Mortality variability and differentials by age and causes of death in rural South Africa, 1994-2018.

INTRODUCTION: Understanding mortality variability by age and cause is critical to identifying intervention and prevention actions to support disadvantaged populations. We assessed mortality changes in two rural South African populations over 25 years covering pre-AIDS and peak AIDS epidemic and subsequent antiretroviral therapy (ART) availability. METHODS: Using population surveillance data from the Agincourt Health and Socio-Demographic Surveillance System (AHDSS; 1994-2018) and Africa Health Research Institute (AHRI; 2000-2018) for 5-year periods, we calculated life expectancy from birth to age 85, mortality age distributions and variation, and life-years lost (LYL) decomposed into four cause-of-death groups. RESULTS: The AIDS epidemic shifted the age-at-death distribution to younger ages and increased LYL. For AHDSS, between 1994-1998 and 1999-2003 LYL increased for females from 13.6 years (95% CI 12.7 to 14.4) to 22.1 (95% CI 21.2 to 23.0) and for males from 19.9 (95% CI 18.8 to 20.8) to 27.1 (95% CI 26.2 to 28.0). AHRI LYL in 2000-2003 was extremely high (females=40.7 years (95% CI 39.8 to 41.5), males=44.8 years (95% CI 44.1 to 45.5)). Subsequent widespread ART availability reduced LYL (2014-2018) for women (AHDSS=15.7 (95% CI 15.0 to 16.3); AHRI=22.4 (95% CI 21.7 to 23.1)) and men (AHDSS=21.2 (95% CI 20.5 to 22.0); AHRI=27.4 (95% CI 26.7 to 28.2)), primarily due to reduced HIV/AIDS/TB deaths in mid-life and other communicable disease deaths in children. External causes increased as a proportion of LYL for men (2014-2018: AHRI=25%, AHDSS=17%). The share of AHDSS LYL 2014-2018 due to non-communicable diseases exceeded pre-HIV levels: females=43%; males=40%. CONCLUSIONS: Our findings highlight shifting burdens in cause-specific LYL and persistent mortality differentials in two populations experiencing complex epidemiological transitions. Results show high contributions of child deaths to LYL at the height of the AIDS epidemic. Reductions in LYL were primarily driven by lowered HIV/AIDS/TB and other communicable disease mortality during the ART periods. LYL differentials persist despite widespread ART availability, highlighting the contributions of other communicable diseases in children, HIV/AIDS/TB and external causes in mid-life and non-communicable diseases in older ages.

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.

Feasibility and acceptability of a contextualized physical activity and diet intervention for the control of hypertension in adults from a rural subdistrict: a study protocol (HYPHEN).

INTRODUCTION: In rural and remote South Africa, most strokes and ischaemic heart diseases are as a consequence of hypertension, which is a modifiable risk factor. The widely recommended therapeutic approaches to control hypertension are through physical activity and diet modifications. However, there is a lack of culturally sensitive community-based, lifestyle interventions to control hypertension among rural African adult populations. We designed an intervention which recommends adjusting daily routine physical activity and dietary behaviour of adults with hypertension. This study aims to evaluate the feasibility and acceptability of HYPHEN in a rural community setting. METHODS: We aim to recruit 30 adult participants with a self-report hypertension diagnosis. A one-arm, prospective design will be used to assess the feasibility and acceptability of recruitment, uptake, engagement, and completion of the 10-week intervention. Recruitment rates will be assessed at week 0. Intervention uptake, engagement, and adherence to the intervention will be assessed weekly via telephone. Blood pressure, body mass index, waist-hip ratio, urinary sodium, accelerometer-measured physical activity, and 24-h diet recall will be assessed at baseline and at 10 weeks. Qualitative semi-structured interviews will be conducted at 10 weeks to explore feasibility and acceptability. DISCUSSION: This study offers a person-centred, sociocultural approach to hypertension control through adaptations to physical activity and dietary intake. This study will determine whether HYPHEN is feasible and acceptable and will inform changes to the protocol/focus that could be tested in a full trial. TRIAL REGISTRATION NUMBER: PACTR202306662753321.

