Secondary distribution of HIV self-test kits by HIV index and antenatal care clients: implementation and costing results from the STAR Initiative in South Africa.

BACKGROUND: Partner-delivered HIV self-testing kits has previously been highlighted as a safe, acceptable and effective approach to reach men. However, less is known about its real-world implementation in reaching partners of people living with HIV. We evaluated programmatic implementation of partner-delivered self-testing through antenatal care (ANC) attendees and people newly diagnosed with HIV by assessing use, positivity, linkage and cost per kit distributed. METHODS: Between April 2018 and December 2019, antenatal care (ANC) clinic attendees and people or those newly diagnosed with HIV clients across twelve clinics in three cities in South Africa were given HIVST kits (OraQuick Rapid HIV-1/2 Antibody Test, OraSure Technologies) to distribute to their sexual partners. A follow-up telephonic survey was administered to all prior consenting clients who were successfully reached by telephone to assess primary outcomes. Incremental economic costs of the implementation were estimated from the provider's perspective. RESULTS: Fourteen thousand four hundred seventy-three HIVST kits were distributed - 10,319 (71%) to ANC clients for their male partner and 29% to people newly diagnosed with HIV for their partners. Of the 4,235 ANC clients successfully followed-up, 82.1% (3,475) reportedly offered HIVST kits to their male partner with 98.1% (3,409) accepting and 97.6% (3,328) using the kit. Among ANC partners self-testing, 159 (4.8%) reported reactive HIVST results, of which 127 (79.9%) received further testing; 116 (91.3%) were diagnosed with HIV and 114 (98.3%) initiated antiretroviral therapy (ART). Of the 1,649 people newly diagnosed with HIV successfully followed-up; 1,312 (79.6%) reportedly offered HIVST kits to their partners with 95.8% (1,257) of the partners accepting and 95.9% (1,206) reported that their partners used the kit. Among these index partners, 297 (24.6%) reported reactive HIVST results of which 261 (87.9%) received further testing; 260 (99.6%) were diagnosed with HIV and 258 (99.2%) initiated ART. The average cost per HIVST distributed in the three cities was US$7.90, US$11.98, and US$14.81, respectively. CONCLUSIONS: Partner-delivered HIVST in real world implementation was able to affordably reach many male partners of ANC attendees and index partners of people newly diagnosed with HIV in South Africa. Given recent COVID-19 related restrictions, partner-delivered HIVST provides an important strategy to maintain essential testing services.

SARS-CoV-2 spike protein diversity at an intra-host level, among SARS-CoV-2 infected individuals in South Africa, 2020 to 2022.

Intra-host diversity studies are used to characterise the mutational heterogeneity of SARS-CoV-2 infections in order to understand the impact of virus-host adaptations. This study investigated the frequency and diversity of the spike (S) protein mutations within SARS-CoV-2 infected South African individuals. The study included SARS-CoV-2 respiratory samples, from individuals of all ages, received at the National Health Laboratory Service at Charlotte Maxeke Johannesburg Academic hospital, Gauteng, South Africa, from June 2020 to May 2022. Single nucleotide polymorphism (SNP) assays and whole genome sequencing were performed on a random selection of SARS-CoV-2 positive samples. The allele frequency (AF) was determined using TaqMan Genotyper software for SNP PCR analysis and galaxy.eu for analysis of FASTQ reads from sequencing. The SNP assays identified 5.3% (50/948) of Delta cases with heterogeneity at delY144 (4%; 2/50), E484Q (6%; 3/50), N501Y (2%; 1/50) and P681H (88%; 44/50), however only heterogeneity for E484Q and delY144 were confirmed by sequencing. From sequencing we identified 9% (210/2381) of cases with Beta, Delta, Omicron BA.1, BA.2.15, and BA.4 lineages that had heterogeneity in the S protein. Heterogeneity was primarily identified at positions 19 (1.4%) with T19IR (AF 0.2-0.7), 371 (92.3%) with S371FP (AF 0.1-1.0), and 484 (1.9%) with E484AK (0.2-0.7), E484AQ (AF 0.4-0.5) and E484KQ (AF 0.1-0.4). Mutations at heterozygous amino acid positions 19, 371 and 484 are known antibody escape mutations, however the impact of the combination of multiple substitutions identified at the same position is unknown. Therefore, we hypothesise that intra-host SARS-CoV-2 quasispecies with heterogeneity in the S protein facilitate competitive advantage of variants that can completely/partially evade host's natural and vaccine-induced immune responses.

