H3Africa: An Africa exemplar? Exploring its framework on protecting human research participants

The Human Heredity and Health in Africa (H3Africa) Consortium is a conglomeration of research and infrastructure projects spread throughout Africa whose aim is to apply genomic methodology to diseases affecting the people in the region. Its operation is innovative in the sense that it is doing something new; that is, filling a hitherto existing void in genomic research capability of African scientists and infusing resources and manpower to institutions and investigators across Africa. But aside from developing and sustaining capacity in genomic research and biorepositories, H3Africa is also invested in developing appropriate ethical regulatory regime to govern research in these areas. This latter concern –research ethics governance – is the major subject of this paper. Specifically, the paper discusses protection of research participants as envisaged by H3Africa in the area of consent, safeguarding privacy, maintaining confidentiality of health information and sharing of data/biospecimens. The ultimate goal is to determine whether H3Africa initiatives and processes are consistent or at odds with international guidelines and best practices.     

The next steps for genomic medicine: challenges and opportunities for the developing world

This is a historical moment on the path to genomic medicine - the point at which theory is about to be translated into practice. We have previously described human genome variation studies taking place in Mexico, India, Thailand, and South Africa. Such investments into science and technology will enable these countries to embark on the path to the medical and health applications of genomics, and to benefit economically. Here we provide a perspective on the challenges and opportunities facing these and other countries in the developing world as they begin to harness genomics for the benefit of their populations.     

Genomics, public health and developing countries: the case of the Mexican National Institute of Genomic Medicine (INMEGEN)

In 2004, the government of Mexico established the National Institute of Genomic Medicine (INMEGEN), to carry out disease-related genomic studies that will address national health problems and stimulate scientific and technological development by generating new commercial products and services in genomic medicine. Towards this end, INMEGEN is carrying out a large-scale genotyping project to map genomic variation within its own population. The initiative is expected to generate a key resource for local researchers to understand disease susceptibility and variation in drug responses, which will contribute to Mexico's goal of developing public health genomics - a field in which Mexico is proving to be a leader amongst emerging economies.     

Comparison of LCI studies in South Africa and Germany

This article investigates the possibilities for and potential applications of Life Cycle Assessments (LCA’s) and specifically of Life Cycle Inventories (LCI’s) in developing countries (e.g. South Africa). The situation in South Africa is compared to that prevailing in Germany, a highly developed country. Although South Africa is unique concerning the different degrees of development within the industry, most of the principles discussed in this article can be applied similarly to other developing countries. No significant full LCI studies have yet been performed in South Africa. Although the immediate local needs for the South Africa enonomy are solving labour problems, creating jobs, building houses, the industries should seriously consider performing LCA and related studies for their products. The concept of quality should be extended to include the environmental performance of a product, process or service.     

Research vulnerability: an illustrative case study from the South African mining industry

The concept of 'vulnerability' is well established within the realm of research ethics and most ethical guidelines include a section on 'vulnerable populations'. However, the term 'vulnerability', used within a human research context, has received a lot of negative publicity recently and has been described as being simultaneously 'too broad' and 'too narrow'. The aim of the paper is to explore the concept of research vulnerability by using a detailed case study - that of mineworkers in post-apartheid South Africa. In particular, the usefulness of Kipnis's taxonomy of research vulnerability will be examined. In recent years the volume of clinical research on human subjects in South Africa has increased significantly. The HIV and TB pandemics have contributed to this increase. These epidemics have impacted negatively on the mining industry; and mining companies have become increasingly interested in research initiatives that address these problems. This case study explores the potential research vulnerability of mineworkers in the context of the South African mining industry and examines measures that can reduce this vulnerability.     

Isolation and the origin of the khoisan: Late pleistocene and early holocene human evolution at the southern end of Africa

The debate between the proponents of the Recent African Origin and the Multiregional Evolution models for the origin of anatomically modern humans has not been of great importance to the interpretation of late Pleistocene human fossils in South Africa. The main reason is that both models propose that evidence of anatomically moderns should happen in South Africa at an early date. A more important issue to the African context is whether or not those early transitions to modernity were accompanied by the development of the distinctive local populations known today as the Khoisan. Serogenetic evidence suggests a relative antiquity for the origins of living Khoisan peoples, but this may simply reflect the longer time that anatomically modern peoples have lived in the sub-continent. A search for features of distinctive Khoisan morphology in the early remains may be of more value as it might indicate the presence of a local adaptive pattern to the special environment conditions of the region.     