Mental distress, food insecurity and university student dropout during the COVID-19 pandemic in 2020: evidence from South Africa.

Background: Student dropout has been a key issue facing universities for many years. The COVID-19 pandemic was expected to exacerbate these trends; however, international literature has produced conflicting findings. Limited literature from Africa has investigated the impact of COVID-19 on student dropout trends, despite the documented devastation, including increased risk of food insecurity and mental distress, caused by the pandemic. Objective: This work seeks to understand the impact of food insecurity and mental distress on student dropout during the COVID-19 pandemic. Methods: Using a cross-sectional research design, first-year undergraduate students from a large South African university were recruited via email to participate in a survey between September and October 2020. The Household Food Insecurity Access Scale (HFIAS) was used to measure food insecurity and the Patient Health Questionnaire Anxiety and Depression Scale (PHQ-ADS) was used to measure mental distress. Multivariate regression was used to investigate factors associated with student dropout. Results: The student dropout rate was 10.5% (95% CI: 8.2-13.2). The prevalence of severe food insecurity was 25.7% (95% CI: 22.3-29.4) and the prevalence of severe mental distress symptoms was 26.7% (95% CI: 23.3-30.4). Dropout rates and levels of food insecurity were highest among students residing in remote areas during the lockdown at 19.2% and 43.6%, respectively. The multivariate logistic regression revealed that being male increased the probability of dropout almost three-fold (odds ratio (OR) = 2.70; 95% CI: 1.48-4.89, p =0.001)). Being moderately food insecure increased the odds of dropout more than two-fold (OR=2.50; 95% CI:1.12-5.55, p=0.025), and experiencing severe mental distress symptoms increased the odds of dropout seven-fold (OR=7.08; 95% CI:2.67-18.81, p<0.001). Conclusion: While acknowledging that various factors and complexities contribute to student dropout, the increased vulnerability to food insecurity and mental distress, stemming from issues such as widespread job losses and isolation experienced during the pandemic, may have also had an impact on dropout. This work reiterates the importance of directing additional support to students who are food insecure and those who are experiencing mental distress in order to mitigate university student dropout.

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.

Incidence and transmission of respiratory syncytial virus in urban and rural South Africa, 2017-2018.

Data on respiratory syncytial virus (RSV) incidence and household transmission are limited. To describe RSV incidence and transmission, we conducted a prospective cohort study in rural and urban communities in South Africa over two seasons during 2017-2018. Nasopharyngeal swabs were collected twice-weekly for 10 months annually and tested for RSV using PCR. We tested 81,430 samples from 1,116 participants in 225 households (follow-up 90%). 32% (359/1116) of individuals had ≥1 RSV infection; 10% (37/359) had repeat infection during the same season, 33% (132/396) of infections were symptomatic, and 2% (9/396) sought medical care. Incidence was 47.2 infections/100 person-years and highest in children <5 years (78.3). Symptoms were commonest in individuals aged <12 and ≥65 years. Individuals 1-12 years accounted for 55% (134/242) of index cases. Household cumulative infection risk was 11%. On multivariable analysis, index cases with ≥2 symptoms and shedding duration >10 days were more likely to transmit; household contacts aged 1-4 years vs. ≥65 years were more likely to acquire infection. Within two South African communities, RSV attack rate was high, and most infections asymptomatic. Young children were more likely to introduce RSV into the home, and to be infected. Future studies should examine whether vaccines targeting children aged <12 years could reduce community transmission.

In-Person Social Interactions and Anxiety During the COVID-19 Pandemic: Exploring the Role of Household Size and Virtual Social Contact Among Midlife and Older Black South African Adults.

