South African Medical Research Council Research Articles

Navigating ethical challenges of integrating genomic medicine into clinical practice: Maximising beneficence in precision oncology

The development of gene expression profiling and next-generation sequencing technologies have steered oncogenomics to the forefront of precision medicine. This created a need for harmonious cooperation between clinicians and researchers to increase access to precision oncology, despite multiple implementation challenges being encountered. The aim is to apply personalised treatment strategies early in cancer management, targeting tumour subtypes and actionable gene variants within the individual’s broader clinical risk profile and wellbeing. A knowledge-generating database linked to the South African Medical Research Council’s Genomic Centre has been created for the application of personalised medicine, using an integrated service and research approach. Insights gained from patient experiences related to tumour heterogeneity, access to targeted therapies and incidental findings of pathogenic germline variants in tumour DNA, provided practice-changing evidence for the implementation of a cost-minimisation pathology-supported genetic testing strategy. Integrating clinical care with genomic research through data sharing advances personalised medicine and maximises precision oncology benefits.

Research ethics and artificial intelligence for global health: perspectives from the global forum on bioethics in research

BackgroundThe ethical governance of Artificial Intelligence (AI) in health care and public health continues to be an urgent issue for attention in policy, research, and practice. In this paper we report on central themes related to challenges and strategies for promoting ethics in research involving AI in global health, arising from the Global Forum on Bioethics in Research (GFBR), held in Cape Town, South Africa in November 2022.MethodsThe GFBR is an annual meeting organized by the World Health Organization and supported by the Wellcome Trust, the US National Institutes of Health, the UK Medical Research Council (MRC) and the South African MRC. The forum aims to bring together ethicists, researchers, policymakers, research ethics committee members and other actors to engage with challenges and opportunities specifically related to research ethics. In 2022 the focus of the GFBR was “Ethics of AI in Global Health Research”. The forum consisted of 6 case study presentations, 16 governance presentations, and a series of small group and large group discussions. A total of 87 participants attended the forum from 31 countries around the world, representing disciplines of bioethics, AI, health policy, health professional practice, research funding, and bioinformatics. In this paper, we highlight central insights arising from GFBR 2022.ResultsWe describe the significance of four thematic insights arising from the forum: (1) Appropriateness of building AI, (2) Transferability of AI systems, (3) Accountability for AI decision-making and outcomes, and (4) Individual consent. We then describe eight recommendations for governance leaders to enhance the ethical governance of AI in global health research, addressing issues such as AI impact assessments, environmental values, and fair partnerships.ConclusionsThe 2022 Global Forum on Bioethics in Research illustrated several innovations in ethical governance of AI for global health research, as well as several areas in need of urgent attention internationally. This summary is intended to inform international and domestic efforts to strengthen research ethics and support the evolution of governance leadership to meet the demands of AI in global health research.

Blood RNA biomarkers for tuberculosis screening in people living with HIV before antiretroviral therapy initiation: a diagnostic accuracy study

Undiagnosed tuberculosis remains a major threat for people living with HIV. Multiple blood transcriptomic biomarkers have shown promise for tuberculosis diagnosis. We sought to evaluate their diagnostic accuracy and clinical utility for systematic pre-antiretroviral therapy (ART) tuberculosis screening. We enrolled consecutive adults (age ≥18 years) referred to start ART at a community health centre in Cape Town, South Africa, irrespective of symptoms. Sputa were obtained (using induction if required) for two liquid cultures. Whole-blood RNA samples underwent transcriptional profiling using a custom Nanostring gene panel. We measured the diagnostic accuracy of seven candidate RNA signatures (one single gene biomarker [BATF2] and six multigene biomarkers) for the reference standard of Mycobacterium tuberculosis culture status, using area under the receiver-operating characteristic curve (AUROC) analysis, and sensitivity and specificity at prespecified thresholds (two standard scores above the mean of healthy controls; Z2). Clinical utility was assessed by calculating net benefit in decision curve analysis. We compared performance with C-reactive protein (CRP; threshold ≥5 mg/L), WHO four-symptom screen (W4SS), and the WHO target product profile for tuberculosis triage tests. A total of 707 people living with HIV (407 [58%] female and 300 [42%] male) were included, with median CD4 count 306 cells per mm3 (IQR 184-486). Of 676 participants with available sputum culture results, 89 (13%) had culture-confirmed tuberculosis. The seven RNA signatures were moderately to highly correlated (Spearman rank coefficients 0·42-0·93) and discriminated tuberculosis culture positivity with similar AUROCs (0·73-0·80), but none statistically better than CRP (AUROC 0·78, 95% CI 0·72-0·83). Diagnostic accuracy was similar across CD4 count strata, but lower among participants with negative W4SS (AUROCs 0·56-0·65) compared with positive (AUROCs 0·75-0·84). The RNA biomarker with the highest AUROC point estimate was a four-gene signature (Suliman4; AUROC 0·80, 95% CI 0·75-0·86), with sensitivity 83% (95% CI 74-90) and specificity 59% (55-63) at the Z2 threshold. In decision curve analysis, Suliman4 and CRP had similar clinical utility to guide confirmatory tuberculosis testing, but both had higher net benefit than W4SS. In exploratory analyses, an approach combining CRP (≥5 mg/L) and Suliman4 (≥Z2) had sensitivity of 80% (70-87), specificity of 70% (66-74), and higher net benefit than either biomarker alone. RNA biomarkers showed better clinical utility to guide confirmatory tuberculosis testing for people living with HIV before ART initiation than symptom-based screening, but their performance did not exceed that of CRP and fell short of WHO recommended targets. Interferon-independent approaches might be required to improve accuracy of host-response biomarkers to support tuberculosis screening before ART initiation. South African Medical Research Council, European and Developing Countries Clinical Trials Partnership 2, National Institutes of Health National Institute of Allergy and Infectious Diseases, The Wellcome Trust, National Institute for Health and Care Research, Royal College of Physicians London.

