Hydrogeochemical processes in groundwater in Uganda: a national-scale analysis

Groundwater represents a vital source of freshwater to meet distributed, rapidly rising demands for safe drinking water, irrigation and industry in low-income countries across the tropics. The hydrochemistry of groundwater within deeply weathered crystalline rock aquifer systems that predominate at low latitudes, is determined primarily by long-term biogeochemical weathering of the parent bedrock. Here, we evaluate geochemical footprints and baseline chemical quality of groundwater that have developed from water-rock interactions across a range of geological environments in Uganda using a national database of hydrochemical and hydrogeological records from 3271 locations. Sampled groundwaters are mostly shallow (69% of samples from depths of <20 m below ground level), fresh at time of drilling (Electrical Conductivity <1000 μS cm−1 in 96% of samples), and of good quality (<8% of samples exceed WHO (2011) guidelines values for chemical parameters in drinking water). Unpalatably high concentrations of total soluble and suspended Fe are, however, common (21%) in meta-igneous, granitic and metamorphic formations. The dominant (95%) anionic facies of groundwater is bicarbonate (HCO3−), indicative of localized flow systems (i.e. discontinuous aquifers) in which chemical evolution of groundwater (e.g. as per Chebotarev sequence) is minimal. Low well yields (82% < 3.6 m3 h−1) and specific capacities (84% < 5 m2 d−1) support this inference; low aquifer transmissivities and storage serve to regulate naturally groundwater withdrawals (i.e. impacts of over-abstraction are localized). Overall, the results attest to the intrinsic high quality of groundwater that occurs in deeply weathered crystalline rock environments in Uganda, which may be expected across tropical Africa

Recent sequence variation in probe binding site affected detection of respiratory syncytial virus group B by real-time RT-PCR

Background Direct immuno-fluorescence test (IFAT) and multiplex real-time RT-PCR have been central to RSV diagnosis in Kilifi, Kenya. Recently, these two methods showed discrepancies with an increasing number of PCR undetectable RSV-B viruses. Objectives Establish if mismatches in the primer and probe binding sites could have reduced real-time RT-PCR sensitivity. Study design Nucleoprotein (N) and glycoprotein (G) genes were sequenced for real-time RT-PCR positive and negative samples. Primer and probe binding regions in N gene were checked for mismatches and phylogenetic analyses done to determine molecular epidemiology of these viruses. New primers and probe were designed and tested on the previously real-time RT-PCR negative samples. Results N gene sequences revealed 3 different mismatches in the probe target site of PCR negative, IFAT positive viruses. The primers target sites had no mismatches. Phylogenetic analysis of N and G genes showed that real-time RT-PCR positive and negative samples fell into distinct clades. Newly designed primers-probe pair improved detection and recovered previous PCR undetectable viruses. Conclusions An emerging RSV-B variant is undetectable by a quite widely used real-time RT-PCR assay due to polymorphisms that influence probe hybridization affecting PCR accuracy

Permeability of the crystalline basement in Uganda : evidence from 665 pumping tests and implications for solar pumping

Crystalline basement rocks of Precambrian age underlie nearly three quarters of Uganda, providing groundwater supplies to meet ever increasing demand from rural areas and urban growth centres. Development of groundwater sources is commonly based on several factors including physical and socio-economic considerations that have a bearing on their functionality and long term reliability. Here we present new transmissivity data from 665 boreholes across basement aquifers in Uganda calculated from previously unanalyzed pumping test data. Other data are available to help interpret the transmissvity values, including borehole lithological logs, weathering thickness, well design and depth to groundwater. Spatial and depth comparisons are made to relate aquifer permeability to lithology and weathering, and also to relate borehole yields to well design. The data provide an improved understanding of the physical permeability of weathered crystalline basement rock aquifers across Uganda, complimenting earlier studies of vertical permeability profiles in focused areas. The analysis helps inform the physical capacity of the aquifer to supply the borehole yields to meet increasing demands, and application the potential for higher abstraction technologies, such as solar pumps