Protocol for the OCAY study: a cohort study of orphanhood and caregiver loss in the COVID-19 era to explore the impact on children and adolescents.

INTRODUCTION: Globally, no person has been untouched by the COVID-19 pandemic. Yet, little attention has been given to children and adolescents in policy, provision and services. Moreover, there is a dearth of knowledge regarding the impact of COVID-19-associated orphanhood and caregiver loss on children. This study aims to provide early insights into the mental health and well-being of children and adolescents experiencing orphanhood or caregiver loss in South Africa. METHODS AND ANALYSIS: Data will be drawn from a quantitative longitudinal study in Cape Town, South Africa. A sample of children and adolescents between the ages of 9 and 18 years, experiencing parental or caregiver loss from COVID-19, will be recruited together with a comparison group of children in similar environments who did not experience loss. The study aims to recruit 500 children in both groups. Mental health and well-being among children will be explored through the use of validated and study-specific measures. Participants will be interviewed at two time points, with follow-up data being collected 12-18 months after baseline. A combination of analytical techniques (including descriptive statistics, regression modelling and structural equation modelling) will be used to understand the experience and inform future policy and service provision. ETHICS AND DISSEMINATION: This study received ethical approval from the Health Research Ethics Committee at Stellenbosch University (N 22/04/040). Results will be disseminated via academic and policy publications, as well as national and international presentations including high-level meetings with technical experts. Findings will also be disseminated at a community level via various platforms.

Ivermectin drug induced liver injury.

Ivermectin remains a popular, albeit unproven, therapy used in both the prevention and treatment of COVID-19. We discuss a patient who developed jaundice and a liver injury 3 weeks after initiating ivermectin for COVID prevention.  Liver histology demonstrated a pattern of injury that was both portal and lobular, with a bile ductulitis as well with marked cholesasis. She was managed with low dose corticosteroids, later tapered and withdrawn. She remains well a year after presenting.

The added value of molecular-based diagnostics in the African forensic medical setting.

Sudden unexpected infant death (SUDI) is reported to be an extraordinarily high burden in sub-Saharan Africa, with the incidence rate in South Africa among the highest in the world. It is common for the cause of many such infant deaths to remain unexplained even after a full medico-legal death investigation, and then to be categorised as a sudden unexplained infant death (SUID). Fortunately, advances in molecular-based diagnostics allow researchers to identify numerous underlying inherited cardiac arrhythmogenic disorders in many SUDI cases, with a predominance of variants identified in the SCN5A gene. Such cardiac arrhythmogenic-related sudden deaths generally present with no structural alterations of the heart that are macroscopically identifiable at autopsy, therefore highlighting the importance of post mortem genetic testing. We report on a significant genetic finding that was made on a SUDI case in which the cause was ascribed to an acute bacterial pneumonia but it was still subjected to post mortem genetic testing of the SCN5A gene. The literature shows that many SUDI cases diagnosed with inherited cardiac arrhythmogenic disorders have demonstrated a viral prodrome within days of their death. It is therefore not uncommon for these cardiac disorders in infants to be mistaken for flu, viral upper respiratory tract infection or pneumonia, and without the incorporation of post mortem genetic testing, any other contributory causes of these deaths are often disregarded. This study highlights the need for research reporting on the genetics of inherited cardiac disorders in Africa.

Understanding the impact of the COVID­19 pandemic on healthcare services for adults during three waves of COVID­19 infections: A South African private sector experience.