The biocultural evolution of Khoisan populations of Southern Africa

The research presented here offers new information on the recent evolution of Khoisan populations of southern Africa through the new study of Holocene skeletons. When combined with subfossil and historical remains, these archeological specimens provide a skeletal record for the last 5000–9000 years of southern African prehistory. Multivariate statistical analyses of cranial measurements were used to determine patterns of morphological variation in the skeletal record with which hypotheses of biocultural evolution were tested. These analyses yielded the following results. First, the traditional distinction between Bushmen and Hottentots holds for recent inland individuals. Second, there is a suggestion of a morphologically distinct San population living on the coast of South Africa. The idea of a “Strandloper” population suggested by early scholars is here revived. The third result is that there is little evidence of complete population succession on the coast of South Africa, suggesting that there were no massive population movements associated with the spread of Hottentot pastoralism throughout southern Africa.     

Local Medicinal Plant Knowledge in South Africa Preserved by Apartheid

Apartheid isolated South Africa economically and politically from the global arena and its citizens culturally from one another. Post-apartheid policymakers have sought to address prior inequalities in education, health care and employment, concerns central to biodiversity conservation initiatives. This article examines the role of school gardening programs on the distribution and transmission of local phytomedicinal knowledge. Urban Cape Town, an area of high biocultural diversity, presents a unique environment in which to observe cultural distinctions in medicinal plant utilization, the impact of school gardening, and the recent cultural amalgamation in local knowledge transmission. Local healers chose 16 common medicinal plants, which were used to examine fifth and seventh graders’ knowledge of local remedies. Results indicate that knowledge of different plants was concentrated in specific ethnic groups and amongst recent migrants. It is proposed that ethnic separation during the apartheid era insulated cultures on socioeconomic and geo-environmental strata, thereby preserving local knowledge.     

Is Younger Really Safer? A Qualitative Study of Perceived Risks and Benefits of Age-Disparate Relationships among Women in Cape Town,South Africa

Young women in age-asymmetric relationships may be at an elevated risk for acquisition of HIV, since relationships with older men are also correlated with other risk behaviors like less condom use. Qualitative studies have shown that women are motivated to participate in these relationships for money and emotional support. However, there is a paucity of research on women’s perceived risks of these relationships, particularly in South Africa. To this end, we conducted in-depth interviews with 23 women recruited from three urban communities in Cape Town. A thematic question guide was used to direct the interviews. Thematic content analysis was used to explore women’s perceived risks of age-disparate and non-age-disparate relationships, the benefits of dating older men, and risk perceptions that influence decisions around beginning or ending a relationship. A plurality of women thought that dating an older man does not bring any adverse consequences, although some thought that older men do not use condoms and may be involved in concurrent partnerships. Many women were less inclined to date same-age or younger men, because they were viewed as being disrespectful and abusive. This study points to the need for more awareness raising about the risks of age-disparate relationships. In addition to these initiatives, there is an urgent need to implement holistic approaches to relationship health, in order to curb intimate partner violence, improve gender equity and make non-age-disparate relationships more attractive.     

Twenty-first century vaccinomics innovation systems: capacity building in the global South and the role of Product Development Partnerships (PDPs)

The availability of sequence information from publicly available complete genomes and data intensive sciences, together with next-generation sequencing technologies offer substantial promise for innovation in vaccinology and global public health in the beginning of the 21st century. This article presents an innovation analysis for the nascent field of vaccinomics by describing one of the major challenges in this endeavor: the need for capacities in "vaccinomics innovation systems" to support the developing countries involved in the creation and testing of new vaccines. In particular, we discuss the need for understanding how institutional frameworks can enhance capacities as intrinsic to a systems approach to health technology development. We focus our attention on the global South, meaning the technically less advanced and developing nations in Africa, Asia, and Latin America. This focus is timely and appropriate because the challenge for innovation in postgenomics medicine is markedly much greater in these regions where basic infrastructures are often underresourced and new or the anticipated institutional relationships can be fragile. Importantly, we examine the role of Product Development Partnerships (PDPs) as a 21st century organizational innovation that contributes to strengthening fragile institutions and capacity building. For vaccinomics innovation systems to stand the test of time in a context of global public health, local communities, knowledge, and cultures need to be collectively taken into account at all stages in programs for vaccinomics-guided vaccine development and delivery in the global South where the public health needs for rational vaccine development are urgent.     

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.     

Human skin color diversity is highest in sub-Saharan African populations

Previous studies of genetic and craniometric traits have found higher levels of within-population diversity in sub-Saharan Africa compared to other geographic regions. This study examines regional differences in within-population diversity of human skin color. Published data on skin reflectance were collected for 98 male samples from eight geographic regions: sub-Saharan Africa, North Africa, Europe, West Asia, Southwest Asia, South Asia, Australasia, and the New World. Regional differences in local within-population diversity were examined using two measures of variability: the sample variance and the sample coefficient of variation. For both measures, the average level of within-population diversity is higher in sub-Saharan Africa than in other geographic regions. This difference persists even after adjusting for a correlation between within-population diversity and distance from the equator. Though affected by natural selection, skin color variation shows the same pattern of higher African diversity as found with other traits.     