Vorkommen von Spurenelementen in Flusssedimenten und Grund- und Oberflächenwasser in der Bergbauregion von Gatumba, Ruanda

Aufgrund der intensiven Landnutzung durch Bergbau und Landwirtschaft sind die Gewässer im Gatumba Mining District durch Stoffaustrag aus Abraumhalden und Erosion stark geprägt. Untersuchungen während einer Trocken- und Regenzeit hinsichtlich der Konzentration von Spurenelemente haben gezeigt, dass von einer Gesundheitsgefährdung der lokalen Bevölkerung derzeit nicht ausgegangen werden kann. In der Regel weisen die Wasserproben der Trockenzeit gegenüber denen der Regenzeit tendenziell höhere Konzentrationen auf. Die Konzentrationen der Sedimente zeigen keinen entsprechenden Trend

Characteristics of high-intensity groundwater abstractions from weathered crystalline bedrock aquifers in East Africa

Weathered crystalline bedrock aquifers sustain water supplies across the tropics, including East Africa. Although well yields are commonly <1 L s−1, more intensive abstraction occurs and provides vital urban and agricultural water supplies. The hydrogeological conditions that sustain such high abstraction from crystalline bedrock aquifers remain, however, poorly characterised. Five sites of intensive groundwater abstraction (multiple boreholes yielding several L s−1 or more) were investigated in Uganda and Tanzania. Analysis of aquifer properties data indicates that the sites have transmissivities of 10–1,000 m2 day−1, which is higher than generally observed in deeply weathered crystalline bedrock aquifers. At four of the five sites, weathered bedrock (saprolite) is overlain by younger superficial sediments, which provide additional storage and raise the water table within the underlying aquifer. Residence-time indicators suggest that: (1) abstracted water derives, in part, from modern recharge (within the last 10–60 years); and (2) intensive abstraction is sustained by recharge occurring over several decades. This range of encountered residence times indicates a degree of resilience to contemporary climate variability (e.g. short-term droughts), although the long-term sustainability of intensive abstractions remains uncertain. Evidence from one site in Tanzania (Makutapora) highlights the value of multi-decadal groundwater-level records in establishing the long-term viability of intensive groundwater abstraction, and demonstrates the influence of intra-decadal climate variability in determining the magnitude and frequency of recharge

Evidence that dicot-infecting mastreviruses are particularly prone to inter-species recombination and have likely been circulating in Australia for longer than in Africa and the Middle East

Viruses of the genus Mastrevirus (family Geminiviridae) are transmitted by leafhoppers and infect either mono- or dicotyledonous plants. Here we have determined the full length sequences of 49 dicot-infecting mastrevirus isolates sampled in Australia, Eritrea, India, Iran, Pakistan, Syria, Turkey and Yemen. Comprehensive analysis of all available dicot-infecting mastrevirus sequences showed the diversity of these viruses in Australia to be greater than in the rest of their known range, consistent with earlier studies, and that, in contrast with the situation in monocot-infecting mastreviruses, detected inter-species recombination events outnumbered intra-species recombination events. Consistent with Australia having the greatest diversity of known dicot-infecting mastreviruses phylogeographic analyses indicating the most plausible scheme for the spread of these viruses to their present locations, suggest that most recent common ancestor of these viruses is likely nearer Australia than it is to the other regions investigated.Department of HE and Training approved lis

Symptom evolution following the emergence of maize streak virus

For pathogens infecting single host species evolutionary trade-offs have previously been demonstrated between pathogen-induced mortality rates and transmission rates. It remains unclear, however, how such trade-offs impact sub-lethal pathogen-inflicted damage, and whether these trade-offs even occur in broad host-range pathogens. Here, we examine changes over the past 110 years in symptoms induced in maize by the broad host-range pathogen, maize streak virus (MSV). Specifically, we use the quantified symptom intensities of cloned MSV isolates in differentially resistant maize genotypes to phylogenetically infer ancestral symptom intensities and check for phylogenetic signal associated with these symptom intensities. We show that whereas symptoms reflecting harm to the host have remained constant or decreased, there has been an increase in how extensively MSV colonizes the cells upon which transmission vectors feed

