Bluetongue virus
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PROVIDER: PRJNA401524 | ENA |
REPOSITORIES: ENA
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Project description:The emergence and fast global spread of COVID-19 has presented one of the greatest public health challenges in modern times with no proven cure or vaccine. Africa is still early in this epidemic, therefore the extent of disease severity is not yet clear. We used a mathematical model to fit to the observed cases of COVID-19 in South Africa to estimate the basic reproductive number and critical vaccination coverage to control the disease for different hypothetical vaccine efficacy scenarios. We also estimated the percentage reduction in effective contacts due to the social distancing measures implemented. Early model estimates show that COVID-19 outbreak in South Africa had a basic reproductive number of 2.95 (95% credible interval [CrI] 2.83–3.33). A vaccine with 70% efficacy had the capacity to contain COVID-19 outbreak but at very higher vaccination coverage 94.44% (95% Crl 92.44–99.92%) with a vaccine of 100% efficacy requiring 66.10% (95% Crl 64.72–69.95%) coverage. Social distancing measures put in place have so far reduced the number of social contacts by 80.31% (95% Crl 79.76–80.85%). These findings suggest that a highly efficacious vaccine would have been required to contain COVID-19 in South Africa. Therefore, the current social distancing measures to reduce contacts will remain key in controlling the infection in the absence of vaccines and other therapeutics.
2024-09-02 | BIOMD0000000978 | BioModels
Project description:Onderstepoort Biological Products Bluetongue Vaccine Genome Sequencing
| PRJNA718723 | ENA
Project description:Bluetongue virus Genome sequencing and assembly
| PRJNA548474 | ENA
Project description:Mycobacterium tuberculosis has the ability to persist within the host in a clinically latent stage. One important condition believed to contribute to latency is reduced access to oxygen but the response of M. tuberculosis to hypoxia is partially characterized. Virtually all dormant models against tuberculosis the vaccine tested in animals used laboratory strains H37Rv or Erdman strains. But major outbreaks of TB occur with the strains that have widely different genotypes and phenotypes compare to H37Rv. In this study, we used a commercial oligonucleotide microarray to determine the overall transcriptional response of lab strain (H37Rv) and most prevalent strains of Mycobacterium tuberculosis from South India S7 and S10 to hypoxia. Analysis of microarray results revealed that a total of 1161 genes are differentially regulated in H37Rv, among them 659 genes are upregulated and 502 genes are down regulated when > 1.5 fold change was taken as cut off. Microarray data of clinical isolates showed total of 790 genes are differentially regulated in S7 clinical isolates among which 453 are upregulated and 337 are down regulated. Interestingly numerous genes are differentially regulated in S10 clinical isolates (total of 2805 genes) and 1463 are upregulated and 1342 genes are down regulated during reduced oxygen model (Wayne’s model). Real-time quantitative RT-PCR was performed for few genes to validate the microarray results. To our knowledge, this genome-wide transcriptomics approach has produced the first insights into the response of South Indian prevalent clinical strains of M. tuberculosis when exposed to reduced oxygen stress.
2014-12-01 | GSE55863 | GEO
Project description:The study aimed to characterize plasmids mediating carbepenem resistance in Klebsiella pneumoniae in Pretoria, South Africa. We analysed 56 K. pneumoniae isolates collected from academic hospital around Pretoria. Based on phenotypic and molecular results of these isolates, 6 representative isolates were chosen for further analysis using long reads sequencing platform. We observed multidrug resistant phenotype in all these isolates, including resistance to aminoglycosides, tetracycline, phenicol, fosfomycin, floroquinolones, and beta-lactams antibiotics. The blaOXA-48/181 and blaNDM-1/7 were manily the plasmid-mediated carbapenemases responsible for carbapenem resistance in the K. pneumoniae isolates in these academic hospitals. These carbapenemase genes were mainly associated with plasmid replicon groups IncF, IncL/M, IncA/C, and IncX3. This study showed plasmid-mediated carbapenemase spread of blaOXA and blaNDM genes mediated by conjugative plasmids in Pretoria hospitals.
