The South African Response to the Pandemic.
Ontology highlight
ABSTRACT:
SUBMITTER: Abdool Karim SS
PROVIDER: S-EPMC7281717 | biostudies-literature | 2020 Jun
REPOSITORIES: biostudies-literature
Publications
The South African Response to the Pandemic.
The New England journal of medicine 20200529 24
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Project description:South African research ethics committees (RECs) faced significant challenges during the COVID-19 pandemic. Research ethics committees needed to find a balance between careful consideration of scientific validity and ethical merit of protocols, and review with the urgency normally associated with public health emergency research. We aimed to explore the views of South African RECs on their pandemic preparedness and response during COVID-19. We conducted in-depth interviews with 21 participants from RECs that were actively involved in the review of COVID-19 related research, at seven academic institutions across South Africa. Interviews were conducted remotely using an in-depth interview guide that included questions regarding REC preparedness and response to COVID-19. Interviews were conducted until data saturation, and audio-recordings were transcribed verbatim and coded. An inductive approach to thematic analysis was used to organise data into themes and sub-themes. This study focused on three main themes: coping during COVID-19, building REC capacity during pandemic times and a consistently cautious approach to mutual recognition of REC reviews. Despite an initial sense of unpreparedness, RECs were able to adapt and maintain careful ethical oversight of both COVID and non-COVID research, and the rigour of REC reviews. Several important lessons for preparedness and response to future pandemics were identified, including heightened awareness of publication, funding and political pressures, the importance of regular training for RECs and researchers, and strategies to enhance moral resilience of REC members. Incremental steps are needed to build trust and authentic partnerships among RECs in inter-pandemic times, to facilitate collaboration during future public health emergencies.
| S-EPMC11619208 | biostudies-literature
Project description:South African abattoir wastewater
| PRJEB70870 | ENA
Project description:South African peritidal stromatolites Metagenome
| PRJNA706574 | ENA
Project description:IntroductionIn South Africa, public perceptions of the COVID-19 pandemic and risk mitigation measures remain mixed. To better understand health behaviours in the context of COVID-19, a qualitative study was conducted, which aimed to investigate perceptions relating to the COVID-19 pandemic among the South African adult population.MethodsTwelve online focus groups were conducted across the following age groups: 18-34, 35-54, 55 + years old (total n = 70) in December 2021. Diversity across socioeconomic status, geographical areas, and urban and rural settings was maximised, with an equal representation of men and women. Focus groups were conducted, and audio recorded using an online platform, transcribed verbatim and thematically analysed using MAXQDA.ResultsThere were mixed perceptions around the pandemic, however, the majority of participants appreciated government actions at the onset of the pandemic and as a result government trust was reported to have initially been high. Nevertheless, as the pandemic progressed, challenges relating to government communication around the pandemic, the inconsistent application of preventative measures by government, the use of soldiers to enforce preventative measures, the banning of alcohol and cigarettes, government corruption and the pervasiveness of social media were reported to have eroded government trust, negatively impacting the uptake of preventative measures. Economic and psychological impacts were experienced differently across income groups. Low-income earners, who already had pre-existing economic challenges reported increased psychological and financial strain. While the once cushioned middle class reported an increase in job insecurity accompanied by psychological challenges. High income earners did not report economic challenges but reported being affected psychologically. Though, low-income earners reported an appreciation of the government financial relief afforded to them middle income earners appeared to not have received adequate financial support.ConclusionWith the existing mistrust of government, there is need for government to leverage existing trusted sources in communities to aid in the implementation of preventative measures. These findings support the development of context specific solutions to address challenges faced at different socioeconomic levels.
