School of Public Health
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Item Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa(2022-02-22) Fiona B Tamburini; Dylan Maghini; Ovokeraye H Oduaran; Ryan Brewster; Michaella R Hulley; Venesa Sahibdeen; Shane A Norris; Stephen Tollman; Kathleen Kahn; Ryan G Wagner; Alisha N Wade; Floidy Wafawanaka; F Xavier Gómez-Olivé; Rhian Twine; Zané Lombard; H3Africa AWI-Gen Collaborative Centre; Scott Hazelhurst; Ami S BhattHuman gut microbiome research focuses on populations living in high-income countries and to a lesser extent, non-urban agriculturalist and hunter-gatherer societies. The scarcity of research between these extremes limits our understanding of how the gut microbiota relates to health and disease in the majority of the world's population. Here, we evaluate gut microbiome composition in transitioning South African populations using short- and long-read sequencing. We analyze stool from adult females living in rural Bushbuckridge (n = 118) or urban Soweto (n = 51) and find that these microbiomes are taxonomically intermediate between those of individuals living in high-income countries and traditional communities. We demonstrate that reference collections are incomplete for characterizing microbiomes of individuals living outside high-income countries, yielding artificially low beta diversity measurements, and generate complete genomes of undescribed taxa, including Treponema, Lentisphaerae, and Succinatimonas. Our results suggest that the gut microbiome of South Africans does not conform to a simple "western-nonwestern" axis and contains undescribed microbial diversity.Item “We Were Afraid”: Mental Health Effects of the COVID-19 Pandemic in Two South African Districts(2022-07-28) Teurai Rwafa-Ponela; Jessica Price; Athini Nyatela; Sizwe Nqakala; Atiya Mosam; Agnes Erzse; Samanta Tresha Lalla-Edward; Jennifer Hove; Kathleen Kahn; Stephen Tollman; Karen Hofman; Susan GoldsteinThe impacts of pandemics are recognized to go beyond infection, physical suffering, and socio-economic disruptions. Other consequences include psychological responses. Using a mental wellbeing lens, we analyzed COVID-19-related stressors in healthcare workers (HCWs) and community members who provided and regularly accessed health services in South Africa, respectively. From February to September 2021, during the second COVID-19 wave we conducted a qualitative study in one urban and one rural district. In-depth interviews and focus group discussions were used to collect data among 43 HCWs and 51 community members purposely and conveniently selected. Most participants experienced mental health challenges regarding multiple aspects of the COVID-19 pandemic and its resulting lockdown, with a few reporting positive adjustments to change. COVID-19 impacts on mental health were consistent among both HCWs and community members in urban and rural alike. Participants’ COVID-19-induced psychological responses included anxiety and fear of the unknown, perceived risk of infection, fear of hospitalization, and fear of dying. Physical effects of the pandemic on participants included COVID-19 infection and associated symptoms, possibilities of severe illness and discomfort of using personal protective equipment. These distresses were exacerbated by social repercussions related to concerns for family wellbeing and infection stigma. Lockdown regulations also intensified anxieties about financial insecurities and social isolation. At times when common coping mechanisms such as family support were inaccessible, cultural consequences related to lack of spiritual gatherings and limited funeral rites posed additional stress on participants. In preparation for future public health emergencies, recognition needs to be given to mental health support and treatment.Item Pension exposure and health: Evidence from a longitudinal study in South Africa(2023-10) Carlos Riumallo Herl; Chodziwadziwa Kabudula; Kathleen Kahn; Stephen Tollman; David CanningSocial protection schemes have been expanding around the world with the objective of protecting older persons during retirement. While theoretically they have been seen as tools to improve individual wellbeing, there are few studies that evaluate whether social pensions can improve health. In this study, we exploit the change in eligibility criteria for the South African Old Age grant to estimate the association between pension exposure eligibility and health of older persons. For this, we use data from the Health and Aging in Africa: A longitudinal Study of an INDEPTH Community in South Africa (HAALSI) and model pension exposure in terms of its cumulative effect. Our results show that pension exposure is associated with better