A rapid and reproducible picture of open access health facility data in Africa to support the COVID-19 response

Background: Open data on the locations and services provided by health facilities in some countries have allowed the development of software tools contributing to COVID-19 response. The UN and WHO encourage countries to make health facility location data open, to encourage use and improvement. We provide a summary of open access health facility location data in Africa using re-useable code. We aim to support data analysts developing software tools to address COVID-19 response in individual countries. In Africa there are currently three main sources of such data; 1) direct from national ministries of health, 2) a database for sub-Saharan Africa collated and published by a team from KEMRI-Wellcome Trust Research Programme and now hosted by WHO, and 3) The Global Healthsites Mapping Project in collaboration with OpenStreetMap. Methods: We searched for and documented official national facility location data that were openly available. We developed re-useable open-source R code to summarise and visualise facility location data by country from the three sources. This re-useable code is used to provide a web user interface allowing data exploration through maps and plots of facility type. Results: Out of 53 African countries, seven provide an official open facility list that can be downloaded and analysed reproducibly. Considering all three sources, there are over 185,000 health facility locations available for Africa. However, there are differences and overlaps between sources and a lack of data on capacities and service provision. Conclusions: We suggest that these summaries and tools will encourage greater use of existing health facility location data, incentivise further improvements in the provision of those data by national suppliers, and encourage collaboration within wider data communities. The tools are a part of the afrimapr project, actively developing R building blocks to facilitate the use of health data in Africa

Responding to Food Price Crisis in Eastern and Southern Africa: Policy Options for National and Regional Action

This paper addresses the magnitude and implications of food price changes in national and regional markets in Eastern and Southern Africa (ESA) with a view to provide the evidence base for effective policy action. Specifically, the paper: - analyses trends and outlooks in country and regional data, presents evidence on the regional food situation, and explores the nexus between high domestic food prices and global food prices, - highlights regional and national dimensions of food price increases and how they are related to food security in the region, and - provides practical short-, medium- and long-term options for governments and other stakeholders for addressing the problem posed by the food price crisis

Greenhouse Gas fluxes from Selected Soil Fertility Management Practices in Humic Nitisols of Upper Eastern Kenya

We quantified soil Carbon dioxide (CO2), Methane (CH4), and Nitrous oxide (N2O) fluxes five soil fertility management practices (Inorganic fertilizer (Mf), maize residue + Inorganic fertilizer (RMf), Maize residue + Inorganic fertilizer + goat manure (RMfM), maize residue + Tithonia diversifolia + goat manure (RTiM), and a Control (CtC)) in Kenya's central highlands using a static chamber method from March 2019 to March 2020. The cumulative annual soil CH4 uptake ranged from -1.07 to -0.64 kg CH4-C ha-1 yr-1, CO2 emissions from 4.59 to 9.01 Mg CO2-C ha-1 yr-1, and N2O fluxes from 104 to 279 g N2O-N ha-1 yr-1. The RTiM produced the highest CO2 emissions (9.01 Mg CO2-C ha-1 yr-1), carbon sequestration (3.99 Mg CO2- eq ha-1), yield scaled N2O emissions (YSE) (0.043 g N2O-N kg-1 grain yield), the lowest net global warming potential (net GWP) (-14.7 Mg CO2-eq ha-1) and greenhouse gas intensities (GHGI) (-2.81 Kg CO2-eq kg-1 grain yield). We observed average maize grain yields of 7.98 Mg ha-1 yr-1 under RMfM treatment. Integrating inorganic fertilizer and maize residue retention resulted in low emissions, increased soil organic carbon sequestration and high maize yields

Spatial variation and inequities in antenatal care coverage in Kenya, Uganda and mainland Tanzania using model-based geostatistics: a socioeconomic and geographical accessibility lens.

