Biotech in South Africa

Cover illustration: Biotech in South Africa. This BTJ special issue is edited by Professor Don Cowan (Cape Town, South Africa) and highlights many aspects on South African research and industry, ecology and economy. Images © Don Cowan (grasslands at the base of the Drakensberg Mountains, KwaZulu-Natal Province, SA), USGS (coal), USFDA (sugarcane) and Corbis Digital Stock (vines).     

Decreasing the Burden of Type 2 Diabetes in South Africa: The Impact of Taxing Sugar-Sweetened Beverages

Introduction

Type 2 diabetes poses an increasing public health burden in South Africa (SA) with obesity as the main driver of the epidemic. Consumption of sugar sweetened beverages (SSBs) is linked to weight gain and reducing SSB consumption may significantly impact the prevalence of obesity and related diseases. We estimated the effect of a 20% SSB tax on the burden of diabetes in SA.

Methods and Findings

We constructed a life table-based model in Microsoft Excel (2010). Consumption data from the 2012 SA National Health and Nutrition Examination Survey, previously published own- and cross-price elasticities of SSBs and energy balance equations were used to estimate changes in daily energy intake and its projected impact on BMI arising from increased SSB prices. Diabetes relative risk and prevalent years lived with disability estimates from the Global Burden of Disease Study and modelled disease epidemiology estimates from a previous study were used to estimate the effect of the BMI changes on diabetes burden. Diabetes cost estimates were obtained from the South African Council for Medical Schemes. Over 20 years, a 20% SSB tax could reduce diabetes incident cases by 106 000 in women (95% uncertainty interval (UI) 70 000–142 000) and by 54 000 in men (95% UI: 33 000–80 000); and prevalence in all adults by 4.0% (95% UI: 2.7%-5.3%). Cumulatively over twenty years, approximately 21 000 (95% UI: 14 000–29 000) adult T2DM-related deaths, 374 000 DALYs attributed to T2DM (95% UI: 299 000–463 000) and over ZAR10 billion T2DM healthcare costs (95% UI: ZAR6.8–14.0 billion) equivalent to USD860 million (95% UI: USD570 million–USD1.2 billion) may be averted.

Conclusion

Fiscal policy on SSBs has the potential to mitigate the diabetes epidemic in South Africa and contribute to the National Department of Health goals stated in the National NCD strategic plan.     

Managing Human Tissue Transfer Across National Boundaries – An Approach from an Institution in South Africa

With biobank research on the increase and the history of exploitation in Africa, it has become necessary to manage the transfer of human tissues across national boundaries. There are many accepted templates of Material Transfer Agreements (MTAs) that currently exist internationally. However, these templates do not address the specific concerns of South Africa and even of Africa as a continent. This article will examine three significantly important ethico‐legal concepts that were deliberated and carefully adapted by a South African Institution to suit the transfer of Human Biological Materials (HBMs) and associated data for biobank research, namely: informed consent; benefit sharing arrangements; and ownership together with intellectual property rights in human tissues. The discussion includes an analysis of current practice; the ethico‐legal challenges in the South African/African context; the decisions made with regard to how the related ethico‐legal challenges were addressed in the MTA; and justifications for implementing these decisions. The processes considered could be of benefit to other developing world countries who consider it necessary to manage the transfer of HBMs across national boundaries.     

The history and composition of the Raymond A. Dart Collection of Human Skeletons at the University of the Witwatersrand,Johannesburg, South Africa

The Raymond A. Dart Collection of Human Skeletons (Dart Collection) is housed in the School of Anatomical Sciences at the University of the Witwatersrand, Johannesburg, South Africa, and comprises one of the largest documented cadaver‐derived human skeletal assemblages in the world. This collection originated in the early 1920s as a result of the efforts of Raymond Dart and continues to grow. The skeletons included represent varied indigenous and immigrant populations from southern Africa, Europe and Asia. This contribution documents the history of the collection and provides an updated inventory and demographic assessment of this valuable research collection. According to a recent inventory the Dart Collection currently comprises 2,605 skeletons representing individuals from regional SA African (76%), White (15%), Coloured (4%) and Indian (0.3%) populations. A large proportion of the skeletons (71%) represent males. The recorded ages at death range from the first year to over 100 years of age, but the majority of individuals died between the ages of 20 and 70. The Dart Collection has been affected by collection procedures based on availability. All of the cadavers collected before 1958, and large proportions subsequently, were derived from unclaimed bodies in regional South African hospitals. Some details of documentation (age at death, population group) are estimates and some aspects of the collection demographics (sex ratios) do not closely reflect any living South African population. Our inventory and analysis of the Dart Collection is aimed to assist researchers planning research on the materials from this collection. Am J Phys Anthropol, 2009. © 2009 Wiley‐Liss, Inc.     