health as measured by a set of health indices. Disentangling these effects, we find that pension exposure is most likely to improve health through the delayed onset of physical disabilities in the elderly population. Our study highlights the relevance of social protection schemes as a mechanism to protect older persons physical health.Item Burden of mortality linked to community-nominated priorities in rural South Africa(2021-11-26) Pyry Mattila; Justine Davies; Denny Mabetha; Stephen Tollman; Lucia D’AmbruosoBackground: Community knowledge is a critical input for relevant health programmes and strategies. How community perceptions of risk reflect the burden of mortality is poorly understood. Objective: To determine the burden of mortality reflecting community-nominated health risk factors in rural South Africa, where a complex health transition is underway. Methods: Three discussion groups (total 48 participants) representing a cross-section of the community nominated health priorities through a Participatory Action Research process. A secondary analysis of Verbal Autopsy (VA) data was performed for deaths in the same community from 1993 to 2015 (n = 14,430). Using population attributable fractions (PAFs) extracted from Global Burden of Disease data for South Africa, deaths were categorised as ‘attributable at least in part’ to community-nominated risk factors if the PAF of the risk factor to the cause of death was >0. We also calculated ‘reducible mortality fractions’ (RMFs), defined as the proportions of each and all community-nominated risk factor(s) relative to all possible risk factors for deaths in the population . Results: Three risk factors were nominated as the most important health concerns locally: alcohol abuse, drug abuse, and lack of safe water. Of all causes of deaths 1993–2015, over 77% (n = 11,143) were attributable at least in part to at least one community-nominated risk factor. Causes of attributable deaths, at least in part, to alcohol abuse were most common (52.6%, n = 7,591), followed by drug abuse (29.3%, n = 4,223), and lack of safe water (11.4%, n = 1,652). In terms of the RMF, alcohol use contributed the largest percentage of all possible risk factors leading to death (13.6%), then lack of safe water (7.0%), and drug abuse (1.3%) . Conclusion: A substantial proportion of deaths are linked to community-nominated risk factors. Community knowledge is a critical input to understand local health risks.Item Coronavirus Host Genomics Study: South Africa (COVIGen-SA)(2022-10-06) Andrew K. May; Heather Seymour; Harriet Etheredge; Heather Maher; Marta C. Nunes; ShabirA.Madhi; SimisoM. Sokhela; W. D. FrancoisVenter; Neil Martinson; Firdaus Nabeemeeah; Cheryl Cohen; Jocelyn Moyes; Sibongile Walaza; Stefano Tempia; Jackie Kleynhans; Anne von Gottberg; Jeremy Nel; Halima Dawood; Ebrahim Variava; Stephen Tollman; Kathleen Kahn; KobusHerbst; EmilyB.Wong; CarolineT.Tiemessen; Alex van Blydenstein; Lyle Murray; Michelle Venter; June Fabian; Miche´le RamsayHowever, continental Africans are yet to be adequately represented in such studies despite the importance of genetic factors in understanding Africa’s response to the pandemic. We describe the development of a research resource for coronavirus host genomics studies in South Africa known as COVIGen-SA—a multicollaborator strategic partnership designed to provide harmonised demographic, clinical, and genetic information specific to Black South Africans with COVID-19. Over 2,000 participants have been recruited to date. Preliminary results on 1,354 SARS-CoV-2 positive participants from four participating studies showed that 64.7% were female, 333 had severe disease, and 329 were people living with HIV. *rough this resource, we aim to provide insights into host genetic factors relevant to African-ancestry populations, using both genome-wide association testing and targeted sequencing of important genomic loci. *is project will promote and enhance partnerships, build skills, and develop resources needed to address the COVID-19 burden and associated risk factors in South African communities.Item Digital delivery of behavioural activation therapy to overcome depression and facilitate social and economic transitions of adolescents in South Africa (the DoBAt study): protocol for a pilot randomised controlled trial(2022-12-05) Bianca D Moffett; Julia R Pozuelo; Alastair van Heerden; Heather A O'Mahen; Michelle Craske; Tholene Sodi; Crick Lund; Kate Orkin; Emma J Kilford; Sarah-Jayne Blakemore; Mahreen Mahmud; Eustasius Musenge; Meghan Davis; Zamakhanya Makhanya; Tlangelani Baloyi; Daniel Mahlangu; Gabriele Chierchia; Sophie L Fielmann; F Xavier Gómez-Olivé; Imraan Valodia; Stephen Tollman; Kathleen Kahn; Alan