Point-of-care C-reactive protein and Xpert MTB/RIF Ultra for tuberculosis screening and diagnosis in unselected antiretroviral therapy initiators: a prospective, cross-sectional, diagnostic accuracy study

Tuberculosis, a major cause of death in people living with HIV, remains challenging to diagnose. Diagnostic accuracy data are scarce for promising triage and confirmatory tests such as C-reactive protein (CRP), sputum and urine Xpert MTB/RIF Ultra (Xpert Ultra), and urine Determine TB LAM Ag (a lateral flow lipoarabinomannan [LF-LAM] test), without symptom selection. We evaluated novel triage and confirmatory tests in ambulatory people with HIV initiating antiretroviral therapy (ART). 897 ART-initiators were recruited irrespective of symptoms and sputum induction offered. For triage (n=800), we evaluated point-of-care blood-based CRP testing, compared with the WHO-recommended four-symptom screen (W4SS). For sputum-based confirmatory testing (n=787), we evaluated Xpert Ultra versus Xpert MTB/RIF (Xpert). For urine-based confirmatory testing (n=732), we evaluated Xpert Ultra and LF-LAM. We used a sputum culture reference standard. 463 (52%) of 897 participants were female. The areas under the receiver operator characteristic curves for CRP was 0·78 (95% CI 0·73-0·83) and for number of W4SS symptoms was 0·70 (0·64-0·75). CRP (≥10 mg/L) had similar sensitivity to W4SS (77% [95% CI 68-85; 80/104] vs 77% [68-85; 80/104]; p>0·99] but higher specificity (64% [61-68; 445/696] vs 48% [45-52; 334/696]; p<0·0001]; reducing unnecessary confirmatory testing by 138 (95% CI 117-160) per 1000 people and number-needed-to-test from 6·91 (95% CI 6·25-7·81) to 4·87 (4·41-5·51). Sputum samples with Xpert Ultra, which required induction in 49 (31%) of 158 of people (95% CI 24-39), had higher sensitivity than Xpert (71% [95% CI 61-80; 74/104] vs 56% [46-66; 58/104]; p<0·0001). Of the people with one or more confirmatory sputum or urine test results that were positive, the proportion detected by Xpert Ultra increased from 45% (26-64) to 66% (46-82) with induction. Programmatically done haemoglobin, triage test combinations, and urine tests showed comparatively worse results. CRP is a more specific triage test than W4SS in those initiating ART. Sputum induction improves diagnostic yield. Sputum samples with Xpert Ultra is a more accurate confirmatory test than with Xpert. South African Medical Research Council, EDCTP2, US National Institutes of Health-National Institute of Allergy and Infectious Diseases.

Determinants of lung function development from birth to age 5 years: an interrupted time series analysis of a South African birth cohort

Early life is a key period that determines long-term health. Lung development in childhood predicts lung function attained in adulthood and morbidity and mortality across the life course. We aimed to assess the effect of early-life lower respiratory tract infection (LRTI) and associated risk factors on lung development from birth to school age in a South African birth cohort. We prospectively followed children enrolled in a population-based cohort from birth (between March 5, 2012 and March 31, 2015) to age 5 years with annual lung function assessment. Data on multiple early-life exposures, including LRTI, were collected. The effect of early-life risk factors on lung function development from birth to age 5 years was assessed using the Generalised Additive Models for Location, Scale and Shape and Interrupted Time Series approach. 966 children (475 [49·2%] female, 491 [50·8%] male) had lung function measured with oscillometry, tidal flow volume loops, and multiple breath washout. LRTI occurred in 484 (50·1%) children, with a median of 2·0 LRTI episodes (IQR 1·0-3·0) per child. LRTI was independently associated with altered lung function, as evidenced by lower compliance (0·959 [95% CI 0·941-0·978]), higher resistance (1·028 [1·016-1·041]), and higher respiratory rate (1·018 [1·063-1·029]) over 5 years. Additional impact on lung function parameters occurred with each subsequent LRTI. Respiratory syncytial virus (RSV) LRTI was associated with lower expiratory flow ratio (0·97 [0·95-0·99]) compared with non-RSV LRTI. Maternal factors including allergy, smoking, and HIV infection were also associated with altered lung development, as was preterm birth, low birthweight, female sex, and coming from a less wealthy household. Public health interventions targeting LRTI prevention, with RSV a priority, are vital, particularly in low-income and middle-income settings. UK Medical Research Council Grant, The Wellcome Trust, The Bill & Melinda Gates Foundation, US National Institutes of Health Human Heredity and Health in Africa, South African Medical Research Council, Hungarian Scientific Research Fund, and European Respiratory Society.