Ethical issues in genomic research on the African continent: experiences and challenges to ethics review committees

This is a report on a workshop titled ‘Ethics for genomic research across five African countries: Guidelines, experiences and challenges’, University of the Witwatersrand, Johannesburg, South Africa, 10 and 11 December 2012. The workshop was hosted by the Wits-INDEPTH partnership, AWI-Gen, as part of the H3Africa Consortium.     

Defective interleukin-1 production by monocytes from patients with malignant disease

Summary Interleukin-1 (IL-1) production by monocytes of patients with various forms of malignant disease was measured after activating the cells with either lipopolysaccharide or malignant K562 cells. Monocytes from all the patients with large tumour masses, including 10 patients with hepatocellular carcinoma, produced considerably less IL-1 than controls or patients with small tumour burdens. After treating control or patient monocytes with human leucocyte interferon for 1 h prior to activation, IL-1 production was markedly improved. Depressed IL-1 production is, therefore, a further aberration in mononuclear function observed in patients with cancer.Supported in part by grants from the South African Medical Research Council, the National Cancer Association of South Africa and the South African Chamber of Mines     

South Africa: from species cradle to genomic applications

The South African government is committed to science and technology innovation, to establishing a knowledge-based economy and to harnessing life-sciences research for health and economic development. Given the constraints and the early stage of development of the field as a whole in South Africa, we found an impressive amount of research on human genomic variation in this country. Encouragingly, South Africa is beginning to apply genomics to address local health needs, including HIV and tuberculosis (TB) infections. We document a number of initiatives in South Africa that are beginning to study genetic variation within the various local indigenous populations. Other early initiatives focus on pharmacogenetic studies, mutation characterization in individual disease genes and genome-wide association studies. Public engagement in genomic issues is spear-headed by The Africa Genome Education Institute.     

Ploidy differences in Cryptococcus albidus

Presumed haploid and diploid cultures ofCryptococcus albidus were analysed for their DNA content per cell. A ratio of approximately 1:2 was obtained by relating the DNA content per cell of the two phases to ploidy. As the diplophase formed neither longitudinally septated cells nor ballistoconidia, the earlier suggestions thatCryptococcus is closely related toTremella seems less likely. On the assumption that the metabasidia ofCryptococcus are gastromycetoid, a closer relationship between this genus and the tulasnelloid fungi appears more probable.Microbiology Research Group, South African Council for Scientific and Industrial Research, Pretoria, South Africa.     

Trends and themes in African ornithology

Ornithology in Africa has a long history. I review trends in the ornithological literature since 1990 within the context of the 14th Pan-African Ornithological Congress. Using full text searches of papers on PubMed® and abstracts from main ornithological journals I found that most papers referencing African bird species are focused on medical-related research questions. Restricting the literature search to journals African ornithologists are most likely to publish in, I found 2 279 relevant papers. These describe work on 29% of African bird species from 82% of African bird families, in all but two African countries. Overall output has increased slightly over time, with more papers tackling more research topics. Most popular research topics were demography, conservation and climate, with disease ecology, physiology and ecological processes the least researched topics. I found that while many authors with African affiliations publish papers, outside of South Africa very few African-based authors reliably publish in the international research literature, perhaps indicating difficulties in establishing a productive research career in much of Africa. I conclude with a call to overseas ornithologists working in Africa and to organisations funding research in Africa to work together to build capacity outside of the few established research centres.     

