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Open science and human genetic data: recommendations on South Africa's Draft National Open Science Policy.

ABSTRACT: The Draft National Open Science Policy, which was shared by the South African government with stakeholders in 2022, is an encouraging step forward as it aims to promote the practice of open science in South Africa through a system of incentives. Since South Africa is constitutionally committed to be an open and democratic society, this approach is preferable to the approach of state control that characterizes the Draft National Policy on Data and Cloud-another data-related policy initiative by the South African government. However, there is room for improvement in the Draft National Open Science Policy. In particular, it should: (a) rely on the right to freedom of scientific research to strengthen the policy; (b) rectify the omission of ownership from its policy analysis; and (c) retain a clear differentiation between human and non-human genetic data. This will ensure that the final policy is clearly anchored in the South African Constitution, and that the principle of "as open as possible, as closed as necessary" can be applied to human genetic data in a legally well informed and accountable way.

SUBMITTER: Thaldar D

PROVIDER: S-EPMC10577200 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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Open science and human genetic data: recommendations on South Africa's Draft National Open Science Policy.

Thaldar Donrich D Gooden Amy A Steytler Michaela M

Frontiers in genetics 20231002

The Draft National Open Science Policy, which was shared by the South African government with stakeholders in 2022, is an encouraging step forward as it aims to promote the practice of open science in South Africa through a system of incentives. Since South Africa is constitutionally committed to be an open and democratic society, this approach is preferable to the approach of state control that characterizes the Draft National Policy on Data and Cloud-another data-related policy i ...[more]

PMID: 37849503

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Project description:BackgroundSouth Africa's National Health Laboratory Service (NHLS), the only clinical laboratory service in the country's public health sector, is an important resource for monitoring public health programmes.ObjectivesWe describe NHLS data quality, particularly patient demographics among infants, and the effect this has on linking multiple test results to a single patient.MethodsRetrospective descriptive analysis of NHLS data from 1st January 2017-1st September 2020 was performed. A validated probabilistic record-linking algorithm linked multiple results to individual patients in lieu of a unique patient identifier. Paediatric HIV PCR data was used to illustrate the effect on monitoring and evaluating a public health programme. Descriptive statistics including medians, proportions and inter quartile ranges are reported, with Chi-square univariate tests for independence used to determine association between variables.ResultsDuring the period analysed, 485 300 007 tests, 98 217 642 encounters and 35 771 846 patients met criteria for analysis. Overall, 15.80% (n = 15 515 380) of all encounters had a registered national identity (ID) number, 2.11% (n = 2 069 785) were registered without a given name, 63.15% (n = 62 020 107) were registered to women and 32.89% (n = 32 304 329) of all folder numbers were listed as either the patient's date of birth or unknown. For infants tested at < 7 days of age (n = 2 565 329), 0.099% (n = 2 534) had an associated ID number and 48.87% (n = 1 253 620) were registered without a given name. Encounters with a given name were linked to a subsequent encounter 40.78% (n = 14 180 409 of 34 775 617) of the time, significantly more often than the 21.85% (n = 217 660 of 996 229) of encounters registered with a baby-derivative name (p-value < 0.001).ConclusionUnavailability and poor capturing of patient demographics, especially among infants and children, affects the ability to accurately monitor routine health programmes. A unique national patient identifier, other than the national ID number, is urgently required and must be available at birth if South Africa is to accurately monitor programmes such as the Prevention of Mother-to-Child Transmission of HIV.

Project description:BackgroundThe number of South African adolescents receiving HIV care and treatment in South Africa is growing. By use of routinely collected laboratory data from South Africa's National HIV Programme, we aimed to quantify the numbers of adolescents accessing HIV care and treatment over time, characterise the role of perinatal infection in these trends, and estimate proportions of adolescents seeking HIV care and antiretroviral therapy (ART) in South Africa's public sector.MethodsWe did a retrospective, descriptive cohort study of children and adolescents aged 1-19 years accessing care in South Africa's public sector HIV treatment programme from 2005 to 2016 with a CD4 cell count or viral load recorded in South Africa's National Health Laboratory Service database. We estimated the total number of children and adolescents entering HIV care with a CD4 cell count or viral load test result by calendar period, as well as the proportion in care and receiving ART with at least one viral load test result. We stratified analyses by gender and by whether the patient entered care at younger than 15 years (probably perinatally infected) or at 15-19 years (probably infected in adolescence).FindingsWe identified 730 882 patients aged 1-19 years at entry to care between Jan 1, 2005, and Dec 31, 2016. 209 205 (54%) of 388 439 patients entering care younger than 15 years and 301 242 (88%) of 342 443 patients entering care aged 15-19 were female. During the study period, the number of virologically monitored patients aged 15-19 years receiving ART increased from 7949 in 2005-08 to 80 918 in 2013-16. 92 783 (66%) of 140 028 patients aged 15-19 years seeking care started ART by 2016, well below UNAID's target of ART for 90% of those diagnosed. We project that the number of adolescents on ART will continue to rise.InterpretationThe many adolescents aged 15-19 years receiving ART reflect the ageing of children entering care at ages 1-14 years, and increases in care-seeking among horizontally infected adolescents aged 15-19 years. However, many adolescents seeking care do not start ART, suggesting an urgent need for interventions to increase uptake of ART and improve services for this population.FundingUS National Institutes of Health, and the President's Emergency Plan for AIDS Relief through the US Agency for International Development.