BACKGROUND: Since the onset of the COVID­19 pandemic, healthcare resources have been repurposed to focus on COVID­19. Resource reallocation and restrictions to movement that affected general access to care may have inadvertently resulted in undue disruptions in the continuum of care for patients requiring non-COVID­19 healthcare services. OBJECTIVES: To describe the change in pattern of health service use in the South African (SA) private sector. METHODS: We conducted a retrospective study of a nationwide cohort of privately insured individuals. An analysis of claims data was performed for non-COVID­19 related healthcare services provided from April 2020 to December 2020 (year 1 of COVID­19) and April 2021 to December 2021 (year 2 of COVID­19) relative to the same period in 2019 prior to the COVID­19 pandemic in SA. Over and above plotting the monthly trends, we tested for statistical significance of the changes using a Wilcoxon test given the non-normality of all the outcomes. RESULTS: Between April and December 2020, relative to the same period in 2021, and also relative to the same period in 2019, we found a 31.9% (p<0.01) and a 16.6% (p<0.01) reduction in emergency room visits, respectively; a 35.9% (p<0.01) and 20.5% (p<0.01) reduction in medical hospital admissions; a 27.4% (p=0.01) and 13.0% (p=0.03) reduction in surgical hospital admissions; a 14.5% (p<0.01) and 4.1% (p=0.16) reduction in face-to-face general practitioner consultations for chronic members; a 24.9% (p=0.06) and 5.2% (p=0.54) reduction in mammography for female members; a 23.4% (p=0.03) and 10.8% (p=0.09) reduction in Pap smear screenings for female members; a 16.5% (p=0.08) and 12.1% (p=0.27) reduction in colorectal cancer registrations and an 18.2% (p=0.08) and 8.9% (p=0.07) decrease in all oncology diagnoses. Uptake of telehealth services throughout the healthcare delivery system increased by 5 708% in 2020 compared with 2019, and 36.1% for 2021 compared with 2020. CONCLUSION: A significant reduction in emergency room visits, hospital admissions and utilisation of primary care services was observed since the start of the pandemic. Further research is required to understand if there are long-term consequences of delayed care. An increase in the use of digital consultations was observed. Research on their acceptability and effectiveness may open new modalities of care, which may have cost- and time-saving benefits.

Burden of disease and barriers to comprehensive care for rheumatic heart disease in South Africa: an updated systematic review protocol.

INTRODUCTION: Rheumatic heart disease (RHD) is responsible for a significant burden of cardiovascular morbidity and mortality, and remains the most common cause of acquired heart disease among children and young adults in low-income and middle-income countries. Additionally, the global COVID-19 pandemic has forced the emergency restructuring of many health systems, which has had a broad impact on health in general, including cardiovascular disease. Despite significant cost to the health system and estimates from 2015 indicating both high incidence and prevalence of RHD in South Africa, no cohesive national strategy exists. An updated review of national burden of disease estimates, as well as literature on barriers to care for patients with RHD, will provide crucial information to assist in the development of a national RHD programme. METHODS AND ANALYSIS: Using predefined search terms that capture relevant disease processes from Group A Streptococcal (GAS) infection through to the sequelae of RHD, a search of PubMed, Scopus, ISI Web of Science, Sabinet African Journals, SA Heart and Current and Completed Research databases will be performed. All eligible studies on RHD, acute rheumatic fever and GAS infection published from April 2014 to December 2022 will be included. Vital registration data for the same period from Statistics South Africa will also be collected. A standardised data extraction form will be used to capture results for both quantitative and qualitative analyses. All studies included in burden of disease estimates will undergo quality assessment using standardised tools. Updated estimates on mortality and morbidity as well as a synthesis of work on primary, secondary and tertiary prevention of RHD will be reported. ETHICS AND DISSEMINATION: No ethics clearance is required for this study. Findings will be disseminated in a peer-reviewed journal and submitted to national stakeholders in RHD. PROSPERO REGISTRATION NUMBER: CRD42023392782.

Factors associated with COVID-19 inpatient mortality cases within 24-hours South Africa.

