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Background: Identification of common spatial disease trends between cattle bovine tuberculosis (BTB) and human extrapulmonary tuberculosis (EPTB) and drug-resistant tuberculosis (DRTB) can support integrated disease control and monitoring programmes. We employed the recently developed multivariate disease mapping methods to examine whether the diseases exhibited any spatial correlation. Methods: A retrospective study of cattle BTB and human EPTB and DRTB cases from 2018 to 2022 was conducted. Bivariate shared spatiotemporal components models were fitted to a) cattle BTB and human EPTB and b) cattle BTB and human DRTB at the district level in Malawi, with cattle density, human density and climatic variables as independent variables. Results: Disease specific spatial effects were higher in the southern half of the country, while the shared spatial effects were more dominant in both the south and western parts of the country. The shared temporal effects showed constant trends, while disease specific temporal effects showed an increasing pattern for cattle BTB and a constant pattern for human EPTB and DRTB. The predicted disease incidence pattern for all forms of TB in the period without data showed a constant pattern over the years. Cattle density was positively associated with cattle BTB (β: 0.022; 95% Credible Interval (CI): 0.004, 0.042). Human density was positively associated with human EPTB (β: 0.005; 95% CI: 0.001, 0.009). Conclusion: Cattle BTB and human EPTB and DRTB have a common spatial pattern in the west and southern parts of Malawi. Integrated interventions targeting high-density areas for cattle and human may have positive impacts on cattle BTB and human EPTB and DRTB.

Introduction Despite a supportive policy environment, little attention has been paid to how to operationalise respectful maternity care in South Africa. This research provides a quantitative, baseline measure of women’s perceptions of person-centred maternity care (PCMC) to identify areas of focus for a participatory intervention with maternity teams.Methods A facility-based cross-sectional survey of postpartum women within 9 weeks postdelivery in two rural districts of KwaZulu-Natal. 908 postpartum women were recruited from postnatal clinics and neonatal units in the district hospitals. The primary outcome was PCMC measured on 30 items with a 4-point Likert scale (0–3). Mixed-effects linear regression analysis was used to identify predictor variables that were significantly associated with PCMC.Results The mean PCMC score was 55.5 (SD 13.6) out of 90 and was significantly higher for women who had caesarean deliveries compared with vaginal births (58.0 (SD 12.8) and 54.5 (SD 13.7), respectively). Around one-fifth of women reported verbal abuse at least once. Over half of women felt that their health information would be kept confidential all of the time, less than 15% of women were allowed to have a companion with them during labour or delivery and less than half of women felt they could completely trust their providers all of the time. Attending eight or more antenatal visits, having a caesarean delivery, being in the age group 30–45 and being in the middle wealth quintile were independently associated with a higher PCMC score while delivering at night was associated with a lower score.Conclusion Women attending rural health facilities experience disrespect and lack of trust in an environment where they have little involvement in decisions about their care and feel unable to ask questions of their providers. These findings support the need for interventions addressing organisational cultures that allow disrespect within maternity units.

Background: In livestock disease surveillance, spatial analysis methods play a major role in the identification of areas where the risk of disease could be higher. Though widely used in human health, their extent and depth of use are not well known in livestock health in sub-Saharan Africa and this has hindered their update in livestock disease modeling. This study set out to provide a comprehensive review of spatial analysis methods and their application in livestock disease data analysis in sub-Saharan Africa. Methods: Articles were searched using keywords related to spatial and spatio-temporal analysis of livestock diseases in sub-Saharan Africa in PubMed, Web of Science, Embase, and Scopus. Articles were reviewed in terms of name of author, country of study area, study design, livestock species, livestock diseases, research tasks, and spatial epidemiological methods in terms of spatial statistics and models among others. Results: A total of 56 articles were selected for review. Descriptive approaches such as simple maps of incidence and prevalence (n = 22) have been commonly used. Spatial scan statistics of the Kulldorff (n = 15) have also been the common spatial statistics employed. Model based spatial analysis has also been used (n = 14). Key research tasks that have been performed include investigating disease distribution, risk factors, space and time interaction and spatial risk prediction. The shortfalls of the reviewed studies include lack of exploration of irregularly shaped cluster scan statistics in case the actual disease clusters are irregular. There is also lack of use of multivariate scan and joint spatial models in case of multiple groups or diseases to show comorbidity. Model based spatial analysis has not accounted for space and time interaction. Machine learning niche models have failed to account for spatial autocorrelation in the data. Model based spatial risk prediction has mainly been retrospective as opposed to prospective for early warning. Conclusion: Future research may consider the application of multivariate scan statistics and joint spatial models for disease comorbidity analysis. It may also explore the use of irregularly shaped cluster scan statistics to enable detection of irregular disease clusters. Research opportunities may also include the use of machine learning models that account for spatial autocorrelation. Future spatial prediction is another area worth exploring to show future disease risk trends for early warning.

Abstract 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.

IntroductionThe 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.MethodsThis 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.ResultsClassifying 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.DiscussionThe 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.

BackgroundThe 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. ObjectiveOur 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. MethodsThis 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. ResultsFrom 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. ConclusionsFew 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

Abstract 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.

