Determining classes of food items for health requirements and nutrition guidelines using Gaussian mixture models.

Introduction: The identification of classes of nutritionally similar food items is important for creating food exchange lists to meet health requirements and for informing nutrition guidelines and campaigns. Cluster analysis methods can assign food items into classes based on the similarity in their nutrient contents. Finite mixture models use probabilistic classification with the advantage of taking into account the uncertainty of class thresholds. Methods: This paper uses univariate Gaussian mixture models to determine the probabilistic classification of food items in the South African Food Composition Database (SAFCDB) based on nutrient content. Results: Classifying food items by animal protein, fatty acid, available carbohydrate, total fibre, sodium, iron, vitamin A, thiamin and riboflavin contents produced data-driven classes with differing means and estimates of variability and could be clearly ranked on a low to high nutrient contents scale. Classifying food items by their sodium content resulted in five classes with the class means ranging from 1.57 to 706.27 mg per 100 g. Four classes were identified based on available carbohydrate content with the highest carbohydrate class having a mean content of 59.15 g per 100 g. Food items clustered into two classes when examining their fatty acid content. Foods with a high iron content had a mean of 1.46 mg per 100 g and was one of three classes identified for iron. Classes containing nutrient-rich food items that exhibited extreme nutrient values were also identified for several vitamins and minerals. Discussion: The overlap between classes was evident and supports the use of probabilistic classification methods. Food items in each of the identified classes were comparable to allowed food lists developed for therapeutic diets. This data-driven ranking of nutritionally similar classes could be considered for diet planning for medical conditions and individuals with dietary restrictions.

Seroprevalence survey of anti-SARS-CoV-2 antibody and associated factors in South Africa: Findings of the 2020-2021 population-based household survey.

Population-based serological testing is important to understand the epidemiology and estimate the true cumulative incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to inform public health interventions. This study reports findings of a national household population SARS-CoV-2 serosurvey in people 12 years and older in South Africa. This cross-sectional multi-stage random stratified cluster survey undertaken from November 2020 to June 2021 collected sociodemographic data, medical history, behavioural data, and blood samples from consenting participants. The samples were tested for SARS-CoV-2 antibodies using the Roche ElecsysAnti-SARS-CoV-2 chemiluminescence immunoassay (CLIA) Total Antibody Test. The survey data were weighted by age, race, sex, and province with final individual weights benchmarked against the 2020 mid-year population estimates and accounted for clustering. Descriptive statistics summarize the characteristics of participants and seroprevalence. Logistic regression analyses were used to identify factors associated with seropositivity. From 13290 survey participants (median age 33 years, interquartile range (IQR) 23-46 years), SARS-CoV-2 seroprevalence was 37.8% [95% Confidence Interval (CI) 35.4-40.4] and varied substantially across the country's nine provinces, and by sex, age and locality type. In the final adjusted model, the odds of seropositivity were higher in women than in men [aOR = 1.3 (95% CI: 1.0-1.6), p = 0.027], and those living with HIV (self-report) [aOR = 1.6 (95% CI: 1.0-2.4), p = 0.031]. The odds were lower among those 50 years and older compared to adolescents 12-19 years old [aOR = 0.6 (95% CI: 0.5-0.8), p<0.001] and in those who did not attend events or gatherings [aOR = 0.7 (95% CI: 0.6-1.0), p = 0.020]. The findings help us understand the epidemiology of SARS-CoV-2 within different regions in a low-middle-income country. The survey highlights the higher risk of infection in women in South Africa likely driven by their home and workplace roles and also highlighted a need to actively target and include younger people in the COVID-19 response.

A Scoping Review Evaluating the Current State of Gut Microbiota Research in Africa.