A genome scan to detect candidate regions influenced by local natural selection in human populations

As human populations dispersed throughout the world, they were subjected to new selective forces, which must have led to local adaptation via natural selection and hence altered patterns of genetic variation. Yet, there are very few examples known in which such local selection has clearly influenced human genetic variation. A potential approach for detecting local selection is to screen random loci across the genome; those loci that exhibit unusually large genetic distances between human populations are then potential markers of genomic regions under local selection. We investigated this approach by genotyping 332 short tandem repeat (STR) loci in Africans and Europeans and calculating the genetic differentiation for each locus. Patterns of genetic diversity at these loci were consistent with greater variation in Africa and with local selection operating on populations as they moved out of Africa. For 11 loci exhibiting the largest genetic differences, we genotyped an additional STR locus located nearby; the genetic distances for these nearby loci were significantly larger than average. These genomic regions therefore reproducibly exhibit larger genetic distances between populations than the "average" genomic region, consistent with local selection. Our results demonstrate that genome scans are a promising means of identifying candidate regions that have been subjected to local selection.     

Bioprospecting the African Renaissance: The new value of <Emphasis Type="Italic">muthi</Emphasis> in South Africa

This article gives an overview of anthropological research on bioprospecting in general and of available literature related to bioprospecting particularly in South Africa. It points out how new insights on value regimes concerning plant-based medicines may be gained through further research and is meant to contribute to a critical discussion about the ethics of Access and Benefit Sharing (ABS). In South Africa, traditional healers, plant gatherers, petty traders, researchers and private investors are assembled around the issues of standardization and commercialization of knowledge about plants. This coincides with a nation-building project which promotes the revitalization of local knowledge within the so called African Renaissance. A social science analysis of the transformation of so called Traditional Medicine (TM) may shed light onto this renaissance by tracing social arenas in which different regimes of value are brought into conflict. When medicinal plants turn into assets in a national and global economy, they seem to be manipulated and transformed in relation to their capacity to promote health, their market value, and their potential to construct new ethics of development. In this context, the translation of socially and culturally situated local knowledge about muthi into global pharmaceuticals creates new forms of agency as well as new power differentials between the different actors involved.     

Questions of khoesan continuity: Dental affinities among the indigenous holocene peoples of South Africa

The present report follows up on the findings of previous research, including recent bioarchaeological study of well‐dated Khoesan skeletal remains, that posits long term biological continuity among the indigenous peoples of South Africa after the Pleistocene. The Arizona State University Dental Anthropology System was used to record key crown, root, and intraoral osseous nonmetric traits in six early‐through‐late Holocene samples from the Cape coasts. Based on these data, phenetic affinities and an identification of traits most important in driving intersample variation were determined using principal components analysis and the mean measure of divergence distance statistic. To expand biological affinity comparisons into more recent times, and thus preliminarily assess the dental impact of disproportionate non‐Khoesan gene flow into local peoples, dental data from historic Khoekhoe and San were also included. Results from the prehistoric comparisons are supportive of population continuity, though a sample from Matjes River Rockshelter exhibits slight phenetic distance from other early samples. This and some insignificant regional divergence among these coastal samples may be related to environmental and cultural factors that drove low‐level reproductive isolation. Finally, a close affinity of historic San to all samples, and a significant difference of Khoekhoe from most early samples is reflective of documented population history following immigration of Bantu‐speakers and, later, Europeans into South Africa. Am J Phys Anthropol 155:33–44, 2014. © 2014 Wiley Periodicals, Inc.     

The disappearing San of southeastern Africa and their genetic affinities

Southern Africa was likely exclusively inhabited by San hunter-gatherers before ~2000 years ago. Around that time, East African groups assimilated with local San groups and gave rise to the Khoekhoe herders. Subsequently, Bantu-speaking farmers, arriving from the north (~1800 years ago), assimilated and displaced San and Khoekhoe groups, a process that intensified with the arrival of European colonists ~350 years ago. In contrast to the western parts of southern Africa, where several Khoe-San groups still live today, the eastern parts are largely populated by Bantu speakers and individuals of non-African descent. Only a few scattered groups with oral traditions of Khoe-San ancestry remain. Advances in genetic research open up new ways to understand the population history of southeastern Africa. We investigate the genomic variation of the remaining individuals from two South African groups with oral histories connecting them to eastern San groups, i.e., the San from Lake Chrissie and the Duma San of the uKhahlamba-Drakensberg. Using ~2.2 million genetic markers, combined with comparative published data sets, we show that the Lake Chrissie San have genetic ancestry from both Khoe-San (likely the ||Xegwi San) and Bantu speakers. Specifically, we found that the Lake Chrissie San are closely related to the current southern San groups (i.e., the Karretjie people). Duma San individuals, on the other hand, were genetically similar to southeastern Bantu speakers from South Africa. This study illustrates how genetic tools can be used to assess hypotheses about the ancestry of people who seemingly lost their historic roots, only recalling a vague oral tradition of their origin.