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.

Abstract To describe the prevalence of unintended pregnancy and its association with HIV status among pregnant women in South Africa. A cross-sectional survey was conducted between October and mid-November 2019 among pregnant women aged 15–49 years in 1589 selected public antenatal care facilities. Pregnancy intention was assessed using two questions from the London Measure of Unplanned Pregnancy. Survey logistic regression examined factors associated with unintended pregnancy. Among 34,946 participants, 51.6% had an unintended pregnancy. On multivariable analysis, the odds of unintended pregnancy was higher among women who knew their HIV-positive status before pregnancy but initiated treatment after the first antenatal visit (adjusted odds ratio [aOR], 1.5 [95% confidence interval (CI):1.2–1.8]), women who initiated treatment before pregnancy (aOR, 1.3 [95% CI:1.2–1.3]), and women with a new HIV diagnosis during pregnancy (aOR, 1.2 [95% CI:1.1–1.3]) compared to HIV-negative women. Women who were single, in a non-cohabiting or a cohabiting relationship, and young women (15–24 years) had significantly higher risk of unintended pregnancy compared to married women and women aged 30–49 years, respectively. A comprehensive approach, including regular assessment of HIV clients’ pregnancy intention, and adolescent and youth-friendly reproductive health services could help prevent unintended pregnancy.

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.

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.

Introduction: The COVID-19 pandemic in Malawi emerged amidst widespread anti-government demonstrations and subsequent mass gatherings. This paper describes the incidence and factors associated with the spread of the COVID-19 pandemic in Malawi. Methodology: This was a retrospective study of public data analysing geopolitical and immigration activities that occurred between 02 April and 08 September 2020. The Chi-square test of independence was used to tabulate sex and age-related fatality ratios among deaths due to COVID-19-related complications. Results: The drivers for COVID-19 spread were mass gatherings secondary to the country’s political landscape and repatriation of citizens from high-risk areas coupled with minimum use of public health interventions. The prevalence was higher in people aged 50–59 years, males and in urban areas. Men had an increased risk of COVID-19-related deaths (Case Fatality Ratio: 1.58 (95% CI 1.11–2.22) compared with women. Furthermore, men and women aged ≥40 years were 16.1 times and 7.1 times more likely to die of COVID-related complications, respectively. Men aged ≥40 years had a 62% increased risk of deaths compared with women of the same age group. Conclusion: Mass political gatherings and cross-border immigration from high-risk areas were drivers for infection. Males, older age and urban residence were associated with increased COVID-19 morbidity and mortality. To control the spread of COVID-19 there is a need to regulate mass gatherings and repatriation of citizens, and strengthen the use of preventive health interventions. Men, the older age groups and urban areas should be prioritised for COVID-19 prevention strategies.

Abstract Background Intimate Partner Violence (IPV) against women is a major public health and human rights problem worldwide. Sub-Saharan Africa (SSA) has one of the highest prevalence of IPV against women in the world. This study used meta-analysis to obtain pooled rural–urban and education attainment differences in the prevalence of IPV among ever-partnered women in SSA, and assessed whether the differences in IPV depended on the SSA region or period or women’s age. Methods We analysed IPV data on 233,585 ever-partnered women aged 15–49 years from 44 demographic and health surveys conducted between 2000 and 2018 in 29 SSA countries. Random-effects meta-analyses were used to estimate overall rural–urban residence and educational differences in IPV rates among the women in SSA. Subgroup analyses were also done to investigate the sources of heterogeneity in the overall meta-analysis findings. Results The pooled prevalence of intimate partner violence was estimated to be 41.3% (37.4–45.2%). Regionally, the highest prevalence of IPV was in Middle Africa (49. 3%; 40.32–58.45), followed by East Africa (44.13%; 36.62–51.67), Southern Africa (39.36%; 34.23–44.49), and West Africa (34.30%; 27.38–41.22). The risks of experiencing IPV were significantly higher if the women had less than secondary education (RR = 1.12; 95% CI 1.07–1.22) compared to those with at least a secondary education. Generally, women who resided in a rural area had their risks of experiencing IPV increased (RR = 1.02; CI 0.96–1.06) compared to those who resided in urban areas, but the IPV increases were only significant in East Africa (RR = 1.13; CI 1.07–1.22). Conclusion In sub-Saharan Africa, intimate partner violence against women is widespread, but the levels are much higher among women with lower levels of education and residing in rural areas. Our findings have provided additional support to policies aimed at achieving SDG goals on the elimination of all forms of violence against women and girls in sub-Saharan Africa. For example, policies that advocate improved educational attainment, especially among women and communities in rural areas.