1498. Geographic differences in weight change on dolutegravir: a prospective cohort study

Abstract Background People with HIV (PWH) on integrase inhibitors may be at increased risk of excess weight gain, but it is unclear if this risk is consistent across settings. Our study objective was to compare weight change over 48 weeks among PWH in Uganda and South Africa.Figure 1.Mean weight change (kg) over 48 weeks among DISCO participants overall (A), among men (B), and among women (C). Methods The Population Effectiveness of Dolutegravir Implementation in Sub-Saharan Africa (DISCO) study is a prospective observational cohort of PWH in routine clinical care at public-sector HIV clinics in Uganda and South Africa. Inclusion criteria were as follows: PWH &amp;gt;18 years old, on NNRTI-based first-line ART for &amp;gt;6 months, and switched to tenofovir disoproxil fumarate, lamivudine, and dolutegravir) by clinic staff. We measured the primary outcomes of weight (in kilograms [kg]) and waist circumference (WC, in centimeters [cm]) at enrollment, 24 weeks, and 48 weeks after switch. The primary outcomes were (1) weight change (kg) and (2) change in WC (cm). We used a linear mixed-effect regression model, adjusted for age, sex, education, duration on ART, and the interaction of study site and visit, to estimate weight. Results 428 individuals in Uganda and 387 in South Africa had data available. The mean weight change over 48 weeks was 0.6 kg [95% CI: 0.1-1.0] in Uganda compared to 2.9 kg [2.4-3.4] in South Africa (p&amp;lt; 0.001); men had significantly smaller mean weight changes than women did in both countries (Figure 1). After adjustment, PWH in South Africa gained significantly more weight than those in Uganda. In participants with available waist data (277 in Uganda and 402 in South Africa), the mean change in WC was significantly greater among those in South Africa (2.3 cm [1.4-3.2]) than those in Uganda (0.8 cm [0.0-1.5]) (p&amp;lt; 0.017). Conclusion PWH in South Africa experienced greater weight gain than in Uganda, suggesting substantial heterogeneity in this risk across settings. Strategies to address obesity risk in PWH should account for regionality. Disclosures W D Francois Venter, MD, FCP, PhD, Gilead Sciences: Grant/Research Support|South African Medical Research Council: Grant/Research Support|Unitaid: Grant/Research Support|USAID: Grant/Research Support|ViiV Healthcare: Grant/Research Support Mark J Siedner, MD, MPH, Viiv Healthcare: Grant/Research Support

Bedaquiline resistance in patients with drug-resistant tuberculosis in Cape Town, South Africa: a retrospective longitudinal cohort study

Bedaquiline is a life-saving tuberculosis drug undergoing global scale-up. People at risk of weak tuberculosis drug regimens are a priority for novel drug access despite the potential source of Mycobacterium tuberculosis-resistant strains. We aimed to characterise bedaquiline resistance in individuals who had sustained culture positivity during bedaquiline-based treatment. We did a retrospective longitudinal cohort study of adults (aged ≥18 years) with culture-positive pulmonary tuberculosis who received at least 4 months of a bedaquiline-containing regimen from 12 drug-resistant tuberculosis treatment facilities in Cape Town, South Africa, between Jan 20, 2016, and Nov 20, 2017. Sputum was programmatically collected at baseline (ie, before bedaquiline initiation) and each month to monitor treatment response per the national algorithm. The last available isolate from the sputum collected at or after 4 months of bedaquiline was designated the follow-up isolate. Phenotypic drug susceptibility testing for bedaquiline was done on baseline and follow-up isolates in MGIT960 media (WHO-recommended critical concentration of 1 μg/mL). Targeted deep sequencing for Rv0678, atpE, and pepQ, as well as whole-genome sequencing were also done. In total, 40 (31%) of 129 patients from an estimated pool were eligible for this study. Overall, three (8%) of 38 patients assessable by phenotypic drug susceptibility testing for bedaquiline had primary resistance, 18 (47%) gained resistance (acquired or reinfection), and 17 (45%) were susceptible at both baseline and follow-up. Several Rv0678 and pepQ single-nucleotide polymorphisms and indels were associated with resistance. Although variants occurred in Rv0676c and Rv1979c, these variants were not associated with resistance. Targeted deep sequencing detected low-level variants undetected by whole-genome sequencing; however, none were in genes without variants already detected by whole-genome sequencing. Patients with baseline fluoroquinolone resistance, clofazimine exposure, and four or less effective drugs were more likely to have bedaquiline-resistant gain. Resistance gain was primarily due to acquisition; however, some reinfection by resistant strains occurred. Bedaquiline-resistance gain, for which we identified risk factors, was common in these programmatically treated patients with sustained culture positivity. Our study highlights risks associated with implementing life-saving new drugs and shows evidence of bedaquiline-resistance transmission. Routine drug susceptibility testing should urgently accompany scale-up of new drugs; however, rapid drug susceptibility testing for bedaquiline remains challenging given the diversity of variants observed. Doris Duke Charitable Foundation, US National Institute of Allergy and Infectious Diseases, South African Medical Research Council, National Research Foundation, Research Foundation Flanders, Stellenbosch University Faculty of Medicine Health Sciences, South African National Research Foundation, Swiss National Science Foundation, and Wellcome Trust.

Alcohol policy framing in South Africa during the early stages of COVID-19: using extraordinary times to make an argument for a new normal

IntroductionPublic health and alcohol industry actors compete to frame alcohol policy problems and solutions. Little is known about how sudden shifts in the political context provide moments for policy actors to re-frame alcohol-related issues. South Africa’s temporary bans on alcohol sales during the COVID-19 pandemic offered an opportunity to study this phenomenon.MethodsWe identified Professor Charles Parry from the South African Medical Research Council as a key policy actor. Parry uses a Twitter account primarily to comment on alcohol-related issues in South Africa. We harvested his tweets posted from March 18 to August 31, 2020, coinciding with the first two alcohol sales bans. We conducted a thematic analysis of the tweets to understand how Parry framed alcohol policy evidence and issues during these ‘extraordinary times.’ResultsParry underlined the extent of alcohol-related harm during ‘normal times’ with scientific evidence and contested industry actors’ efforts to re-frame relevant evidence in a coherent and well-constructed argument. Parry used the temporary sales restrictions to highlight the magnitude of the health and social harms resulting from alcohol consumption, particularly trauma, rather than the COVID-19 transmission risks. Parry portrayed the sales ban as a policy learning opportunity (or ‘experiment’) for South Africa and beyond.ConclusionsCrisis conditions can provide new openings for public health (and industry) actors to make salient particular features of alcohol and alcohol policy evidence.

