Variation in SARS-CoV-2 outbreaks across sub-Saharan Africa.
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ABSTRACT:
SUBMITTER: Rice BL
PROVIDER: S-EPMC8590469 | biostudies-literature | 2021 Mar
REPOSITORIES: biostudies-literature
Publications
Variation in SARS-CoV-2 outbreaks across sub-Saharan Africa.
Rice Benjamin L BL Annapragada Akshaya A Baker Rachel E RE Bruijning Marjolein M Dotse-Gborgbortsi Winfred W Mensah Keitly K Miller Ian F IF Motaze Nkengafac Villyen NV Raherinandrasana Antso A Rajeev Malavika M Rakotonirina Julio J Ramiadantsoa Tanjona T Rasambainarivo Fidisoa F Yu Weiyu W Grenfell Bryan T BT Tatem Andrew J AJ Metcalf C Jessica E CJE
Nature medicine 20210202 3
A surprising feature of the SARS-CoV-2 pandemic to date is the low burdens reported in sub-Saharan Africa (SSA) countries relative to other global regions. Potential explanations (for example, warmer environments<sup>1</sup>, younger populations<sup>2-4</sup>) have yet to be framed within a comprehensive analysis. We synthesized factors hypothesized to drive the pace and burden of this pandemic in SSA during the period from 25 February to 20 December 2020, encompassing demographic, comorbidity, ...[more]
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Project description:A surprising feature of the SARS-CoV-2 pandemic to date is the low burdens reported in sub-Saharan Africa (SSA) countries relative to other global regions. Potential explanations (e.g., warmer environments1, younger populations2-4) have yet to be framed within a comprehensive analysis accounting for factors that may offset the effects of climate and demography. Here, we synthesize factors hypothesized to shape the pace of this pandemic and its burden as it moves across SSA, encompassing demographic, comorbidity, climatic, healthcare and intervention capacity, and human mobility dimensions of risk. We find large scale diversity in probable drivers, such that outcomes are likely to be highly variable among SSA countries. While simulation shows that extensive climatic variation among SSA population centers has little effect on early outbreak trajectories, heterogeneity in connectivity is likely to play a large role in shaping the pace of viral spread. The prolonged, asynchronous outbreaks expected in weakly connected settings may result in extended stress to health systems. In addition, the observed variability in comorbidities and access to care will likely modulate the severity of infection: We show that even small shifts in the infection fatality ratio towards younger ages, which are likely in high risk settings, can eliminate the protective effect of younger populations. We highlight countries with elevated risk of 'slow pace', high burden outbreaks. Empirical data on the spatial extent of outbreaks within SSA countries, their patterns in severity over age, and the relationship between epidemic pace and health system disruptions are urgently needed to guide efforts to mitigate the high burden scenarios explored here.
| S-EPMC7386522 | biostudies-literature
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:BackgroundDespite the high COVID-19 morbidity and mortality rates across the world, the reported rates in sub-Saharan Africa (SSA), which has a higher burden of other infectious diseases and overwhelmed healthcare systems, remain relatively low. This study aims to better understand the potential factors that contribute to this phenomenon, especially among cancer patients who are considered as a high-risk group for developing severe COVID-19.MethodsPlasma samples collected during the COVID-19 pandemic from SARS-CoV-2 unvaccinated cancer and potential blood donor populations were analyzed for SARS-CoV-2 (spike and nucleocapsid proteins) antibodies by an immunofluorescence assay. The relationships between SARS-CoV-2 seroprevalences and study variables were determined using a logistic regression analysis.ResultsHigh seroprevalence against the SARS-CoV-2 spike and nucleocapsid proteins were found among the SARS-CoV-2 unvaccinated COVID-19 pandemic populations in SSA. However, the cancer patients demonstrated a lower seroprevalence compared to potential blood donors. There was also an association between mild COVID-19 symptoms with prior tuberculosis vaccination among cancer patients.ConclusionCancer patients in SSA tend to have a relatively lower SARS-CoV-2 seroprevalence compared to potential blood donors recruited from the same geographic locations during the COVID-19 pandemic. More study is required to determine its cause and potential impact on SARS-CoV-2 vaccination among cancer patients.
| S-EPMC9369079 | biostudies-literature
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:BackgroundCholera remains a public health threat but is inequitably distributed across sub-Saharan Africa. Lack of standardized reporting and inconsistent outbreak definitions limit our understanding of cholera outbreak epidemiology.MethodsFrom a database of cholera incidence and mortality, we extracted data from sub-Saharan Africa and reconstructed outbreaks of suspected cholera starting in January 2010 to December 2019 based on location-specific average weekly incidence rate thresholds. We then described the distribution of key outbreak metrics.ResultsWe identified 999 suspected cholera outbreaks in 744 regions across 25 sub-Saharan African countries. The outbreak periods accounted for 1.8 billion person-months (2% of the total during this period) from January 2010 to January 2020. Among 692 outbreaks reported from second-level administrative units (e.g., districts), the median attack rate was 0.8 per 1000 people (interquartile range (IQR), 0.3-2.4 per 1000), the median epidemic duration was 13 weeks (IQR, 8-19), and the median early outbreak reproductive number was 1.8 (range, 1.1-3.5). Larger attack rates were associated with longer times to outbreak peak, longer epidemic durations, and lower case fatality risks.ConclusionsThis study provides a baseline from which the progress toward cholera control and essential statistics to inform outbreak management in sub-Saharan Africa can be monitored.