Abstract Background The rising burden of the ongoing COVID-19 epidemic in South Africa has motivated the application of modeling strategies to predict the COVID-19 cases and deaths. Reliable and accurate short and long-term forecasts of COVID-19 cases and deaths, both at the national and provincial level, are a key aspect of the strategy to handle the COVID-19 epidemic in the country. Methods In this paper we apply the previously validated approach of phenomenological models, fitting several non-linear growth curves (Richards, 3 and 4 parameter logistic, Weibull and Gompertz), to produce short term forecasts of COVID-19 cases and deaths at the national level as well as the provincial level. Using publicly available daily reported cumulative case and death data up until 22 June 2020, we report 5, 10, 15, 20, 25 and 30-day ahead forecasts of cumulative cases and deaths. All predictions are compared to the actual observed values in the forecasting period. Results We observed that all models for cases provided accurate and similar short-term forecasts for a period of 5 days ahead at the national level, and that the three and four parameter logistic growth models provided more accurate forecasts than that obtained from the Richards model 10 days ahead. However, beyond 10 days all models underestimated the cumulative cases. Our forecasts across the models predict an additional 23,551–26,702 cases in 5 days and an additional 47,449–57,358 cases in 10 days. While the three parameter logistic growth model provided the most accurate forecasts of cumulative deaths within the 10 day period, the Gompertz model was able to better capture the changes in cumulative deaths beyond this period. Our forecasts across the models predict an additional 145–437 COVID-19 deaths in 5 days and an additional 243–947 deaths in 10 days. Conclusions By comparing both the predictions of deaths and cases to the observed data in the forecasting period, we found that this modeling approach provides reliable and accurate forecasts for a maximum period of 10 days ahead.

Objective: South Africa has used antenatal HIV surveys for HIV surveillance in pregnant women since 1990. We assessed South Africa’s readiness to transition to programme data based antenatal HIV surveillance with respect to PMTCT uptake, accuracy of point-of-care rapid testing (RT) and selection bias with using programme data in the context of the 2017 antenatal HIV survey. Methods: Between 1 October and 15 November 2017, the national survey was conducted in 1,595 public antenatal facilities selected using stratified multistage cluster sampling method. Results of point-of-care RT were obtained from medical records. Blood samples were taken from eligible pregnant women and tested for HIV using immunoassays (IA) in the laboratory. Descriptive statistics were used to report on: PMTCT uptake; agreement between HIV point-of-care RT and laboratory-based HIV-1 IA; and selection bias associated with using programme data for surveillance. Results: PMTCT HIV testing uptake was high (99.8%). The positive percent agreement (PPA) between RT and IA was lower than the World Health Organization (WHO) benchmark (97.6%) at 96.3% (95% confidence interval (CI): 95.9%–96.6%). The negative percent agreement was above the WHO benchmark (99.5%), at 99.7% (95% CI: 99.6%–99.7%) nationally. PPA markedly varied by province (92.9%–98.3%). Selection bias due to exclusion of participants with no RT results was within the recommended threshold at 0.3%. Conclusion: For the three components assessed, South Africa was close to meeting the WHO standard for transitioning to routine RT data for antenatal HIV surveillance. The wide variations in PPA across provinces should be addressed. Keywords: Pregnant women, Surveillance, Test agreement, PMTCT, Rapid testing, South Africa

Objectives About half of the pregnancies among women living with HIV (WLWH) receiving antiretroviral therapy (ART) in sub-Saharan African countries are reported to be unintended. Unintended pregnancy is associated with late initiation of antenatal care (ANC), and may delay provision of viral load monitoring services, antenatal adherence counselling and support, and other services that promote sustained viral suppression throughout pregnancy. This study examines the association between unsuppressed viral load during the third trimester of pregnancy and unintended pregnancy among women who initiated ART before pregnancy. Methods This was an analysis of data from a national antenatal survey conducted at 1 589 public health facilities in South Africa between 1 October and 15 November 2019. Consenting pregnant women aged 15–49 years attending ANC during the survey period were enrolled. Demographic and clinical data were collected through interview and medical record review. Pregnancy intention was assessed using two questions from the London Measure of Unplanned Pregnancy, and responses were categorized as “unintended,” “undecided,” and “intended.” Blood specimens were collected from all women and tested for HIV; and if positive, a viral load test was performed. A survey domain-based poisson regression model examined the association between unsuppressed viral load during the third trimester of pregnancy and unintended pregnancy among women who initiated ART before pregnancy. Viral suppression was defined as viral load Results Of 10 901 WLWH with viral load data available, 63.3% (95% confidence interval (CI): 62.4%-64.1%) were virally suppressed. Among the 2 681 women (representing 24.1% of all WLWH with viral load data) who initiated ART before pregnancy and were in their third trimester at the time of enrolment, 74.4% (95% CI: 73.0%-75.8%) were virally suppressed. In the same population, the proportion virally suppressed was lower among women whose current pregnancies were unintended (72.1%, 95% CI: 70.1%-74.1%) compared to women whose pregnancies were intended (78.3%, 95% CI: 75.9%-80.5%). In multivariable analyses adjusted for age, gravity, marital status, education, location of facility and syphilis status, unintended pregnancy was associated with unsuppressed viral load during the third trimester (adjusted relative risk: 1.3, 95% CI: 1.1–1.4) among women who initiated ART before pregnancy. Conclusion The identified association between unsuppressed viral load and unintended pregnancy among pregnant women who initiated ART before pregnancy highlights the need to strengthen routine assessment of fertility preferences and provision of contraceptive services to reproductive age WLWH receiving ART.