The met and unmet health needs for HIV, hypertension, and diabetes in rural KwaZulu-Natal, South Africa: analysis of a cross-sectional multimorbidity survey

The convergence of infectious diseases and non-communicable diseases in South Africa is challenging to health systems. In this analysis, we assessed the multimorbidity health needs of individuals and communities in rural KwaZulu-Natal and established a framework to quantify met and unmet health needs for individuals living with infectious and non-communicable diseases. We analysed data collected between May 25, 2018, and March 13, 2020, from participants of a large, community-based, cross-sectional multimorbidity survey (Vukuzazi) that offered community-based HIV, hypertension, and diabetes screening to all residents aged 15 years or older in a surveillance area in the uMkhanyakude district in KwaZulu-Natal, South Africa. Data from the Vukuzazi survey were linked with data from demographic and health surveillance surveys with a unique identifier common to both studies. Questionnaires were used to assess the diagnosed health conditions, treatment history, general health, and sociodemographic characteristics of an individual. For each condition (ie, HIV, hypertension, and diabetes), individuals were defined as having no health needs (absence of condition), met health needs (condition that is well controlled), or one or more unmet health needs (including diagnosis, engagement in care, or treatment optimisation). We analysed met and unmet health needs for individual and combined conditions and investigated their geospatial distribution. Of 18 041 participants who completed the survey (12 229 [67·8%] were female and 5812 [32·2%] were male), 9898 (54·9%) had at least one of the three chronic diseases measured. 4942 (49·9%) of these 9898 individuals had at least one unmet health need (1802 [18·2%] of 9898 needed treatment optimisation, 1282 [13·0%] needed engagement in care, and 1858 [18·8%] needed a diagnosis). Unmet health needs varied by disease; 1617 (93·1%) of 1737 people who screened positive for diabetes, 2681 (58·2%) of 4603 people who screened positive for hypertension, and 1321 (21·7%) of 6096 people who screened positive for HIV had unmet health needs. Geospatially, met health needs for HIV were widely distributed and unmet health needs for all three conditions had specific sites of concentration; all three conditions had an overlapping geographical pattern for the need for diagnosis. Although people living with HIV predominantly have a well controlled condition, there is a high burden of unmet health needs for people living with hypertension and diabetes. In South Africa, adapting current, widely available HIV care services to integrate non-communicable disease care is of high priority. Fogarty International Center and the National Institutes of Health, the Bill & Melinda Gates Foundation, the South African Department of Science and Innovation, the South African Medical Research Council, the South African Population Research Infrastructure Network, and the Wellcome Trust. For the isiZulu translation of the abstract see Supplementary Materials section.

Safety of COVID-19 booster dose: is the juice worth the squeeze?

Safety of COVID-19 booster dose: is the juice worth the squeeze?

Effect of compensatory evolution in the emergence and transmission of rifampicin-resistant Mycobacterium tuberculosis in Cape Town, South Africa: a genomic epidemiology study

Experimental data show that drug-resistance-conferring mutations are often associated with a decrease in the replicative fitness of bacteria in vitro, and that this fitness cost can be mitigated by compensatory mutations; however, the role of compensatory evolution in clinical settings is less clear. We assessed whether compensatory evolution was associated with increased transmission of rifampicin-resistant tuberculosis in Khayelitsha, Cape Town, South Africa. We did a genomic epidemiological study by analysing available M tuberculosis isolates and their associated clinical data from individuals routinely diagnosed with rifampicin-resistant tuberculosis in primary care and hospitals in Khayelitsha, Cape Town, South Africa. Isolates were collected as part of a previous study. All individuals diagnosed with rifampicin-resistant tuberculosis and with linked biobanked specimens were included in this study. We applied whole-genome sequencing, Bayesian reconstruction of transmission trees, and phylogenetic multivariable regression analysis to identify individual and bacterial factors associated with the transmission of rifampicin-resistant M tuberculosis strains. Between Jan 1, 2008, and Dec 31, 2017, 2161 individuals were diagnosed with multidrug-resistant or rifampicin-resistant tuberculosis in Khayelitsha, Cape Town, South Africa. Whole-genome sequences were available for 1168 (54%) unique individual M tuberculosis isolates. Compensatory evolution was associated with smear-positive pulmonary disease (adjusted odds ratio 1·49, 95% CI 1·08-2·06) and a higher number of drug-resistance-conferring mutations (incidence rate ratio 1·38, 95% CI 1·28-1·48). Compensatory evolution was also associated with increased transmission of rifampicin-resistant disease between individuals (adjusted odds ratio 1·55; 95% CI 1·13-2·12), independent of other patient and bacterial factors. Our findings suggest that compensatory evolution enhances the in vivo fitness of drug-resistant M tuberculosis genotypes, both within and between patients, and that the in vitro replicative fitness of rifampicin-resistant M tuberculosis measured in the laboratory correlates with the bacterial fitness measured in clinical settings. These results emphasise the importance of enhancing surveillance and monitoring efforts to prevent the emergence of highly transmissible clones capable of rapidly accumulating new drug resistance mutations. This concern becomes especially crucial at present, because treatment regimens incorporating novel drugs are being implemented. Funding for this study was provided by a Swiss and South Africa joint research award (grant numbers 310030_188888, CRSII5_177163, and IZLSZ3_170834), the European Research Council (grant number 883582), and a Wellcome Trust fellowship (to HC; reference number 099818/Z/12/Z). ZS-D was funded through a PhD scholarship from the South African National Research Foundation and RMW was funded through the South African Medical Research Council.

