Seeding COVID-19 across Sub-Saharan Africa: An Analysis of Reported Importation Events across 49 Countries.
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ABSTRACT:
SUBMITTER: Skrip LA
PROVIDER: S-EPMC8103462 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Sub-Saharan Africa represents 69% of the total number of individuals living with HIV infection worldwide and 72% of AIDS deaths globally. Pulmonary infection is a common and frequently fatal complication, though little is known regarding the lower airway microbiome composition of this population. Our objectives were to characterize the lower airway microbiome of Ugandan HIV-infected patients with pneumonia, to determine relationships with demographic, clinical, immunological, and microbiological variables and to compare the composition and predicted metagenome of these communities to a comparable cohort of patients in the US (San Francisco). Bronchoalveolar lavage samples from a cohort of 60 Ugandan HIV-infected patients with acute pneumonia were collected. Amplified 16S ribosomal RNA was profiled and aforementioned relationships examined. Ugandan airway microbiome composition and predicted metagenomic function were compared to US HIV-infected pneumonia patients. Among the most common bacterial pulmonary pathogens, Pseudomonas aeruginosa was most prevalent in the Ugandan cohort. Patients with a richer and more diverse airway microbiome exhibited lower bacterial burden, enrichment of members of the Lachnospiraceae and sulfur-reducing bacteria and reduced expression of TNF-alpha and matrix metalloproteinase-9. Compared to San Franciscan patients, Ugandan airway microbiome were significantly richer, and compositionally distinct with predicted metagenomes that encoded a multitude of distinct pathogenic pathways e.g secretion systems. Ugandan pneumonia-associated airway microbiome is compositionally and functionally distinct from those detected in comparable patients in developed countries, a feature which may contribute to adverse outcomes in this population. Please note that the data from the comparable cohort of patients in the USUS data was published as supplemental material of PMID: 22760045 but not submitted to GEO The 'patient_info.txt' contains 12 clinical, 7 immunological and 3 microbiological variables for each patient.
2014-02-20 | GSE52791 | GEO
Project description:Konzo, a disease characterized by sudden, irreversible spastic paraparesis, affecting up to 10% of the population in some regions of Sub-Saharan Africa during outbreaks and is strongly associated with dietary exposure to cyanogenic bitter cassava. The molecular mechanisms underlying the development of konzo, remain largely unknown. Here, through an analysis of 16 individuals with konzo and matched healthy controls from the same outbreak zones, we identified 117 differentially methylated loci involved in numerous biological processes that may identify cyanogenic- sensitive regions of the genome, providing the first study of epigenomic alterations associated with sub-lethal cyanide exposure and a clinical phenotype.
2022-12-31 | GSE180119 | GEO
Project description:Sub-Saharan Africa represents 69% of the total number of individuals living with HIV infection worldwide and 72% of AIDS deaths globally. Pulmonary infection is a common and frequently fatal complication, though little is known regarding the lower airway microbiome composition of this population. Our objectives were to characterize the lower airway microbiome of Ugandan HIV-infected patients with pneumonia, to determine relationships with demographic, clinical, immunological, and microbiological variables and to compare the composition and predicted metagenome of these communities to a comparable cohort of patients in the US (San Francisco). Bronchoalveolar lavage samples from a cohort of 60 Ugandan HIV-infected patients with acute pneumonia were collected. Amplified 16S ribosomal RNA was profiled and aforementioned relationships examined. Ugandan airway microbiome composition and predicted metagenomic function were compared to US HIV-infected pneumonia patients. Among the most common bacterial pulmonary pathogens, Pseudomonas aeruginosa was most prevalent in the Ugandan cohort. Patients with a richer and more diverse airway microbiome exhibited lower bacterial burden, enrichment of members of the Lachnospiraceae and sulfur-reducing bacteria and reduced expression of TNF-alpha and matrix metalloproteinase-9. Compared to San Franciscan patients, Ugandan airway microbiome were significantly richer, and compositionally distinct with predicted metagenomes that encoded a multitude of distinct pathogenic pathways e.g secretion systems. Ugandan pneumonia-associated airway microbiome is compositionally and functionally distinct from those detected in comparable patients in developed countries, a feature which may contribute to adverse outcomes in this population. Please note that the data from the comparable cohort of patients in the USUS data was published as supplemental material of PMID: 22760045 but not submitted to GEO The 'patient_info.txt' contains 12 clinical, 7 immunological and 3 microbiological variables for each patient. The G2 PhyloChip microarray platform (commercially available from Second Genome, Inc.) was used to profile bacteria in lower airway samples from 60 subjects
2014-02-20 | E-GEOD-52791 | biostudies-arrayexpress
Project description:ObjectiveThe aim of this study was to identify the range and frequency of patient-reported barriers and facilitators to antiretroviral treatment (ART) adherence in sub-Saharan Africa (SSA).DesignStudies from 2005 to 2016 were identified by searching 10 electronic databases and through additional hand and web-searching.MethodsInclusion criteria were HIV-positive adults taking ART based in any SSA country, qualitative study or quantitative survey and included at least one patient-reported barrier or facilitator to ART adherence. Exclusion criteria were only including data from treatment-naive patients initiating ART, only single-dose treatment, participants residing outside of SSA and reviews.ResultsAfter screening 11 283 records, 154 studies (161 papers) were included in this review. Forty-three barriers and 30 facilitators were reported across 24 SSA countries. The most frequently identified barriers across studies were forgetting (n = 76), lack of access to adequate food (n = 72), stigma and discrimination (n = 68), side effects (n = 67) and being outside the house or travelling (n = 60). The most frequently identified facilitators across studies were social support (n = 60), reminders (n = 55), feeling better or healthier after taking ART (n = 35), disclosing their HIV status (n = 26) and having a good relationship with a health provider (n = 22).ConclusionThis review addresses the gap in knowledge by collating all the patient-reported barriers and facilitators to ART adherence in SSA. Current barriers measures need to be adapted or new tools developed to include the wide variety of factors identified. The factors that have the greatest impact need to be isolated so interventions are developed that reduce the barriers and enhance the facilitators.
