Development of a customised design flood estimation tool to estimate floods in gauged and ungauged catchments

Published ArticleThe estimation of design flood events, i.e., floods characterised by a specific magnitude-frequency relationship, at a particular site in a specific region is necessary for the planning, design and operation of hydraulic structures. Both the occurrence and frequency of flood events, along with the uncertainty involved in the estimation thereof, contribute to the practising engineers’ dilemma to make a single, justifiable decision based on the results obtained from the plethora of ‘outdated’ design flood estimation methods available in South Africa. The objectives of this study were: (i) to review the methods currently used for design flood estimation in South Africa for single-site analysis, (ii) to develop a customised, user-friendly Design Flood Estimation Tool (DFET) containing the latest design rainfall information and recognised estimation methods used in South African flood hydrology, and (iii) to demonstrate the use and functionality of the developed DFET by comparing and assessing the performance of the various design flood estimation methods in gauged catchments with areas ranging from 100 km² to 10 000 km² in the C5 secondary drainage region, South Africa. The results showed that the developed DFET will provide designers with an easy-to-use software tool for the rapid estimation and evaluation of alternative design flood estimation methods currently available in South Africa for applications at a site-specific scale in both gauged/ungauged and small/large catchments. In applying the developed DFET to gauged catchments, the simplified ‘small catchment’ (A ≤ 15 km²) deterministic flood estimation methods provided acceptable results when compared to the probabilistic analyses applicable to all of the catchment sizes and return periods, except for the 2-year return period. Less acceptable results were demonstrated by the ‘medium catchment’ (15 km² 5 000 km²) empirical flood estimation methods. It can be concluded that there is no single design flood estimation method that is superior to all other methods used to address the wide variety of flood magnitude-frequency problems that are encountered in practice. Practising engineers’ still have to apply their own experience and knowledge to these particular problems until the gap between flood research and practice in South Africa is narrowed by improving existing (outdated) design flood estimation methods and/or evaluating methods used internationally and developing new methods for application in South Africa

A model to assess water tariffs as part of water demand management

Water Conservation and Water Demand Management (WC/WDM) forms part of integrated water resource management and can be used as an economically viable alternative to the upgrade of infrastructure to balance supply and demand. In order to enable effective decision-making, a model was developed in this study to estimate expected water savings and the financial impact of a change in water tariff as a WC/WDM measure. This paper describes a model that was developed for municipalities to calculate the predicted change in water use and the associated income. The model takes into account variation in price elasticity per tariff block. The effectiveness of the model as a planning tool is illustrated through an appropriate example.Keywords: water demand management, price elasticity, change in water tariff, block tariff, WC/WDM mode

Unit Reference Value: Application in appraising inter-basin water transfer projects

Unit Reference Value (URV) is a common measure in South Africa to assess the economic efficiency of proposed water projects. This is a companion article to an earlier one establishing that the current approach of appraisal of inter-basin water transfer projects (IBTs) with significant pumping costs overestimates likely future water transfers and thereby variable operational costs. Those findings are taken further and it is established that the URV, as currently applied, fails as a suitable measure to appraise such IBTs. From rooting URVs in fundamental cost effectiveness analysis theory a revised URV approach is proposed that provides for a conceptual separation between water transfers affecting operating costs and water transfers used as a proxy measure for effectiveness. The prominent effect of the revised URV approach is demonstrated by means of the example of the proposed Thukela Water Project in South Africa.Keywords: unit reference value, cost effectiveness analysis, inter-basin water transfers, project appraisa

Hydrologic-economic appraisal of life-cycle costs of inter-basin water transfer projects

This article describes research that compares actual water transfers of an inter-basin transfer (IBT) scheme with its original, appraisal stage, prediction. Transfers are shown to be significantly less and also more variable than predicted. Further research reveals that the state of the receiving system has a large bearing on year-to-year decisions regarding water transfers. Past appraisals, following what is called the Incremental Approach, do not adequately consider the stochastic nature of the likely future inter-basin transfer operating regime. Examination of six case studies, four South African, one Chinese and one Australian, shows that the Incremental Approach is still in general use – despite tools available for an improved approach. A new approach, called the Comprehensive Approach, is proposed to upgrade estimations of variable costs associated with water transfers – often substantial life-cycle cost components of IBTs.A demonstration of the Comprehensive Approach, by means of an example of an IBT with significant pumping costs associated with water transfers, is provided. Uncertainty regarding future water transfers and associated variable costs are provided for by stochastic simulation  modelling. The Incremental Approach is shown to be severely biased with respect to variable costs and it is shown that this bias leads to significantly different estimations of likely life-cycle project costs. Such differences conceivably lead to suboptimal decision-making.Keywords: Water resources, inter-basin water transfer, project appraisal, life-cycle costs, stochastic modellin

