Characteristics of infections with ancestral, Beta and Delta variants of SARS-CoV-2 in the PHIRST-C community cohort study, South Africa, 2020-2021.

BACKGROUND: Data on the characteristics of individuals with mild and asymptomatic infections with different SARS-CoV-2 variants are limited. We therefore compared the characteristics of individuals infected with ancestral, Beta and Delta SARS-CoV-2 variants in South Africa. METHODS: We conducted a prospective cohort study in a rural and an urban site during July 2020-August 2021. Mid-turbinate nasal swabs were collected twice-weekly from household members irrespective of symptoms and tested for SARS-CoV-2 using real-time reverse transcription polymerase chain reaction (rRT-PCR). Differences in demographic and clinical characteristics, shedding and cycle threshold (Ct) value of infection episodes by variant were evaluated using multinomial regression. Overall and age-specific incidence rates of infection were compared by variant. RESULTS: We included 1200 individuals from 222 households and 648 rRT-PCR-confirmed infection episodes (66, 10% ancestral, 260, 40% Beta, 322, 50% Delta). Symptomatic proportion was similar for ancestral (7, 11%), Beta (44, 17%), and Delta (46, 14%) infections (p=0.4). After accounting for previous infection, peak incidence shifted to younger age groups in successive waves (40-59 years ancestral, 19-39 years Beta, 13-18 years Delta). On multivariable analysis, compared to ancestral, Beta infection was more common in individuals aged 5-12 years (vs 19-39)(adjusted odds ratio (aOR) 2.6, 95% confidence interval (CI)1.1-6.6) and PCR cycle threshold (Ct) value <30 (vs >35)(aOR 3.2, 95%CI 1.3-7.9), while Delta was more common in individuals aged <5 (aOR 6.7, 95%CI1.4-31.2) and 5-12 years (aOR 6.6 95%CI2.6-16.7)(vs 19-39) and Ct value <30 (aOR 4.5, 95%CI 1.3-15.5) and 30-35 (aOR 6.0, 95%CI 2.3-15.7)(vs >35). CONCLUSIONS: Consecutive SARS-CoV-2 waves with Beta and Delta variants were associated with a shift to younger individuals. Beta and Delta infections were associated with higher peak viral loads, potentially increasing infectiousness.

Understanding Household Dynamics From the Ground Up: A Longitudinal Study From a Rural South African Setting.

Investigations into household structure in low- and middle-income countries (LMICs) provide important insight into how families manage domestic life in response to resource allocation and caregiving needs during periods of rapid sociopolitical and health-related challenges. Recent evidence on household structure in many LMICs contrasts with long-standing viewpoints of worldwide convergence to a Western nuclearized household model. Here, we adopt a household-centered theoretical and methodological framework to investigate longitudinal patterns and dynamics of household structure in a rural South African setting during a period of high AIDS-related mortality and socioeconomic change. Data come from the Agincourt Health and Socio-Demographic Surveillance System (2003-2015). Using latent transition models, we derived six distinct household types by examining conditional interdependency between household heads' characteristics, members' age composition, and migration status. More than half of households were characterized by their complex and multigenerational profiles, with considerable within-typology variation in household size and dependency structure. Transition analyses showed stability of household types under female headship, while higher proportions of nuclearized household types dissolved over time. Household dissolution was closely linked to prior mortality experiences-particularly, following death of a male head. Our findings highlight the need to better conceptualize and contextualize household changes across populations and over time.

Unmasking Pneumococcal Carriage in a High Human Immunodeficiency Virus (HIV) Prevalence Population in two Community Cohorts in South Africa, 2016-2018: The PHIRST Study.

