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South Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Despite clear linguistic and geographic diversity, the genetic differences between these groups have not been systematically investigated. Based on genome-wide data of over 5000 individuals, representing eight major SEB groups, we provide strong evidence for fine-scale population structure that broadly aligns with geographic distribution and is also congruent with linguistic phylogeny (separation of Nguni, Sotho-Tswana and Tsonga speakers). Although differential Khoe-San admixture plays a key role, the structure persists after Khoe-San ancestry-masking. The timing of admixture, levels of sex-biased gene flow and population size dynamics also highlight differences in the demographic histories of individual groups. The comparisons with five Iron Age farmer genomes further support genetic continuity over ~400 years in certain regions of the country. Simulated trait genome-wide association studies further show that the observed population structure could have major implications for biomedical genomics research in South Africa. Despite linguistic and geographic diversity in South Eastern Bantu-speaking (SEB) groups of South Africa, genetic variation in these groups has not been investigated in depth. Here, the authors analyse genome-wide data from 5056 individuals, providing insights into demographic history across SEB groups.

The aim of the study was to determine the prevalence and determinants of chronic non-communicable disease (NCD) risk factors in a rural community in the Limpopo Province of South Africa. This survey was conducted using the WHO \"STEPwise approach to the surveillance of non-communicable diseases\" (STEPS) methodology. Participants were residents of the Dikgale HDSS site and standardised international protocols were used to measure behavioural risk factors (smoking, alcohol consumption, fruit and vegetable intake and, physical activity) and physical characteristics (weight, height, waist and hip circumferences and blood pressure-BP). Fasting blood glucose, triglyceride, cholesterol and HDL-C were determined in 732 participants. Data were analysed using STATA 12 for Windows. The prevalence of current smokers amongst the participants was 13.7%, of which 81.3% were daily smokers. Alcohol was consumed by 16.3% of the participants. The majority of participants (88.6%) had low daily intake of fruit and vegetables and low physical activity (66.5%). The prevalence of hypertension amongst the participants was 38.2%. Overweight, obesity and high waist circumference were prevalent in females. The cardio-metabolic risk profile was not significantly different between men and women. People who were older than 40 years, overweight or obese and those who consumed alcohol were more likely to be hypertensive. Smoking was associated significantly with older age, males, never married and divorced people. Alcohol consumption was associated with older age, males, low educational status and low income. High levels of risk factors for NCDs among adults in the Dikgale HDSS suggest an urgent need for health interventions to control these risk factors at the population level in order to reduce the prevalence of NCDs.

Objectives To investigate the descriptive nature of objectively-measured, free-living sleep quantity and quality, and the relationship to adiposity, in a rural African setting in 145 adults (≥ 40 years, female: n = 104, male: n = 41). Wrist-mounted, triaxial accelerometry data was collected over 9 days. Measures of sleep quantity and quality, and physical activity were extracted from valid minute-by-minute data. Adiposity indices were body-mass-index, waist circumference and conicity index. Self-reported data included behavioural, health and socio-demographic variables. Community consultation followed the quantitative data analyses, for validation and interpretation of findings. Results Females had more nocturnal sleep than males (7.2 vs. 6.8 h/night, p  = 0.0464) while males recorded more diurnal sleep time ( p  = 0.0290). Wake after sleep onset and number of awakenings were higher in females, and sleep efficiency was higher in males ( p  ≤ 0.0225). Sleep indices were generally similar between weekdays and weekends, except for sleep fragmentation index ( p  = 0.0458). Sleep quantity, but not sleep quality was independently and inversely associated with adiposity ( p  = 0.0453). Physical activity and morbidity measures were significantly and consistently associated with sleep and adiposity measures ( p  < 0.0458). The preliminary qualitative data suggests that future studies should include more detailed data around contextual issues of sleep (social, cultural, economic, environment).

Background: The study was conducted in the Dikgale Health and Demographic Surveillance System (DHDSS) site where we have observed increasing obesity levels, particularly in women, despite evidence of high physical activity (PA) and a relatively low daily energy intake. Objective: This study aimed to assess the socio-demographic, behavioural and biological determinants of body mass index (BMI) in adult residents permanently residing in the DHDSS. Methods: A cross-sectional study was conducted in which socio-demographic, behavioural and biological characteristics from 1143 participants (aged 40-60 years) were collected using a paper questionnaire and standard anthropometric measures. Human immunodeficiency virus (HIV) testing was performed on all participants except those who indicated that they had tested positive. Chi-square and Mann-Whitney tests were used to analyze categorical and continuous variables, respectively, while hierarchical multivariate regression was used to analyze predictors of BMI. Results: The median age of women and men was 51 (46-56) and 50 (45-55) years, respectively. The prevalence of overweight-obesity was 76% in women and 21% in men. A significant negative association of BMI with HIV and smoking and a significant positive association with socio-economic status (SES) was observed in both sexes. In women, BMI was negatively associated with sleep duration (p = 0.015) and age (p = 0.012), but positively associated with sugar-sweetened beverages (SSBs) (p = 0.08). In men, BMI was negatively associated with alcohol use (p = 0.016) and positively associated with being married (p < 0.001). PA was not associated with BMI in either sexes. Full models explained 9.2% and 20% of the variance in BMI in women and men, respectively. Conclusion: BMI in DHDSS adults is not associated with physical inactivity but is associated wealth, marital status, sleep, smoking, alcohol use, and HIV status. Future studies should explore the contribution of nutrition, stunting, psycho-social and genetic factors to overweight and obesity in DHDSS.