Project description:BackgroundSince its introduction, telemedicine for patients with chronic diseases has been studied in various clinical settings. However, there is limited evidence of the effectiveness and medical safety of the nationwide adoption of telemedicine.ObjectiveThis study aimed to analyze the effects of telemedicine on chronic diseases during the COVID-19 pandemic under a temporary telemedicine policy in South Korea using national claims data.MethodsHealth insurance claims data were extracted over 2 years: 1 year before (from February 24, 2019, to February 23, 2020) and 1 year after the policy was implemented (from February 24, 2020, to February 23, 2021). We included all patients who used telemedicine at least once in the first year after the policy was implemented and compared them with a control group of patients who never used telemedicine. The comparison focused on health care use; the medication possession ratio (MPR); and admission rates to general wards (GWs), emergency departments (EDs), and intensive care units (ICUs) using difference-in-differences analysis. A total of 4 chronic diseases were targeted: hypertension, diabetes mellitus (DM), chronic obstructive pulmonary disease (COPD), and common mental disorders.ResultsA total of 1,773,454 patients with hypertension; 795,869 patients with DM; 37,460 patients with COPD; and 167,084 patients with common mental disorders were analyzed in this study. Patients diagnosed with hypertension or DM showed increased MPRs without an increase in GW, ED, or ICU admission rates during the policy year. Moreover, patients in the DM group who did not use telemedicine had higher rates of ED, GW, and ICU admissions, and patients in the hypertension group had higher rates of GW or ICU admissions after 1 year of policy implementation. This trend was not evident in COPD and common mental disorders.ConclusionsThe temporary telemedicine policy was effective in increasing medication adherence and reducing admission rates for patients with hypertension and DM; however, the efficacy of the policy was limited for patients with COPD and common mental disorders. Future studies are required to demonstrate the long-term effects of telemedicine policies with various outcome measures reflecting disease characteristics.

Project description:BackgroundResearch out of South Africa estimates the total unmet need for care for those with type 2 diabetes mellitus (diabetes) at 80%. We evaluated the care cascade using South Africa's National Health Laboratory Service (NHLS) database and assessed if HIV infection impacts progression through its stages.MethodsThe cohort includes patients from government facilities with their first glycated hemoglobin A1c (HbA1c) or plasma glucose (fasting (FPG); random (RPG)) measured between January 2012 to March 2015 in the NHLS. Lab-diagnosed diabetes was defined as HbA1c ≥ 6.5%, FPG ≥ 7.0mmol/l, or RPG ≥ 11.1mmol/l. Cascade stages post diagnosis were retention-in-care and glycaemic control (defined as an HbA1c < 7.0% or FPG < 8.0mmol/l or RPG < 10.0mmol/l) over 24-months. We estimated gaps at each stage nationally and by people living with HIV (PLWH) and without (PLWOH).ResultsOf the 373,889 patients tested for diabetes, 43.2% had an HbA1c or blood glucose measure indicating a diabetes diagnosis. Amongst those with lab-diagnosed diabetes, 30.9% were retained-in-care (based on diabetes labs) and 8.7% reached glycaemic control by 24-months. Prevalence of lab-diagnosed diabetes in PLWH was 28.6% versus 47.3% in PLWOH. Among those with lab-diagnosed diabetes, 34.3% of PLWH were retained-in-care versus 30.3% PLWOH. Among people retained-in-care, 33.8% of PLWH reached glycaemic control over 24-months versus 28.6% of PLWOH.ConclusionsIn our analysis of South Africa's NHLS database, we observed that 70% of patients diagnosed with diabetes did not maintain in consistent diabetes care, with fewer than 10% reaching glycemic control within 24 months. We noted a disparity in diabetes prevalence between PLWH and PLWOH, potentially linked to different screening methods. These differences underscore the intricacies in care but also emphasize how HIV care practices could guide better management of chronic diseases like diabetes. Our results underscore the imperative for specialized strategies to bolster diabetes care in South Africa.