BACKGROUND: Longitudinal pneumococcus colonization data in high human immunodeficiency virus (HIV) prevalence settings following pneumococcal conjugate vaccine introduction are limited. METHODS: In 327 randomly selected households, 1684 individuals were enrolled and followed-up for 6 to 10 months during 2016 through 2018 from 2 communities. Nasopharyngeal swabs were collected twice weekly and tested for pneumococcus using quantitative lytA real-time polymerase chain reaction. A Markov model was fitted to the data to define the start and end of an episode of colonization. We assessed factors associated with colonization using logistic regression. RESULTS: During the study period, 98% (1655/1684) of participants were colonized with pneumococcus at least once. Younger age (<5 years: adjusted odds ratio [aOR], 14.1; 95% confidence [CI], 1.8-111.3, and 5-24 years: aOR, 4.8, 95% CI, 1.9-11.9, compared with 25-44 years) and HIV infection (aOR, 10.1; 95% CI, 1.3-77.1) were associated with increased odds of colonization. Children aged <5 years had fewer colonization episodes (median, 9) than individuals ≥5 years (median, 18; P < .001) but had a longer episode duration (<5 years: 35.5 days; interquartile range, 17-88) vs. ≥5 years: 5.5 days (4-12). High pneumococcal loads were associated with age (<1 year: aOR 25.4; 95% CI, 7.4-87.6; 1-4 years: aOR 13.5, 95% CI 8.3-22.9; 5-14 years: aOR 3.1, 95% CI, 2.1-4.4 vs. 45-65 year old patients) and HIV infection (aOR 1.7; 95% CI 1.2-2.4). CONCLUSIONS: We observed high levels of pneumococcus colonization across all age groups. Children and people with HIV were more likely to be colonized and had higher pneumococcal loads. Carriage duration decreased with age highlighting that children remain important in pneumococcal transmission.

Patterns of engagement in HIV care during pregnancy and breastfeeding: findings from a cohort study in North-Eastern South Africa.

BACKGROUND: Eliminating mother-to-child transmission of HIV (MTCT) in sub-Saharan Africa is hindered by limited understanding of HIV-testing and HIV-care engagement among pregnant and breastfeeding women. METHODS: We investigated HIV-testing and HIV-care engagement during pregnancy and breastfeeding from 2014 to 2018 in the Agincourt Health and Demographic Surveillance System (HDSS). We linked HIV patient clinic records to HDSS pregnancy data. We modelled time to a first recorded HIV-diagnosis following conception, and time to antiretroviral therapy (ART) initiation following diagnosis using Kaplan-Meier methods. We performed sequence and cluster analyses for all pregnancies linked to HIV-related clinic data to categorise MTCT risk period engagement patterns and identified factors associated with different engagement patterns using logistic regression. We determined factors associated with ART resumption for women who were lost to follow-up (LTFU) using Cox regression. RESULTS: Since 2014, 15% of 10,735 pregnancies were recorded as occurring to previously (51%) or newly (49%) HIV-diagnosed women. New diagnoses increased until 2016 and then declined. We identified four MTCT risk period engagement patterns (i) early ART/stable care (51.9%), (ii) early ART/unstable care (34.1%), (iii) late ART initiators (7.6%), and (iv) postnatal seroconversion/early, stable ART (6.4%). Year of delivery, mother's age, marital status, and baseline CD4 were associated with these patterns. A new pregnancy increased the likelihood of treatment resumption following LTFU. CONCLUSION: Almost half of all pregnant women did not have optimal ART coverage during the MTCT risk period. Programmes need to focus on improving retention, and leveraging new pregnancies to re-engage HIV-positive women on ART.

Prevalence and socio-demographic correlates of tobacco and alcohol use in four sub-Saharan African countries: a cross-sectional study of middle-aged adults.

BACKGROUND: Substance misuse is a global public health problem. In addition to social and economic concerns, consumption of tobacco and alcohol is associated with susceptibility to cardiovascular, respiratory, and infectious diseases, cancers, and risk of transition to substance use disorders. African data suggest regional differences in the prevalence and patterns of substance use, but a number of key questions remain. This cross-sectional population-based study of middle-aged adults aims to examine prevalence and socio-demographic correlates of substance use in four sub-Saharan African countries, in rural and urban settings. METHODS: Participants aged between 40 and 60 years were recruited from six research centres as part of the Africa Wits-INDEPTH partnership for Genomic Research study. Data on patterns of tobacco and alcohol consumption was captured, and the latter further assessed using the CAGE (cut-annoyed-guilty-eye) questionnaire. RESULTS: Data from 10,703 participants suggested that more men (68.4%) than women (33.3%) were current substance users. The prevalence of current smoking was significantly higher in men than in women (34.5% vs 2.1%, p < 0.001). Smokeless tobacco was used more by women than men (14.4% vs 5.3%, p < 0.001). Current smoking was associated with alcohol consumption in men, and smoking cessation in men was associated with being a former drinker, having higher socio-economic status, and if married or cohabiting. Current alcohol consumption was higher in men, compared to women (60.3% vs 29.3%), and highest in men from Soweto (70.8%) and women from Nanoro (59.8%). The overall prevalence of problematic alcohol consumption among men was 18.9%, and women 7.3%. Men were significantly more likely to develop problematic drinking patterns, and this was more common in those who were divorced or widowed, and in current smokers. CONCLUSIONS: Regional variation in the patterns and prevalence of substance use was observed across study sites, and in rural and urban settings. The high levels of substance use recorded in this study are of concern due to the increased risk of associated morbidities. Further longitudinal data will be valuable in determining trends in substance misuse in Africa.