Background Chronic disease management (CDM) is an approach to health care that keeps people as healthy as possible through the prevention, early detection and management of chronic diseases. The aim of this study was to develop interventions to improve management of chronic diseases in the form of an integrated, evidence-based chronic disease management model in Dikgale, a rural area of Limpopo Province in South Africa. Methods A multifaceted intervention, called ‘quality circles’ (QCs) was developed to improve the quality and the management of chronic diseases in the Dikgale Health and Demographic Surveillance System (HDSS). These QCs used the findings from previous studies which formed part of the larger project in the study area, namely, the quantitative study using STEPwise survey and qualitative studies using focus group discussions and semi-structured interviews. Results The findings from previous studies in Dikgale HDSS revealed that an epidemiological transition is occurring. Again, the most widely reported barriers from previous studies in this rural area were: lack of knowledge of NCDs; shortages of medication and shortages of nurses in the clinics, which results in patients having long waiting-time at clinics. Lack of training of health care providers on the management of chronic diseases and the lack of supervision by the district and provincial health managers, together with poor dissemination of guidelines, were contributing factors to the lack of knowledge of non-communicable diseases (NCDs) management among nurses and community health care workers (CHWs). Consideration of all of these findings led to the development of model which focuses on integrating nursing services, CHWs and traditional health practitioners (THPs), including a well-established clinical information system for health care providers. A novel aspect of the model is the inclusion of community ambassadors who are on treatment for NCDs and are, thus, repositories of knowledge who can serve as a bridge between health care workers and community members. Conclusion The model developed highlights the need for health interventions that aim to control risk factors at the population level, the need for availability of NCD-trained nurses, functional equipment and medication and a need to improve the link with traditional healers.

Objective: The present study evaluated the prevalence of anaemia and its determinants in one- and three-year-old children from the Capricorn District of Limpopo Province, South Africa. Methods: A prospective cohort study conducted in rural villages in the Capricorn District of Limpopo Province, South Africa. At birth, a cohort of 219 children was followed until they were one and three years of age. Data collected included the children’s anthropometric measurements, blood for biochemical analysis (full blood count, ferritin, folate and vitamin B12) and socio-demographic status.Results: At one year, anaemia (Hb < 11 g/dL) was present in 52% of the children, decreasing to 22% by the third year. Iron deficiency (ferritin < 12 µg/mL) was common in these children (39% and 33% at one year and three years, respectively) particularly in the presence of anaemia. Folate and vitamin B12 deficiencies (< 5 ng/mL and < 145 pg/mL, respectively) were common at one year, with the children accumulating enough vitamin B12 by three years; however, folate deficiency levels remained fairly constant between the two time points.Conclusion: There was a high prevalence of anaemia in the study participants at one year and three years of age. Factors that increased the risk of anaemia at three years were: a mother with only a primary school education, anaemia at one year, male gender, overweight, and combined overweight and stunting. Protective factors against anaemia were having a younger mother who served as the main caregiver.

To determine the prevalence of stunting, wasting and overweight and their determinants in 3-year-old children in the Central Region of Limpopo Province, South Africa. Prospective cohort study. Rural villages in the Central Region of the Limpopo Province, South Africa. One hundred and sixty-two children who were followed from birth were included in the study. Anthropometric measurements and sociodemographic characteristics of the children were recorded. Height-for-age Z-scores were low, with a high prevalence of stunting (48%). The children also exhibited a high prevalence of overweight (22%) and obesity (24%). Thirty-one (19%) children were both stunted and overweight. Gaining more weight within the first year of life increased the risk of being overweight at 3 years by 2.39 times (95% confidence interval (CI) 1.96-4.18) while having a greater length at 1 year was protective against stunting (odds ratio (OR) 0.41; 95% CI 0.17-0.97). Having a mother as a student increased the risk for stunting at 3 years by 18.21 times (95% CI 9.46-34.74) while having a working mother increased the risk for overweight by 17.87 times (95% CI 8.24-38.78). All these factors also appeared as risks or as being protective in children who were both overweight and stunted, as did living in a household having nine or more persons (OR 5.72; 95% CI 2.7-12.10). The results of this study highlight the importance of evaluating anthropometric status in terms of both stunting and overweight. Furthermore, it is important to realise the importance of normal length and weight being attained at 1 year of age, since these in turn predict nutritional status at 3 years of age.