The Spread of Tomato Yellow Leaf Curl Virus from the Middle East to the World

The ongoing global spread of Tomato yellow leaf curl virus (TYLCV; Genus Begomovirus, Family Geminiviridae) represents a serious looming threat to tomato production in all temperate parts of the world. Whereas determining where and when TYLCV movements have occurred could help curtail its spread and prevent future movements of related viruses, determining the consequences of past TYLCV movements could reveal the ecological and economic risks associated with similar viral invasions. Towards this end we applied Bayesian phylogeographic inference and recombination analyses to available TYLCV sequences (including those of 15 new Iranian full TYLCV genomes) and reconstructed a plausible history of TYLCV's diversification and movements throughout the world. In agreement with historical accounts, our results suggest that the first TYLCVs most probably arose somewhere in the Middle East between the 1930s and 1950s (with 95% highest probability density intervals 1905–1972) and that the global spread of TYLCV only began in the 1980s after the evolution of the TYLCV-Mld and -IL strains. Despite the global distribution of TYLCV we found no convincing evidence anywhere other than the Middle East and the Western Mediterranean of epidemiologically relevant TYLCV variants arising through recombination. Although the region around Iran is both the center of present day TYLCV diversity and the site of the most intensive ongoing TYLCV evolution, the evidence indicates that the region is epidemiologically isolated, which suggests that novel TYLCV variants found there are probably not direct global threats. We instead identify the Mediterranean basin as the main launch-pad of global TYLCV movements

A reduced-carbohydrate and lactose-free formulation for stabilization among hospitalized children with severe acute malnutrition: A double-blind, randomized controlled trial

BackgroundChildren with medically complicated severe acute malnutrition (SAM) have high risk of inpatient mortality. Diarrhea, carbohydrate malabsorption, and refeeding syndrome may contribute to early mortality and delayed recovery. We tested the hypothesis that a lactose-free, low-carbohydrate F75 milk would serve to limit these risks, thereby reducing the number of days in the stabilization phase.Methods and findingsIn a multicenter double-blind trial, hospitalized severely malnourished children were randomized to receive standard formula (F75) or isocaloric modified F75 (mF75) without lactose and with reduced carbohydrate. The primary endpoint was time to stabilization, as defined by the World Health Organization (WHO), with intention-to-treat analysis. Secondary outcomes included in-hospital mortality, diarrhea, and biochemical features of malabsorption and refeeding syndrome. The trial was registered at clinicaltrials.gov (NCT02246296). Four hundred eighteen and 425 severely malnourished children were randomized to F75 and mF75, respectively, with 516 (61%) enrolled in Kenya and 327 (39%) in Malawi. Children with a median age of 16 months were enrolled between 4 December 2014 and 24 December 2015. One hundred ninety-four (46%) children assigned to F75 and 188 (44%) to mF75 had diarrhea at admission. Median time to stabilization was 3 days (IQR 2–5 days), which was similar between randomized groups (0.23 [95% CI −0.13 to 0.60], P = 0.59). There was no evidence of effect modification by diarrhea at admission,age, edema, or HIV status. Thirty-six and 39 children died before stabilization in the F75 and in mF75 arm, respectively (P = 0.84). Cumulative days with diarrhea (P = 0.27), enteral (P = 0.42) or intravenous fluids (P = 0.19), other serious adverse events before stabilization, and serum and stool biochemistry at day 3 did not differ between groups. The main limitation was that the primary outcome of clinical stabilization was based on WHO guidelines, comprising clinical evidence of recovery from acute illness as well as metabolic stabilization evidenced by recovery of appetite. ConclusionsEmpirically treating hospitalized severely malnourished children during the stabilization phase with lactose-free, reduced-carbohydrate milk formula did not improve clinical outcomes. The biochemical analyses suggest that the lactose-free formulae may still exceed a carbohydrate load threshold for intestinal absorption, which may limit their usefulness in the context of complicated SAM