scholarly journals Genetic diversity of Ehrlichia ruminantium field strains from selected farms in South Africa

2020 ◽  
Vol 87 (1) ◽  
Author(s):  
Helena C. Steyn ◽  
Alri Pretorius
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Vaccine Development ◽  
Quantitative Polymerase Chain Reaction ◽  
Gene Region ◽  
Economic Losses ◽  
Ehrlichia Ruminantium ◽  
Field Samples ◽  
Endemic Areas

Heartwater is a tick-borne disease caused by the intracellular rickettsial parasite Ehrlichia ruminantium and transmitted by Amblyomma hebraeum ticks. Heartwater is problematic in endemic areas because it causes high mortality in ruminants and leads to economic losses that threaten productivity and food security. This may indicate that there is augmented genetic diversity in the field, which may result in isolates that are more virulent than the Ball3 and Welgevonden isolates. The genetic diversity of E. ruminantium was investigated in this study, focussing on the pCS20 gene region and four polymorphic open reading frames (ORFs) identified by subtractive hybridisation. The 16S ribosomal ribonucleic acid gene confirmed E. ruminantium in brain, blood and tick genomic deoxyribonucleic acid samples (n = 3792) collected from 122 farms that were randomly selected from seven provinces of South Africa where heartwater is endemic. The conserved E. ruminantium pCS20 quantitative polymerase chain reaction (qPCR) assay was used to scan all collected field samples. A total of 433 samples tested positive with the qPCR using the pCS20 gene region, of which 167 were sequenced. The known stocks and field samples were analysed, and phylogenetic trees were generated from consensus sequences. A total of 25 new clades were identified; of these, nine isolates from infected blood could be propagated in cell cultures. These clades were not geographically confined to a certain area but were distributed amongst heartwater-endemic areas in South Africa. Thus, the knowledge of strain diversity of E. ruminantium is essential for control of heartwater and provides a basis for further vaccine development.

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.

scholarly journals Computational Analysis of African Swine Fever Virus Protein Space for the Design of an Epitope-Based Vaccine Ensemble

Pathogens ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1078 ◽  
Author(s):  
Albert Ros-Lucas ◽  
Florencia Correa-Fiz ◽  
Laia Bosch-Camós ◽  
Fernando Rodriguez ◽  
Julio Alonso-Padilla
Keyword(s):  
T Cell ◽  
Vaccine Development ◽  
De Novo ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Economic Losses ◽  
Virus Protein ◽  
Hemorrhagic Disease ◽  
Starting Point

African swine fever virus is the etiological agent of African swine fever, a transmissible severe hemorrhagic disease that affects pigs, causing massive economic losses. There is neither a treatment nor a vaccine available, and the only method to control its spread is by extensive culling of pigs. So far, classical vaccine development approaches have not yielded sufficiently good results in terms of concomitant safety and efficacy. Nowadays, thanks to advances in genomic and proteomic techniques, a reverse vaccinology strategy can be explored to design alternative vaccine formulations. In this study, ASFV protein sequences were analyzed using an in-house pipeline based on publicly available immunoinformatic tools to identify epitopes of interest for a prospective vaccine ensemble. These included experimentally validated sequences from the Immune Epitope Database, as well as de novo predicted sequences. Experimentally validated and predicted epitopes were prioritized following a series of criteria that included evolutionary conservation, presence in the virulent and currently circulating variant Georgia 2007/1, and lack of identity to either the pig proteome or putative proteins from pig gut microbiota. Following this strategy, 29 B-cell, 14 CD4+ T-cell and 6 CD8+ T-cell epitopes were selected, which represent a starting point to investigating the protective capacity of ASFV epitope-based vaccines.

scholarly journals Molecular detection and genetic diversity of Leucocytozoon sabrazesi in chickens in Thailand

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Runglawan Chawengkirttikul ◽  
Witchuta Junsiri ◽  
Amaya Watthanadirek ◽  
Napassorn Poolsawat ◽  
Sutthida Minsakorn ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Egg Production ◽  
Control Strategies ◽  
Amino Acid Sequences ◽  
Economic Losses ◽  
Nested Polymerase Chain Reaction ◽  
Blood Samples ◽  
Tropical Regions ◽  
Vaccination Programs ◽  
High Entropy