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Project description:BackgroundAlthough religious affiliation has been identified as a potential barrier to immunization in some African countries, there are no systematic multi-country analyses, including within-country variability, on this issue. We investigated whether immunization varied according to religious affiliation and sex of the child in sub-Saharan African (SSA) countries.MethodsWe used data from 15 nationally representative surveys from 2010 to 2016. The major religious groups were described by country in terms of wealth, residence, and education. Proportions of fully immunized and unvaccinated children were stratified by country, maternal religion, and sex of the child. Poisson regression with robust variance was used to assess whether the outcomes varied according to religion, with and without adjustment for the above cited sociodemographic confounders. Interactions between child sex and religion were investigated.ResultsFifteen countries had >10% of families affiliated with Christianity and >10% affiliated with Islam, and four also had >10% practicing folk religions. In general, Christians were wealthier, more educated and more urban. Nine countries had significantly lower full immunization coverage among Muslims than Christians (pooled prevalence ratio = 0.81; 95%CI: 0.79-0.83), of which seven remained significant after adjustment for confounders (pooled ratio = 0.90; 0.87-0.92). Four countries had higher coverage among Muslims, of which two remained significant after adjustment. Regarding unvaccinated children, six countries showed higher proportions among Muslims, all of which remained significant after adjustment [crude pooled ratio = 1.83 (1.59-2.07); adjusted = 1.31 (1.14-1.48)]. Children from families practicing folk religions did not show any consistent patterns in immunization. Child sex was not consistently associated with vaccination.ConclusionMuslim religion was associated with lower vaccine coverage in several SSA countries, both for boys and girls. The involvement of religious leaders is essential for increasing immunization coverage and supporting the leave no one behind agenda of the Sustainable Development Goals.
| S-EPMC6995994 | biostudies-literature
Project description:Measurement of incidence rates of childhood cancer in Africa is difficult. The study 'Cancer of Childhood in sub Saharan Africa' [Stefan C, Bray F, Ferlay J, Parkin DM and Liu B (2017) Cancer of Childhood in sub-Saharan Africaecancer11(755)] brings together results from 16 population-based registries which, as members of the African Cancer Registry Network (AFCRN), have been evaluated as achieving adequate coverage of their target population. The cancers are classified according to the third revision of the International Classification of Childhood Cancer (ICCC-3) and recorded rates in Africa are compared with those in childhood populations in the UK, France, and the USA. It is clear that, in many centres, lack of adequate diagnostic and treatment facilities, leads to under-diagnosis (and enumeration) of leukaemias and brain cancers. However, for several childhood cancers, incidence rates in Africa are higher than those in high income countries. This applies to infection-related cancers such as Kaposi sarcoma, Burkitt lymphoma, Hodgkin lymphoma and hepatocellular carcinoma, and also to two common embryonal cancers-retinoblastoma and nephroblastoma. These (and other) observations are unlikely to be artefact, and are of considerable interest when considering possible aetiological factors, including ethnic differences in risk (and hence genetic/familial antecedents). The data reported are the most extensive so far available on the incidence of cancer in sub Saharan Africa, and clearly indicate the need for more resources to be devoted to cancer registration, especially in the childhood age range, as part of an overall programme to improve the availability of diagnosis and treatment of this group of cancers, many of which have-potentially-an excellent prognosis.
| S-EPMC5533598 | biostudies-other
Project description:BACKGROUND:Although under-five mortality reduced globally from 93 per 1000 live births in 1990 to 39 in 2018, sub-Saharan Africa witnessed an increase from 31% in 1990 to 54% in 2018. Morbidity has been reported to contribute largely to these deaths. This study examined the factors that are associated with childhood morbidity in sub-Saharan Africa. METHODS:Demographic and Health Surveys of 31 countries in sub-Saharan Africa were used in this study. The study involved 189 069 children who had or did not have fever, cough or diarrhoea in the 2 weeks preceding the surveys. Descriptive statistics and binary logistic regression were applied in the analysis. RESULTS:About 22% of the children suffered from fever, 23% suffered from cough and 16% suffered from diarrhoea. While the odds of experiencing fever increased by 37% and 18%, respectively, for children from poorest and poorer households, children of women aged 15-24 and 25-34 years are 47% and 23%, respectively, more likely to experience diarrhoea. The probability of suffering from morbidity increased for children who are 12-23 months, of higher order birth, small in size at birth and from households with non-improved toilet facility. CONCLUSIONS:This study has shown that childhood morbidity remains a major health challenge in sub-Saharan Africa with socioeconomic, maternal, child's and environmental factors playing significant roles. Efforts at addressing this problem should consider these factors.