The gut microbiota has emerged as a key human health and disease determinant. However, there is a significant knowledge gap regarding the composition, diversity, and function of the gut microbiota, specifically in the African population. This scoping review aims to examine the existing literature on gut microbiota research conducted in Africa, providing an overview of the current knowledge and identifying research gaps. A comprehensive search strategy was employed to identify relevant studies. Databases including MEDLINE (PubMed), African Index Medicus (AIM), CINAHL (EBSCOhost), Science Citation index (Web of Science), Embase (Ovid), Scopus (Elsevier), WHO International Clinical Trials Registry Platform (ICTRP), and Google Scholar were searched for relevant articles. Studies investigating the gut microbiota in African populations of all age groups were included. The initial screening included a total of 2136 articles, of which 154 were included in this scoping review. The current scoping review revealed a limited number of studies investigating diseases of public health significance in relation to the gut microbiota. Among these studies, HIV (14.3%), colorectal cancer (5.2%), and diabetes mellitus (3.9%) received the most attention. The top five countries that contributed to gut microbiota research were South Africa (16.2%), Malawi (10.4%), Egypt (9.7%), Kenya (7.1%), and Nigeria (6.5%). The high number (n = 66) of studies that did not study any specific disease in relation to the gut microbiota remains a gap that needs to be filled. This scoping review brings attention to the prevalent utilization of observational study types (38.3%) in the studies analysed and emphasizes the importance of conducting more experimental studies. Furthermore, the findings reflect the need for more disease-focused, comprehensive, and population-specific gut microbiota studies across diverse African regions and ethnic groups to better understand the factors shaping gut microbiota composition and its implications for health and disease. Such knowledge has the potential to inform targeted interventions and personalized approaches for improving health outcomes in African populations.

A novel outlier statistic in multivariate survival models and its application to identify unusual under-five mortality sub-districts in Malawi.

Although under-five mortality (U5M) rates have declined worldwide, many countries in sub-Saharan Africa still have much higher rates. Detection of subnational areas with unusually higher U5M rates could support targeted high impact child health interventions. We propose a novel group outlier detection statistic for identifying areas with extreme U5M rates under a multivariate survival data model. The performance of the proposed statistic was evaluated through a simulation study. We applied the proposed method to an analysis of child survival data in Malawi to identify sub-districts with unusually higher or lower U5M rates. The simulation study showed that the proposed outlier statistic can detect unusual high or low mortality groups with a high accuracy of at least 90%, for datasets with at least 50 clusters of size 80 or more. In the application, at most 7 U5M outlier sub-districts were identified, based on the best fitting model as measured by the Akaike information criterion (AIC).

Motivational interviewing and problem-solving therapy intervention for patients on antiretroviral therapy for HIV in Tshwane, South Africa: A randomized controlled trial to assess the impact on alcohol consumption.

BACKGROUND AND AIMS: Reduction of alcohol consumption is important for people undergoing treatment for HIV. We tested the efficacy of a brief intervention for reducing the average volume of alcohol consumed among patients on HIV antiretroviral therapy (ART). DESIGN, SETTING AND PARTICIPANTS: This study used a two-arm multi-centre randomized controlled trial with follow-up to 6 months. Recruitment occurred between May 2016 and October 2017 at six ART clinics at public hospitals in Tshwane, South Africa. Participants were people living with HIV, mean age 40.8 years [standard deviation (SD) = 9.07], 57.5% female, and on average 6.9 years (SD = 3.62) on ART. At baseline (BL), the mean number of drinks consumed over the past 30 days was 25.2 (SD = 38.3). Of 756 eligible patients, 623 were enrolled. INTERVENTION: Participants were randomly assigned to a motivational interviewing (MI)/problem-solving therapy (PST) intervention arm (four modules of MI and PST delivered over two sessions by interventionists) or a treatment as usual (TAU) comparison arm. People assessing outcomes were masked to group assignment. MEASUREMENTS: The primary outcome was the number of standard drinks (15 ml pure alcohol) consumed during the past 30 days assessed at 6-month follow-up (6MFU). FINDINGS: Of the 305 participants randomized to MI/PST, 225 (74%) completed the intervention (all modules). At 6MFU, retention was 88% for the control and 83% for the intervention arm. In support of the hypothesis, an intention-to-treat-analysis for the primary outcome at 6MFU was -0.410 (95% confidence interval = -0.670 to -0.149) units lower on log scale in the intervention group than in the control group (P = 0.002), a 34% relative reduction in the number of drinks. Sensitivity analyses were undertaken for patients who had alcohol use disorders identification test (AUDIT) scores ≥ 8 at BL (n = 299). Findings were similar to those of the whole sample. CONCLUSIONS: In South Africa, a motivational interviewing/problem-solving therapy intervention significantly reduced drinking levels in HIV-infected patients on antiretroviral therapy at 6-month follow-up.