Background: Underweight in human immunodeficiency virus (HIV)-infected people on antiretroviral therapy (ART) complicates the management of HIV infection and contributes to mortality, whereas overweight increases the risk of cardiovascular disease (CVD). Aim: The study determined weight status and associated factors in people with HIV infection receiving ART. Setting: Rural primary health care clinics in Dikgale, Limpopo province, South Africa. Methods: A cross-sectional study in which data were collected using the World Health Organization (WHO) stepwise approach to surveillance (STEPS) questionnaire and calculated using WHO analysis programmes guide. Weight and height were measured using standard WHO procedures, and body mass index was calculated as weight (kg)/height (m 2 ). Data on ART duration were extracted from patients’ files. CD4 lymphocyte counts and viral load were determined using standard laboratory techniques. Results: Of the 214 participants, 8.9%, 54.7% and 36.4% were underweight, normal weight and overweight, respectively. Physical activity (OR: 0.99, p = 0.001) and male gender (OR: 0.29, p = 0.04) were negatively associated with overweight. Men who used tobacco were more likely to be underweight than non-tobacco users (OR: 10.87, p = 0.02). Neither ART duration nor viral load or CD4 count was independently associated with underweight or overweight in multivariate analysis. Conclusion: A high proportion of people on ART were overweight and a smaller proportion underweight. There is a need to simultaneously address the two extreme weight problems in this vulnerable population through educating them on benefits of avoiding tobacco, engaging in physical activity and raising awareness of CVD risk.

Background We investigated the criterion validity of a physical activity index (PAI) derived from socio-demographic variables obtained from convenience samples of rural African women. Methods We used a sample (N = 206) from a larger dataset which surveyed adult rural Africans during 1997, and data collected during 2003/4 from 138 adult rural African women. A three-point PAI (low-, medium- and high-subsistence) was constructed from four socio-demographic questions related to electricity, cooking methods, water collection and availability of motorized transport. Criterion measures included measures of adiposity, blood biochemistry, resting blood pressure (RBP), physical fitness (VO 2max ) and single-plane accelerometry (ACC). Results Age, educational level and health status were not related to PAI level (p > 0.1). There was a significant negative, linear trend between the PAI level and adiposity level (p < 0.04), and fasting blood glucose concentration (p < 0.0001), while VO 2max was positively related to PAI level (p = 0.0190). The PAI level was positively and linearly related to ACC output, namely counts.day -1 (p = 0.0044), steps.day -1 (p = 0.0265), min.day -1 of moderate-to-vigorous activity (p = 0.0040), and the percentage of subjects adhering to physical activity public health guidelines (p = 0.0157). Other criterion measures did not reach significance, but were in the expected direction (sedentary behaviour: p > 0.08, RBP: p > 0.07). Conclusion The PAI derived from a socio-demographic questionnaire is a valid instrument for broadly categorizing levels of physical activity for this specific population of rural African women. As the epidemiological transition progresses, validity will need to be re-established.

Objective: The objective was to determine lipid levels and cardiovascular risk factors in treatment-naïve, human immunodeficiency virus (HIV)-infected rural African people in Limpopo province.Design: This was a case control study.Setting and subjects: The setting was Dikgale Health and Demographic Surveillance System Centre, Limpopo province. Treatment naïve, HIV-infected and HIV-negative people participated in the study. Outcome measures: Demographic, lifestyle and chronic disease data were collected using the World Health Organization stepwise approach to surveillance (STEPS) questionnaire. Biochemical parameters were tested using standard biochemical methods. HIV testing and CD4 counts were performed using the Alere Determine™ HIV 1/2 Ag/Ab kit and The Alere Pima™ Analyser. Insulin resistance, low-density lipoprotein cholesterol (LDL cholesterol), and non-high-density lipoprotein cholesterol (non-HDL cholesterol) levels were calculated.Results: The mean age of participants (years) was 49.7 ± 16.6. More HIV-infected than HIV-uninfected women consumed alcohol (25.4% vs. 11.9%, p-value < 0.05), and the prevalence of abdominal obesity was higher in HIV-uninfected than in HIV-infected women (74.6% vs. 54.8%, p-value < 0.05). Levels of total cholesterol (TC), HDL cholesterol, non-HDL cholesterol, LDL cholesterol and apolipoprotein A1 (ApoA1) were significantly lower in the HIV-infected than in the HIV-uninfected group. The prevalence of low HDL cholesterol was higher in HIV-infected than in HIV-uninfected people (62.4% vs. 41.6%, p-value < 0.01). HIV infection increased the likelihood of low HDL cholesterol by 2.7 times (p-value 0.001). Male gender and alcohol use decreased the likelihood of low HDL cholesterol by 61% (p-value 0.002) and 48% (p-value 0.048), respectively. HIV infection was associated with low HDL cholesterol, ApoA1, LDL cholesterol and TC. Low CD4 count was associated with low body mass index, LDL cholesterol and high diastolic blood pressure.Conclusion: The prevalence of cardiovascular risk factors was equally high in HIV-infected and in HIV-uninfected rural people, except for low HDL and alcohol consumption, which were significantly higher in HIV-infected people, while abdominal obesity was significantly higher in HIV-uninfected people. There is a need to raise awareness of cardiovascular risk factors in rural people in Limpopo province.