HIV treatment cascade for older adults in rural South Africa.

OBJECTIVES: The HIV treatment cascade is a powerful framework for understanding progress from initial diagnosis to successful treatment. Data sources for cascades vary and often are based on clinical cohorts, population cohorts linked to clinics, or self-reported information. We use both biomarkers and self-reported data from a large population-based cohort of older South Africans to establish the first HIV cascade for this growing segment of the HIV-positive population and compare results using the different data sources. METHODS: Data came from the Health and Aging in Africa: A Longitudinal Study of an INDEPTH Community in South Africa (HAALSI) 2015 baseline survey of 5059 adults aged 40+ years. Dried blood spots (DBS) were screened for HIV, antiretroviral drugs and viral load. In-home surveys asked about HIV testing, diagnosis and antiretroviral therapy (ART) use. We calculated proportions and CIs for each stage of the cascade, conditional on attainment of the previous stage, using (1) biomarkers, (2) self-report and (3) both biomarkers and self-report, and compared with UNAIDS 90-90-90 targets. RESULTS: 4560 participants had DBS results, among whom 1048 (23%) screened HIV-positive and comprised the denominator for each cascade. The biomarker cascade showed 63% (95% CI 60 to 66) on ART and 72% (95% CI 69 to 76) of those on ART with viral suppression. Self-reports underestimated testing, diagnosis and ART, with only 47% (95% CI 44 to 50) of HIV-positive individuals reporting ART use. The combined cascade indicated high HIV testing (89% (95% CI 87 to 91)), but lower knowledge of HIV-positive status (71% (95% CI 68 to 74)). CONCLUSIONS: Older South Africans need repeated HIV testing and sustained ART to reach 90-90-90 targets. HIV cascades relying on self-reports are likely to underestimate true cascade attainment, and biomarkers provide substantial improvements to cascade estimates.

Clusters of HIV Risk and Protective Sexual Behaviors in Agincourt, Rural South Africa: Findings from the Ha Nakekela Population-Based Study of Ages 15 and Older.

Understanding how sexual behaviors cluster in distinct population subgroups along the life course is critical for effective targeting and tailoring of HIV prevention messaging and intervention activities. We examined interrelatedness of sexual behaviors and variation between men and women across a wide age range in a rural South African setting with a high HIV burden. Data come from the Ha Nakekela population-based survey of people aged 15-85-plus drawn from the Agincourt Health and Socio-Demographic Surveillance System. We used latent class analysis of six sexual behavior indicators to identify distinct subgroup sexual behavior clusters. We then examined associations between class membership and sociodemographic and other behavioral risk factors and assessed the accuracy of a reduced set of sexual behavior indicators to classify individuals into latent classes. We identified three sexual behavior classes: (1) single with consistent protective behaviors; (2) risky behaviors; and (3) in union with lack of protective behaviors. Patterns of sexual behaviors varied by gender. Class membership was also associated with age, HIV status, nationality, and alcohol use. With only two sexual behavior indicators (union status and multiple sexual partners), individuals were accurately assigned to their most likely predicted class. There were distinct multidimensional sexual behavior clusters in population subgroups that varied by sex, age, and HIV status. In this population, only two brief questions were needed to classify individuals into risk classes. Replication in other situations is needed to confirm these findings.

Pensions, consumption and health: evidence from rural South Africa.