SteinIntroduction Scalable psychological treatments to address depression among adolescents are urgently needed. This is particularly relevant to low-income and middle-income countries where 90% of the world’s adolescents live. While digital delivery of behavioural activation (BA) presents a promising solution, its feasibility, acceptability and effectiveness among adolescents in an African context remain to be shown. Methods and analysis This study is a two-arm singleblind individual-level randomised controlled pilot trial to assess the feasibility, acceptability and initial efficacy of digitally delivered BA therapy among adolescents with depression. The intervention has been coproduced with adolescents at the study site. The study is based in the rural northeast of South Africa in the Bushbuckridge subdistrict of Mpumalanga province. A total of 200 adolescents with symptoms of mild to moderately severe depression on the Patient Health Questionnaire Adolescent Version will be recruited (1:1 allocation ratio). The treatment group will receive BA therapy via a smartphone application (the Kuamsha app) supported by trained peer mentors. The control group will receive an enhanced standard of care. The feasibility and acceptability of the intervention will be evaluated using a mixed methods design, and signals of the initial efficacy of the intervention in reducing symptoms of depression will be determined on an intention-to-treat basis. Secondary objectives are to pilot a range of cognitive, mental health, risky behaviour and socioeconomic measures; and to collect descriptive data on the feasibility of trial procedures to inform the development of a further larger trial.Item Building knowledge, optimising physical and mental health and setting up healthier life trajectories in South African women (Bukhali): a preconception randomised control trial part of the Healthy Life Trajectories Initiative (HeLTI)(2022-03-25) Shane A Norris; Catherine E Draper; Alessandra Prioreschi; CM Smuts; Lisa Jayne Ware; CindyLee Dennis; Philip Awadalla; D Bassani; Zulfiqar Bhutta; Laurent Briollais; D William Cameron; Tobias Chirwa; B Fallon; CM Gray; Jill Hamilton; J Jamison; Heather Jaspan; Jennifer Jenkins; Kathleen Kahn; AP Kengne; Estelle V Lambert; Naomi Levitt; Marie-Claude Martin; Michele Ramsay; Daniel Roth; Stephen Scherer; Daniel Sellen; Wiedaad Slemming; Deborah Sloboda; M Szyf; Stephen Tollman; Mark Tomlinson; Suzanne Tough; Stephen G Matthews; Linda Richter; Stephen Lyeis challenging due to a persistent infectious disease, burgeoning obesity, most notably among women and rising rates of non-communicable diseases (NCDs). With two thirds of women presenting at their first antenatal visit either overweight or obese in urban South Africa (SA), the preconception period is an opportunity to optimise health and offset transgenerational risk of both obesity and NCDs. Methods and analysis Bukhali is the first individual randomised controlled trial in Africa to test the efficacy of a complex continuum of care intervention and forms part of the Healthy Life Trajectories Initiative (HeLTI) consortium implementing harmonised trials in Canada, China, India and SA. Starting preconception and continuing through pregnancy, infancy and childhood, the intervention is designed to improve nutrition, physical and mental health and health behaviours of South African women to offset obesity-risk (adiposity) in their offspring. Women aged 18–28 years (n=6800) will be recruited from Soweto, an urban-poor area of Johannesburg. The primary outcome is dual-energy X-ray absorptiometry derived fat mass index (fat mass divided by height2 ) in the offspring at age 5 years. Community health workers will deliver the intervention randomly to half the cohort by providing health literacy material, dispensing a multimicronutrient supplement, providing health services and feedback, and facilitating behaviour change support sessions to optimise: (1) nutrition, (2) physical and mental health and (3) lay the foundations for healthier pregnancies and early child development. Ethics and dissemination Ethical approval has been obtained from the Human Ethics Research Committee University of the Witwatersrand, Johannesburg, South Africa (M1811111), the University of Toronto, Canada (19-0066-E) and the WHO Ethics Committee (ERC.0003328). Data and biological sample sharing policies are consistent with the governance policy of the HeLTI Consortium (https://helti.org) and South African government legislation (POPIA). The recruitment and research team will obtain informed consent.Item Performance of four computer-coded verbal autopsy methods for cause of death assignment compared with physician coding on 24,000 deaths in low- and