AbstractLeucocytozoon sabrazesi is the intracellular protozoa of leucocytozoonosis, which is transmitted by the insect vectors and affects chickens in most subtropical and tropical regions of the globe, except South America, and causing enormous economic losses due to decreasing meat yield and egg production. In this study, L. sabrazesi gametocytes have been observed in the blood smears, and molecular methods have been used to analyse the occurrence and genetic diversity of L. sabrazesi in blood samples from 313 chickens raised in northern, western and southern parts of Thailand. The nested polymerase chain reaction (nested PCR) assay based on the cytb gene revealed that 80.51% (252/313) chickens were positive of L. sabrazesi. The phylogenetic analysis indicated that L. sabrazesi cytb gene is conserved in Thailand, showed 2 clades and 2 subclades with similarity ranged from 89.5 to 100%. The diversity analysis showed 13 and 18 haplotypes of the sequences from Thailand and from other countries, respectively. The entropy analyses of nucleic acid sequences showed 26 high entropy peaks with values ranging from 0.24493 to 1.21056, while those of amino acid sequences exhibited 5 high entropy peaks with values ranging from 0.39267 to 0.97012. The results; therefore, indicate a high molecular occurrence of L. sabrazesi in chicken blood samples with the associated factors that is statistically significant (p < 0.05). Hence, our results could be used to improve the immunodiagnostic methods and to find appropriate preventive control strategies or vaccination programs against leucocytozoonosis in order to mitigate or eliminate the harmful impact of this infection on chicken industry.

scholarly journals Porcine Reproductive and Respiratory Syndrome Virus: Immune Escape and Application of Reverse Genetics in Attenuated Live Vaccine Development

Vaccines ◽  
2021 ◽  
Vol 9 (5) ◽  
pp. 480
Author(s):  
Honglei Wang ◽  
Yangyang Xu ◽  
Wenhai Feng
Keyword(s):  
Immune Responses ◽  
Reverse Genetics ◽  
Vaccine Development ◽  
Immune Escape ◽  
Rna Virus ◽  
Economic Losses ◽  
Respiratory Syndrome Virus ◽  
Live Vaccines ◽  
Host Immune Responses ◽  
Inactivated Vaccines

Porcine reproductive and respiratory syndrome virus (PRRSV), an RNA virus widely prevalent in pigs, results in significant economic losses worldwide. PRRSV can escape from the host immune response in several processes. Vaccines, including modified live vaccines and inactivated vaccines, are the best available countermeasures against PRRSV infection. However, challenges still exist as the vaccines are not able to induce broad protection. The reason lies in several facts, mainly the variability of PRRSV and the complexity of the interaction between PRRSV and host immune responses, and overcoming these obstacles will require more exploration. Many novel strategies have been proposed to construct more effective vaccines against this evolving and smart virus. In this review, we will describe the mechanisms of how PRRSV induces weak and delayed immune responses, the current vaccines of PRRSV, and the strategies to develop modified live vaccines using reverse genetics systems.

Lantana camara (lantana).

2021 ◽  
Author(s):  
Sarah E. Thomas ◽  
Julissa Rojas-Sandoval ◽  
Pedro Acevedo-Rodríguez
Keyword(s):  
South Africa ◽  
Biological Control ◽  
Control Measures ◽  
Economic Losses ◽  
Pests And Diseases ◽  
Control Programmes ◽  
Agricultural Weed ◽  
Successful Control ◽  
The Tropics ◽  
Ornamental Shrub

Abstract L. camara is a highly variable ornamental shrub, native of the neotropics. It has been introduced to most of the tropics and subtropics as a hedge plant and has since been reported as extremely weedy and invasive in many countries. It is generally deleterious to biodiversity and has been reported as an agricultural weed resulting in large economic losses in a number of countries. In addition to this, it increases the risk of fire, is poisonous to livestock and is a host for numerous pests and diseases. L. camara is difficult to control. In Australia, India and South Africa aggressive measures to eradicate L. camara over the last two centuries have been largely unsuccessful, and the invasion trajectory has continued upwards despite control measures. This species has been the target of biological control programmes for over a century, with successful control only being reported in a few instances.

scholarly journals Recent Progress in the Development of Liver Fluke and Blood Fluke Vaccines

Vaccines ◽  
2020 ◽  
Vol 8 (3) ◽  
pp. 553 ◽  
Author(s):  
Donald P. McManus
Keyword(s):  
Vaccine Development ◽  
Neglected Tropical Diseases ◽  
Clonorchis Sinensis ◽  
Economic Losses ◽  
Helminth Parasites ◽  
Blood Fluke ◽  
Parasitic Helminths ◽  
The Status ◽  
Liver Flukes ◽  
Fasciola Spp