A prediction risk score for HIV among adolescent girls and young women in South Africa: identifying those in need of HIV pre-exposure prophylaxis.

BACKGROUND: In sub-Saharan Africa (SSA), adolescent girls and young women (AGYW) have the highest risk of acquiring HIV. This has led to several studies aimed at identifying risk factors for HIV in AGYM. However, a combination of the purported risk variables in a multivariate risk model could be more useful in determining HIV risk in AGYW than one at a time. The purpose of this study was to develop and validate an HIV risk prediction model for AGYW. METHODS: We analyzed HIV-related HERStory survey data on 4,399 AGYW from South Africa. We identified 16 purported risk variables from the data set. The HIV acquisition risk scores were computed by combining coefficients of a multivariate logistic regression model of HIV positivity. The performance of the final model at discriminating between HIV positive and HIV negative was assessed using the area under the receiver-operating characteristic curve (AUROC). The optimal cut-point of the prediction model was determined using the Youden index. We also used other measures of discriminative abilities such as predictive values, sensitivity, and specificity. RESULTS: The estimated HIV prevalence was 12.4% (11.7% - 14.0) %. The score of the derived risk prediction model had a mean and standard deviation of 2.36 and 0.64 respectively and ranged from 0.37 to 4.59. The prediction model's sensitivity was 16. 7% and a specificity of 98.5%. The model's positive predictive value was 68.2% and a negative predictive value of 85.8%. The prediction model's optimal cut-point was 2.43 with sensitivity of 71% and specificity of 60%. Our model performed well at predicting HIV positivity with training AUC of 0.78 and a testing AUC of 0.76. CONCLUSION: A combination of the identified risk factors provided good discrimination and calibration at predicting HIV positivity in AGYW. This model could provide a simple and low-cost strategy for screening AGYW in primary healthcare clinics and community-based settings. In this way, health service providers could easily identify and link AGYW to HIV PrEP services.

Syphilis screening coverage and positivity by HIV treatment status among South African pregnant women enrolled in the 2019 antenatal HIV sentinel survey.

We describe coverage of maternal syphilis screening, syphilis positivity, coverage of treatment and their association with maternal HIV infection and antiretroviral treatment (ART) status among pregnant women attending South African antenatal clinics. The 2019 antenatal care sentinel survey was a cross-sectional survey conducted from 1 October to 15 November 2019 at 1589 sentinel sites in all nine provinces of the country and aimed to enrol 36,000 pregnant women ages 15-49 years regardless of HIV, ART or syphilis status. Data collection procedures included obtaining written informed consent, a brief interview, medical record review and blood specimen collection. Completed data collection forms and specimens were sent to designated regional laboratories for data capture and HIV serology testing. Data analysis determined four outcomes i) syphilis screening coverage ii) syphilis positivity iii) coverage of any treatment and iv) with Benzathine penicillin G (BPG). Multivariable logistic regression models with or without interaction between HIV infection and ART status with province were used to determine factors associated with syphilis positivity. Of the 41 598 women enrolled, 35 900 were included in the analysis for syphilis screening coverage. The weighted syphilis screening coverage was 96.4% [95% Confidence Interval (CI) 95.9-96.7%] nationally and was lowest among HIV positive women not on ART at 93.5% (95% CI 92.2-94.5%). Syphilis positivity was 2.6% (95% CI 2.4-2.9%) nationally. Among those who were syphilis positive, 91.9% (95% CI 89.8-93.7%) had documentation of syphilis treatment status, of whom 92.0% (95% CI 89.8-93.9%) were treated, with the majority treated with one or more doses of BPG [92.2% (95% CI 89.8-94.3%)]. HIV-positive women, not on ART [adjusted odd ratio (aOR) 2.24 (95% 1.71-2.93)] and those on ART [aOR 2.25 (95% CI 1.91-2.64)] were more likely to be syphilis positive compared to those who were HIV negative. The national syphilis screening coverage met the global screening target of 95%. Syphilis positivity was higher among HIV positive women compared to negative women. Introduction of rapid syphilis testing and ensuring a universal supply of appropriate treatment for syphilis will reduce the likelihood of mother-to-child transmission of syphilis.