OBJECTIVES: The current study investigates how physical distancing during the coronavirus disease 2019 (COVID-19) pandemic was associated with increased anxiety among a cohort of midlife older Black South African adults and the extent to which household size and virtual social contact modify this association for men and women. METHODS: We analyze data from a phone survey conducted from July 2021 to March 2022 as part of Health and Aging in Africa: A Longitudinal Study of an INDEPTH Community in South Africa (n = 2,080). We employ logistic regression to estimate the association between changes in in-person social interactions and anxiety symptoms and examine whether the association is modified by household size and changes in virtual social contact. We perform analyses separately for women and men. RESULTS: Declines in in-person social interactions were associated with increased anxiety for women and men (odds ratios [OR] = 2.52, p < .001). For women only, declines were greater for those living in larger households (OR = 1.11, p = .032). Declines were buffered by increased virtual social contact for both women (OR = 0.55, p = .025) and men (OR = 0.45, p = .019). DISCUSSION: Although the anxiety symptoms of women and men were similarly affected by declines in in-person social interaction, the modifying influence of household size is unique to women, likely due to gender-specific social roles. For women, living in larger households may mean greater caregiving burden, exacerbating the detrimental association between physical distancing and anxiety. On the other hand, both women and men may have used virtual means to connect with friends and family living outside their homes, buffering against increased anxiety.

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.

Home-based HIV testing strategies for middle-aged and older adults in rural South Africa.

OBJECTIVE: More than one in four adults over 40 years with HIV in South Africa are unaware of their status and not receiving antiretroviral therapy (ART). HIV self-testing may offer a powerful approach to closing this gap for aging adults. Here, we report the results of a randomized comparative effectiveness trial of three different home-based HIV testing strategies for middle-aged and older adults in rural South Africa. DESIGN: Two thousand nine hundred and sixty-three individuals in the 'Health and Ageing in Africa: a Longitudinal Study of an INDEPTH Community in South Africa (HAALSI)' cohort study were randomized 1 : 1 : 1 to one of three types of home-based and home-delivered HIV testing modalities: rapid testing with counseling; self-testing, and both rapid testing with counselling and self-testing. METHOD: In OLS regression analyses, we estimated the treatment effects on HIV testing and HIV testing frequency at about 1 year after delivery. Finally, we assessed the potential adverse effects of these strategies on the secondary outcomes of depressive symptom as assessed by the CESD-20, linkage to care, and risky sexual behavior. RESULTS: There were no significant differences in HIV testing uptake or testing frequency across groups. However, respondents in the self-testing treatment arms were more likely to shift from testing at home and a facility [self-testing (HIVST), -8 percentage points (pp); 95% confidence interval (CI) -14 to -2 pp; self-testing plus rapid testing and counselling (ST+RT+C); -9 pp, 95% CI -15 to -3 pp] to testing only at home (HIVST 5 pp; 95% CI 2 to 9 pp; ST+RT+C: 5 pp, 95% CI 1 to 9 pp) - suggesting a revealed preference for self-testing in this population. We also found no adverse effects of this strategy on linkage to care for HIV and common comorbidities, recent sexual partners, or condom use. Finally, those in the self-testing only arm had significantly decreased depressive symptom scores by 0.58 points (95% CI -1.16 to -0.01). CONCLUSION: We find HIV self-testing to be a well tolerated and seemingly preferred home-based testing option for middle-aged and older adults in rural South Africa. This approach should be expanded to achieve the UNAIDS 95-95-95 targets.

Association of alcohol use and multimorbidity among adults aged 40 years and above in rural South Africa.