BACKGROUND: Increasing numbers of older people in sub-Saharan Africa are gaining access to pension benefits and it is often claimed that these benefits promote healthy forms of consumption, which contribute to significant improvements in their health status. However, evidence to support these claims is limited. METHODS: The paper uses data for 2701 people aged 60 or over who participated in a population-based study in rural north-eastern South Africa. It analyses effects of receiving a pension on reported food scarcity, body mass index and patterns of consumption. RESULTS: The paper finds that living in a pension household is associated with a reduced risk of reported food scarcity and with higher levels of consumption of food and drink. The paper does not find that living in a pension household is associated with a higher prevalence of current smoking nor current alcohol consumption. However, the paper still finds that tobacco and alcohol make up over 40% of reported food and drink consumption, and that the correlation between reported food scarcity and body mass index status is imperfect. CONCLUSIONS: The paper does not show significant associations between pension receipt and the selected risk factors. However, the context of prevalent obesity and high shares of household spending allocated to tobacco and alcohol call into question widely-made claims that pensions enhance healthy consumption among older people in low and middle-income countries.

Implementing prevention policies for mother-to-child transmission of HIV in rural Malawi, South Africa and United Republic of Tanzania, 2013-2016.

OBJECTIVE: To assess adoption of World Health Organization (WHO) guidance into national policies for prevention of mother-to-child transmission (PMTCT) of human immunodeficiency virus (HIV) and to monitor implementation of guidelines at facility level in rural Malawi, South Africa and the United Republic of Tanzania. METHODS: We summarized national PMTCT policies and WHO guidance for 15 indicators across the cascades of maternal and infant care over 2013-2016. Two survey rounds were conducted (2013-2015 and 2015-2016) in 46 health facilities serving five health and demographic surveillance system populations. We administered structured questionnaires to facility managers to describe service delivery. We report the proportions of facilities implementing each indicator and the frequency and durations of stock-outs of supplies, by site and survey round. FINDINGS: In all countries, national policies influencing the maternal and infant PMTCT cascade of care aligned with WHO guidelines by 2016; most inter-country policy variations concerned linkage to routine HIV care. The proportion of facilities delivering post-test counselling, same-day antiretroviral therapy (ART) initiation, antenatal care and ART provision in the same building, and Option B+ increased or remained at 100% in all sites. Progress in implementing policies on infant diagnosis and treatment varied across sites. Stock-outs of HIV test kits or antiretroviral drugs in the past year declined overall, but were reported by at least one facility per site in both rounds. CONCLUSION: Progress has been made in implementing PMTCT policy in these settings. However, persistent gaps across the infant cascade of care and supply-chain challenges, risk undermining infant HIV elimination goals.

Policy Shift: South Africa's Old Age Pensions' Influence on Perceived Quality of Life.

Noncontributory pensions serve as an important resource for poverty-affected households in low- and middle-income countries. This study explores how a recent policy change to pension receipt influences perceived quality of life among older South Africans. We use survey data from the longitudinal World Health Organization Study on global AGEing and adult health and from the Agincourt Health and Socio-Demographic Surveillance System census. We find pension receipt to have a positive impact on both men's and women's perceived quality of life. These findings hold when controlling for prior well-being status. We find a significant moderating factor of physical limitations on the relationship between pension receipt and quality of life. Individuals reporting the highest levels of physical limitation report a larger increase in their quality of life upon pension receipt than those with less severe physical limitations. We conclude that despite the well-documented household income-pooling in this population, pension receipt still leads to a significant positive impact on pensioners' perceived quality of life.

Rural-urban variations in age at menarche, adult height, leg-length and abdominal adiposity in black South African women in transitioning South Africa.

BACKGROUND: The pre-pubertal socioeconomic environment may be an important determinant of age at menarche, adult height, body proportions and adiposity: traits closely linked to adolescent and adult health. AIMS: This study explored differences in age at menarche, adult height, relative leg-length and waist circumference between rural and urban black South African young adult women, who are at different stages of the nutrition and epidemiologic transitions. SUBJECTS AND METHODS: We compared 18-23 year-old black South African women, 482 urban-dwelling from Soweto and 509 from the rural Mpumalanga province. Age at menarche, obstetric history and household socio-demographic and economic information were recorded using interview-administered questionnaires. Height, sitting-height, hip and waist circumference were measured using standardised techniques. RESULTS: Urban and rural black South African women differed in their age at menarche (at ages 12.7 and 14.5 years, respectively). In urban women, a one-year increase in age at menarche was associated with a 0.65 cm and 0.16% increase in height and relative leg-length ratio, respectively. In both settings, earlier age at menarche and shorter relative leg-length were independently associated with an increase in waist circumference. CONCLUSIONS: In black South African women, the earlier onset of puberty, and consequently an earlier growth cessation process, may lead to central fat mass accumulation in adulthood.