Population genetics of Eldana saccharina Walker (Lepidoptera: Pyralidae) and the implications for management using biocontrol

The African sugarcane stalk borer, Eldona saccharina Walker (Lepidoptera: Pyralidae), is widely distributed throughout sub-Saharan Africa and is an important insect pest of maize and sugarcane. The insect shows significant variation in behaviour, host plant and natural enemy guild in different regions. Several attempts to redistribute the natural enemies of E. saccharina from West Africa to South Africa were unsuccessful. The significant behavioural, host plant and natural enemy variations as well as failures of biocontrol attempts evoked a hypothesis of genetic diversification. To evaluate this hypothesis a molecular analysis was conducted on geographically isolated populations of E. saccharina from East, North, South and West Africa, using the cytochrome c oxidase subunit I (COI) region of the mitochondrial genome. The results revealed that E. saccharina populations are separated into four major units corresponding to the West Africa, Rift Valley, South/East Africa and southern African populations. Mitochondrial DNA divergence among the four populations ranged from 1% to 4.98%. To examine the impact of the observed genetic variation on the fertility of inter-population crosses, a mating experiment was conducted between the Rift valley and South African population to produce an F1 generation, and these were backcrossed with the South African parent population. Fertility of eggs produced by the F1/parent population cross was significantly reduced when compared to fertility of the "true" South African line, and the F1/F1 cross. The contributions of the observed genetic differences and inter population incompatibility for the failure of previous biocontrol attempts are discussed and recommendations on future biocontrol practices are given.     

African Female Physicians and Nurses in the Global Care Chain: Qualitative Explorations from Five Destination Countries

Migration of health professionals is an important policy issue for both source and destination countries around the world. The majority of migrant care workers in industrialized countries today are women. However, the dimension of mobility of highly skilled females from countries of the global south has been almost entirely neglected for many years. This paper explores the experiences of high-skilled female African migrant health-workers (MHW) utilising the framework of Global Care Chain (GCC) research. In the frame of the EU-project HURAPRIM (Human Resources for Primary Health Care in Africa), the research team conducted 88 semi-structured interviews with female and male African MHWs in five countries (Botswana, South Africa, Belgium, Austria, UK) from July 2011 until April 2012. For this paper we analysed the 34 interviews with female physicians and nurses using the qualitative framework analysis approach and the software atlas.ti. In terms of the effect of the migration on their career, almost all of the respondents experienced short-term, long-term or permanent inability to work as health-care professionals; few however also reported a positive career development post-migration. Discrimination based on a foreign nationality, race or gender was reported by many of our respondents, physicians and nurses alike, whether they worked in an African or a European country. Our study shows that in addition to the phenomenon of deskilling often reported in GCC research, many female MHW are unable to work according to their qualifications due to the fact that their diplomas are not recognized in the country of destination. Policy strategies are needed regarding integration of migrants in the labour market and working against discrimination based on race and gender.     

How to deal with neglected tropical diseases in the light of an African ethic

Many countries in Africa, and more generally those in the Global South with tropical areas, are plagued by illnesses that the wealthier parts of the world (mainly ‘the West’) neither suffer from nor put systematic effort into preventing, treating or curing. What does an ethic with a recognizably African pedigree entail for the ways various agents ought to respond to such neglected diseases? As many readers will know, a characteristically African ethic prescribes weighty duties to aid on the part of those in a position to do so, and it therefore entails that there should have been much more contribution from the Western, ‘developed’ world. However, what else does it prescribe, say, on the part of sub‐Saharan governments and the African Union, and are they in fact doing it? I particularly seek to answer these questions here, by using the 2013‐16 Ebola crisis in West Africa to illustrate what should have happened but what by and large did not.     