BACKGROUND: Pregnant women in sub-Saharan Africa (SSA) experience the highest levels of maternal mortality and stillbirths due to predominantly avoidable causes. Antenatal care (ANC) can prevent, detect, alleviate, or manage these causes. While eight ANC contacts are now recommended, coverage of the previous minimum of four visits (ANC4+) remains low and inequitable in SSA. METHODS: We modelled ANC4+ coverage and likelihood of attaining district-level target coverage of 70% across three equity stratifiers (household wealth, maternal education, and travel time to the nearest health facility) based on data from malaria indicator surveys in Kenya (2020), Uganda (2018/19) and Tanzania (2017). Geostatistical models were fitted to predict ANC4+ coverage and compute exceedance probability for target coverage. The number of pregnant women without ANC4+ were computed. Prediction was at 3 km spatial resolution and aggregated at national and district -level for sub-national planning. RESULTS: About six in ten women reported ANC4+ visits, meaning that approximately 3 million women in the three countries had  20,000 women having <ANC4+ visits were 38%, 1% and 1%, respectively. In many districts, ANC4+ coverage and likelihood of attaining the target coverage was lower among the poor, uneducated and those geographically marginalized from healthcare. CONCLUSIONS: These findings will be invaluable to policymakers for annual appropriations of resources as part of efforts to reduce maternal deaths and stillbirths

Smallholder cropping systems contribute limited greenhouse gas fluxes in upper Eastern Kenya

The contribution of smallholder farming systems to the National greenhouse gas (GHG) budget is missing in most developing countries, including Kenya. Data on the contribution of smallholder cropping systems to the GHG balance is essential for realising Sustainable Development Goal 13 on climate action, i.e., on nationally determined contributions (NDCs) and in compliance with the Paris Agreement. Do smallholder farming systems act as nature-based solutions for greenhouse gas emissions reduction? This study evaluated GHG emissions from cropping systems under on-farm smallholder farming conditions. We had five cropping systems on two smallholder farms: sole maize, maize-bean intercrop, coffee, banana, and agroforestry. Gas samples were collected using three static chambers per cropping system. The gas samples were analysed using gas chromatography (GC) fitted with a 63Ni-electron capture detector (ECD) for N2O and flame ionisation detector (FID) for CH4 and CO2 using N as carrier gas. Cumulative annual fluxes of (CH4, N2O, and CO2) varied significantly in farms one and two across the cropping systems. The cumulative soil GHG fluxes ranged from -1.34kg CH4single bondC ha−1 yr−1 under agroforestry to -0.77kg CH4single bondC ha−1 yr−1 under banana for CH4, 0.30kg N2Osingle bondN ha−1 yr−1 to 1.23kg N2Osingle bondN ha−1 yr−1 for N2O and 5949kg CO2single bondC ha−1 yr−1 to 12,954kg CO2single bondC ha−1 yr−1 for CO2. The maize grain yields ranged from 0 to 3.38 Mg ha−1. The N2O yields scaled emissions ranged from 0.10 to 0.26g kg−1 maize and 0.68 to 1.30g kg−1 beans. Smallholder farmers in Upper Eastern Kenya contribute a limited amount of soil GHG emissions and thus could act as a nature-based solution for lowering agricultural emissions

Malaria protection due to sickle haemoglobin depends on parasite genotype.

Host genetic factors can confer resistance against malaria1, raising the question of whether this has led to evolutionary adaptation of parasite populations. Here we searched for association between candidate host and parasite genetic variants in 3,346 Gambian and Kenyan children with severe malaria caused by Plasmodium falciparum. We identified a strong association between sickle haemoglobin (HbS) in the host and three regions of the parasite genome, which is not explained by population structure or other covariates, and which is replicated in additional samples. The HbS-associated alleles include nonsynonymous variants in the gene for the acyl-CoA synthetase family member2-4 PfACS8 on chromosome 2, in a second region of chromosome 2, and in a region containing structural variation on chromosome 11. The alleles are in strong linkage disequilibrium and have frequencies that covary with the frequency of HbS across populations, in particular being much more common in Africa than other parts of the world. The estimated protective effect of HbS against severe malaria, as determined by comparison of cases with population controls, varies greatly according to the parasite genotype at these three loci. These findings open up a new avenue of enquiry into the biological and epidemiological significance of the HbS-associated polymorphisms in the parasite genome and the evolutionary forces that have led to their high frequency and strong linkage disequilibrium in African P. falciparum populations