Progression of the epidemiological transition in a rural South African setting: findings from population surveillance in Agincourt, 1993-2013.

BACKGROUND: Virtually all low- and middle-income countries are undergoing an epidemiological transition whose progression is more varied than experienced in high-income countries. Observed changes in mortality and disease patterns reveal that the transition in most low- and middle-income countries is characterized by reversals, partial changes and the simultaneous occurrence of different types of diseases of varying magnitude. Localized characterization of this shifting burden, frequently lacking, is essential to guide decentralised health and social systems on the effective targeting of limited resources. Based on a rigorous compilation of mortality data over two decades, this paper provides a comprehensive assessment of the epidemiological transition in a rural South African population. METHODS: We estimate overall and cause-specific hazards of death as functions of sex, age and time period from mortality data from the Agincourt Health and socio-Demographic Surveillance System and conduct statistical tests of changes and differentials to assess the progression of the epidemiological transition over the period 1993-2013. RESULTS: From the early 1990s until 2007 the population experienced a reversal in its epidemiological transition, driven mostly by increased HIV/AIDS and TB related mortality. In recent years, the transition is following a positive trajectory as a result of declining HIV/AIDS and TB related mortality. However, in most age groups the cause of death distribution is yet to reach the levels it occupied in the early 1990s. The transition is also characterized by persistent gender differences with more rapid positive progression in females than males. CONCLUSIONS: This typical rural South African population is experiencing a protracted epidemiological transition. The intersection and interaction of HIV/AIDS and antiretroviral treatment, non-communicable disease risk factors and complex social and behavioral changes will impact on continued progress in reducing preventable mortality and improving health across the life course. Integrated healthcare planning and program delivery is required to improve access and adherence for HIV and non-communicable disease treatment. These findings from a local, rural setting over an extended period contribute to the evidence needed to inform further refinement and advancement of epidemiological transition theory.

Relationships between structure, process and outcome to assess quality of integrated chronic disease management in a rural South African setting: applying a structural equation model.

BACKGROUND: South Africa faces a complex dual burden of chronic communicable and non-communicable diseases (NCDs). In response, the Integrated Chronic Disease Management (ICDM) model was initiated in primary health care (PHC) facilities in 2011 to leverage the HIV/ART programme to scale-up services for NCDs, achieve optimal patient health outcomes and improve the quality of medical care. However, little is known about the quality of care in the ICDM model. The objectives of this study were to: i) assess patients' and operational managers' satisfaction with the dimensions of ICDM services; and ii) evaluate the quality of care in the ICDM model using Avedis Donabedian's theory of relationships between structure (resources), process (clinical activities) and outcome (desired result of healthcare) constructs as a measure of quality of care. METHODS: A cross-sectional study was conducted in 2013 in seven PHC facilities in the Bushbuckridge municipality of Mpumalanga Province, north-east South Africa - an area underpinned by a robust Health and Demographic Surveillance System (HDSS). The patient satisfaction questionnaire (PSQ-18), with measures reflecting structure/process/outcome (SPO) constructs, was adapted and administered to 435 chronic disease patients and the operational managers of all seven PHC facilities. The adapted questionnaire contained 17 dimensions of care, including eight dimensions identified as priority areas in the ICDM model - critical drugs, equipment, referral, defaulter tracing, prepacking of medicines, clinic appointments, waiting time, and coherence. A structural equation model was fit to operationalise Donabedian's theory, using unidirectional, mediation, and reciprocal pathways. RESULTS: The mediation pathway showed that the relationships between structure, process and outcome represented quality systems in the ICDM model. Structure correlated with process (0.40) and outcome (0.75). Given structure, process correlated with outcome (0.88). Of the 17 dimensions of care in the ICDM model, three structure (equipment, critical drugs, accessibility), three process (professionalism, friendliness and attendance to patients) and three outcome (competence, confidence and coherence) dimensions reflected their intended constructs. CONCLUSION: Of the priority dimensions, referrals, defaulter tracing, prepacking of medicines, appointments, and patient waiting time did not reflect their intended constructs. Donabedian's theoretical framework can be used to provide evidence of quality systems in the ICDM model.

A comparative analysis of national HIV policies in six African countries with generalized epidemics.