BackgroundEvidence 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 findingsThis 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.ConclusionsThese 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.

ObjectivesThe 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.MethodData 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 ResultsOf 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).ConclusionAlthough 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.

In the longitudinal data analysis we integrate flexible linear predictor link function and high-correlated predictor variables. Our approach uses B-splines for non-parametric part in the linear predictor component. A generalized estimation equation is used to estimate the parameters of the proposed model. We assess the performance of our proposed model using simulations and an application to an analysis of acquired immunodeficiency syndrome data set.

The gut microbiota has been immensely studied over the past years because of its involvement in the pathogenesis of numerous diseases. However, gut microbiota data in Africa are limited. Therefore, it is crucial to have studies that reflect various populations in order to fully capture global microbial diversity. In the proposed scoping review, we will describe the gut microbiota’s appearance in terms of gut microbiota markers, in both health and disease in African populations. Relevant publications will be searched for in the PubMed, Scopus, Web of Science, Academic Search Premier, Africa-Wide Information, African journals online, CINAHL, and EBSCOhost and Embase databases. We will focus on articles published between January 2005 and March 2023. We will also determine if the studies to be included in the review would provide enough data to identify quantifiable gut microbiome traits that could be used as health or disease markers, identify the types of diseases that were mostly focused on in relation to gut microbiota research in Africa, as well as to discover and analyze knowledge gaps in the gut microbiota research field in the continent. We will include studies involving African countries regardless of race, gender, age, health status, disease type, study design, or care setting. Two reviewers will conduct a literature search and screen the titles/abstracts against the eligibility criteria. The reviewers will subsequently screen full-text articles and identify studies that meet the inclusion criteria. This will be followed by charting the data using a charting tool and analysis of the evidence. The proposed scoping review will follow a qualitative approach such that a narrative summary will accompany the tabulated/graphical results which will describe how the results relate to the review objectives and questions. As a result, this review may play a significant role in the identification of microbiota-related adjunctive therapies in the African region where multiple comorbidities coexist. Scoping review registration: Open Science Framework.

Background: Identification of the geographical areas with low uptake of HIV testing could assist in spatial targeting of interventions to improve the uptake of HIV testing. Objectives: The objective of this research study was to map the uptake of HIV testing at the district level in South Africa. Method: The secondary analysis used data from the Human Sciences Research Council’s 2017 National HIV Prevalence, Incidence, Behaviour and Communication Survey, where data were collected using a multistage stratified random cluster sampling approach. Descriptive spatial methods were used to assess disparities in the proportion of those ever tested for HIV at the district level in South Africa. Results: The districts with the highest overall coverage of people ever having tested for HIV ( 85%) include West Rand in Gauteng, Lejweleputswa and Thabo Mofutsanyane in Free State, and Ngaka Modiri Molema in North-West. These provinces also had the least variation in HIV testing coverage between their districts. Districts in KwaZulu-Natal had the widest variation in coverage of HIV testing. The districts with the lowest uptake of HIV testing were uMkhanyakude (54.7%) and Ugu (61.4%) in KwaZulu-Natal and Vhembe (61.0%) in Limpopo. Most districts had a higher uptake of HIV testing amongst female than male participants. Conclusion: The uptake of HIV testing across various districts in South Africa seems to be unequal. Intervention programmes must improve the overall uptake of HIV testing, especially in uMkhanyakude and Ugu in KwaZulu-Natal and Vhembe in Limpopo. Interventions must also focus on enhancing uptake of HIV testing amongst male participants in most districts. Strategies that would improve the uptake of HIV testing include HIV self-testing and community HIV testing, specifically home-based testing.

Background Little is known about the contribution of community health posts and community health workers (CHWs) to geographical accessibility of primary healthcare (PHC) services at community level and strategies for optimising geographical accessibility to these services.Methods Using a complete georeferenced census of community health posts and CHWs in Niger and other high-resolution spatial datasets, we modelled travel times to community health posts and CHWs between 2000 and 2013, accounting for training, commodities and maximum population capacity. We estimated additional CHWs needed to optimise geographical accessibility of the population beyond the reach of the existing community health post network. We assessed the efficiency of geographical targeting of the existing community health post network compared with networks designed to optimise geographical targeting of the estimated population, under-5 deaths and Plasmodium falciparum malaria cases.Results The per cent of the population within 60-minute walking to the nearest community health post with a CHW increased from 0.0% to 17.5% between 2000 and 2013. An estimated 10.4 million people (58.5%) remained beyond a 60-minute catchment of community health posts. Optimal deployment of 7741 additional CHWs could increase geographical coverage from 41.5% to 82.9%. Geographical targeting of the existing community health post network was inefficient but optimised networks could improve efficiency by 32.3%–47.1%, depending on targeting metric.Interpretations We provide the first estimates of geographical accessibility to community health posts and CHWs at national scale in Niger, highlighting improvements between 2000 and 2013, geographies where gaps remained and approaches for optimising geographical accessibility to PHC services at community level.