BACKGROUND: African countries with limited healthcare capacity are particularly vulnerable to the novel coronavirus. The pandemic has left health systems short on resources to safely manage patients and protect health care workers. South Africa is still battling the epidemic of HIV/AIDS and tuberculosis which have had their programme/services interrupted due to the effects of the pandemic. Lessons learned from the HIV/AIDS and TB programme have shown that South Africans delay seeking health services when a new disease presents itself. OBJECTIVE: The study sought to investigate the risk factors for COVID-19 inpatients' mortality within 24-hours of hospital admission in Public health facilities in Limpopo Province, South Africa. METHODS: The study used retrospective secondary data obtained from the 1 067 clinical records of patients admitted between March 2020 and June 2021 by the Limpopo Department of Health (LDoH). A multivariable logistic regression model, both adjusted and unadjusted, was used to assess the risk factors associated with COVID-19 mortality within 24 hours of admission. RESULTS: This study, which was conducted in Limpopo public hospitals, discovered that 411 (40%) of COVID-19 patients died within 24-hours of admission. The majority of the patients were 60 years or older, mostly of female gender and had co-morbidities. In terms of vital signs, most had body temperatures less than 38°C. Our study findings revealed that COVID-19 patients who present with fever and shortness of breath are 1.8 and 2.5 times more likely to die within 24-hours of admission to the hospital, than patients without fever and normal respiratory rate . Hypertension was independently associated with mortality in COVID-19 patients within 24-hours of admission, with a high odds ratio for hypertensive patients (OR = 1.451; 95% CI = 1.013; 2.078) compared to non-hypertensive patients. CONCLUSION: Assessing demographic and clinical risk factors for COVID-19 mortality within 24-hours of admission aids in understanding and prioritising patients with severe COVID-19 and hypertension. Finally, this will provide guidelines for planning and optimising the use of LDoH healthcare resources and also aid in public awareness endeavours.

Two years on and four waves later: Johannesburg diagnostic radiographers' experiences of COVID-19.

INTRODUCTION: At the onset of COVID-19 diagnostic radiographers from Gauteng, South Africa, shared their experiences of the new workflow and operations, their well-being and their resilience during this time. They experienced emotional, physical and financial fatigue. It is now over two years later, and South Africa has experienced four waves of COVID-19. Therefore, this study explored diagnostic radiographers' experience of COVID-19 after two years and four waves. METHODS: A qualitative explorative, descriptive and contextual study was conducted by collecting data through nine virtual individual in-depth interviews. Responses from the diagnostic radiographers in Johannesburg, Gauteng, South Africa, underwent thematic analysis. RESULTS: Thematic analysis revealed two themes and related categories. Theme one: participants shared synchronistic experiences with the four COVID-19 waves, the heterogeneous vaccination ideologies and their support and coping skills. Theme two: lessons learnt and the way forward. CONCLUSION: Participants shared feeling overwhelmed at the onset of COVID-19 and feared infecting their family, friends and colleagues. However, their anxiety and fear decreased with time. They experienced the Delta variant as the worst and felt supported by their colleagues more than by management. They recounted observations of vaccine hesitancy but acknowledged that vaccination had alleviated some of the fear and anxiety. Participants' coping skills varied, and reflecting on their experience, they shared the lessons learnt and the way forward.

Declining trends in vaccine confidence across sub-Saharan Africa: A large-scale cross-sectional modeling study.

Current WHO/UNICEF estimates of routine childhood immunization coverage reveal the largest sustained decline in uptake in three decades with pronounced setbacks across Africa. Although the COVID-19 pandemic has induced significant supply and delivery disruptions, the impact of the pandemic on vaccine confidence is less understood. We here examine trends in vaccine confidence across eight sub-Saharan countries between 2020 and 2022 via a total of 17,187 individual interviews, conducted via a multi-stage probability sampling approach and cross-sectional design and evaluated using Bayesian methods. Multilevel regression combined with poststratification weighting using local demographic information yields national and sub-national estimates of vaccine confidence in 2020 and 2022 as well as its socio-demographic associations. We identify declines in perceptions toward the importance of vaccines for children across all eight countries, with mixed trends in perceptions toward vaccine safety and effectiveness. We find that COVID-19 vaccines are perceived to be less important and safe in 2022 than in 2020 in six of the eight countries, with the only increases in COVID-19 vaccine confidence detected in Ivory Coast. There are substantial declines in vaccine confidence in the Democratic Republic of Congo and South Africa, notably in Eastern Cape, KwaZulu-Natal, Limpopo, and Northern Cape (South Africa) and Bandundu, Maniema, Kasaï-Oriental, Kongo-Central, and Sud-Kivu (DRC). While over 60-year-olds in 2022 have higher vaccine confidence in vaccines generally than younger age groups, we do not detect other individual-level socio-demographic associations with vaccine confidence at the sample sizes studied, including sex, age, education, employment status, and religious affiliation. Understanding the role of the COVID-19 pandemic and associated policies on wider vaccine confidence can inform post-COVID vaccination strategies and help rebuild immunization system resilience.