Invasive <Emphasis Type="Italic">Tamarix</Emphasis> (Tamaricaceae) in South Africa: current research and the potential for biological control

Most species of Tamarix originate in Eurasia and at least five species have become invasive around the world, including South Africa. However, T. usneoides is indigenous to southern Africa, where the potential for biological control of the invasive species is being investigated. Recent research on the invasive species is reviewed here with particular reference to these South African biocontrol efforts. The successful biological control programme against invasive Tamarix in the USA, using several species of “Tamarisk beetle”, is being used as a guide for the South African research. The South African programme is complicated by firstly, the presence of the indigenous T. usneoides which raises the precision of host-specificity required, and secondly, the introduced and indigenous Tamarix have a high intrinsic value for phytoremediation of mine tailings dams in South Africa. The phylogenetic proximity of these Tamarix species to each other has contributed to this challenge, which has nevertheless been successfully addressed by molecular techniques used to separate the species. In addition, classical morphological techniques have been used to separate the Tamarisk beetles, so that now they can generally be matched to Tamarix tree species. Overall, it is concluded that given the broad knowledge now available on the ecology and identity of both the trees and their biocontrol agents, the prospects for successful biological control of Tamarix in South Africa are good.     

Comparative evaluation of Life Cycle Impact assessment methods with a South African case study

Goal and Background  LCIA procedures that have been used in the South Africa manufacturing industry include the CML, Ecopoints, EPS and Eco-indicators 95 and 99 procedures. The aim of this paper is to evaluate and compare the applicability of these European LCIA procedures within the South African context, using a case study. Methods  The five European methods have been evaluated based on the applicability of the respective classification, characterisation, normalization and weighting approaches for the South African situation. Impact categories have been grouped into air, water, land and mined abiotic resources for evaluation purposes. The evaluation and comparison is further based on a cradle-to-gate Screening Life Cycle Assessment (SLCA) case study of the production of dyed two-fold wool yarn in South Africa. Results and Discussion  Where land is considered as a separate category (CML, Eco-indicator 99 and EPS), the case study highlights this inventory constituent as the most important. Similarly, water usage is shown as the second most important in one LCIA procedure (EPS) where it is taken into account. However, the impact assessment modelling for these categories may not be applicable for the variance in South African ecosystems. If land and water is excluded from the interpretation, air emissions, coal usage, ash disposal, pesticides and chrome emissions to water are the important constituents in the South African wool industry. Conclusions  In most cases impact categories and procedures defined in the LCIA methods for air pollution, human health and mined abiotic resources are applicable in South Africa. However, the relevance of the methods is reduced where categories are used that impact ecosystem quality, as ecosystems differ significantly between South Africa and the European continent. The methods are especially limited with respect to water and land resources. Normalisation and weighting procedures may also be difficult to adapt to South African conditions, due to the lack of background information and social, cultural and political differences. Recommendations and Outlook  Further research is underway to develop a framework for a South African LCIA procedure, which will be adapted from the available European procedures. The wool SLCA must be revisited to evaluate and compare the proposed framework with the existing LCIA procedures.     

The ethnobotany of South African medicinal orchids

Orchidaceae, the largest and most diverse family of flowering plants is widespread, with a broad range of ethnobotanical applications. Southern Africa is home to approximately 494 terrestrial and epiphytic orchid species, of which, 49 are used in African traditional medicine to treat cough and diarrheal symptoms, madness, promote conception, relieve pain, induce nausea, and expel intestinal worms and for many cultural practices. The biological activity and chemical composition of South African medicinal orchid species are yet to be explored fully. In this review we highlight the potential for pharmacological research on South African medicinal orchid species based on their traditional medicinal uses.     

Compatibility of codling moths Cydia pomonella (Linnaeus) (Lepidoptera: Tortricidae) from South Africa with codling moths shipped from Canada

The sterile insect technique (SIT) has been successfully applied against codling moth Cydia pomonella (Linnaeus) (Lepidoptera; Tortricidae) in British Columbia since 1992 where the mass‐rearing facility produces between 15 and 16 million moths per week. Due to the seasonality of this pest, the facility is only fully utilized for part of the year. The time and expense of implementing SIT against codling moth in South Africa may be substantially reduced if moths from Canada were sexually compatible with those from South Africa. In addition, because the pome fruit‐growing season in both countries is opposite, the programme in Canada might benefit by maintaining moth production year‐round and selling moths to South Africa. Semi‐field studies in small cages and release‐recapture studies were conducted in an unsprayed apple orchard in South Africa to assess mating compatibility of laboratory‐reared codling moth from Canada and wild codling moths from South Africa. The results suggest that Canadian codling moth males were equally attracted to calling Canadian and South African females despite the fact that Canadian moths had been transported (from Canada to South Africa) for 48 h as both pupae and adults. The data also suggest that at lower field temperatures Canadian moths were more active than South African moths. Results from the release‐recapture field trials indicated that Canadian and South African males were equally attracted to Canadian and South African females. These results suggest that codling moths from Canada and South Africa are fully compatible and indicate that Canadian moths can be used for SIT studies in South Africa. As these studies were conducted with moths from two very different climatic and time zones, it is proposed that populations of codling moth in other pome fruit production areas may also be compatible with the Canadian moths.     