IntroductionNew HIV infection during pre-conception and pregnancy is a significant contributor of mother-to-child transmission of HIV in South Africa. This study estimated HIV incidence (defined as new infection within the last one year from the time of the survey which included both new infections occurred during pregnancy or just before pregnancy) among pregnant women and described the characteristics of recently infected pregnant women at national level.MethodsBetween 1 October and 15 November 2017, we conducted a national cross-sectional survey among pregnant women aged 15-49 years old attending antenatal care at 1,595 public facilities. Blood specimens were collected from pregnant women and tested for HIV in a centralised laboratory. Plasma viral load and Limiting Antigen Avidity Enzyme Immunosorbent Assay (LAg) tests were further performed on HIV positive specimens to differentiate between recent and long-term infections. Recent infection was defined as infection that occurred within one year from the date of collection of blood specimen for the survey. Data on age, age of partner, and marital status were collected through interviews. Women whose specimens were classified as recent by LAg assay and with viral loads >1,000 copies/mL were considered as recently infected. The calculated proportion of HIV positive women with recent infection was adjusted for assay-specific parameters to estimate annual incidence. Survey multinomial logistic regression was used to examine factors associated with being recently infected using HIV negative women as a reference group. Age-disparate relationship was defined as having a partner 5 or more years older.ResultsOf 10,049 HIV positive participants with LAg and viral load data, 1.4% (136) were identified as recently infected. The annual HIV incidence was 1.5% (95% confidence interval (CI): 1.2-1.7). In multivariable analyses, being single (adjusted odds ratio, aOR: 3.4, 95% CI: 1.8-6.2) or cohabiting (aOR: 3.8, 95% CI: 1.8-7.7), compared to being married as well as being in an age-disparate relationship among young women (aOR: 3.1, 95% CI: 2.0-4.7; reference group: young women (15-24years) whose partners were not 5 years or more older) were associated with higher odds of recent infection.ConclusionsCompared to previous studies among pregnant women, the incidence estimated in this study was substantially lower. However, the UNAIDS target to reduce incidence by 75% by 2020 (which is equivalent to reducing incidence to

The vision of health for all by Dr. Halfdan Mahler, Director General of the World Health Organization (WHO) 1973 to 1988, guided public health approaches towards improving life for all those mired in poverty and disease. Research on the Neglected Tropical Diseases (NTDs) of the world’s poor was advancing strongly when the coronavirus disease 2019 (COVID-19) struck. Although work on the NTDs did not grind to a halt, the situation is reminiscent of the author Stefan Zweig’s passionate account of culture destruction in his book The World of Yesterday from 1941, which gives an insight as to how the war ended traditional life. His thoughts parallel the present situation; however, this time societies are not torn apart by war but instead isolated by a pandemic. It comes upon today’s scientists to move fast to make COVID-19 less devastating than the Spanish flu of 1918-1920 that killed more than 3% of the world population...

Objectives We report the effectiveness of a mentoring approach to improve health workers’ (HWs’) knowledge, attitudes and confidence with counselling on HIV and infant feeding.Design Quasi-experimental controlled before–after study.Setting Randomly selected primary healthcare clinics (n=24 intervention, n=12 comparison); two districts, South Africa.Participants All HWs providing infant feeding counselling in selected facilities were invited.Interventions Three 1–2 hours, on-site workshops over 3–6 weeks.Primary outcome measures Knowledge (22 binary questions), attitude (21 questions—5-point Likert Scale) and confidence (19 questions—3-point Likert Scale). Individual item responses were added within each of the attitude and confidence domains. The respective sums were taken to be the domain composite index and used as a dependent variable to evaluate intervention effect. Linear regression models were used to estimate the mean score difference between intervention and comparison groups postintervention, adjusting for the mean score difference between them at baseline. Analyses were adjusted for participant baseline characteristics and clustering at health facility level.Results In intervention and comparison sites, respectively: 289 and 131 baseline and 253 and 114 follow-up interviews were conducted (August–December 2017). At baseline there was no difference in mean number of correctly answered knowledge questions; this differed significantly at follow-up (15.2 in comparison; 17.2 in intervention sites (p