Barriers affecting COVID­19 vaccination in Phalombe District, Malawi: A qualitative study.

BACKGROUND: In Malawi, only 1 072 229 people out of a national target population of 13 546 324 had received at least one dose of the AstraZeneca COVID­19 vaccine by 26 December 2021, and only 672 819 people were classified as fully vaccinated. Phalombe District in Malawi had particularly low COVID­19 vaccine uptake, with only 4% (n=8 538) of 225 219 people being fully vaccinated by 26 December. OBJECTIVES: To explore reasons for vaccine hesitancy and refusal among people living in Phalombe District. METHODS: This cross-sectional qualitative study employed six focus group discussions (FGDs) and 19 in-depth interviews (IDIs) to collect data. We purposefully selected two traditional authorities (TAs), Nazombe and Nkhumba, as study areas, and conducted FGDs and IDIs in 6 randomly selected villages in these two TAs. Participants were religious leaders, traditional leaders, youths, traditional healers and ordinary community members. We explored reasons for vaccine refusal and hesitancy, how contextual cultural beliefs influenced people's decision to receive the COVID­19 vaccine, and which sources of information were trusted in the community. Data were analysed using thematic content analysis. RESULTS: We conducted 19 IDIs and six FGDs. Themes that emerged from the data were reasons for vaccine refusal and hesitancy, contextual cultural beliefs affecting the decision whether to be vaccinated, ways to improve COVID­19 vaccine uptake, and means of communicating information about COVID­19 vaccines. Participants mentioned that myths contributing to vaccine refusal and hesitancy circulated in the community through social media. With regard to contextual cultural beliefs, most participants believed that COVID­19 was a disease of rich people, while others believed that it signalled the end of the world and that it could not be cured. CONCLUSION: Health systems should recognise and acknowledge the reasons leading to vaccine hesitancy and refusal and address these appropriately to improve vaccine uptake. Effective community sensitisation and engagement should be enhanced to clarify myths and address misinformation about the COVID­19 vaccine.

Investigating blood alcohol concentrations in injury-related deaths before and during the COVID-19 National lockdown in Western Cape, South Africa: A cross-sectional retrospective review.

BACKGROUND: Alcohol is a significant contributor to injury-related morbidity and mortality in South Africa (SA).  During the COVID-19 global pandemic, restrictions to movement and to the legal access of alcohol* were introduced in SA.  This study aimed to investigate the effect of alcohol bans during the COVID-19 lockdown periods on injury-related mortality and the blood alcohol concentrations (BAC) in these deaths. METHODS: A retrospective, cross-sectional analysis of injury-related deaths in Western Cape (WC) province, SA, between 1 January 2019 to 31 December 2020 was conducted. Cases where BAC testing was performed were further examined according to the periods of lockdown (AL5-1) and alcohol restrictions. RESULTS: A total of 16,027 injury-related cases were admitted to Forensic Pathology Service mortuaries in the WC over the two-year period.  An average decrease of 15.7% injury-related deaths in 2020 compared to 2019 was noted, as well as a 47.7% decrease in injury-related deaths during hard lockdown (April -May 2020) compared to the same period in 2019. In the injury-related deaths, 12,077 (75.4%) had blood specimens collected for BAC testing. In 5,078 (42.0%) of submitted cases, a positive BAC (≥0.01g/100 mL) was reported. No significant difference was observed in the mean positive BAC between 2019 and 2020, however in April and May 2020, the mean BACs observed (0.13 g/100 mL) was less than that in 2019 (0.18 g/100 mL). A high number of positive BACs in the 12-17-year age group (±23.4%) was observed. CONCLUSION: There was a clear decrease in injury-related deaths in the WC during the COVID-19-related lockdown periods that coincided with the alcohol ban and restriction of movement and an increase following relaxation of restrictions on alcohol sales and movement. The data illustrated that mean BACs were similar between all periods of alcohol restriction compared to 2019, apart from hard lockdown in April-May, 2020.  This coincided with a smaller mortuary intake during the level 5 and 4 lockdown periods.   Keywords: Alcohol; blood alcohol concentration; COVID-19; injury; lockdown; South Africa; violent death; Western Cape   * Alcohol refers to ethanol.