We assessed the prevalence of reported alcohol use and its association with multimorbidity among adults aged 40 years and above in a rural, transitioning South African setting. Findings could potentially inform alcohol interventions integration in the prevention and treatment of chronic conditions. We analysed data from the first wave of The Health and Ageing in Africa-a longitudinal Study in an INDEPTH community (HAALSI) nested within the Agincourt Health and Demographic Surveillance Systems, conducted between November 2014 and November 2015 (n = 5059). We computed descriptive statistics and performed univariate analysis to determine factors independently associated with multimorbidity. Age, Body Mass Index, education, sex, and household wealth status and variables with a p-value < 0.20 in univariate analysis were included in multivariable Modified Poisson regression models. Any factors with a p-value of < 0.05 in the final models were considered statistically significant. The first wave of HAALSI was completed by 5059 participants aged 40 years and above and included 2714 (53.6%) females. The prevalence of reported ever alcohol use was 44.6% (n = 2253) and of these 51.9% (n = 1171) reported alcohol use in the last 30 days. The prevalence of HIV multimorbidity was 59.6% (3014/5059) and for multimorbidity without HIV 52.5% (2657/5059). Alcohol use was associated with HIV multimorbidity among all participants (RR: 1.05, 95% CI: 1.02-1.08), and separately for males (RR: 1.05, 95% CI: 1.00-1.10) and females (RR: 1.06, 95%CI: 1.02-1.11). Similarly, alcohol use was associated with multimorbidity without HIV among all participants (RR: 1.05, 95% CI: 1.02-1.09), and separately for males (RR: 1.06, 95% CI: 1.00-1.12) and females (RR: 1.06, 95% CI: 1.01-1.11). Reported alcohol use was common and associated with HIV multimorbidity and multimorbidity without HIV among older adults in rural northeast South Africa. There is a need to integrate Screening, Brief Interventions, and Referral for alcohol Treatment in the existing prevention and treatment of multimorbidity in South Africa.

Intergenerational spillover effects of antiretroviral therapy in sub-Saharan Africa: a scoping review and future directions for research.

BACKGROUND: Antiretroviral therapy (ART) may influence individuals who do not receive the intervention but who are connected in some way to the person who does. Relatively little is known, however, about the size and scope of, what we term, spillover effects of ART. We explored intergenerational spillover effects of ART in sub-Saharan Africa (SSA) and identified several directions for future research. METHODS: We conducted a scoping review between March and April 2022. We systematically searched PubMed, PsycINFO, EconLit, OTseeker, AIDSInfo, Web of Science, CINHAL, Google Scholar and African Index Medicus. We analysed the distribution of included studies over time and summarised their findings. We examined the intergenerational impact of ART provision to working-age adults living with HIV on children ('downward' spillover effects) and older adults ('upward' spillover effects). We categorised types of intergenerational spillover effects according to broad themes which emerged from our analysis of included studies. FINDINGS: We identified 26 studies published between 2005 and 2022 with 16 studies assessing spillover effects from adults to children (downward), and 1 study explicitly assessing spillover effects from working-age adults to older adults (upward). The remaining studies did not fully specify the direction of spillover effects. Most spillover effects of ART to household and family members were beneficial and included improvements in wealth, labour market outcomes, health outcomes and health services utilisation, schooling, and household composition. Both children and older adults benefited from ART availability among adults. Detrimental spillover effects were only reported in three studies and included financial and opportunity costs associated with health services utilisation and food insecurity in the first year after ART. CONCLUSIONS: ART may lead to substantial spillover effects across generations and sectors in SSA. Further research is needed to capitalise on positive spillover effects while mitigating potential negative spillover effects. The returns to investments in large-scale health interventions such as ART may be underestimated without considering these societal benefits.

Identifying the prevalence and correlates of multimorbidity in middle-aged men and women: a cross-sectional population-based study in four African countries.