An intergenerational life-course approach to address early childhood obesity and adiposity: the Healthy Life Trajectories Initiative (HeLTI)

BackgroundInteractions between genes and early-life exposures during conception, fetal life, infancy, and early childhood have been shown to affect an individual's health later in life. Maternal undernutrition and obesity, gestational diabetes, and impaired growth in utero and in early life are associated with adiposity and overweight and obesity in childhood, which are risk factors for poor health trajectories and non-communicable diseases. In Canada, China, India, and South Africa, 10–30% of children aged 5–16 years are overweight or obese. MethodsThe application of developmental origins of health and disease principles offers a novel approach to prevention of overweight and obesity and reduction of adiposity by delivering integrated interventions across the life course, starting before conception and continuing through early childhood. The Healthy Life Trajectories Initiative (HeLTI) was established in 2017 through a unique collaboration between national funding agencies in Canada, China, India, South Africa, and WHO. The aim of HeLTI is to evaluate the effect of an integrated four-phase intervention starting preconceptionally and continuing through pregnancy, infancy, and early childhood on reducing childhood adiposity (fat mass index) and overweight and obesity, and optimising early child development, nutrition, and other healthy behaviours. FindingsApproximately 22 000 women are being recruited in Shanghai (China), Mysore (India), Soweto (South Africa), and across various provinces of Canada. Women who conceive (an expected 10 000) and their children will be followed up until the child reaches the age of 5 years. InterpretationHeLTI has harmonised the intervention, measures, tools, biospecimen collection, and analysis plans for the trial to be run across four countries. HeLTI will help establish whether an intervention aimed at addressing maternal health behaviours, nutrition, and weight; providing psychosocial support to reduce maternal stress and prevent mental illness; optimising infant nutrition, physical activity, and sleep; and promoting parenting skills can reduce the intergenerational risk of excess childhood adiposity and overweight and obesity across diverse settings. FundingCanadian Institutes of Health Research; National Science Foundation of China; Department of Biotechnology, India; and South African Medical Research Council.

Developing Indicators to Measure the Implementation of the Western Cape Alcohol Harms Reduction Strategy in South Africa

This manuscript describes a process to develop a set of indicators to monitor and evaluate the implementation of the Western Cape Alcohol-Related Harms Reduction (AHR) White Paper in South Africa and provide a final set of indicators. Drawing on the framework in Andréasson et al. (2009), a logic model with categories and types of indicators (i.e. prevention, determinants, consumption, and alcohol-related harms) was used to develop an initial set of 255 indicators. The methodological process followed involved a) scoping of a large electronic database maintained by the South African Medical Research Council, b) a comprehensive literature review and, c) reaching out to18 international key informants. Iterative communications with stakeholders from diverse government entities via email, telephone calls and individual and multi-person face-to-face meetings, together with a consensus process involving the study team was used to refine the indicators. The final set included 176 indicators; 108, (61.4%) of these were “core” indicators, and 68 (38.6%) were “expanded” indicators, meaning they added to the core indicators in given areas which would be useful to have but are of a lower priority or are likely to be less easy to obtain. Of the core indicators, 45 (42.4%) were deemed by policy makers/researchers in the Premier’s office as “high-level indicators,” denoting that they were the most essential. This manuscript demonstrates that it is possible to develop evidence-based, location-specific indicators to evaluate policy implementation.

Pregnancy and neonatal safety outcomes of timing of initiation of daily oral tenofovir disoproxil fumarate and emtricitabine pre-exposure prophylaxis for HIV prevention (CAP016): an open-label, randomised, non-inferiority trial

The safety of tenofovir disoproxil fumarate and emtricitabine as pre-exposure prophylaxis (PrEP) in pregnant women not living with HIV is uncertain. We aimed to compare pregnancy and neonatal outcomes in women exposed and not exposed to PrEP during pregnancy. In this single-site, open-label, randomised, non-inferiority trial in Durban, South Africa, we evaluated pregnancy and neonatal outcomes in pregnant women aged 18 years or older, not living with HIV, and at 14-28 weeks' gestation at the time of enrolment. Eligible participants were randomly assigned (1:1) using a computer-generated permuted block (block size of ten) randomisation list to immediate initiation or deferred initiation of PrEP until breastfeeding cessation. Participants in the immediate PrEP group received a monthly supply of once daily oral tenofovir disoproxil fumarate 300 mg and emtricitabine 200 mg. Participants in the deferred PrEP group received standard of care for HIV prevention. The primary outcomes were the occurrence of preterm live birth (<37 weeks gestational age) and very preterm birth (<34 weeks gestational age) determined by menstrual dating, low birthweight (<2500 g), very low birthweight (<1500 g), stillbirth (≥20 weeks gestational age), and small for gestational age (birthweight less than the tenth percentile). Post-natal safety outcomes will be reported elsewhere. We used binomial regression models to estimate risk differences and two-sided 90% CIs. Immediate PrEP was non-inferior to deferred PrEP if the upper bound of the 90% CI of the risk difference was less than the upper predefined non-inferiority margin for preterm birth (7·5%), very preterm birth (2·6%), low birthweight (5·5%), very low birthweight (1·2%), stillbirth (1·0%), and small for gestational age (3·7%). All outcomes were analysed in the intention-to-treat population. This study is registered with ClinicalTrials.gov, NCT3227731. Between Sept 25, 2017, and Dec 6, 2019, we screened 693 women, of whom 540 were randomly assigned to immediate PrEP (n=271) or deferred PrEP (n=269). The median gestational age was 19 weeks (IQR 15-23 for immediate PrEP and 16-23 for deferred PrEP). The risk difference between the immediate PrEP group and the deferred PrEP group for preterm birth was -4·7% (90% CI -10·7 to 1·2; immediate PrEP was non-inferior), for very preterm birth was 0·6% (-3·4 to 4·6; upper limit exceeded the non-inferiority margin), for low birthweight was 2·5% (-1·6 to 6·6; upper limit exceeded the non-inferiority margin), for very low birthweight was 0% (-1·4 to 1·4; upper limit exceeded the non-inferiority margin), for stillbirth was 1·2% (-1·5 to 3·8; upper limit exceeded the non-inferiority margin), and for small for gestational age was 0·9% (-1·2 to 2·9; immediate PrEP was non-inferior). In our study, PrEP was not associated with preterm birth or small for gestational age infants. Our data support the use of tenofovir disoproxil fumarate and emtricitabine in pregnancy and our reassuring findings can be used to allay safety concerns among pregnant women. South African Medical Research Council and Gilead Sciences.