middle-income countries(2014) Nikita Desai; Lukasz Aleksandrowicz; Pierre Miasnikof; Ying Lu; Jordana Leitao; Peter Byass; Stephen Tollman; Paul Mee; Dewan Alam; Suresh Kumar Rathi; Abhishek Singh; Rajesh Kumar; Faujdar Ram; Prabhat JhaBackground: Physician-coded verbal autopsy (PCVA) is the most widely used method to determine causes of death (CODs) in countries where medical certification of death is uncommon. Computer-coded verbal autopsy (CCVA) methods have been proposed as a faster and cheaper alternative to PCVA, though they have not been widely compared to PCVA or to each other. Methods: We compared the performance of open-source random forest, open-source tariff method, InterVA-4, and the King-Lu method to PCVA on five datasets comprising over 24,000 verbal autopsies from low- and middle-income countries. Metrics to assess performance were positive predictive value and partial chance-corrected concordance at the individual level, and cause-specific mortality fraction accuracy and cause-specific mortality fraction error at the population level. Results: The positive predictive value for the most probable COD predicted by the four CCVA methods averaged about 43% to 44% across the datasets. The average positive predictive value improved for the top three most probable CODs, with greater improvements for open-source random forest (69%) and open-source tariff method (68%) than for InterVA-4 (62%). The average partial chance-corrected concordance for the most probable COD predicted by the open-source random forest, open-source tariff method and InterVA-4 were 41%, 40% and 41%, respectively, with better results for the top three most probable CODs. Performance generally improved with larger datasets. At the population level, the King-Lu method had the highest average cause-specific mortality fraction accuracy across all five datasets (91%), followed by InterVA-4 (72% across three datasets), open-source random forest (71%) and open-source tariff method (54%). Conclusions: On an individual level, no single method was able to replicate the physician assignment of COD more than about half the time. At the population level, the King-Lu method was the best method to estimate cause-specific mortality fractions, though it does not assign individual CODs. Future testing should focus on combining different computer-coded verbal autopsy tools, paired with PCVA strengths. This includes using open-source tools applied to larger and varied datasets (especially those including a random sample of deaths drawn from the population), so as to establish the performance for age- and sex-specific CODsItem SARS-CoV-2 Seroprevalence after Third Wave of Infections, South Africa(2022-05) Jackie Kleynhans; Stefano Tempia; Nicole Wolter; Anne von Gottberg; Jinal N. Bhiman; Amelia Buys; Jocelyn Moyes; Meredith L. McMorrow; Kathleen Kahn; F. Xavier Gómez-Olivé; Stephen Tollman; Neil A. Martinson; Floidy Wafawanaka; Limakatso Lebina; Jacques D. du Toit; Waasila Jassat; Mzimasi Neti; Marieke Brauer; Cheryl CohenBy November 2021, after the third wave of severe acute respiratory syndrome coronavirus 2 infections in South Africa, seroprevalence was 60% in a rural community and 70% in an urban community. High seroprevalence before the Omicron variant emerged may have contributed to reduced illness severity observed in the fourth wave.Item TRENDS IN HOUSEHOLD MATERIAL RESOURCES AND COGNITIVE HEALTH IN A LONGITUDINAL COHORT STUDY OF AGING IN SOUTH AFRICA(2022) Lindsay Kobayashi; Chodziwadziwa Kabudula; Mohammed Kabeto; Xuexin Yu; Stephen Tollman; Kathleen Kahn; Lisa Berkman; Molly RosenbergMaterial resources that affect daily living conditions may be salient for cognitive aging in low-income settings, but evidence is limited on this topic. We investigated relationships between long-term trends in household material resources and subsequent cognitive function among 4,580 adults aged ≥40 in a population-representative cohort in Agincourt sub-district, South Africa, from 2001-2015. Household material resources (dwelling materials, water, sanitation, sources of power, modern amenities, and livestock) were assessed biennially from 2001- 2013. We evaluated mean resources, volatility in resources, and change in resources over this period in relation to cognitive function in 2014/2015. Higher mean household resources and larger improvements over time in resources were positively associated with subsequent cognitive function, independent of confounders. Findings were largely driven by modern amenities for food preparation, transportation, and communication outside of the household. Access to these amenities may support cognitive aging through boosting nutrition and cognitive reserve and should be investigated further.