OBJECTIVES: To determine the prevalence of multimorbidity, to identify which chronic conditions cluster together and to identify factors associated with a greater risk for multimorbidity in sub-Saharan Africa (SSA). DESIGN: Cross-sectional, multicentre, population-based study. SETTING: Six urban and rural communities in four sub-Saharan African countries. PARTICIPANTS: Men (n=4808) and women (n=5892) between the ages of 40 and 60 years from the AWI-Gen study. MEASURES: Sociodemographic and anthropometric data, and multimorbidity as defined by the presence of two or more of the following conditions: HIV infection, cardiovascular disease, chronic kidney disease, asthma, diabetes, dyslipidaemia, hypertension. RESULTS: Multimorbidity prevalence was higher in women compared with men (47.2% vs 35%), and higher in South African men and women compared with their East and West African counterparts. The most common disease combination at all sites was dyslipidaemia and hypertension, with this combination being more prevalent in South African women than any single disease (25% vs 21.6%). Age and body mass index were associated with a higher risk of multimorbidity in men and women; however, lifestyle correlates such as smoking and physical activity were different between the sexes. CONCLUSIONS: The high prevalence of multimorbidity in middle-aged adults in SSA is of concern, with women currently at higher risk. This prevalence is expected to increase in men, as well as in the East and West African region with the ongoing epidemiological transition. Identifying common disease clusters and correlates of multimorbidity is critical to providing effective interventions.

Physical Activity and Its Association With Body Mass Index: A Cross-Sectional Analysis in Middle-Aged Adults From 4 Sub-Saharan African Countries.

BACKGROUND: This study aimed to explore association of self-reported physical activity domains of work, leisure, and transport-related physical activity and body mass index (BMI) in 9388 adult men and women from the Africa-Wits-INDEPTH partnership for Genomic (AWI-Gen) study in Africa. Africa-Wits-INDEPTH partnership for Genomic is a large, population-based cross-sectional cohort with participants from 6 sites from rural and urban areas in 4 sub-Saharan African countries. METHODS: A sex-stratified meta-analysis of cross-sectional data from men and women aged 29-82 years was used to assess the association of physical activity with BMI. RESULTS: Overall, meeting physical activity guidelines of at least 150 minutes per week was associated with 0.82 kg/m2 lower BMI in men (ß = -0.80 kg/m2; 95% confidence interval [CI], -1.14 to -0.47) and 0.68 kg/m2 lower BMI in women (ß = -0.68 kg/m2; 95% CI, -1.03 to -0.33). Sex and site-specific differences were observed in the associations between physical activity domains and BMI. Among those who met physical activity guidelines, there was an inverse association between transport-related physical activity and BMI in men from Nanoro (Burkina Faso) (ß = -0.79 kg/m2; 95% CI, -1.25 to -0.33) as well as work-related physical activity and BMI in Navrongo men (Ghana) (ß = -0.76 kg/m2; 95% CI, -1.25 to -0.27) and Nanoro women (ß = -0.90 kg/m2; 95% CI, -1.44 to -0.36). CONCLUSIONS: Physical activity may be an effective strategy to curb rising obesity in Africa. More studies are needed to assess the impact of sex and geographic location-specific physical activity interventions on obesity.

Indirect effects of COVID-19 on maternal and child health in South Africa.

BACKGROUND: The unfinished burden of poor maternal and child health contributes to the quadruple burden of disease in South Africa with the direct and indirect effects of the COVID-19 pandemic yet to be fully documented. OBJECTIVE: To investigate the indirect effects of COVID-19 on maternal and child health in different geographical regions and relative wealth quintiles. METHODS: We estimated the effects of COVID-19 on maternal and child health from April 2020 to June 2021. We estimated this by calculating mean changes across facilities, relative wealth index (RWI) quintiles, geographical areas and provinces. To account for confounding by underlying seasonal or linear trends, we subsequently fitted a segmented fixed effect panel model. RESULTS: A total of 4956 public sector facilities were included in the analysis. Between April and September 2020, full immunisation and first dose of measles declined by 6.99% and 2.44%, respectively. In the follow-up months, measles first dose increased by 4.88% while full immunisation remained negative (-0.65%) especially in poorer quintiles. At facility level, the mean change in incidence and mortality due to pneumonia, diarrhoea and severe acute malnutrition was negative. Change in first antenatal visits, delivery by 15-19-year olds, delivery by C-section and maternal mortality was positive but not significant. CONCLUSION: COVID-19 disrupted utilisation of child health services. While reduction in child health services at the start of the pandemic was followed by an increase in subsequent months, the recovery was not uniform across different quintiles and geographical areas. This study highlights the disproportionate impact of the pandemic and the need for targeted interventions to improve utilisation of health services.