| S-EPMC9439956 | biostudies-literature
Project description:Low crop yields in Sub-Saharan Africa are associated with low fertilizer use. To better understand patterns of, and opportunities for, fertilizer use, location specific fertilizer price data may be relevant. We compiled local market price data for urea fertilizer, a source of inorganic nitrogen, in 1729 locations in eighteen countries in two regions (West and East Africa) from 2010-2018 to understand patterns in the spatial variation in fertilizer prices. The average national price was lowest in Ghana (0.80 USD kg-1), Kenya (0.97 USD kg-1), and Nigeria (0.99 USD kg-1). Urea was most expensive in three landlocked countries (Burundi: 1.51, Uganda: 1.49, and Burkina Faso: 1.49 USD kg-1). Our study uncovers considerable spatial variation in fertilizer prices within African countries. We show that in many countries this variation can be predicted for unsampled locations by fitting models of prices as a function of longitude, latitude, and additional predictor variables that capture aspects of market access, demand and environmental conditions. Predicted within-country urea price variation (as a fraction of the median price) was particularly high in Kenya (0.77-1.12), Nigeria (0.83-1.34), Senegal (0.73-1.40), Tanzania (0.90-1.29) and Uganda (0.93-1.30), but much lower in Burkina Faso (0.96-1.04), Burundi (0.95-1.05), and Togo (0.94-1.05). The correlation coefficient of the country level models was between 0.17 to 0.83 (mean 0.52) and the RMSE varies from 0.005 to 0.188 (mean 0.095). In 10 countries, predictions were at least 25% better than a null-model that assumes no spatial variation. Our work indicates new opportunities for incorporating spatial variation in prices into efforts to understand the profitability of agricultural technologies across rural areas in Sub-Saharan Africa.
| S-EPMC6959603 | biostudies-literature
Project description:Introduction: For the COVID-19 (SARS-CoV-2) response, COVID-19 antigen (Ag), and antibody (Ab) rapid diagnostic tests (RDTs) are expected to complement central molecular testing particularly in low-resource settings. The present review assesses requirements for implementation of COVID-19 RDTs in sub-Saharan Africa. Methods: Review of PubMed-published articles assessing COVID-19 RDTs complemented with Instructions for Use (IFU) of products. Results: In total 47 articles on two COVID-19 Ag RDTs and 54 COVID-19 Ab RDTs and IFUs of 20 COVID-19 Ab RDTs were retrieved. Only five COVID-19 Ab RDTs (9.3%) were assessed with capillary blood sampling at the point-of-care; none of the studies were conducted in sub-Saharan Africa. Sampling: Challenges for COVID-19 Ag RDTs include nasopharyngeal sampling (technique, biosafety) and sample stability; for COVID-19 Ab RDTs equivalence of whole blood vs. plasma/serum needs further validation (assessed for only eight (14.8%) products). Sensitivity-Specificity: sensitivity of COVID-19 Ag and Ab RDTs depend on viral load (antigen) and timeframe (antibody), respectively; COVID-19 Ab tests have lower sensitivity compared to laboratory test platforms and the kinetics of IgM and IgG are very similar. Reported specificity was high but has not yet been assessed against tropical pathogens. Kit configuration: For COVID-19 Ag RDTs, flocked swabs should be added to the kit; for COVID-19 Ab RDTs, finger prick sampling materials, transfer devices, and controls should be added (currently only supplied in 15, 5, and 1/20 products). Usability and Robustness: some COVID-19 Ab RDTs showed high proportions of faint lines (>40%) or invalid results (>20%). Shortcomings were reported for buffer vials (spills, air bubbles) and their instructions for use. Stability: storage temperature was ≤ 30°C for all but one RDT, in-use and result stability were maximal at 1 h and 30 min, respectively. Integration in the healthcare setting requires a target product profile, landscape overview of technologies, certified manufacturing capacity, a sustainable market, and a stringent but timely regulation. In-country deployment depends on integration in the national laboratory network. Discussion/Conclusion: Despite these limitations, successful implementation models in triage, contact tracing, and surveillance have been proposed, in particular for COVID-19 Ab RDTs. Valuable experience is available from implementation of other disease-specific RDTs in sub-Saharan Africa.
| S-EPMC7662157 | biostudies-literature
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: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:Ebolaviruses have the ability to infect a wide variety of species, with many African mammals potentially serving either as primary reservoirs or secondary amplifying hosts. Previous work has shown that frugivorous bats and primates are often associated with spillover and outbreaks. Yet the role that patterns of biodiversity, either of mammalian hosts or of common fruiting species such as Ficus (figs, fruit resources used by a wide variety of species), play in driving outbreak risk remains unclear. We investigated what factors most directly influence Ebolavirus outbreak risk in Sub-Saharan Africa by using a phylogenetically informed path analysis to compare a wide array of potential models (path diagrams) of spatial dynamics. We considered mammalian frugivore richness, cercopithecid and hominid primate richness, richness of pteropodid (fruit) bats, the spatial distribution of species that have tested positive for Ebolavirus antibodies in the wild, Ficus habitat suitability, and environmental conditions (mean annual and variability in temperature and rainfall). The proximate factors that most influenced whether a given host species range contained a site of a previous outbreak event were 1) habitat suitability for Ficus and 2) the diversity of cercopithecid primates. Frugivore richness overall (including bats, primates, and a few other mammals) and the richness of bats in the family Pteropodidae had a strong effect on which species tested positive for Ebolavirus antibodies, but did not influence outbreak risk directly in pathways explored. We interpret this as evidence that foraging around Ficus and frugivorous mammals (such as cercopithecid primates which are commonly hunted for food) play a prominent role in driving outbreaks into human communities, relative to other factors we considered which influence outbreak risk more indirectly.
| S-EPMC11867621 | biostudies-literature