Abstract Background Noncommunicable diseases (NCDs) including cardiovascular diseases (CVDs), diabetes, cancer and chronic lung disease are increasingly emerging as major contributors to morbidity and mortality in developing countries. For example, in South Africa, 195 people died per day between 1997 and 2004 from CVDs related causes. Access to efficient and effective health facility and care is an important contributing factor to overall population health and addressing prognosis, care and management CVD disease burden. This study aimed to spatially evaluate geographic health care access of people diagnosed with CVD to health facilities and to evaluate the density of the existing health facility network in South Africa. Methods Data was obtained from the National Income Dynamics Study (NIDS) conducted in 4 waves (phases) between 2008 and 2014. The participants who responded as having heart problems that were diagnosed by a health practitioner were extracted for use in this study. Network analyst in ArcGIS ® was used to generate a least-cost path, which refers to the best path that one can travel. The residential locations of participants diagnosed with heart problems were put into the network analysis model as origins and the location of health facilities were destinations. District averages were used to protect the identity of studied participants. Results There were a total of 51, 42, 43, 43 health districts out the 52 that had recorded subjects with a heart condition in the 2008, 2010–2011, 2012 and 2014–2015 waves, respectively. The mean distance from a case household to a health facility per wave was 2, 2.3, 2.1 and 2.1 km in 2008, 2010–2011 and 2014–2015 respectively. The maximum individual distances travelled per wave were 41.4 km, 40,5 km, 44,2 km and 39.6 km for the 2008, 2010–2011, 2012 and 2014–2015 waves respectively. For district level analysis, participants with CVD residing in the districts found to be among the poorest in the country travelled the longest distances. These were located in the provinces of Limpopo and KwaZulu Natal. It was also found that districts with large proportions of their population living in rural settings had among the lowest densities of health facilities. Significant percentages of study participants were exposed to numerous CVD risk factors, the commonly reported one being high blood pressure. A lack of regular exercise was also commonly reported in each of the waves. Conclusion A lack of accessible healthcare in already impoverished municipalities could result in an increase lack of timely diagnosis, CVD case management. This could result in increased CVD-related morbidity and mortality. GIS methods have the potential to assist national health programs to develop policies that target issues such as areas or populations being underserved by health facilities and populations that must travel long distances to receive healthcare. These policies will be key in preventing and controlling the emerging CVD burden through an accessible primary healthcare system for early detection and case management.

IntroductionKnowledge of HIV status in South Africa (SA) is reported to be 90% among people living with HIV. National level estimates could mask population-specific levels, which are critical to monitor program coverage and potential impact. Using data from the 2017 national antenatal sentinel survey, we assessed knowledge of HIV-positive status, initiation of antiretroviral therapy (ART), and socio-demographic characteristics associated with knowledge of HIV-positive status prior to the current pregnancy among women attending antenatal care.MethodsBetween 1 October and 15 November 2017, a nationally representative sample of 32,716 pregnant women were enrolled from 1,595 public health facilities selected from all districts of SA. Data on age, gravidity, knowledge of HIV-positive status and ART initiation prior to pregnancy were extracted from medical records. A blood sample was collected from each woman regardless of prior knowledge of HIV status or ART history, and tested for HIV in the laboratory. All HIV-positive pregnant women enrolled in the survey were eligible for inclusion in the analysis. Multivariable survey logistic regression was used to examine factors associated with knowledge of HIV-positive status prior to the current pregnancy.ResultsOf 10,065 eligible HIV-positive women, 60.8% (95% confidence interval (CI):59.9%-61.7%) knew their HIV status prior to the current pregnancy, of whom 91.1% (95% CI: 90.4%-91.7%) initiated ART prior to the current pregnancy. Knowledge of HIV-positive status was lower among adolescent girls and young women (15-24 years) (38.9%) and primigravid women (40.5%) compared with older women (35-49 years) (75.5%) and multigravid women (64.7%). In a multivariable analysis, significant effect modification was found between gravidity and age (P value = 0.047). Being in the age group 15-24 years compared to the age group 35-49 years decreased the odds of knowing HIV-positive status by 80% (adjusted odds ratio (AOR): 0.2, 95% CI:0.1-0.4) among primigravid women and by 60%(AOR: 0.4, 95% CI:0.3-0.4) among multigravid women.ConclusionKnowledge of HIV-positive status prior to the current pregnancy fell short of the target of 90% among pregnant women living with HIV. This was especially low among adolescent girls and young women, highlighting the gap in youth friendly reproductive health and HIV testing services.

BackgroundOf the total 56 million deaths worldwide during 2012, 38 million (68%) were due to noncommunicable diseases (NCDs), particularly cardiovascular diseases (17.5 million deaths) cancers (8.2 million) which represents46.2% and 21.7% of NCD deaths, respectively). Nearly 80 percent of the global CVD deaths occur in low- and middle-income countries. Some of the major CVDs such as ischemic heart disease (IHD) and stroke and CVD risk conditions, namely, hypertension and dyslipidaemia share common modifiable risk factors including smoking, unhealthy diets, harmful use of alcohol and physical inactivity. The CVDs are now putting a heavy strain of the health systems at both national and local levels, which have previously largely focused on infectious diseases and appalling maternal and child health. We set out to estimate district-level co-occurrence of two cardiovascular diseases (CVDs), namely, ischemic heart disease (IHD) and stroke; and two major risk conditions for CVD, namely, hypertension and dyslipidaemia in South Africa.MethodThe analyses were based on adults health collected as part of the 2012 South African National Health and Nutrition Examination Survey (SANHANES). We used joint disease mapping models to estimate and map the spatial distributions of risks of hypertension, self-report of ischaemic heart disease (IHD), stroke and dyslipidaemia at the district level in South Africa. The analyses were adjusted for known individual social demographic and lifestyle factors, household and district level poverty measurements using binary spatial models.ResultsThe estimated prevalence of IHD, stroke, hypertension and dyslipidaemia revealed high inequality at the district level (median value (range): 5.4 (0-17.8%); 1.7 (0-18.2%); 32.0 (12.5-48.2%) and 52.2 (0-71.7%), respectively). The adjusted risks of stroke, hypertension and IHD were mostly high in districts in the South-Eastern parts of the country, while that of dyslipidaemia, was high in Central and top North-Eastern corridor of the country.ConclusionsThe study has confirmed common modifiable risk factors of two cardiovascular diseases (CVDs), namely, ischemic heart disease (IHD) and stroke; and two major risk conditions for CVD, namely, hypertension and dyslipidaemia. Accordingly, an integrated intervention approach addressing cardiovascular diseases and associated risk factors and conditions would be more cost effective and provide stronger impacts than individual tailored interventions only. Findings of excess district-level variations in the CVDs and their risk factor profiles might be useful for developing effective public health policies and interventions aimed at reducing behavioural risk factors including harmful use of alcohol, physical inactivity and high salt intake.