A desalination guide for South African municipal engineers

Municipalities need to develop Water Services Development Plans (WSDPs) as a first requirement in their budgetary process, and need to be made aware of the options that are available to provide more than basic services. While 25./personEd has been set as the minimum basic water supply and while many consumers receive far in excess of this amount, there are areas of the country where water of acceptable quality is not available for household use. However, in many areas adequate quantities of saline water may be, or are, readily available. This is especially the case for coastal cities and towns.The cost of treating water is only part of the total cost of making drinking water available to the consumer. This together with the fact that membrane technology is becoming more affordable and that energy can be recovered, makes the desalination of water viable for domestic purposes.A desk study, funded by the Department Water Affairs and Forestry and managed by the Water Research Commission, was undertaken to identify treatment options for desalinating seawater from both the Indian and Atlantic oceans or brackish water from boreholes. The specific objectives of the project were to compile a Guide on the technologies that can be implemented in South Africa to treat saline water to drinking water standards, to identify the pretreatment that is necessary, and to present guidelines on operational, maintenance, management and environmental aspects relevant to the selection and use of these technologies. An important aspect was also to quantify the capital and operating costs for planning purposes of the different components needed to successfully bring the water to the accepted standards for potable and domestic use.Of particular importance for the South African application was to identify the level of skills required for daily operation of the desalination plants, the level of skills required to provide technical back-up and advice, and to identify and advise on the competencies, training needs and capacity building required at operator and management levels. Lastly, the relevant local environmental legislations governing desalination were also identified

An atypical carbohydrate deficient glycoprotein (CDG) syndrome patient in South Africa

No Abstrac

Longitudinal monitoring of Ehrlichia ruminantium infection in Gambian lambs and kids by pCS20 PCR and MAP1-B ELISA

<p>Abstract</p> <p>Background</p> <p>The epidemiology of <it>E. ruminantium </it>infection in extensively managed young animals is not adequately understood. Thus in this study, we monitored the onset (age at first infection) and kinetics of <it>E. ruminantium </it>infection and antibody response in extensively managed newborn lambs and kids at three sites in The Gambia.</p> <p>Methods</p> <p>We used a nested pCS20 PCR and MAP1-B ELISA in a longitudinal study to monitor the onset (age at first infection) and kinetics of <it>E. ruminantium </it>infection and antibody response respectively, in 77 newborn lambs and kids under a traditional husbandry system at three sites (Kerr Seringe, Keneba, Bansang) in The Gambia where heartwater is known to occur. The animals were monitored for field tick infestation and the comparative performance of the two assays in detecting <it>E. ruminantium </it>infection was also assessed.</p> <p>Results</p> <p>The infection rate detected by pCS20 PCR varied between 8.6% and 54.8% over the 162-day study period. Nineteen per cent of the animals in week 1 post-partum tested positive by pCS20 PCR with half of these infections (7/14) detected in the first 3 days after birth, suggesting that transmission other than by tick feeding had played a role. The earliest detectable <it>A. variegatum </it>infestation in the animals occurred in week 16 after birth. Antibodies detected by MAP1-B ELISA also varied, between 11.5% and 90%. Although there is considerable evidence that this assay can detect false positives and due to this and other reasons serology is not a reliable predictor of infection at least for heartwater. In contrast to the pCS20 PCR, the serological assay detected the highest proportion of positive animals in week 1 with a gradual decline in seropositivity with increasing age. The pCS20 PCR detected higher <it>E. ruminantium </it>prevalence in the animals with increasing age and both the Spearman's rank test (<it>r</it>_{<it>s </it>}= -0.1512; P = 0.003) and <it>kappa </it>statistic (-0.091 to 0.223) showed a low degree of agreement between the two assays.</p> <p>Conclusion</p> <p>The use of pCS20 PCR supported by transmission studies and clinical data could provide more accurate information on heartwater epidemiology in endemic areas and single-occasion testing of an animal may not reveal its true infection status. The view is supported because both the vector and vertical transmission may play a vital role in the epidemiology of heartwater in young small ruminants; the age range of 4 and 12 weeks corresponds to the period of increased susceptibility to heartwater in traditionally managed small ruminants.</p