“Respiratory Syncytial Viruses (RSV) Infection in Children”: A Scientometric Analysis of Global Publications during 2002-21

International Journal of Medicine and Public Health,2022,12,4,156-164.DOI:10.5530/ijmedph.2021.4.29Published:January 2023Type:Review Article“Respiratory Syncytial Viruses (RSV) Infection in Children”: A Scientometric Analysis of Global Publications during 2002-21BM Gupta, Manish Mohan Gore, Atul Gupta, and Avadhesh Kumar Patel BM Gupta1,*, Manish Mohan Gore2, Atul Gupta3, Avadhesh Kumar Patel4 1Formerly with CSIR-NISTADS, New Delhi, INDIA. 2National Institute of Science Communication & Policy Research, New Delhi, INDIA. 3Dr. Rajendra Prasad Government Medical College, Kangra at Tanda, Himachal Pradesh, INDIA. 4Banaras Hindu University, Department of Library and Information Science, Varanasi, Uttar Pradesh, INDIA. Abstract:The study reviewed the publication growth and identified key players and traced the evolution of research themes on “RSV Infection in Children”. Using Scopus database, a keyword search was undertaken, which yielded 917 research records during 2002 to 2021. The retrieved research data was analyzed using a bibliometric analysis techniques and MS-Excel software. The co-authorship network visualization of authors, organizations and countries and cooccurrence network visualization of all keywords are visualized using VOSviewer software. The 917 papers were written by 4902 authors employed at 710 organizations based in 104 countries/territories and were published in 273 journals in the field. The top journals ranked by publication productivity were Pediatric Infectious Disease Journal, Journal of Infectious Diseases and PLOS One and by citation impact per paper were American Journal of Respiratory and Critical Care Medicine, Infectious Diseases and Therapy and Journal of Pediatrics. Authors from countries contributed the most publications were USA, U.K. and China, and those contributing the most impactful publications were France, Japan and Spain. Center for Disease Control and Prevention, USA, University Medical Center Utrecht, Netherlands, and MedImmune LLC Inc. USA are the three organizations with the most productive publications and Kenya Medical Research Institute, South African Medical Research Council, South Africa and University of Witwatersrand, Johannesburg, South Africa are the organizations with most impactful organizations. Authors contributing the most were O. Ramilo (USA), E.A.F. Simoes (USA) and R.A. Karron (USA) and the most impactful papers were D.J. Nokes (U.K.), K.M. Edwards (USA) and C.B. Hall (USA). Based on collaboration network maps, there were significant collaborations based on common interests. According to the keyword co-occurrence diagram, the most frequent keywords are “Respiratory Synctial Virus”, “Respiratory Syncytial Pneumovirus”, “Human Respiratory Syncytial Virus”, “Hospitalization”, “Respiratory Tract Infection” and “Brochiolitis”. Analysis of 44 significant keywords showed that the research was distributed into 4 clusters, which indicates the most significant areas of current research. With the acceleration of the child diseases, the number of articles on “RSV in Children” is increasing rapidly. Bibliometric analysis of global research in this area for the last 20 years can provide useful information and meaningful reference to funding agencies and researchers, enabling them to explore current research status and identify the future areas and hotspots. Keywords:Bibliometrics., Children, Global publications, Respiratory Syncytial Viruses Infection, Respiratory Virus, RSV Infection, scientometricsView:PDF (1.59 MB)

Early childhood wheezing phenotypes and determinants in a South African birth cohort: longitudinal analysis of the Drakenstein Child Health Study