OBJECTIVE: To compare national human immunodeficiency virus (HIV) policies influencing access to HIV testing and treatment services in six sub-Saharan African countries. METHODS: We reviewed HIV policies as part of a multi-country study on adult mortality in sub-Saharan Africa. A policy extraction tool was developed and used to review national HIV policy documents and guidelines published in Kenya, Malawi, South Africa, Uganda, the United Republic of Tanzania and Zimbabwe between 2003 and 2013. Key informant interviews helped to fill gaps in findings. National policies were categorized according to whether they explicitly or implicitly adhered to 54 policy indicators, identified through literature and expert reviews. We also compared the national policies with World Health Organization (WHO) guidance. FINDINGS: There was wide variation in policies between countries; each country was progressive in some areas and not in others. Malawi was particularly advanced in promoting rapid initiation of antiretroviral therapy. However, no country had a consistently enabling policy context expected to increase access to care and prevent attrition. Countries went beyond WHO guidance in certain areas and key informants reported that practice often surpassed policy. CONCLUSION: Evaluating the impact of policy differences on access to care and health outcomes among people living with HIV is challenging. Certain policies will exert more influence than others and official policies are not always implemented. Future research should assess the extent of policy implementation and link these findings with HIV outcomes.

Relationship between community-level alcohol outlet accessibility and individual-level herpes simplex virus type 2 infection among young women in South Africa.

BACKGROUND: Exposure to alcohol outlets may influence sexual health outcomes at the individual and community levels. Visiting alcohol outlets facilitates alcohol consumption and exposes patrons to a risky environment and network of potential partners, whereas the presence of alcohol outlets in the community may shift social acceptance of riskier behavior. We hypothesize that living in communities with more alcohol outlets is associated with increased sexual risk. METHODS: We performed a cross-sectional analysis in a sample of 2174 South African schoolgirls (ages 13-21 years) living across 24 villages in the rural Agincourt subdistrict, underpinned by long-term health and sociodemographic surveillance. To examine the association between number of alcohol outlets in village of residence and individual-level prevalent herpes simplex virus type 2 (HSV-2) infection, we used generalized estimating equations with logit links, adjusting for individual- and village-level covariates. RESULTS: The median number of alcohol outlets per village was 3 (range, 0-7). Herpes simplex virus type 2 prevalence increased from villages with no outlets (1.4% [95% confidence interval, 0.2-12.1]), to villages with 1 to 4 outlets (4.5% [3.7-5.5]), and to villages with more than 4 outlets (6.3% [5.6, 7.1]). An increase of 1 alcohol outlet per village was associated with an 11% increase in the odds of HSV-2 infection (adjusted odds ratio [95% confidence interval], 1.11 [0.98-1.25]). CONCLUSIONS: Living in villages with more alcohol outlets was associated with increased prevalence of HSV-2 infection in young women. Structural interventions and sexual health screenings targeting villages with extensive alcohol outlet environments could help prevent the spread of sexually transmitted infections.

The promise of record linkage for assessing the uptake of health services in resource constrained settings: a pilot study from South Africa.

BACKGROUND: Health and Demographic Surveillance Systems (HDSS) have been instrumental in advancing population and health research in low- and middle- income countries where vital registration systems are often weak. However, the utility of HDSS would be enhanced if their databases could be linked with those of local health facilities. We assess the feasibility of record linkage in rural South Africa using data from the Agincourt HDSS and a local health facility. METHODS: Using a gold standard dataset of 623 record pairs matched by means of fingerprints, we evaluate twenty record linkage scenarios (involving different identifiers, string comparison techniques and with and without clerical review) based on the Fellegi-Sunter probabilistic record linkage model. Matching rates and quality are measured by their sensitivity and positive predictive value (PPV). Background characteristics of matched and unmatched cases are compared to assess systematic bias in the resulting record-linked dataset. RESULTS: A hybrid approach of deterministic followed by probabilistic record linkage, and scenarios that use an extended set of identifiers including another household member's first name yield the best results. The best fully automated record linkage scenario has a sensitivity of 83.6% and PPV of 95.1%. The sensitivity and PPV increase to 84.3% and 96.9%, respectively, when clerical review is undertaken on 10% of the record pairs. The likelihood of being linked is significantly lower for females, non-South Africans and the elderly. CONCLUSION: Using records matched by means of fingerprints as the gold standard, we have demonstrated the feasibility of fully automated probabilistic record linkage using identifiers that are routinely collected in health facilities in South Africa. Our study also shows that matching statistics can be improved if other identifiers (e.g., another household member's first name) are added to the set of matching variables, and, to a lesser extent, with clerical review. Matching success is, however, correlated with background characteristics that are indicative of the instability of personal attributes over time (e.g., surname in the case of women) or with misreporting (e.g., age).

