrence of AR by Salmonella isolates from animals, humans, and environmental samples in South Africa and this calls for a consolidated “One Health” approach for antimicrobial resistance epidemiological research, as well as the formulation of necessary intervention measures to prevent further spread.

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