Modeling the positive testing rate of COVID-19 in South Africa using a semi-parametric smoother for binomial data.

Identification and isolation of COVID-19 infected persons plays a significant role in the control of COVID-19 pandemic. A country's COVID-19 positive testing rate is useful in understanding and monitoring the disease transmission and spread for the planning of intervention policy. Using publicly available data collected between March 5th, 2020 and May 31st, 2021, we proposed to estimate both the positive testing rate and its daily rate of change in South Africa with a flexible semi-parametric smoothing model for discrete data. There was a gradual increase in the positive testing rate up to a first peak rate in July, 2020, then a decrease before another peak around mid-December 2020 to mid-January 2021. The proposed semi-parametric smoothing model provides a data driven estimates for both the positive testing rate and its change. We provide an online R dashboard that can be used to estimate the positive rate in any country of interest based on publicly available data. We believe this is a useful tool for both researchers and policymakers for planning intervention and understanding the COVID-19 spread.

Intervention in Mothers and Newborns to Reduce Maternal and Perinatal Mortality in 3 Provinces in South Africa Using a Quality Improvement Approach: Protocol for a Mixed Method Type 2 Hybrid Evaluation.

BACKGROUND: The COVID-19 pandemic undermined gains in reducing maternal and perinatal mortality in South Africa. The Mphatlalatsane Initiative is a health system intervention to reduce mortality and morbidity in women and newborns to desired levels. OBJECTIVE: Our evaluation aims to determine the effect of various exposures, including the COVID-19 pandemic, and a system-level, complex, patient-centered quality improvement (QI) intervention (the Mphatlalatsane Initiative) on maternal and neonatal health services at 21 selected South African facilities. The objectives are to determine whether Mphatlalatsane reduces the institutional maternal mortality ratio, neonatal mortality rate, and stillbirth rate (objective 1) and improves patients' experiences (objective 2) and quality of care (objective 3). Objective 4 assesses the contextual and implementation process factors, including the COVID-19 pandemic, that shape Mphatlalatsane uptake and variation. METHODS: This study is an implementation science type 2 hybrid effectiveness, controlled before-and-after design with quantitative and qualitative components. The Mphatlalatsane intervention commenced at the end of 2019. For objective 1, intervention and control facility-level data from the District Health Information System are compared for changes in institutional maternal and neonatal mortality and stillbirth rates and associations with QI, the COVID-19 pandemic, and both. This first analysis includes data from 18 facilities, regardless of their allocation to intervention or comparison, to obtain a general idea of the effect of the COVID-19 pandemic. For objectives 2 to 3, data collectors abstract data from maternal and neonatal records, interview participants, and conduct neonatal facility assessments. For objective 4, interviews, program documentation, surveys, and observations are used to assess how contextual factors at the macro-, meso-, and microlevels explain variation in intervention uptake and outcome. The intervention dose is measured at the microlevel only in the intervention facilities. The study assesses the Mphatlalatsane Initiative from 2020 to 2022. RESULTS: From preliminary analysis, across the 3 provinces, maternal and neonatal deaths increased during the COVID-19 pandemic, whereas stillbirths remained unchanged. Maternal satisfaction with quality of care was >90%. The COVID-19 pandemic severely disrupted the QI teams functioning. However, the QI teams regained their pre-COVID-19 momentum by adapting the QI model, with advisers providing mentoring and support. Variation in adoption at the mesolevel was related to stable and motivated leadership (particularly at the facility level), poor integration into routine processes, and buy-in from senior district managers who were affected by competing priorities. Varying referral and specialist outreach systems, staff availability and development, and service delivery infrastructure are plausible factors in variable outcomes. CONCLUSIONS: Few evaluations rigorously evaluated the effect of health system interventions on improving health services and outcomes. Results will inform the scaling up of successful intervention components and strategies to mitigate the effects of the COVID-19 pandemic or similar emerging epidemics on maternal and neonatal mortality. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/42041.

Assessing spatial patterns of HIV prevalence and interventions in semi-urban settings in South Africa. Implications for spatially targeted interventions.