| S-EPMC10091320 | biostudies-literature
Project description:Background: Tuberculosis (TB) remains a global health problem, with vaccination likely to be a necessary part of a successful control strategy. Results of the first Phase 2b efficacy trial of a candidate vaccine, MVA85A, evaluated in BCG-vaccinated infants were published last year. Although no improvement in efficacy above BCG alone was seen, cryopreserved samples from this trial provide an opportunity to study the immune response to vaccination in this population. Methods: We investigated blood samples taken before vaccination (baseline) and one and 28 days post-vaccination with MVA85A or placebo (Candin). The IFN-γ ELISpot assay was performed at baseline and on day 28 to quantify the adaptive response to Ag85A peptides. Gene expression analysis was performed at all three timepoints to identify early gene signatures predictive of the magnitude of the subsequent adaptive T cell response using the significance analysis of microarrays (SAM) statistical package and gene set enrichment analysis. Results: One day post-MVA85A, there is an induction of inflammatory pathways compared to placebo samples. Modules associated with myeloid cells and inflammation pre- and one day post-MVA85A correlate with a higher IFN-γ ELISpot response post-vaccination. By contrast, previous work done in UK adults shows early inflammation in this population is not associated with a strong T cell response but that induction of regulatory pathways inversely correlates with the magnitude of the T cell response. This may be indicative of important mechanistic differences in how T cell responses develop in these two populations following vaccination with MVA85A. Conclusion: The results suggest the capacity of MVA85A to induce a strong innate response is key to the initiation of an adaptive immune response in South African infants but induction of regulatory pathways may be more important in UK adults. Understanding differences in immune response to vaccination between populations is likely to be an important aspect of developing successful vaccines and vaccination strategies. Trial registration: ClinicalTrials.gov number NCT00953927
2014-06-11 | GSE56559 | GEO
Project description:BackgroundGiven the economic and social divide that exists in South Africa, it is critical to manage the health response of its residents to the Covid-19 pandemic within the different socio-economic contexts that define the lived realities of individuals.ObjectiveThe objective of this study is to analyse the Covid-19 preventive behaviour and the socio-economic drivers behind the health-response behaviour.DataThe study employs data from waves 1 and 2 of South Africa's nationally representative National Income Dynamics Study (NIDS)-Coronavirus Rapid Mobile Survey (CRAM). The nationally representative panel data has a sample of 7073 individuals in Wave 1 and 5676 individuals in Wave 2.MethodsThe study uses bivariate statistics, concentration indices and multivariate estimation techniques, ranging from a probit, control-function approach, special-regressor method and seemingly unrelated regression to account for endogeneity while identifying the drivers of the response behaviour.FindingsThe findings indicate enhanced behavioural responsiveness to Covid-19. Preventive behaviour is evolving over time; the use of face mask has overtaken handwashing as the most utilised preventive measure. Other measures, like social distancing, avoiding close contact, avoiding big groups and staying at home, have declined between the two periods of the study. There is increased risk perception with significant concentration among the higher income groups, the educated and older respondents. Our findings validate the health-belief model, with perceived risk, self-efficacy, perceived awareness and barriers to preventive strategy adoption identified as significant drivers of health-response behaviour. Measures such as social distancing, avoiding close contact, and the use of sanitisers are practised more by the rich and educated, but not by the low-income respondents.ConclusionThe respondents from lower socio-economic backgrounds are associated with optimism bias and face barriers to the adoption of preventive strategies. This requires targeted policy attention in order to make response behaviour effective.
| S-EPMC8051761 | biostudies-literature
Project description:RNA was extracted from all instar (insect developmental) stages for both D. noxia biotypes SA1 and SAM with the purpose to capture as many expressed transcripts as possible. South African D. noxia biotype SA1 is known to be the least virulent aphid, while its offspring, the South African D. noxia biotype SAM is the most virulent. The overall purpose of the experiment was to establish a baseline availability of transcripts to the aphids as well as help improve on current genome assemblies. Three biological replicates of 100 aphids each was collected from both biotypes SA1 and SAM that were respectively reared on preference host cultivars. Whole aphids were flash frozen in liquid nitrogen, ground to a powder with micro pistils and RNA was extracted making use of a Qiagen RNeasy kit. Library preparation for sequencing was performed using an Illumina TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E protocol. The replicate samples from the SAM biotype yielded between 120 – 140 million 100bp PE reads and the replicate samples from the SA1 biotype yielded between 113 – 137 million 100bp PE reads (with a Q20 phred score above 98% for all replicates) after sequencing on the NovaSeq6000 system. De novoassembly was performed making use of the Trinity package.