South Africa is experiencing an increasing burden of noncommunicable diseases (NCDs). There is evidence of co-morbidity of several NCDs at small geographical areas in the country. However, the extent to which this applies to joint spatial autocorrections of NCDs is not known. The objective of this study was to derive and quantify multivariate spatial autocorrections for NCDrelated mortality in South Africa. The study used mortality attributable to cerebrovascular, ischaemic heart failure and hypertension captured by the country’s Department of Home Affairs for the years 2001, 2007 and 2011. Both univariate and pairwise spatial clustering measures were derived using observed, empirical Bayes smoothed and age-adjusted standardised mortality rates. Cerebrovascular and ischaemic heart co-clustering was significant for the years 2001 and 2011. Cerebrovascular and hypertension co-clustering was significant for the years 2007 and 2011, while hypertension and ischaemic heart co-clustering was significant for the year 2011. Co-clusters of cerebrovascular-ischaemic heart disease are the most profound and located in the south-western part of the country. It was successfully demonstrated that bivariate spatial autocorrelations can be derived for spatially dependent mortality rates as exemplified by mortality rates attributed to three cardiovascular conditions. The identified co-clusters of spatially dependent health outcomes may be targeted for an integrated intervention and monitoring programme.

Infectious diseases transmitted by vectors/intermediate hosts constitute a major part of the economic burden related to public health in the endemic countries of the tropics, which challenges local welfare and hinders development. The World Health Organization, in partnership with pharmaceutical companies, major donors, endemic countries and non-governmental organizations, aims to eliminate the majority of these infections in the near future. To succeed, the ecological requirements and real-time distributions of the causative agents (bacteria, parasites and viruses) and their vectors must not only be known to a high degree of accuracy, but the data must also be updated more rapidly than has so far been the case. Current approaches include data collection through terrestrial capture on site and satellite-generated information. This article provides an update of currently available sources of remotely-sensed data, including specific information on satellite-borne sensors, and how such data can be handled by Geographical Information Systems (GIS). Computers, when equipped with GIS software based on common spatial denominators, can connect remotely-sensed environmental records with terrestrial-captured data and apply spatial statistics in ways uniquely suited to manage control activities in areas where vector-borne infections dominate.

Background: The Demographic and Health Surveys (DHS) and Multiple Indicator Cluster Surveys (MICS) are the major data sources in low- and middle-income countries (LMICs) for evaluating health service coverage. For certain maternal and child health (MCH) indicators, the two surveys use different recall periods: 5 years for DHS and 2 years for MICS. Objective: We explored whether the different recall periods for DHS and MICS affect coverage trend analyses as well as missing data and coverage estimates. Designs: We estimated coverage, using proportions with 95% confidence intervals, for four MCH indicators: intermittent preventive treatment of malaria in pregnancy, tetanus vaccination, early breastfeeding and postnatal care. Trends in coverage were compared using data from 1) standard 5-year DHS and 2-year MICS recall periods (unmatched) and 2) DHS restricted to 2-year recall to match the MICS 2-year recall periods (matched). Linear regression was used to explore the relationship between length of recall, missing data and coverage estimates. Results: Differences in coverage trends were observed between matched and unmatched data in 7 of 18 (39%) comparisons performed. The differences were in the direction of the trend over time, the slope of the coverage change or the significance levels. Consistent trends were seen in 11 of the 18 (61%) comparisons. Proportion of missing data was inversely associated with coverage estimates in both short (2 years) and longer (5 years) recall of the DHS (r=−0.3, p=0.02 and r=−0.4, p=0.004, respectively). The amount of missing information was increased for longer recall compared with shorter recall for all indicators (significant odds ratios ranging between 1.44 and 7.43). Conclusions: In a context where most LMICs are dependent on population-based household surveys to derive coverage estimates, users of these types of data need to ensure that variability in recall periods and the proportion of missing data across data sources are appropriately accounted for when trend analyses are conducted.