Equitable allocation of resources targeting the human immunodeficiency virus (HIV) at the local level requires focusing interventions in areas of the greatest need. Understanding the geographical variation in the HIV epidemic and uptake of selected HIV prevention and treatment programmes are necessary to identify such areas. Individual-level HIV data were obtained from a 2012 national HIV survey in South Africa. Spatial regression models on each outcome measure (HIV infection, sub-optimal condom use or non-anti-retroviral treatment (ART) adjusted for spatial random effects at the ward level were fitted using WINBUGS software. In addition, ward-level data was utilized to estimate condom use coverage and ART initiation rates which were obtained from routinely collected data in 2012. Ordinary Kriging was used to produce smoothed maps of HIV infection, condom use coverage and ART initiation rates. HIV infection was associated with individuals undertaking tertiary education [posterior odds ratio (POR): 19.53; 95% credible intervals (CrI): 3.22- 84.93]. Sub-optimal condom use increased with age (POR: 1.09; 95%CrI: 1.06-1.11) and was associated with being married (POR: 4.14; 95%CrI: 1.23-4.28). Non-ART use was associated with being married (POR: 6.79; 95%CrI: 1.43-22.43). There were clusters with high HIV infection, sub-optimal condom use, and non- ART use in Ekurhuleni, an urban and semi-urban district in Gauteng province, South Africa. Findings show the need for expanding condom programmes and/or strengthening other HIV prevention programmes such as pre-exposure prophylaxis and encouraging sustained engagement in HIV care and treatment in the identified areas with the greatest need in Ekurhuleni Metropolitan Municipality.

Estimating Unhealthy Food Effects on Childhood Overweight in Malawi Using an Observational Study.

INTRODUCTION: Consumption of unhealthy foods in children contributes to high levels of childhood obesity globally. In developing countries there is paucity of empirical studies on the association.  This study employed propensity-score methods to evaluate the effect of unhealthy foods on overweight among children in Malawi using observational data. METHODS: Data on 4625 children aged 6 to 59 months from the 2015-16 Malawi Demographic and Health Survey (MDHS) were analyzed. A multivariable logistic regression model of unhealthy foods (yes or no) on purported confounders of childhood overweight was used to obtain a child's unhealthy food propensity score. The propensity scores were then used to form matched sets of healthy and unhealthy fed children. The association between unhealthy foods and childhood overweight was assessed using the conditional logistic regression model. RESULTS: The prevalence of overweight (body mass index (BMI) z-score > 2 standard deviations) was estimated at 4.5% (3.8%, 5.3%). The proportion of children who consumed unhealthy foods was estimated at 14.6% (95% CI: 13.1%, 16.2%). Our propensity score matching achieved a balance in the distribution of the confounders between children in the healthy and unhealthy food groups. Children fed unhealthy foods were significantly more likely to be overweight than those fed healthy foods (OR = 2.5, 95% CI: (1.2, 5.2)). CONCLUSION: The findings suggest the adverse effects of unhealthy foods on childhood overweight in Malawi. Thus, efforts to reduce unhealthy food consumption among children should be implemented and supported to address the problem of childhood overweight in Malawi and the sub-Saharan African region.

Progress towards the UNAIDS 95-95-95 targets among pregnant women in South Africa: Results from the 2017 and 2019 national Antenatal HIV Sentinel Surveys.