Developmental trajectories of childhood wheezing in low-income and middle-income countries (LMICs) have not been well described. We aimed to derive longitudinal wheeze phenotypes from birth to 5 years in a South African birth cohort and compare those with phenotypes derived from a UK cohort. We used data from the Drakenstein Child Health Study (DCHS), a longitudinal birth cohort study in a peri-urban area outside Cape Town, South Africa. Pregnant women (aged ≥18 years) were enrolled during their second trimester at two public health clinics. We followed up children from birth to 5 years to derive six multidimensional indicators of wheezing (including duration, temporal sequencing, persistence, and recurrence) and applied Partition Around Medoids clustering to derive wheeze phenotypes. We compared phenotypes with a UK cohort (the Avon Longitudinal Study of Parents and Children [ALSPAC]). We investigated associations of phenotypes with early-life exposures, including all-cause lower respiratory tract infection (LRTI) and virus-specific LRTI (respiratory syncytial virus, rhinovirus, adenovirus, influenza, and parainfluenza virus) up to age 5 years. We investigated the association of phenotypes with lung function at 6 weeks and 5 years. Between March 5, 2012, and March 31, 2015, we enrolled 1137 mothers and there were 1143 livebirths. Four wheeze phenotypes were identified among 950 children with complete data: never (480 children [50%]), early transient (215 children [23%]), late onset (104 children [11%]), and recurrent (151 children [16%]). Multivariate adjusted analysis indicated that LRTI and respiratory syncytial virus-LRTI, but not other respiratory viruses, were associated with increased risk of recurrent wheeze (odds ratio [OR] 2·79 [95% CI 2·05-3·81] for all LTRIs; OR 2·59 [1·30-5·15] for respiratory syncytial virus-LRTIs). Maternal smoking (1·88 [1·12-3·02]), higher socioeconomic status (2·46 [1·23-4·91]), intimate partner violence (2·01 [1·23-3·29]), and male sex (2·47 [1·50-4·04]) were also associated with recurrent wheeze. LRTI and respiratory syncytial virus-LRTI were also associated with early transient and late onset clusters. Wheezing illness architecture differed between DCHS and ALSPAC; children included in ALSPAC in the early transient cluster wheezed for a longer period before remission and late-onset wheezing started at an older age, and no persistent phenotype was identified in DCHS. At 5 years, airway resistance was higher in children with early or recurrent wheeze compared with children who had never wheezed. Airway resistance increased from 6 weeks to 5 years among children with recurrent wheeze. Effective strategies to reduce maternal smoking and psychosocial stressors and new preventive interventions for respiratory syncytial virus are urgently needed to optimise child health in LMICs. UK Medical Research Council; The Bill & Melinda Gates Foundation; National Institutes of Health Human Heredity and Health in Africa; South African Medical Research Council; Wellcome Trust.

Durability of ChAdOx1 nCoV-19 (AZD1222) vaccine and hybrid humoral immunity against variants including omicron BA.1 and BA.4 6 months after vaccination (COV005): a post-hoc analysis of a randomised, phase 1b–2a trial

BackgroundCOVID-19 vaccine rollout is lagging in Africa, where there has been a high rate of SARS-CoV-2 infection. We aimed to evaluate the effect of SARS-CoV-2 infection before vaccination with the ChAdOx-nCoV19 (AZD1222) vaccine on antibody responses through to 180 days.MethodsWe did an unmasked post-hoc immunogenicity analysis after the first and second doses of AZD1222 in a randomised, placebo-controlled, phase 1b–2a study done in seven locations in South Africa. AZD1222 recipients who were HIV-uninfected, were stratified into baseline seropositive or seronegative groups using the serum anti-nucleocapsid (anti-N) immunoglobulin G (IgG) electroluminescence immunoassay to establish SARS-CoV-2 infection before the first dose of AZD1222. Binding IgG to spike (anti-S) and receptor binding domain (anti-RBD) were measured before the first dose (day 0), second dose (day 28), day 42, and day 180. Neutralising antibody (NAb) against SARS-CoV-2 variants D614G, beta, delta, gamma, and A.VOI.V2, and omicron BA1 and BA.4 variants, were measured by pseudovirus assay (day 28, day 42, and day 180). This trial is registered with ClinicalTrials.gov, NCT04444674, and the Pan African Clinicals Trials Registry, PACTR202006922165132.FindingsOf 185 individuals who were randomly assigned to AZD1222, we included 91 individuals who were baseline seropositive and 58 who were baseline seronegative, in the final analysis. In the seropositive group, there was little change of anti-S IgG (and anti-RBD IgG) or neutralising antibody (NAb) titres at day 42 compared with at day 28. Anti-S (and anti-RBD) IgG geometric mean concentrations (GMCs) were higher throughout in the seropositive compared with the seronegative group, including at day 180 (GMCs 517·8 [95% CI 411·3–651·9] vs 82·1 [55·2–122·3] BAU/mL). Also D614G NAb geometric mean titres (GMTs) were higher in the seropositive group than the seronegative group, as was the percentage with titres of at least 185 (80% putative risk reduction threshold [PRRT] against wild-type–alpha COVID-19), including at day 180 (92·0% [74·0–99·0] vs 18·2% [2·3–51·8). Similar findings were observed for beta, A.VOI.V2, and gamma. For delta, BA.1, and BA.4, NAb GMTs and the proportion with titres above the PRRT were substantially higher in the seropositive compared with seronegative group at day 28 and day 42, but no longer differed between the groups by day 180.InterpretationA single dose of AZD1222 in the general African population, where COVID-19 vaccine coverage is low and SARS-CoV-2 seropositivity is 90%, could enhance the magnitude and quality of antibody responses to SARS-CoV-2.FundingThe Bill & Melinda Gates Foundation, the South African Medical Research Council, the UK Research and Innovation, the UK National Institute for Health Research, and the South African Medical Research Council.TranslationFor the Zulu translation of the abstract see Supplementary Materials section.