Intervention effects and long-term changes in physical activity and cardiometabolic outcomes among children at risk of noncommunicable diseases in South Africa: a cluster-randomized controlled trial and follow-up analysis.

Introduction: Risk factors for noncommunicable diseases such as insufficient physical activity (PA), overweight or hypertension are becoming increasingly predominant among children globally. While school-based interventions are promising preventive strategies, evidence of their long-term effectiveness, especially among vulnerable populations, is scarce. We aim to assess the short-term effects of the physical and health KaziKidz intervention on cardiometabolic risk factors and the long-term, pre-and post-COVID-19 pandemic changes thereof in high-risk children from marginalized communities. Methods: The intervention was tested in a cluster-randomized controlled trial between January and October 2019 in eight primary schools near Gqeberha, South Africa. Children with overweight, elevated blood pressure, pre-diabetes, and/or borderline dyslipidemia were identified and re-assessed 2 years post-intervention. Study outcomes included accelerometry-measured PA (MVPA), body mass index (BMI), mean arterial pressure (MAP), glucose (HbA1c), and lipid levels (TC to HDL ratio). We conducted mixed regression analyses to assess intervention effects by cardiometabolic risk profile, and Wilcoxon signed-rank tests to evaluate longitudinal changes in the high-risk subpopulation. Results: We found a significant intervention effect on MVPA during school hours for physically inactive children, and among active as well as inactive girls. In contrast, the intervention lowered HbA1c and TC to HDL ratio only in children with glucose or lipid values within the norm, respectively. At follow-up, the intervention effects were not maintained in at-risk children, who showed a decline in MVPA, and an increase in BMI-for-age, MAP, HbA1c and TC to HDL ratio. Conclusion: We conclude that schools are key settings in which to promote PA and improve health; however, structural changes are necessary to ensure that effective interventions reach marginalized school populations and achieve sustainable impact.

Performance of rapid antigen tests in identifying Omicron BA.4 and BA.5 infections in South Africa.

BACKGROUND: Concerns around accuracy and performance of rapid antigen tests continue to be raised with the emergence of new SARS-CoV-2 variants. OBJECTIVE: To evaluate the performance of two widely used SARS-CoV-2 rapid antigen tests during BA.4/BA.5 SARS-CoV-2 wave in South Africa (May - June 2022). STUDY DESIGN: A prospective field evaluation compared the SARS-CoV-2 Antigen Rapid test from Hangzhou AllTest Biotech (nasal swab) and the Standard Q COVID-19 Rapid Antigen test from SD Biosensor (nasopharyngeal swab) to the Abbott RealTime SARS-CoV-2 assay (nasopharyngeal swab) on samples collected from 540 study participants. RESULTS: Overall 28.52% (154/540) were SARS-CoV-2 RT-PCR positive with median cycle number value of 12.30 (IQR 9.30-19.40). Out of the 99 successfully sequenced SARS-CoV-2 positive samples, 18 were classified as BA.4 and 56 were classified as BA.5. The overall sensitivities of the AllTest SARS-CoV-2 Ag test and Standard Q COVID-19 Ag test were 73.38% (95% CI 65.89-79.73) and 74.03% (95% CI 66.58-80.31) and their specificities were 97.41% (95% CI 95.30-98.59) and 99.22% (95% CI 97.74-99.74) respectively. Sensitivity was >90% when the cycle number value was <20. The sensitivity of both rapid tests was >90% in samples infected with Omicron sub-lineage BA.4 and BA.5. CONCLUSION: Accuracy of tested rapid antigen tests that target the nucleocapsid SARS-CoV-2 protein, were not adversely affected by BA.4 and BA.5 Omicron sub-variants.