OBJECTIVES: The UNAIDS 95-95-95 global targets for epidemic control aim to ensure by 2030 that 95% of HIV-positive people know their HIV status, 95% of people diagnosed with HIV receive sustained antiretroviral therapy (ART), and 95% of people on ART have viral suppression. While data on the first and second 95 targets are routinely reported nationally, data on the third 95 target are not available for pregnant women in South Africa. The lack of data on the third 95 target limits the inclusion of low viral suppression as one of the contributing factors in MTCT root cause analyses. This study assessed progress towards the 95-95-95 targets among pregnant women between the ages of 15-49 years attending public health facilities in South Africa. METHOD: Data were obtained from two consecutive national cross-sectional antenatal HIV sentinel surveys conducted between 1 October and 15 November in both 2017 and 2019. In each survey, data on age, knowledge of HIV status, ART initiation, and geographical location (province) were extracted from medical records. A blood specimen was collected from each woman and tested for HIV. Viral load tests were performed on HIV-positive specimens. Descriptive and multiple logistic regression analyses were performed to examine association between province and viral suppression (defined as viral load <50 copies/mL) using the combined dataset (i.e., both 2017 and 2019 data combined). All analyses considered the survey design. RESULTS: Of 10 065 and 11 321 HIV-positive women included in the 2017 and 2019 surveys, respectively, 96.0% (95% confidence interval (CI): 95.6-96.4%) and 97.6% (95% CI: 97.3-97.8%) knew their HIV-positive status; 86.6% (95% CI: 85.9-87.3%) and 96.0% (95% CI: 95.6-96.4%) of those who knew their HIV status were receiving ART; while 64.2% (95% CI: 63.2-65.2%) and 66.0% (95% CI: 65.1-66.8%) of those receiving ART were virally suppressed. Achievement of the third 95 target significantly varied by province ranging from 33.9-72.6% in 2017 and 43.4-77.3% in 2019. Knowledge of HIV-positive status, ART initiation, and viral suppression increased in both 15-24 and 25-49 year age groups between 2017 and 2019. In a multivariable analysis adjusting for survey year, gravidity, and education, the odds of viral suppression significantly varied by province (except KwaZulu-Natal and Western Cape, other provinces were less likely to attain viral suppression compared to Gauteng), age (adjusted odds ratio (AOR) for 15-24 years vs 25-49 years: 0.7, 95% CI: 0.6-0.8), and timing of ART initiation (AOR for ART initiation during pregnancy vs before pregnancy: 0.4, 95% CI: 0.5-0.6). CONCLUSION: Although in 2019 the first and second 95 targets were achieved among pregnant women, meeting the third 95 target remains a challenge. This study highlighted the importance of promoting early ART initiation and the need to target young women in efforts to improve progress towards the third 95 target. Additionally, the provincial variation in viral suppression could be further investigated in future studies to identify and address the root causes underlying these differences.

Statistical Methods for the Analysis of Food Composition Databases: A Review.

Evidence-based knowledge of the relationship between foods and nutrients is needed to inform dietary-based guidelines and policy. Proper and tailored statistical methods to analyse food composition databases (FCDBs) could assist in this regard. This review aims to collate the existing literature that used any statistical method to analyse FCDBs, to identify key trends and research gaps. The search strategy yielded 4238 references from electronic databases of which 24 fulfilled our inclusion criteria. Information on the objectives, statistical methods, and results was extracted. Statistical methods were mostly applied to group similar food items (37.5%). Other aims and objectives included determining associations between the nutrient content and known food characteristics (25.0%), determining nutrient co-occurrence (20.8%), evaluating nutrient changes over time (16.7%), and addressing the accuracy and completeness of databases (16.7%). Standard statistical tests (33.3%) were the most utilised followed by clustering (29.1%), other methods (16.7%), regression methods (12.5%), and dimension reduction techniques (8.3%). Nutrient data has unique characteristics such as correlated components, natural groupings, and a compositional nature. Statistical methods used for analysis need to account for this data structure. Our summary of the literature provides a reference for researchers looking to expand into this area.

Inter-Country COVID-19 Contagiousness Variation in Eight African Countries.