2019-10-17 | GSE138949 | GEO
Project description:Background Bordetella pertussis is a Gram-negative bacterium that infects the human respiratory tract and causes pertussis or whooping cough. The disease has resurged in many countries including Finland where the whole-cell pertussis vaccine has been used for more than 50 years. Antigenic divergence has been observed between vaccine strains and clinical isolates in Finland. To better understand genome evolution in B. pertussis circulating in the immunized population, we developed an oligonucleotide-based microarray for comparative genomic analysis of Finnish strains isolated during the period of 50 years. Methodology/Principal Findings The microarray consisted of 3,582 oligonucleotides (70-mer) and covered 94% of the genome of Tohama I, the strain of which the genome has been sequenced [21]. Twenty isolates from 1953 to 2004 were studied together with two Finnish vaccine strains and two international reference strains. The isolates were selected according to their characteristics, e.g. the year and place of isolation and pulsed-field gel electrophoresis profiles. Genomic DNA of the tested strains, along with reference DNA of Tohama I strain, was labelled and hybridized. The absence of genes as established with microarrays, was confirmed by PCR. Compared to the Tohama I strain, Finnish isolates lost 7 (8.6 kb) to 49 (55.3 kb) genes, clustered in one to four distinct loci. The number of lost genes increased with time, and one third of lost genes had functions related to ion transport, metabolism, or energy production and conversion. All four loci of lost genes were flanked by the insertion sequence element IS481. Conclusion/Significance Our results showed that the progressive gene loss occurred in Finnish B. pertussis strains isolated during a period of 50 years and confirmed that B. pertussis is dynamic and is continuously evolving, suggesting that the bacterium may use gene loss as one strategy to adapt to highly immunized populations. Keywords: comparetive genomic hybridisation
2007-09-20 | GSE8092 | GEO
Project description:Gray leaf spot (GLS) disease of maize is caused by the fungus Cercospora zeina in African countries, such as South Africa. The plant material was from maize inbred line B73-QTL, which was introgressed with a QTL region for resistance to GLS from the maize inbred line CML444 (Berger et al (2014) BMC Genetics 15 60 www.biomedcentral.com/1471-2156/15/60 ). This QTL was named 10G2_GLS and 10H_GLS from two field trials in KwaZulu-Natal province, South Africa in that study. B73-QTL plants were planted in the field, and subjected to natural infection with C. zeina. This was the same field trial as B73 plants that were sampled for RNAseq and the data reported in Swart et al (2017) Mol Plant Microbe Interact 30 710-724 (2017)(GSE94442). Samples were collected from lower leaves with moderate GLS lesions and younger upper leaves of the same B73-QTL plants with very few immature GLS lesions. The first aim of the experiment was to compare the maize transcriptomes during C.zeina challenge between B73 (from GSE94442 data) and B73-QTL plants (this study). The second aim was to identify novel transcripts expressed from the QTL region, which may underlie the quantitative disease resistance to GLS. The third aim was to identify C. zeina genes expressed in planta during infection.
2020-02-14 | GSE137198 | GEO
Project description:Despite high vaccination coverage, pertussis is on the rise in many countries including Czech Republic. To better understand B. pertussis resurgence we compared the changes in genome structures between Czech vaccine and circulating strains and subsequently, we determined how these changes translated into global transcriptomic and proteomic profiles. The whole-genome sequencing revealed that both historical and recent isolates of B. pertussis display substantial variation in genome organization and cluster separately. The RNA-seq and LC-MS/MS analyses indicate that these variations translated into discretely separated transcriptomic and proteomic profiles. Compared to vaccine strains, recent isolates displayed increased expression of flagellar genes and decreased expression of polysaccharide capsule operon. Czech strains (Bp46, K10, Bp155, Bp318 and Bp6242)exhibited increased expression of T3SS and sulphate metabolism genes when compared to Tohama I. In spite of 50 years of vaccination the Czech vaccine strains (VS67, VS393 and VS401) differ from recent isolates to a lesser extent than from another vaccine strain Tohama I.
2021-09-08 | PXD015184 | Pride
Project description:Resurgence of pertussis has been observed in many countries with high vaccination coverage and clonal expansion of certain Bordetella pertussis strains has been associated with recent epidemics in Europe. It is known that vaccinations have selected strains which are different from those used for vaccine production. However, little is known about the differences in genomic content of strains circulating before the vaccination was introduced. In this study, we compared the genomes of 39 vaccine strains and old clinical isolates collected from Finland (N=5), Poland (N=14), Serbia (N=10) and the UK (N=10). The analysis included genotyping, pulsed-field gel electrophoresis (PFGE) and comparative genomic hybridisation (CGH). Compared to the strain Tohama I, the European strains analyzed have lost three major regions of difference (RD3, 5 and 29). However, difference in frequency of the absent RDs 3, 5 or 29 was observed among the four countries. Of the strains with absent RD5, half had also a duplicated region in the genome. All four RDs (RD22, 23, 24 and 26) absent in Tohama I were present in majority of the tested strains. Results obtained from PFGE analysis correlated well with those of CGH. Recently a novel pertussis toxin promoter allele (ptxP3) was described. Strains with ptxP3 have replaced resident ptxP1 strains. When the recent strains (N=22) selected from the four countries were examined, the ptxP3 allele was found in all countries except Poland. Our result indicates that at least three clusters of B. pertussis circulated in Europe in pre-vaccine era and their genomes were distinct from that of the reference strain Tohama I. Although progressive gene loss occurs in B. pertussis population with time, difference in frequency of the lost genes were observed among the countries. The observed differences in genomic content might be vaccine-driven.
2011-10-04 | GSE29579 | GEO
Project description:Transcription profiles of a field collection of Anopheles gambiae M molecular form (i.e. Anopheles coluzzii) from a population from Cote d'Ivoire (West Africa) were compared to two laboratory strains and to a wild caught field strain (all carbamate insecticide susceptible) to investigate their differences in insecticide resistance. Both carbamate-exposed and carbamate-unexposed Cote d'Ivoire samples were compared to each susceptible strain, and also directly to one another (i.e. exposed vs. unexposed).
2013-12-03 | E-MTAB-1903 | biostudies-arrayexpress