Barriers to and facilitators of the provision of a youth-friendly health services programme in rural South Africa.

BACKGROUND: Youth-friendly health services are a key strategy for improving young people's health. This is the first study investigating provision of the Youth Friendly Services programme in South Africa since the national Department of Health took over its management in 2006. In a rural area of South Africa, we aimed to describe the characteristics of the publicly-funded primary healthcare facilities, investigate the proportion of facilities that provided the Youth Friendly Services programme and examine healthcare workers' perceived barriers to and facilitators of the provision of youth-friendly health services. METHODS: Semi-structured interviews were conducted with nurses of all eight publicly-funded primary healthcare facilities in Agincourt sub-district, Mpumalanga Province, South Africa. Thematic analysis of interview transcripts was conducted and data saturation was reached. RESULTS: Participants largely felt that the Youth Friendly Services programme was not implemented in their primary healthcare facilities, with the exception of one clinic. Barriers to provision reported by nurses were: lack of youth-friendly training among staff and lack of a dedicated space for young people. Four of the eight facilities did not appear to uphold the right of young people aged 12 years and older to access healthcare independently. Breaches in young people's confidentiality to parents were reported. CONCLUSIONS: Participants reported that provision of the Youth Friendly Services programme is limited in this sub-district, and below the Department of Health's target that 70% of primary healthcare facilities should provide these services. Whilst a dedicated space for young people is unlikely to be feasible or necessary, all facilities have the potential to be youth-friendly in terms of staff attitudes and actions. Training and on-going support should be provided to facilitate this; the importance of such training is emphasised by staff. More than one member of staff per facility should be trained to allow for staff turnover. As one of a few countrywide, government-run youth-friendly clinic programmes in a low or middle-income country, these results may be of interest to programme managers and policy makers in such settings.

Changing use of traditional healthcare amongst those dying of HIV related disease and TB in rural South Africa from 2003 - 2011: a retrospective cohort study.

BACKGROUND: In 2011 there were 5.5 million HIV infected people in South Africa and 71% of those requiring antiretroviral therapy (ART) received it. The effective integration of traditional medical practitioners and biomedical providers in HIV prevention and care has been demonstrated. However concerns remain that the use of traditional treatments for HIV-related disease may lead to pharmacokinetic interactions between herbal remedies and ART drugs and delay ART initiation. Here we analyse the changing prevalence and determinants of traditional healthcare use amongst those dying of HIV-related disease, pulmonary tuberculosis and other causes in a rural South African community between 2003 and 2011. ART was made available in this area in the latter part of this period. METHODS: Data was collected during household visits and verbal autopsy interviews. InterVA-4 was used to assign causes of death. Spatial analyses of the distribution of traditional healthcare use were performed. Logistic regression models were developed to test associations of determinants with traditional healthcare use. RESULTS: There were 5929 deaths in the study population of which 47.7% were caused by HIV-related disease or pulmonary tuberculosis (HIV/AIDS and TB). Traditional healthcare use declined for all deaths, with higher levels throughout for those dying of HIV/AIDS and TB than for those dying of other causes. In 2003-2005, sole use of biomedical treatment was reported for 18.2% of HIV/AIDS and TB deaths and 27.2% of other deaths, by 2008-2011 the figures were 49.9% and 45.3% respectively. In bivariate analyses, higher traditional healthcare use was associated with Mozambican origin, lower education levels, death in 2003-2005 compared to the later time periods, longer illness duration and moderate increases in prior household mortality. In the multivariate model only country of origin, time period and illness duration remained associated. CONCLUSIONS: There were large decreases in reported traditional healthcare use and increases in the sole use of biomedical treatment amongst those dying of HIV/AIDS and TB. No associations between socio-economic position, age or gender and the likelihood of traditional healthcare use were seen. Further qualitative and quantitative studies are needed to assess whether these figures reflect trends in healthcare use amongst the entire population and the reasons for the temporal changes identified.