The estimates of contiguousness parameters of an epidemic have been used for health-related policy and control measures such as non-pharmaceutical control interventions (NPIs). The estimates have varied by demographics, epidemic phase, and geographical region. Our aim was to estimate four contagiousness parameters: basic reproduction number (R0), contact rate, removal rate, and infectious period of coronavirus disease 2019 (COVID-19) among eight African countries, namely Angola, Botswana, Egypt, Ethiopia, Malawi, Nigeria, South Africa, and Tunisia using Susceptible, Infectious, or Recovered (SIR) epidemic models for the period 1 January 2020 to 31 December 2021. For reference, we also estimated these parameters for three of COVID-19's most severely affected countries: Brazil, India, and the USA. The basic reproduction number, contact and remove rates, and infectious period ranged from 1.11 to 1.59, 0.53 to 1.0, 0.39 to 0.81; and 1.23 to 2.59 for the eight African countries. For the USA, Brazil, and India these were 1.94, 0.66, 0.34, and 2.94; 1.62, 0.62, 0.38, and 2.62, and 1.55, 0.61, 0.39, and 2.55, respectively. The average COVID-19 related case fatality rate for 8 African countries in this study was estimated to be 2.86%. Contact and removal rates among an affected African population were positively and significantly associated with COVID-19 related deaths (p-value < 0.003). The larger than one estimates of the basic reproductive number in the studies of African countries indicate that COVID-19 was still being transmitted exponentially by the 31 December 2021, though at different rates. The spread was even higher for the three countries with substantial COVID-19 outbreaks. The lower removal rates in the USA, Brazil, and India could be indicative of lower death rates (a proxy for good health systems). Our findings of variation in the estimate of COVID-19 contagiousness parameters imply that countries in the region may implement differential COVID-19 containment measures.

COVID-19 hospitalization and mortality and hospitalization-related utilization and expenditure: Analysis of a South African private health insured population.

BACKGROUND: Evidence on the risk factors for COVID-19 hospitalization, mortality, hospital stay and cost of treatment in the African context is limited. This study aims to quantify the impact of known risk factors on these outcomes in a large South African private health insured population. METHODS AND FINDINGS: This is a cross sectional analytic study based on the analysis of the records of members belonging to health insurances administered by Discovery Health (PTY) Ltd. Demographic data for 188,292 members who tested COVID-19 positive over the period 1 March 2020-28 February 2021 and the hospitalization data for these members up until 30 June 2021 were extracted. Logistic regression models were used for hospitalization and death outcomes, while length of hospital stay and (log) cost per patient were modelled by negative binominal and linear regression models. We accounted for potential differences in the population served and the quality of care within different geographic health regions by including the health district as a random effect. Overall hospitalization and mortality risk was 18.8% and 3.3% respectively. Those aged 65+ years, those with 3 or more comorbidities and males had the highest hospitalization and mortality risks and the longest and costliest hospital stays. Hospitalization and mortality risks were higher in wave 2 than in wave 1. Hospital and mortality risk varied across provinces, even after controlling for important predictors. Hospitalization and mortality risks were the highest for diabetes alone or in combination with hypertension, hypercholesterolemia and ischemic heart disease. CONCLUSIONS: These findings can assist in developing better risk mitigation and management strategies. It can also allow for better resource allocation and prioritization planning as health systems struggle to meet the increased care demands resulting from the pandemic while having to deal with these in an ever-more resource constrained environment.

Prevalence of bacteriologically confirmed pulmonary tuberculosis in South Africa, 2017-19: a multistage, cluster-based, cross-sectional survey.

BACKGROUND: Tuberculosis remains an important clinical and public health issue in South Africa, which has one of the highest tuberculosis burdens in the world. We aimed to estimate the burden of bacteriologically confirmed pulmonary tuberculosis among people aged 15 years or older in South Africa. METHODS: This multistage, cluster-based, cross-sectional survey included eligible residents (age ≥15 years, who had slept in a house for ≥10 nights in the preceding 2 weeks) in 110 clusters nationally (cluster size of 500 people; selected by probability proportional-to-population size sampling). Participants completed face-to-face symptom questionnaires (for cough, weight loss, fever, and night sweats) and manually read digital chest X-ray screening. Screening was recorded as positive if participants had at least one symptom or an abnormal chest X-ray suggestive of tuberculosis, or a combination thereof. Sputum samples from participants who were screen-positive were tested by the Xpert MTB/RIF Ultra assay (first sample) and Mycobacteria Growth Indicator Tube culture (second sample), with optional HIV testing. Participants with a positive Mycobacterium tuberculosis complex culture were considered positive for bacteriologically confirmed pulmonary tuberculosis; when culture was not positive, participants with a positive Xpert MTB/RIF Ultra result with an abnormal chest X-ray suggestive of active tuberculosis and without current or previous tuberculosis were considered positive for bacteriologically confirmed pulmonary tuberculosis. FINDINGS: Between Aug 15, 2017, and July 28, 2019, 68 771 people were enumerated from 110 clusters, with 53 250 eligible to participate in the survey, of whom 35 191 (66·1%) participated. 9066 (25·8%) of 35 191 participants were screen-positive and 234 (0·7%) were identified as having bacteriologically confirmed pulmonary tuberculosis. Overall, the estimated prevalence of bacteriologically confirmed pulmonary tuberculosis was 852 cases (95% CI 679-1026) per 100 000 population; the prevalence was highest in people aged 35-44 years (1107 cases [95% CI 703-1511] per 100 000 population) and those aged 65 years or older (1104 cases [680-1528] per 100 000 population). The estimated prevalence was approximately 1·6 times higher in men than in women (1094 cases [95% CI 835-1352] per 100 000 population vs 675 cases [494-855] per 100 000 population). 135 (57·7%) of 234 participants with tuberculosis screened positive by chest X-ray only, 16 (6·8%) by symptoms only, and 82 (35·9%) by both. 55 (28·8%) of 191 participants with tuberculosis with known HIV status were HIV-positive. INTERPRETATION: Pulmonary tuberculosis prevalence in this survey was high, especially in men. Despite the ongoing burden of HIV, many participants with tuberculosis in this survey did not have HIV. As more than half of the participants with tuberculosis had an abnormal chest X-ray without symptoms, prioritising chest X-ray screening could substantially increase case finding. FUNDING: Global Fund, Bill & Melinda Gates Foundation, USAID.