Immunologic and vascular biomarkers of mortality in critical COVID-19 in a South African cohort

Introduction: Biomarkers predicting mortality among critical Coronavirus disease 2019 (COVID-19) patients provide insight into the underlying pathophysiology of fatal disease and assist with triaging of cases in overburdened settings. However, data describing these biomarkers in Sub-Saharan African populations are sparse. Methods: We collected serum samples and corresponding clinical data from 87 patients with critical COVID-19 on day 1 of admission to the intensive care unit (ICU) of a tertiary hospital in Cape Town, South Africa, during the second wave of the COVID-19 pandemic. A second sample from the same patients was collected on day 7 of ICU admission. Patients were followed up until in-hospital death or hospital discharge. A custom-designed 52 biomarker panel was performed on the Luminex® platform. Data were analyzed for any association between biomarkers and mortality based on pre-determined functional groups, and individual analytes. Results: Of 87 patients, 55 (63.2%) died and 32 (36.8%) survived. We found a dysregulated cytokine response in patients who died, with elevated levels of type-1 and type-2 cytokines, chemokines, and acute phase reactants, as well as reduced levels of regulatory T cell cytokines. Interleukin (IL)-15 and IL-18 were elevated in those who died, and levels reduced over time in those who survived. Procalcitonin (PCT), C-reactive protein, Endothelin-1 and vascular cell adhesion molecule-1 were elevated in those who died. Discussion: These results show the pattern of dysregulation in critical COVID-19 in a Sub-Saharan African cohort. They suggest that fatal COVID-19 involved excessive activation of cytotoxic cells and the NLRP3 (nucleotide-binding domain, leucine-rich–containing family, pyrin domain–containing-3) inflammasome. Furthermore, superinfection and endothelial dysfunction with thrombosis might have contributed to mortality. HIV infection did not affect the outcome. A clinically relevant biosignature including PCT, pH and lymphocyte percentage on differential count, had an 84.8% sensitivity for mortality, and outperformed the Luminex-derived biosignature

International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact

Background: Pneumococcal conjugate vaccines have reduced the incidence of invasive pneumococcal disease, caused by vaccine serotypes, but non-vaccine-serotypes remain a concern. We used whole genome sequencing to study pneumococcal serotype, antibiotic resistance and invasiveness, in the context of genetic background. / Methods: Our dataset of 13,454 genomes, combined with four published genomic datasets, represented Africa (40%), Asia (25%), Europe (19%), North America (12%), and South America (5%). These 20,027 pneumococcal genomes were clustered into lineages using PopPUNK, and named Global Pneumococcal Sequence Clusters (GPSCs). From our dataset, we additionally derived serotype and sequence type, and predicted antibiotic sensitivity. We then measured invasiveness using odds ratios that relating prevalence in invasive pneumococcal disease to carriage. / Findings: The combined collections (n = 20,027) were clustered into 621 GPSCs. Thirty-five GPSCs observed in our dataset were represented by >100 isolates, and subsequently classed as dominant-GPSCs. In 22/35 (63%) of dominant-GPSCs both non-vaccine serotypes and vaccine serotypes were observed in the years up until, and including, the first year of pneumococcal conjugate vaccine introduction. Penicillin and multidrug resistance were higher (p < .05) in a subset dominant-GPSCs (14/35, 9/35 respectively), and resistance to an increasing number of antibiotic classes was associated with increased recombination (R2 = 0.27 p < .0001). In 28/35 dominant-GPSCs, the country of isolation was a significant predictor (p < .05) of its antibiogram (mean misclassification error 0.28, SD ± 0.13). We detected increased invasiveness of six genetic backgrounds, when compared to other genetic backgrounds expressing the same serotype. Up to 1.6-fold changes in invasiveness odds ratio were observed. / Interpretation: We define GPSCs that can be assigned to any pneumococcal genomic dataset, to aid international comparisons. Existing non-vaccine-serotypes in most GPSCs preclude the removal of these lineages by pneumococcal conjugate vaccines; leaving potential for serotype replacement. A subset of GPSCs have increased resistance, and/or serotype-independent invasiveness