The impact of COVID-19 on a South African pediatric cardiac service: implications and insights into service capacity.

Background and Objectives: The Western Cape public pediatric cardiac service is under-resourced. COVID-19 regulations are likely to have long-term effects on patient care but may provide insight into service capacity requirements. As such, we aimed to quantify the impact of COVID-19 regulations on this service. Methods: An uncontrolled retrospective pre-post study of all presenting patients over two, one-year periods; the pre-COVID-19 period (01/03/2019-29/02/2020) and the peri-COVID-19 period (01/03/2020-28/02/2021). Results: Admissions decreased by 39% (624 to 378) and cardiac surgeries decreased by 29% (293 to 208) in the peri-COVID-19 period, with an increase in urgent cases (PR:5.99, 95%CI:3.58-10.02, p < 0.001). Age at surgery was lower in the peri-COVID-19 period, 7.2 (2.4-20.4) vs. 10.8 (4.8-49.2) months (p < 0.05), likewise, age at surgery for transposition of the great arteries (TGA) was lower peri-COVID-19, 15 (IQR:11.2-25.5) vs. 46 (IQR:11-62.5) days (p < 0.05). Length of stay 6 (IQR:2-14) vs. 3 days (IQR:1-9) (p < 0.001), complications (PR:1.21, 95%CI:1.01-1.43, p < 0.05), and age-adjusted delayed-sternal-closure rates (PR:3.20, 95%CI:1.09-9.33, p < 0.05) increased peri-COVID-19. Conclusion: Cardiac procedures were significantly reduced in the peri-COVID-19 period which will have implications on an overburdened service and ultimately, patient outcomes. COVID-19 restrictions on elective procedures freed capacity for urgent cases, demonstrated by the absolute increase in urgent cases and significant decrease in age at TGA-surgery. This facilitated intervention at the point of physiological need, albeit at the expense of elective procedures, and also revealed insights into capacity requirements of the Western Cape. These data emphasize the need for an informed strategy to increase capacity and reduce backlog whilst ensuring minimal morbidity and mortality.Graphical Abstract.

Metagenomics characterization of respiratory viral RNA pathogens in children under five years with severe acute respiratory infection in the Free State, South Africa.

Prompt detection of viral respiratory pathogens is crucial in managing respiratory infection including severe acute respiratory infection (SARI). Metagenomics next-generation sequencing (mNGS) and bioinformatics analyses remain reliable strategies for diagnostic and surveillance purposes. This study evaluated the diagnostic utility of mNGS using multiple analysis tools compared with multiplex real-time PCR for the detection of viral respiratory pathogens in children under 5 years with SARI. Nasopharyngeal swabs collected in viral transport media from 84 children admitted with SARI as per the World Health Organization definition between December 2020 and August 2021 in the Free State Province, South Africa, were used in this study. The obtained specimens were subjected to mNGS using the Illumina MiSeq system, and bioinformatics analysis was performed using three web-based analysis tools; Genome Detective, One Codex and Twist Respiratory Viral Research Panel. With average reads of 211323, mNGS detected viral pathogens in 82 (97.6%) of the 84 patients. Viral aetiologies were established in nine previously undetected/missed cases with an additional bacterial aetiology (Neisseria meningitidis) detected in one patient. Furthermore, mNGS enabled the much needed viral genotypic and subtype differentiation and provided significant information on bacterial co-infection despite enrichment for RNA viruses. Sequences of nonhuman viruses, bacteriophages, and endogenous retrovirus K113 (constituting the respiratory virome) were also uncovered. Notably, mNGS had lower detectability rate for severe acute respiratory syndrome coronavirus 2 (missing 18/32 cases). This study suggests that mNGS, combined with multiple/improved bioinformatics tools, is practically feasible for increased viral and bacterial pathogen detection in SARI, especially in cases where no aetiological agent could be identified by available traditional methods.