Accounting for Sampling Weights in the Analysis of Spatial Distributions of Disease Using Health Survey Data, with an Application to Mapping Child Health in Malawi and Mozambique.

Most analyses of spatial patterns of disease risk using health survey data fail to adequately account for the complex survey designs. Particularly, the survey sampling weights are often ignored in the analyses. Thus, the estimated spatial distribution of disease risk could be biased and may lead to erroneous policy decisions. This paper aimed to present recent statistical advances in disease-mapping methods that incorporate survey sampling in the estimation of the spatial distribution of disease risk. The methods were then applied to the estimation of the geographical distribution of child malnutrition in Malawi, and child fever and diarrhoea in Mozambique. The estimation of the spatial distributions of the child disease risk was done by Bayesian methods. Accounting for sampling weights resulted in smaller standard errors for the estimated spatial disease risk, which increased the confidence in the conclusions from the findings. The estimated geographical distributions of the child disease risk were similar between the methods. However, the fits of the models to the data, as measured by the deviance information criteria (DIC), were different.

Assessment of prevalence and risk factors of diabetes and pre-diabetes in South Africa.

BACKGROUND: Diabetes prevalence, as well as that of pre-diabetes, is rapidly increasing in South Africa. Individuals with pre-diabetes have a high risk of developing type 2 diabetes, which is reversible with a change in lifestyle. If left untreated, diabetes can lead to serious health complications. Our objective was to assess the prevalence of diabetes and pre-diabetes, and to investigate the associated risk factors of each in the South African population. METHOD: This study made use of the South African Demographic Health Survey 2016 data. The study participants included 6442 individuals aged 15 years and older. A generalized additive mixed model was employed to account for the complex survey design of the study as well as well spatial autocorrelation in the data. RESULTS: The observed prevalence of pre-diabetes and diabetes was 67% and 22%, respectively. Among those who had never been tested for diabetes prior to the survey, 10% of females and 6% of males were found to be diabetic, and 67% of both males and females were found to be pre-diabetic. Thus, a large proportion of the South African population remains undiagnosed. The model revealed both common and uncommon factors significantly associated with pre-diabetes and diabetes. This highlights the importance of considering diabetic status as a three-level categorical outcome, rather than binary. In addition, significant interactions between some of the lifestyle factors, demographic factors and anthropometric measures were revealed, which indicates that the effects each these factors have on the likelihood of an individual being pre-diabetic or diabetic is confounded by other factors. CONCLUSION: The risk factors for diabetes and pre-diabetes are many and complicated. Individuals need to be aware of their diabetic status before health complications arise. It is therefore important for all stakeholders in government and the private sector of South Africa to get involved in providing education and creating awareness about diabetes. Regular testing of diabetes, as well as leading a healthy lifestyle, should be encouraged.