Genetic Variation in TLR Genes in Ugandan and South African Populations and Comparison with HapMap Data

Genetic epidemiological studies of complex diseases often rely on data from the International HapMap Consortium for identification of single nucleotide polymorphisms (SNPs), particularly those that tag haplotypes. However, little is known about the relevance of the African populations used to collect HapMap data for study populations conducted elsewhere in Africa. Toll-like receptor (TLR) genes play a key role in susceptibility to various infectious diseases, including tuberculosis. We conducted full-exon sequencing in samples obtained from Uganda (n = 48) and South Africa (n = 48), in four genes in the TLR pathway: TLR2, TLR4, TLR6, and TIRAP. We identified one novel TIRAP SNP (with minor allele frequency [MAF] 3.2%) and a novel TLR6 SNP (MAF 8%) in the Ugandan population, and a TLR6 SNP that is unique to the South African population (MAF 14%). These SNPs were also not present in the 1000 Genomes data. Genotype and haplotype frequencies and linkage disequilibrium patterns in Uganda and South Africa were similar to African populations in the HapMap datasets. Multidimensional scaling analysis of polymorphisms in all four genes suggested broad overlap of all of the examined African populations. Based on these data, we propose that there is enough similarity among African populations represented in the HapMap database to justify initial SNP selection for genetic epidemiological studies in Uganda and South Africa. We also discovered three novel polymorphisms that appear to be population-specific and would only be detected by sequencing efforts.     

Genetic identification of members of the Bemisia tabaci cryptic species complex from South Africa reveals native and introduced haplotypes

The whitefly Bemisia tabaci cryptic species complex contains some important agricultural pest and virus vectors. Members of the complex have become serious pests in South Africa (SA) because of their feeding habit and their ability to transmit begomovirus species. Despite their economic importance, studies on the biology and distribution of B. tabaci in SA are limited. To this end, a survey was made to investigate the diversity and distribution of B. tabaci cryptic species in eight geographical locations (provinces) in SA, between 2002 and 2009, using the mitochondrial cytochrome oxidase I (mtCOI) sequences. Phylogenetic analysis revealed the presence of members from two endemic sub‐Saharan Africa (SSAF) subclades coexisting with two introduced putative species. The SSAF‐1 subclade includes cassava host‐adapted B. tabaci populations, whereas the whiteflies collected from cassava and non‐cassava hosts formed a distinct subclade, referred to as SSAF‐5, and represent a new subclade among previously recognized southern Africa clades. Two introduced cryptic species, belonging to the Mediterranean and Middle East–Asia minor 1 clades, were identified and include the B and Q types. The B type showed the widest distribution, being present in five of the eight provinces explored in SA, infesting several host plants and predominating over the indigenous haplotypes. This is the first report of the occurrence of the exotic Q type in SA alongside the more widely distributed B type. Furthermore, mtCOI PCR‐RFLP was developed for the SA context to allow rapid discrimination between the B, Q and SSAF putative species. The capacity to manage pests and disease effectively relies on knowledge of the identity of the agents causing the damage. Therefore, this study contributes to the understanding of South African B. tabaci species diversity, information needed for the development of knowledge‐based disease management practices.     