Liver flukes (Fasciola spp., Opisthorchis spp., Clonorchis sinensis) and blood flukes (Schistosoma spp.) are parasitic helminths causing neglected tropical diseases that result in substantial morbidity afflicting millions globally. Affecting the world’s poorest people, fasciolosis, opisthorchiasis, clonorchiasis and schistosomiasis cause severe disability; hinder growth, productivity and cognitive development; and can end in death. Children are often disproportionately affected. F. hepatica and F. gigantica are also the most important trematode flukes parasitising ruminants and cause substantial economic losses annually. Mass drug administration (MDA) programs for the control of these liver and blood fluke infections are in place in a number of countries but treatment coverage is often low, re-infection rates are high and drug compliance and effectiveness can vary. Furthermore, the spectre of drug resistance is ever-present, so MDA is not effective or sustainable long term. Vaccination would provide an invaluable tool to achieve lasting control leading to elimination. This review summarises the status currently of vaccine development, identifies some of the major scientific targets for progression and briefly discusses future innovations that may provide effective protective immunity against these helminth parasites and the diseases they cause.

scholarly journals Amblyomma hebraeum is the predominant tick species on goats in the Mnisi Community Area of Mpumalanga Province South Africa and is co-infected with Ehrlichia ruminantium and Rickettsia africae

2019 ◽  
Author(s):  
Frans Jongejan ◽  
Laura Berger ◽  
Suzanne Busser ◽  
Iris Deetman ◽  
Manon Jochems ◽  
...  
Keyword(s):  
South Africa ◽  
Tick Species ◽  
Amblyomma Hebraeum ◽  
Ehrlichia Ruminantium ◽  
Mpumalanga Province ◽  
Rickettsia Africae ◽  
Community Area

Abstract The authors have withdrawn this preprint from Research Square

scholarly journals Whole genome sequencing reveals the genomic diversity, taxonomic classification, and evolutionary relationships of the genus Nocardia

2021 ◽  
Vol 15 (8) ◽  
pp. e0009665
Author(s):  
Shuai Xu ◽  
Zhenpeng Li ◽  
Yuanming Huang ◽  
Lichao Han ◽  
Yanlin Che ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Gene Families ◽  
Single Copy ◽  
Taxonomic Classification ◽  
Genomic Diversity ◽  
Evolutionary Relationships ◽  
Taxonomic Structure ◽  
Pan Genome ◽  
Dipeptidyl Aminopeptidase

Nocardia is a complex and diverse genus of aerobic actinomycetes that cause complex clinical presentations, which are difficult to diagnose due to being misunderstood. To date, the genetic diversity, evolution, and taxonomic structure of the genus Nocardia are still unclear. In this study, we investigated the pan-genome of 86 Nocardia type strains to clarify their genetic diversity. Our study revealed an open pan-genome for Nocardia containing 265,836 gene families, with about 99.7% of the pan-genome being variable. Horizontal gene transfer appears to have been an important evolutionary driver of genetic diversity shaping the Nocardia genome and may have caused historical taxonomic confusion from other taxa (primarily Rhodococcus, Skermania, Aldersonia, and Mycobacterium). Based on single-copy gene families, we established a high-accuracy phylogenomic approach for Nocardia using 229 genome sequences. Furthermore, we found 28 potentially new species and reclassified 16 strains. Finally, by comparing the topology between a phylogenomic tree and 384 phylogenetic trees (from 384 single-copy genes from the core genome), we identified a novel locus for inferring the phylogeny of this genus. The dapb1 gene, which encodes dipeptidyl aminopeptidase BI, was far superior to commonly used markers for Nocardia and yielded a topology almost identical to that of genome-based phylogeny. In conclusion, the present study provides insights into the genetic diversity, contributes a robust framework for the taxonomic classification, and elucidates the evolutionary relationships of Nocardia. This framework should facilitate the development of rapid tests for the species identification of highly variable species and has given new insight into the behavior of this genus.

scholarly journals Not Tripping over TRIPS: An Analysis of Necessity and Legality of the COVID-19 TRIPS Waiver Proposal

2022 ◽  
Vol 10 (5) ◽  
pp. 61-65
Author(s):  
Ahan Gadkari ◽  
◽  
Sofia Dash ◽  
Keyword(s):  
South Africa ◽  
Intellectual Property ◽  
Property Rights ◽  
World Trade Organization ◽  
Intellectual Property Rights ◽  
World Trade ◽  
Vaccine Development ◽  
Pharmaceutical Manufacturing ◽  
The World ◽  
Fair Distribution

The availability of vaccinations against COVID-19 provides hope for containing the epidemic, which has already claimed over 2.84 million lives. However, inoculating millions of individuals worldwide would need large vaccine manufacturing followed by fair distribution. A barrier to vaccine development and dissemination is the developers' intellectual property rights. India and South Africa have jointly sought to the World Trade Organization that certain TRIPS rules of COVID-19 vaccines, medicines, and treatments be waived. This piece argues for such a waiver, highlighting the unique circumstances that exist. It believes that TRIPS's flexibilities are inadequate to cope with the present epidemic, particularly for nations without pharmaceutical manufacturing competence.

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