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.

SARS-CoV-2 transmission, persistence of immunity, and estimates of Omicron's impact in South African population cohorts.

Understanding the build-up of immunity with successive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and the epidemiological conditions that favor rapidly expanding epidemics will help facilitate future pandemic control. We analyzed high-resolution infection and serology data from two longitudinal household cohorts in South Africa to reveal high cumulative infection rates and durable cross-protective immunity conferred by prior infection in the pre-Omicron era. Building on the history of past exposures to different SARS-CoV-2 variants and vaccination in the cohort most representative of South Africa's high urbanization rate, we used mathematical models to explore the fitness advantage of the Omicron variant and its epidemic trajectory. Modeling suggests that the Omicron wave likely infected a large fraction (44 to 81%) of the population, leaving a complex landscape of population immunity primed and boosted with antigenically distinct variants. We project that future SARS-CoV-2 resurgences are likely under a range of scenarios of viral characteristics, population contacts, and residual cross-protection.

SARS-CoV-2 incidence, transmission, and reinfection in a rural and an urban setting: results of the PHIRST-C cohort study, South Africa, 2020-21.

BACKGROUND: By August, 2021, South Africa had been affected by three waves of SARS-CoV-2; the second associated with the beta variant and the third with the delta variant. Data on SARS-CoV-2 burden, transmission, and asymptomatic infections from Africa are scarce. We aimed to evaluate SARS-CoV-2 burden and transmission in one rural and one urban community in South Africa. METHODS: We conducted a prospective cohort study of households in Agincourt, Mpumalanga province (rural site) and Klerksdorp, North West province (urban site) from July, 2020 to August, 2021. We randomly selected households for the rural site from a health and sociodemographic surveillance system and for the urban site using GPS coordinates. Households with more than two members and where at least 75% of members consented to participate were eligible. Midturbinate nasal swabs were collected twice a week from household members irrespective of symptoms and tested for SARS-CoV-2 using real-time RT-PCR (RT-rtPCR). Serum was collected every 2 months and tested for anti-SARS-CoV-2 antibodies. Main outcomes were the cumulative incidence of SARS-CoV-2 infection, frequency of reinfection, symptomatic fraction (percent of infected individuals with ≥1 symptom), the duration of viral RNA shedding (number of days of SARS-CoV-2 RT-rtPCR positivity), and the household cumulative infection risk (HCIR; number of infected household contacts divided by the number of susceptible household members). FINDINGS: 222 households (114 at the rural site and 108 at the urban site), and 1200 household members (643 at the rural site and 557 at the urban site) were included in the analysis. For 115 759 nasal specimens from 1200 household members (follow-up 92·5%), 1976 (1·7%) were SARS-CoV-2-positive on RT-rtPCR. By RT-rtPCR and serology combined, 749 of 1200 individuals (62·4% [95% CI 58·1-66·4]) had at least one SARS-CoV-2 infection episode, and 87 of 749 (11·6% [9·4-14·2]) were reinfected. The mean infection episode duration was 11·6 days (SD 9·0; range 4-137). Of 662 RT-rtPCR-confirmed episodes (>14 days after the start of follow-up) with available data, 97 (14·7% [11·9-17·9]) were symptomatic with at least one symptom (in individuals aged <19 years, 28 [7·5%] of 373 episodes symptomatic; in individuals aged ≥19 years, 69 [23·9%] of 289 episodes symptomatic). Among 222 households, 200 (90·1% [85·3-93·7]) had at least one SARS-CoV-2-positive individual on RT-rtPCR or serology. HCIR overall was 23·9% (195 of 817 susceptible household members infected [95% CI 19·8-28·4]). HCIR was 23·3% (20 of 86) for symptomatic index cases and 23·9% (175 of 731) for asymptomatic index cases (univariate odds ratio [OR] 1·0 [95% CI 0·5-2·0]). On multivariable analysis, accounting for age and sex, low minimum cycle threshold value (≤30 vs >30) of the index case (OR 5·3 [2·3-12·4]) and beta and delta variant infection (vs Wuhan-Hu-1, OR 3·3 [1·4-8·2] and 10·4 [4·1-26·7], respectively) were associated with increased HCIR. People living with HIV who were not virally supressed (≥400 viral load copies per mL) were more likely to develop symptomatic illness when infected with SAR-CoV-2 (OR 3·3 [1·3-8·4]), and shed SARS-CoV-2 for longer (hazard ratio 0·4 [95% CI 0·3-0·6]) compared with HIV-uninfected individuals. INTERPRETATION: In this study, 565 (85·3%) SARS-CoV-2 infections were asymptomatic and index case symptom status did not affect HCIR, suggesting a limited role for control measures targeting symptomatic individuals. Increased household transmission of beta and delta variants was likely to have contributed to successive waves of SARS-CoV-2 infection, with more than 60% of individuals infected by the end of follow-up. FUNDING: US CDC, South Africa National Institute for Communicable Diseases, and Wellcome Trust.