2020-12-31 | GSE143502 | GEO
Project description:Background: Tuberculosis (TB) remains a global health problem, with vaccination likely to be a necessary part of a successful control strategy. Results of the first Phase 2b efficacy trial of a candidate vaccine, MVA85A, evaluated in BCG-vaccinated infants were published last year. Although no improvement in efficacy above BCG alone was seen, cryopreserved samples from this trial provide an opportunity to study the immune response to vaccination in this population. Methods: We investigated blood samples taken before vaccination (baseline) and one and 28 days post-vaccination with MVA85A or placebo (Candin). The IFN-γ ELISpot assay was performed at baseline and on day 28 to quantify the adaptive response to Ag85A peptides. Gene expression analysis was performed at all three timepoints to identify early gene signatures predictive of the magnitude of the subsequent adaptive T cell response using the significance analysis of microarrays (SAM) statistical package and gene set enrichment analysis. Results: One day post-MVA85A, there is an induction of inflammatory pathways compared to placebo samples. Modules associated with myeloid cells and inflammation pre- and one day post-MVA85A correlate with a higher IFN-γ ELISpot response post-vaccination. By contrast, previous work done in UK adults shows early inflammation in this population is not associated with a strong T cell response but that induction of regulatory pathways inversely correlates with the magnitude of the T cell response. This may be indicative of important mechanistic differences in how T cell responses develop in these two populations following vaccination with MVA85A. Conclusion: The results suggest the capacity of MVA85A to induce a strong innate response is key to the initiation of an adaptive immune response in South African infants but induction of regulatory pathways may be more important in UK adults. Understanding differences in immune response to vaccination between populations is likely to be an important aspect of developing successful vaccines and vaccination strategies. Trial registration: ClinicalTrials.gov number NCT00953927
2014-06-11 | GSE56561 | GEO
Project description:In susceptible plant hosts, co-evolution has favoured viral strategies to evade host defenses and utilize resources to their own benefit. The degree of manipulation of host gene expression is dependent on host-virus specificity and certain abiotic factors. In order to gain insight into global transcriptomic changes for a geminivirus pathosystem, South African cassava mosaic virus [ZA:99] (SACMV-ZA:99]) and Arabidopsis thaliana, 4 x 44K Agilent microarrays were adopted. After normalization, a 2-fold change filtering of data (p<0.05) identified 1,820 differentially expressed genes in apical leaf tissue. A significant increase in differential gene expression over time (451 genes at 14 dpi, 742 genes at 24 dpi, and 1011 genes at 36 dpi) was observed. This increase in expression, correlated with an increase in SACMV accumulation as virus copies were 5-fold higher at 24 dpi and 6-fold higher at 36 dpi than at 14 dpi (1.1x104 virus copies present at 14 dpi, 5.7x104 copies at 24 dpi, and 6.3x104 copies at 36 dpi). Many 2-fold genes were primarily involved in stress and defense responses, phytohormone signalling pathways, cellular transport, cell-cycle regulation, transcription, oxidation-reduction, and other metabolic processes. Forty-one genes (2.3%) were shown to be continuously expressed across the infection period, indicating that the majority of genes were transient and unique to a particular time point. Plant signalling networks were disrupted and manipulated by SACMV-[ZA:99] in order to affect homeostasis and antagonize host’s defense responses. At the same time, an adaptive response was initiated to reprogramme metabolism and divert energy from growth-related processes to defense, all leading to disruption of normal biological host processes. Comparisons between SACMV-[ZA:99] with plant-infecting RNA and DNA viruses revealed similarities and differences in expression patterns among viruses, showing either general defense or virus-specific responses. Within the Geminiviridae family in particular, similarities in cell-cycle regulation and gene expression patterns correlated between SACMV-[ZA:99] and Cabbage leaf curl virus (CaLCuV) but differences were also evident. For instance, CaLCuV showed antagonistic interactions between Salicyclic Acid (SA) and Jasmonic Acid (JA) pathways, whereas SACMV displayed synergism. Differences in gene induction, repression and outcome between the two geminiviruses clearly demonstrated host-specific interactions with SACMV-[ZA:99] leading to infection. To our knowledge this is the first geminivirus study identifying differentially expressed transcripts across 3 time points
2013-01-07 | GSE43282 | GEO
Project description:IntroductionThere was a low level of pandemic preparedness in South Asia, but the region has done well in mounting an appropriate response to the coronavirus disease 2019 (COVID-19) pandemic. The rate and proportion of deaths attributed to COVID-19 are lower despite case surges similar to the rest of the world.ResultsThe COVID-19 pandemic has revealed the glaring vulnerabilities of the health system. In addition, the high burden of non-communicable diseases in South Asia multiplies the complexities in combating present and future health crises. The advantage offered by the younger population demographics in South Asia may not be sustained with the rising burden of non-communicable diseases and lack of priority setting for improving health systems.ConclusionThe COVID-19 pandemic has provided a window for introspection, scaling up preparedness for future pandemics, and improving the health of the population overall.
| S-EPMC7836380 | biostudies-literature