Neighbourliness, conviviality, and the sacred in Athens’ refugee squats

To better understand the range of possibilities and opportunities for (co)existence available to displacement‐affected people, attention must be given to the thick webs of sociality shaping interactions in situations of mass displacement. This paper makes the case that refugee squats in Athens are distinct spaces wherein different understandings of (co)existence converge – spaces whose production is contingent on support from neighbourly relations and networks that are mediated in moments through conceptions of conviviality informed by religion. Based on ethnographic work carried out in 2016 and a spatial analysis of refugee squats in Athens, this paper emphasises neighbourliness and conviviality as they relate to sacred understandings of coexistence. This helps highlight the limits built in to thinking about the movement of refugees from the global South through Euro‐centric ontologies of the social. More than this, following postcolonial debates on the decentring of knowledge production, the research makes manifest how Islamic socio‐cultural memories of jiwār or a right of neighbourliness complicate geographies of humanitarianism that make stark binary assumptions between religious and secular space. In turn, the evidence from Athens indicates that refugee perspectives on neighbourliness are imperfectly translated by migrant rights activists as solidarity, obscuring the different ways Muslim structures of feeling contribute to the production of refugee squats

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2–4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

A novel formulation of inhaled sodium cromoglicate (PA101) in idiopathic pulmonary fibrosis and chronic cough: a randomised, double-blind, proof-of-concept, phase 2 trial

Background Cough can be a debilitating symptom of idiopathic pulmonary fibrosis (IPF) and is difficult to treat. PA101 is a novel formulation of sodium cromoglicate delivered via a high-efficiency eFlow nebuliser that achieves significantly higher drug deposition in the lung compared with the existing formulations. We aimed to test the efficacy and safety of inhaled PA101 in patients with IPF and chronic cough and, to explore the antitussive mechanism of PA101, patients with chronic idiopathic cough (CIC) were also studied. Methods This pilot, proof-of-concept study consisted of a randomised, double-blind, placebo-controlled trial in patients with IPF and chronic cough and a parallel study of similar design in patients with CIC. Participants with IPF and chronic cough recruited from seven centres in the UK and the Netherlands were randomly assigned (1:1, using a computer-generated randomisation schedule) by site staff to receive PA101 (40 mg) or matching placebo three times a day via oral inhalation for 2 weeks, followed by a 2 week washout, and then crossed over to the other arm. Study participants, investigators, study staff, and the sponsor were masked to group assignment until all participants had completed the study. The primary efficacy endpoint was change from baseline in objective daytime cough frequency (from 24 h acoustic recording, Leicester Cough Monitor). The primary efficacy analysis included all participants who received at least one dose of study drug and had at least one post-baseline efficacy measurement. Safety analysis included all those who took at least one dose of study drug. In the second cohort, participants with CIC were randomly assigned in a study across four centres with similar design and endpoints. The study was registered with ClinicalTrials.gov (NCT02412020) and the EU Clinical Trials Register (EudraCT Number 2014-004025-40) and both cohorts are closed to new participants. Findings Between Feb 13, 2015, and Feb 2, 2016, 24 participants with IPF were randomly assigned to treatment groups. 28 participants with CIC were enrolled during the same period and 27 received study treatment. In patients with IPF, PA101 reduced daytime cough frequency by 31·1% at day 14 compared with placebo; daytime cough frequency decreased from a mean 55 (SD 55) coughs per h at baseline to 39 (29) coughs per h at day 14 following treatment with PA101, versus 51 (37) coughs per h at baseline to 52 (40) cough per h following placebo treatment (ratio of least-squares [LS] means 0·67, 95% CI 0·48–0·94, p=0·0241). By contrast, no treatment benefit for PA101 was observed in the CIC cohort; mean reduction of daytime cough frequency at day 14 for PA101 adjusted for placebo was 6·2% (ratio of LS means 1·27, 0·78–2·06, p=0·31). PA101 was well tolerated in both cohorts. The incidence of adverse events was similar between PA101 and placebo treatments, most adverse events were mild in severity, and no severe adverse events or serious adverse events were reported. Interpretation This study suggests that the mechanism of cough in IPF might be disease specific. Inhaled PA101 could be a treatment option for chronic cough in patients with IPF and warrants further investigation