Project description:ObjectivesHIV counselling and testing is critical to HIV prevention and treatment efforts. Mass campaigns may be an effective strategy to increase HIV testing in countries with generalized HIV epidemics. We assessed the self-reported uptake of HIV testing among individuals who had never previously tested for HIV, particularly those in high-risk populations, during the period of a national, multisector testing campaign in South Africa (April 2010 and June 2011).DesignThis study was a prospective cohort study.MethodsWe analyzed data from two waves (2010/2011, n=16,893; 2012, n=18,707) of the National Income Dynamics Study, a nationally representative cohort that enabled prospective identification of first-time testers. We quantified the number of adults (15 years and older) testing for the first time nationally. To assess whether the campaign reached previously underserved populations, we examined changes in HIV testing coverage by age, gender, race and province sub-groups. We also estimated multivariable logistic regression models to identify socio-economic and demographic predictors of first-time testing.ResultsOverall, the proportion of adults ever tested for HIV increased from 43.7% (95% confidence interval (CI): 41.48, 45.96) to 65.2% (95% CI: 63.28, 67.10) over the study period, with approximately 7.6 million (95% CI: 6,387,910; 8,782,986) first-time testers. Among black South Africans, the country's highest HIV prevalence sub-group, HIV testing coverage improved among poorer and healthier individuals, thus reducing gradients in testing by wealth and health. In contrast, HIV testing coverage remained lower for men, younger individuals and the less educated, indicating persistent if not widening disparities by gender, age and education. Large geographic disparities in coverage also remained as of 2012.ConclusionsMass provision of HIV testing services can be effective in increasing population coverage of HIV testing. The geographic and socio-economic disparities in programme impacts can help guide best practices for future efforts. These efforts should focus on hard-to-reach populations, including men and less-educated individuals.

Project description:BackgroundChronic kidney disease (CKD) has emerged as a substantial global health challenge, with a marked rise in associated mortality. However, it often goes undetected until advanced stages, particularly in low-income and middle-income countries such as South Africa. We investigated the prevalence and progression of CKD in South Africa, utilising a subset of data from the National Health Laboratory Services Multi-morbidity Cohort.MethodsThis study was a retrospective analysis of adults aged 18-85 years who underwent initial creatinine laboratory testing at government hospitals and clinics from January 2012 to January 2016. CKD was assessed using the Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equation, excluding the race factor, with a cut-off of CKD-EPI<60 mL/min/1.73 m2. Lab-diagnosed CKD was defined as two estimated glomerular filtration rate measurements <60 mL/min/1.73 m2 at least 90 days apart. Cox regression and survival curves were used to estimate HRs and rates of progression.ResultsAmong 6 106 521 adults tested between 2012 and 2016, 1.5% (95% CI 1.4% to 1.5%) were diagnosed with CKD, with the majority in stage 3. Over follow-up (median: 2 years, IQR: 0.8-3.6 years), 28.2% (95% CI 27.7% to 28.6%) of patients diagnosed as stage 3a progressed to a more severe disease state. Among patients who were in stage 3b at diagnosis, 29.6% (95% CI 29.0% to 30.1%) progressed and 33.3% (95% CI 32.5% to 34.1%) of stage 4 patients progressed. We estimated a 48% higher adjusted hazard of CKD progression for individuals with diabetes (adjusted HR 1.48, 95% CI 1.41 to 1.57) compared with those without. Advancing age also increased the risk, particularly for those aged >50 years.ConclusionsThis study underscores the urgency for early detection and management of CKD in South Africa, particularly for high-risk individuals. Strengthening primary healthcare systems and raising CKD awareness are vital for improved patient outcomes and to alleviate the burden on healthcare resources. Early intervention can delay CKD progression, thus reducing the need for costly treatments like dialysis and transplantation.

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Open science and human genetic data: recommendations on South Africa's Draft National Open Science Policy.

Publications

Open science and human genetic data: recommendations on South Africa's <i>Draft National Open Science Policy</i>.

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