Genetic associations with carotid intima-media thickness link to atherosclerosis with sex-specific effects in sub-Saharan Africans.

Atherosclerosis precedes the onset of clinical manifestations of cardiovascular diseases (CVDs). We used carotid intima-media thickness (cIMT) to investigate genetic susceptibility to atherosclerosis in 7894 unrelated adults (3963 women, 3931 men; 40 to 60 years) resident in four sub-Saharan African countries. cIMT was measured by ultrasound and genotyping was performed on the H3Africa SNP Array. Two new African-specific genome-wide significant loci for mean-max cIMT, SIRPA (p = 4.7E-08), and FBXL17 (p = 2.5E-08), were identified. Sex-stratified analysis revealed associations with one male-specific locus, SNX29 (p = 6.3E-09), and two female-specific loci, LARP6 (p = 2.4E-09) and PROK1 (p = 1.0E-08). We replicate previous cIMT associations with different lead SNPs in linkage disequilibrium with SNPs primarily identified in European populations. Our study find significant enrichment for genes involved in oestrogen response from female-specific signals. The genes identified show biological relevance to atherosclerosis and/or CVDs, sex-differences and transferability of signals from non-African studies.

Investigating clinic transfers among HIV patients considered lost to follow-up to improve understanding of the HIV care cascade: Findings from a cohort study in rural north-eastern South Africa.

Investigating clinical transfers of HIV patients is important for accurate estimates of retention and informing interventions to support patients. We investigate transfers for adults reported as lost to follow-up (LTFU) from eight HIV care facilities in the Agincourt health and demographic surveillance system (HDSS), South Africa. Using linked clinic and HDSS records, outcomes of adults more than 90 days late for their last scheduled clinic visit were determined through clinic and routine tracing record reviews, HDSS data, and supplementary tracing. Factors associated with transferring to another clinic were determined through Cox regression models. Transfers were graphically and geospatially visualised. Transfers were more common for women, patients living further from the clinic, and patients with higher baseline CD4 cell counts. Transfers to clinics within the HDSS were more likely to be undocumented and were significantly more likely for women pregnant at ART initiation. Transfers outside the HDSS clustered around economic hubs. Patients transferring to health facilities within the HDSS may be shopping for better care, whereas those who transfer out of the HDSS may be migrating for work. Treatment programmes should facilitate transfer processes for patients, ensure continuity of care among those migrating, and improve tracking of undocumented transfers.