A chronotype comparison of South African and Dutch marathon runners: The role of scheduled race start times and effects on performance

Recently, a high prevalence of morning-types was reported among trained South African endurance athletes. Proposed explanations for this observation were that either the chronotype of these athletes is better suited to coping with the early-morning start times of endurance events in South Africa; or habitual early waking for training or endurance events may have conditioned the athletes to adapt and become morning-types. The South African endurance athletes also had earlier chronotypes compared to a control population of less active individuals, suggesting that individuals who are more physically active may have earlier chronotypes. However, since both the South African athlete and control groups showed an overrepresentation of morning-types compared to European and American populations, the South African climate may in part have explained this bias towards morningness. Given the latitude and climate differences between South Africa and the Netherlands, and that South African marathons typically start at about 06:30 while those in the Netherlands start later (±11:00), comparison of South African and Dutch marathon runners and active controls would allow for simultaneous assessment of the effects of marathon start time, degree of physical activity and climate on chronotype. Therefore, the primary aims of this study were: (i) to assess the effect of marathon start time on chronotype in marathon runners and (ii) to determine the extent to which either degree of physical activity or climate might explain the bias towards morningness observed in South African athletes and controls. A secondary aim was to determine whether any relationships exist between chronotype, PERIOD3 (PER3) variable number tandem repeat (VNTR) polymorphism genotype, habitual training habits and marathon performance. Trained male marathon runners from South Africa (n?=?95) and the Netherlands (n?=?90), and active but non-competitive male controls from South Africa (n?=?97) and the Netherlands (n?=?98) completed a questionnaire capturing demographics, training and race history, as well as the Horne–Östberg morningness–eveningness personality questionnaire. All participants donated buccal cell samples from which genomic DNA was extracted and polymerase chain reaction analysis was used to genotype them for the PER3 VNTR polymorphism, which has previously been associated with chronotype. The main finding was that South African runners were significantly more morning-orientated than Dutch runners suggesting that participation in an endurance sport with an earlier start time may influence chronotype. Secondly, both the South African and Dutch runners were significantly more morning-orientated than their respective control groups, indicating that individuals who train for and participate in recreational endurance sport races have an earlier chronotype than physically active but non-competitive males. Thirdly, mean chronotype scores were similar between the South African and Dutch control groups, suggesting that climate does not seem to affect chronotype in these groups. Fourthly, the PER3 VNTR polymorphism distribution was similar between the four groups and was not associated with chronotype, suggesting that the difference in chronotype between the four groups in this study is not explained by the PER3 VNTR genotype. Lastly, in the South African runners group, a higher preference for mornings was associated with a better personal best half-marathon and current marathon performance.     

Molecular Analysis of South African Ovine Herpesvirus 2 Strains Based on Selected Glycoprotein and Tegument Genes

Ovine herpesvirus 2 (OvHV-2), is the causative agent of sheep-associated malignant catarrhal fever (SA-MCF), a generally fatal disease of cattle and other captive wild ruminants. Information on the OvHV-2 strains circulating in South Africa (SA) and other African countries with regard to genetic structure and diversity, and pattern of distribution is not available. This study aimed to characterize the OvHV-2 strains circulating in SA using selected genes encoding glycoproteins and tegument proteins. To establish the genetic diversity of OvHV-2 strains, four genes, Ov 7, Ov 8 ex2, ORF 27 and ORF 73 were selected for analysis by PCR and DNA sequencing. Nucleotide and amino acid multiple sequence analyses revealed two genotypes for ORF 27 and ORF 73, and three genotypes for Ov 7 and Ov 8 ex2, randomly distributed throughout the regions. Ov 7 and ORF 27 nucleotide sequence analysis revealed variations that distinguished SA genotypes from those of reference OvHV-2 strains. Epitope mapping analysis showed that mutations identified from the investigated genes are not likely to affect the functions of the gene products, particularly those responsible for antibody binding activities associated with B-cell epitopes. Knowledge of the extent of genetic diversity existing among OvHV-2 strains has provided an understanding on the distribution patterns of OvHV-2 strains or genotypes across the regions of South Africa. This can facilitate the management of SA-MCF in SA, in terms of introduction of control measures or safe practices to monitor and control OvHV-2 infection. The products encoded by the Ov 7, Ov 8 ex2 and ORF 27 genes are recommended for evaluation of their coded proteins as possible antigens in the development of an OvHV-2 specific serodiagnostic assay.