The clinical and biochemical effects of atrial fibrillation on heart failure with reduced ejection fraction; a sub-saharan African perspective

Abstract Background Sub Saharan Africa (SSA) has seen one of the sharpest increases in cardiovascular disease-related mortality. This increase is evidenced by a growing burden of heart failure and atrial fibrillation (AF) risk factors. Atrial fibrillation is a common comorbidity of heart failure with reduced ejection fraction (HFrEF) which predisposes to an increased risk of morbidity and mortality. Studies done in high income countries (HIC) suggest that there may be an essential role for ethnic differences. However, in the absence of accurate epidemiological data in Sub-Saharan Africa, this cannot be proven. To date, there has never been a prospective systematic description of patients with HFrEF/AF and HFrEF/sinus rhythm (SR). Aim Our study aimed to describe the clinical and biochemical profile of patients with HFrEF/AF and HFrEF/SR in a Sub-Saharan African cohort. Methods The study was conducted inthe division of our Academic Hospital in South Africa. We enrolled 141 patients, consecutively, with HFrEF. Baseline clinical characteristics and exploratory biomarkers were recorded. All participants underwent comprehensive echocardiography. Novel left atrial strain was measured using 2D-speckle tracking echocardiography. These values were compared between patients in SR and in AF. Results The prevalence of AF was 21.38%. Hypertensive heart disease was the leading cause of HFrEF (36%). HFrEF/AF patients were significantly older (66.7±11.9) than those in SR (53.7±14.4) (p=0.000) with significantly different racial proportions (p=0.001). Coronary artery disease was prevalent in patients with HFrEF/AF. Patients with HFrEF/AF had significantly lower Kansas City Cardiomyopathy Questionnaire scores (29.83±15.27) compared to those in SR (44.26±16.30) (p=0.000) as well as worsening functional class (NYHA III–IV; 64.3% vs 22.7%, p=0.000). Measured levels of sST2 were greater in HFrEF/AF patients 40.45ng/mL (17.6–68.6) vs 20.8 (7.9–44.0) in HFrEF/SR (p=0.031). Patients with HFrEF/AF had a significantly greater left atrial volume (ml) (83.9 [64–99.9]) than those with HFrEF/SR (61.53±25.46) (p=0.038). Left atrial strain reservoir function (%) was significantly lower in patients with HFrEF/AF (29.00±13.60) compared to those with HFrEF/SR (41.56±15.46) (p=0.0004) Conclusion Our findings demonstrate that patients with HFrEF/AF are older than those in SR but much younger compared to patients in HICs. Hypertensive heart disease is a major cause of HFrEF in South Africa. We demonstrate that patients with HFrEF/AF are clinically worse off than those with HFrEF/SR. Atrial fibrillation is a marker of fibrosis and disease severity in HFrEF. Patients with HFrEF/AF had elevated sST2 levels a more deformed left atrium morphologically and poor tissue doppler function. On strain imaging, HFrEF/AF patients had poor left atrial reservoir function. Funding Acknowledgement Type of funding sources: Private grant(s) and/or Sponsorship. Main funding source(s): The South African Medical Research Council

HIV incidence estimation among female sex workers in South Africa: a multiple methods analysis of cross-sectional survey data

Although numerous studies have investigated HIV risk factors and shown high HIV prevalence among female sex workers in South Africa, no national HIV incidence estimate exists for this potentially important group for HIV transmission. We aimed to estimate HIV incidence among female sex workers in South Africa who could be accessed through sex worker programmes, and to refine and describe the methods that enabled analysis. This study was embedded in a cross-sectional national survey of female sex workers who were linked to sex worker programmes. We aimed to enrol 3000 female sex workers aged at least 18 years who had sold or transacted in sex in the preceding 6 months in 12 randomly selected districts of the 22 districts with sex worker programmes, ensuring coverage of all provinces of South Africa. Women who self-reported as current victims of human trafficking were excluded from enrolment. We used a multistep process to sample districts and then hotspots, and a chain referral method to recruit participants. We collected cross-sectional data for self-reported HIV status, demographic characteristics, and exposure to violence. Two rapid tests were used to ascertain diagnostic markers, a viral load assay was used to ascertain clinical markers, and the Maxim Limiting Antigen Avidity EIA was used to ascertain infection-staging HIV markers. Given the challenges of estimating HIV incidence, especially cross-sectionally, multiple methods of estimation were adapted to our setting, leveraging the age structure of HIV prevalence, recency-of -infection biomarker results (ie, where recent infection is classified as ≤1·5 normalised optical density [ODn] on the avidity assay and viral load of ≥1000 copies per mL), and reported testing histories. Of 3005 female sex workers who were enrolled and interviewed between Feb 4 and June 26, 2019, 2999 who had HIV test results were included in this analysis. The median age of participants was 32 years (IQR 27-38). 1714 (57·2%) of 2999 participants self-reported as being HIV positive, and 1447 (48·3%) of 2993 participants reported client sexual violence in the past year. The measured HIV prevalence was 62·1% (95% CI 60·3-65·7) and peaked at approximately age 40 years. Using recency-of-infection biomarker results, we obtained a base case estimate of HIV incidence of 4·60 cases per 100 person-years (95% CI 1·53-8·45) for the population. Estimates were generally consistent by method, and outlying incidence estimates calculated by self-reported testing histories were considered unreliable. Various sensitivity analyses produced estimates up to 11 cases per 100 person-years, and we did not detect differences by age and region. We found that female sex workers have extraordinarily high HIV incidence of approximately 5 cases per 100 person-years, emphasising the need to sustain and strengthen efforts to mitigate risk and provide adequate care. The notable role that sex work has in HIV transmission demands substantial investment in ongoing epidemiological monitoring. South African Medical Research Council, South African National Treasury, Global Fund, South African Department of Science and Innovation, Wellcome Trust.

Keystone Malaria Symposium 2022: a vibrant discussion of progress made and challenges ahead from drug discovery to treatment

Keystone Malaria Symposium 2022: a vibrant discussion of progress made and challenges ahead from drug discovery to treatment