Background Monitoring prevalence of smoking is essential for evaluating the impact of national tobacco control policies. This study aims to estimate national pooled smoking prevalence trends over a 16 year period for adult South Africans. Methods Smoking prevalence by age, sex and race from 14 South African population and national household surveys conducted between 1998 - 2014 were used to generate trends over time by 1) performing a series of transformations of the aggregated prevalence data, 2) investigating interactions with race/time, and 3) using a posthumous regression. Bias within surveys were adjusted for by using a risk-of-bias weight. Results The overall observed smoking prevalence decreased from 23.7 (22.4; 24.9) in 1998 to 20.3 (19.3; 21.4) in 2014. Downward trends were observed in both males and females, although it was steeper in males. There were significant differences between race groups, as well as within race groups across age, most notably Asian males, which also seemed to drive the steep decline among males. Whilst the downward trend was evident in older ages (25 + years), the youngest group (15 - 24 years) had a non-linear trend differing from the linear trend in the older group. Conclusions Pooling estimates from different national surveys over time, gave an effective picture of trends in smoking in South Africa. Although not directly observable, the trends reported indicate that the South African Tobacco Control Act of 1993 had influenced and maintained decreasing smoking trends in the last couple of decades, albeit to a lesser extent among females.

BACKGROUND:Household surveys undertaken in Niger since 1998 have revealed steady declines in under-5 mortality which have placed the country 'on track' to reach the fourth Millennium Development goal (MDG). This paper explores Niger's mortality and health coverage data for children under-5 years of age up to 2012 to describe trends in high impact interventions and the resulting impact on childhood deaths averted. The sustainability of these trends are also considered. METHODS AND FINDINGS:Estimates of child mortality using the 2012 Demographic and Health Survey were developed and maternal and child health coverage indicators were calculated over four time periods. Child survival policies and programmes were documented through a review of documents and key informant interviews. The Lives Saved Tool (LiST) was used to estimate the number of child lives saved and identify which interventions had the largest impact on deaths averted. The national mortality rate in children under-5 decreased from 286 child deaths per 1000 live births (95% confidence interval 177 to 394) in the period 1989-1990 to 128 child deaths per 1000 live births in the period 2011-2012 (101 to 155), corresponding to an annual rate of decline of 3.6%, with significant declines taking place after 1998. Improvements in the coverage of maternal and child health interventions between 2006 and 2012 include one and four or more antenatal visits, maternal Fansidar and tetanus toxoid vaccination, measles and DPT3 vaccinations, early and exclusive breastfeeding, oral rehydration salts (ORS) and proportion of children sleeping under an insecticide-treated bed net (ITN). Approximately 26,000 deaths of children under-5 were averted in 2012 due to decreases in stunting rates (27%), increases in ORS (14%), the Hib vaccine (14%), and breastfeeding (11%). Increases in wasting and decreases in vitamin A supplementation negated some of those gains. Care seeking at the community level was responsible for an estimated 7,800 additional deaths averted in 2012. A major policy change occurred in 2006 enabling free health care provision for women and children, and in 2008 the establishment of a community health worker programme. CONCLUSION:Increases in access and coverage of care for mothers and children have averted a considerable number of childhood deaths. The 2006 free health care policy and health post expansion were paramount in reducing barriers to care. However the sustainability of this policy and health service provision is precarious in light of persistently high fertility rates, unpredictable GDP growth, a high dependence on donor support and increasing pressures on government funding.

Malawi is estimated to have achieved its Millennium Development Goal (MDG) 4 target. This paper explores factors influencing progress in child survival in Malawi including coverage of interventions and the role of key national policies. We performed a retrospective evaluation of the Catalytic Initiative (CI) programme of support (2007–2013). We developed estimates of child mortality using four population household surveys undertaken between 2000 and 2010. We recalculated coverage indicators for high impact child health interventions and documented child health programmes and policies. The Lives Saved Tool (LiST) was used to estimate child lives saved in 2013. The mortality rate in children under 5 years decreased rapidly in the 10 CI districts from 219 deaths per 1000 live births (95% confidence interval (CI) 189 to 249) in the period 1991–1995 to 119 deaths (95% CI 105 to 132) in the period 2006–2010. Coverage for all indicators except vitamin A supplementation increased in the 10 CI districts across the time period 2000 to 2013. The LiST analysis estimates that there were 10 800 child deaths averted in the 10 CI districts in 2013, primarily attributable to the introduction of the pneumococcal vaccine (24%) and increased household coverage of insecticide–treated bednets (19%). These improvements have taken place within a context of investment in child health policies and scale up of integrated community case management of childhood illnesses. Malawi provides a strong example for countries in sub–Saharan Africa of how high impact child health interventions implemented within a decentralised health system with an established community–based delivery platform, can lead to significant reductions in child mortality.

Abstract Evolutionary annotation of genome maintenance (GM) proteins has conventionally been established by remote relationships within protein sequence databases. However, often no significant relationship can be established. Highly sensitive approaches to attain remote homologies based on iterative profile-to-profile methods have been developed. Still, these methods have not been systematically applied in the evolutionary annotation of GM proteins. Here, by applying profile-to-profile models, we systematically survey the repertoire of GM proteins from bacteria to man. We identify multiple GM protein candidates and annotate domains in numerous established GM proteins, among other PARP, OB-fold, Macro, TUDOR, SAP, BRCT, KU, MYB (SANT), and nuclease domains. We experimentally validate OB-fold and MIS18 (Yippee) domains in SPIDR and FAM72 protein families, respectively. Our results indicate that, surprisingly, despite the immense interest and long-term research efforts, the repertoire of genome stability caretakers is still not fully appreciated.