| S-EPMC7552796 | biostudies-literature
Project description:There is an urgent need for data to inform coronavirus disease (COVID-19) pandemic response efforts. At the same time, the pandemic has created challenges for data collection, one of which is interviewer training in the context of social distancing. In sub-Saharan Africa, in-person interviewer training and face-to-face data collection remain the norm, requiring researchers to think creatively about transitioning to remote settings to allow for safer data collection that respects government guidelines. Performance Monitoring for Action (PMA, formerly PMA2020) has collected both cross-sectional and longitudinal data on key reproductive health measures in Africa and Asia since 2013. Relying on partnerships with in-country research institutes and cadres of female interviewers recruited from sampled communities, the project was well-positioned to transition to collecting data on COVID-19 from the onset of the pandemic. This article presents PMA's development of a remote training system for COVID-19 surveys in the Democratic Republic of the Congo, Kenya, and Nigeria, including challenges faced and lessons learned. We demonstrate that remote interviewer training can be a viable approach when data are critically needed and in-person learning is not possible. We also argue against systematic replacement of in-person trainings with remote learning, instead recommending consideration of local context and a project's individual circumstances when contemplating a transition to remote interviewer training.
| S-EPMC8087422 | biostudies-literature
Project description:IntroductionHandwashing is fundamentally an inexpensive means of reducing the spread of communicable diseases. In developing countries, many people die due to infectious diseases that could be prevented by proper hand hygiene. The recent coronavirus (COVID-19) pandemic is a threat to people who are living in resource-limited countries including sub-Saharan Africa (SSA). Effective hand hygiene requires sufficient water from reliable sources, preferably accessible on premises, and access to handwashing facility (water and or soap) that enable hygiene behaviors. Therefore, this study aims to determine the prevalence of limited handwashing facility and its associated factors in sub-Saharan Africa.MethodsData from the Demographic and Health Surveys (DHS) were used, which have been conducted in 29 sub-Saharan African countries since January 1, 2010. A two-stage stratified random cluster sampling strategy was used to collect the data. This study comprised a total of 237,983 weighted samples. The mixed effect logistic regression model with a cluster-level random intercept was fitted. Meta-analysis and sub-group analysis were performed to establish the pooled prevalence.ResultsThe pooled prevalence of limited handwashing facility was found to be 66.16% (95% CI; 59.67%-72.65%). Based on the final model, household head with age group between 35 and 60 [AOR = 0.89, 95% CI; 0.86-0.91], households with mobile type of hand washing facility [AOR = 1.73, 95% CI; 1.70-1.77], unimproved sanitation facility [AOR = 1.58, 95% CI; 1.55-1.62], water access more than 30 min round trip [AOR = 1.16, 95% CI; 1.13-1.19], urban residential area [AOR = 2.08, 95% CI; 2.04-2.13], low media exposure [AOR = 1.47, 95% CI; 1.31-1.66], low educational level [AOR = 1.30, 95% CI; 1.14-1.48], low income level [AOR = 2.41, 95% CI; 2.33-2.49] as well as lower middle-income level [AOR = 2.10, 95% CI; 2.14-2.17] and households who had more than three children [AOR = 1.25, 95% CI; 1.20-1.31] were associated with having limited handwashing facility.Conclusion and recommendationThe pooled coverage of limited handwashing facility was high in sub-Saharan Africa. Raising awareness of the community and promoting access to handwashing materials particularly in poorer and rural areas will reduce its coverage.
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Project description:A characteristic of Plasmodium falciparum infections is the gradual acquisition of clinical immunity resulting from repeated exposures to the parasite. While the molecular basis of protection against clinical malaria remains unresolved, its effects on epidemiological patterns are well recognized. Accumulating epidemiological data constitute a valuable resource that must be intensively explored and interpreted as to effectively inform control planning.Here we apply a mathematical model to clinical data from eight endemic regions in sub-Saharan Africa. The model provides a quantitative framework within which differences in age distribution of clinical disease are assessed in terms of the parameters underlying transmission. The shorter infectious periods estimated for clinical infections induce a regime of bistability of endemic and malaria-free states in regions of mesoendemic transmission. The two epidemiological states are separated by a threshold that provides a convenient measure for intervention design. Scenarios of eradication and resurgence are simulated.In regions that support mesoendemic transmission, intervention success depends critically on reducing prevalence below a threshold which separates endemic and malaria-free regimes.
| S-EPMC2262141 | biostudies-other