Multidimensions of sleep health among in-school adolescents in rural and urban areas in southwestern Nigeria.

INTRODUCTION: Previous studies have focused on sleep inequities among disadvantaged populations in high-income countries. However, little is known about the differences in sleep health among adolescents in Africa. We aimed to compare the multidimensions of sleep health in adolescents living in rural vs. urban communities in Nigeria. METHODS: This cross-sectional study enrolled adolescents aged 13-19 in six rural and six urban schools in Osun State, Nigeria. We measured the prevalence of poor sleep quality (Pittsburgh Sleep Quality Index score >5), daytime sleepiness (Epworth Sleepiness Scale for Children and Adolescents score >10), and risk of sleep apnea (Teen STOPBANG). We compared the sleep health variables between the rural and urban populations using multivariable logistic regression. RESULTS: Of the 900 participants (51% rural; 59% female; average age (SD)= 15.1(1.4) years), 79% had short sleep duration (<8.5 hours), 14.9% poor sleep quality, 9.6% excessive daytime sleepiness and 9.8% risk of sleep apnea. Urban adolescents had a higher prevalence of poor sleep quality (p = .004), short sleep duration (p < .001), daytime sleepiness (p = .044), and risk of sleep apnea (p = .006) compared to rural adolescents. The adjusted odds of having poor sleep quality (p = .008) and daytime sleepiness (p = .007) were about 2-fold higher among urban compared to rural adolescents. Later school end time, having single/separated parent(s), absence of parental setting of bedtime were independently associated with poorer sleep health. CONCLUSION: Adolescents in rural communities had better sleep health than adolescents in urban communities. There is a need to develop interventions to improve the sleep quality and overall sleep health of urban-dwelling adolescents.

Moving towards a person-centred HIV care cascade: An exploration of potential biases and errors in routine data in South Africa.

In 2022, in recognition of lags in data infrastructure, the World Health Organisation (WHO) recommended the use of routinely linked individual patient data to monitor HIV programmes. The WHO also recommended a move to person-centred care to better reflect the experiences of people living with HIV. The switch from aggregated service level data to person-centred data will likely introduce some biases and errors. However, little is understood about the direction and magnitude of these biases. We investigated HIV-testing and HIV-care engagement from 2014 to 2018 in the Agincourt Health and Demographic Surveillance System (HDSS). We digitised and linked HIV patient clinic records to HDSS population data in order to estimate biases in routine clinical data. Using this linked data, we followed all individuals linked to HIV-related clinic data throughout their care pathway. We built sequences to represent these pathways. We performed sequence and cluster analyses for all individuals to categorise patterns of care engagement and identified factors associated with different engagement patterns using multinomial logistic regression. Our analyses included 4947 individuals who were linked to 5084 different patient records. We found that routine data would have inflated patient numbers by 2% due to double counting. We also found that 2% of individuals included in our analyses had received multiple HIV tests. These phenomena were driven by undocumented transfers. Further analysis of engagement patterns found a low level of stable engagement in care (<33%). Engagement fell into three distinct clusters: (i) characterised by high rates of late ART initiation, unstable engagement in care, and high mortality (53.9%), (ii) characterised by early ART initiation followed by prolonged periods of LTFU (13.7%), and (iii) characterised by early ART initiation followed by stable engagement in care (32.4%). Compared to cluster (i) older individuals were less likely to be in cluster (ii) and more likely to be in cluster (iii). Those who initiated ART prior to 2016 were more likely to be in cluster (ii) and (iii) compared to cluster (i). Those who initiated ART for PMTCT (RRR: 1.88 (95% CI: 1.45, 2.44)) or TB coinfection (RRR: 2.11 (95% CI: 1.27, 3.50)) were more likely to be in cluster (ii) when compared to those who initiated ART due to CD4 eligibility criteria. Males (RRR: 0.63 (95% CI: 0.51, 0.77)) were less likely to be in cluster (iii) compared to cluster (i) as were those who initiated ART for PMTCT (RRR: 0.77 (95% CI: 0.62, 0.97)) or under test and treat guidelines when compared to those who initiated ART due to CD4 eligibility. Only a minority of patients are consistently engaged in care while the majority cycle between engagement and disengagement. Individual level data could be useful in monitoring programmes and accurately reporting patient figures if it is of high quality, has minimal missingness and is properly linked in order to account for biases that accrue from using this kind of data.