Evaluating systematic targeted universal testing for tuberculosis in primary care clinics of South Africa: A cluster-randomized trial (The TUTT Trial).

BACKGROUND: The World Health Organization (WHO) recommends systematic symptom screening for tuberculosis (TB). However, TB prevalence surveys suggest that this strategy does not identify millions of TB patients, globally. Undiagnosed or delayed diagnosis of TB contribute to TB transmission and exacerbate morbidity and mortality. We conducted a cluster-randomized trial of large urban and rural primary healthcare clinics in 3 provinces of South Africa to evaluate whether a novel intervention of targeted universal testing for TB (TUTT) in high-risk groups diagnosed more patients with TB per month compared to current standard of care (SoC) symptom-directed TB testing. METHODS AND FINDINGS: Sixty-two clinics were randomized; with initiation of the intervention clinics over 6 months from March 2019. The study was prematurely stopped in March 2020 due to clinics restricting access to patients, and then a week later due to the Coronavirus Disease 2019 (COVID-19) national lockdown; by then, we had accrued a similar number of TB diagnoses to that of the power estimates and permanently stopped the trial. In intervention clinics, attendees living with HIV, those self-reporting a recent close contact with TB, or a prior episode of TB were all offered a sputum test for TB, irrespective of whether they reported symptoms of TB. We analyzed data abstracted from the national public sector laboratory database using Poisson regression models and compared the mean number of TB patients diagnosed per clinic per month between the study arms. Intervention clinics diagnosed 6,777 patients with TB, 20.7 patients with TB per clinic month (95% CI 16.7, 24.8) versus 6,750, 18.8 patients with TB per clinic month (95% CI 15.3, 22.2) in control clinics during study months. A direct comparison, adjusting for province and clinic TB case volume strata, did not show a significant difference in the number of TB cases between the 2 arms, incidence rate ratio (IRR) 1.14 (95% CI 0.94, 1.38, p = 0.46). However, prespecified difference-in-differences analyses showed that while the rate of TB diagnoses in control clinics decreased over time, intervention clinics had a 17% relative increase in TB patients diagnosed per month compared to the prior year, interaction IRR 1.17 (95% CI 1.14, 1.19, p < 0.001). Trial limitations were the premature stop due to COVID-19 lockdowns and the absence of between-arm comparisons of initiation and outcomes of TB treatment in those diagnosed with TB. CONCLUSIONS: Our trial suggests that the implementation of TUTT in these 3 groups at extreme risk of TB identified more TB patients than SoC and could assist in reducing undiagnosed TB patients in settings of high TB prevalence. TRIAL REGISTRATION: South African National Clinical Trials Registry DOH-27-092021-4901.

Realising radical potential: building community power in primary health care through Participatory Action Research.

BACKGROUND: While community participation is an established pro-equity approach in Primary Health Care (PHC), it can take many forms, and the central category of power is under-theorised. The objectives were to (a) conduct theory-informed analysis of community power-building in PHC in a setting of structural deprivation and (b) develop practical guidance to support participation as a sustainable PHC component. METHODS: Stakeholders representing rural communities, government departments and non-governmental organisations engaged through a participatory action research (PAR) process in a rural sub-district in South Africa. Three reiterative cycles of evidence generation, analysis, action, and reflection were progressed. Local health concerns were raised and framed by community stakeholders, who generated new data and evidence with researchers. Dialogue was then initiated between communities and the authorities, with local action plans coproduced, implemented, and monitored. Throughout, efforts were made to shift and share power, and to adapt the process to improve practical, local relevance. We analysed participant and researcher reflections, project documents, and other project data using power-building and power-limiting frameworks. RESULTS: Co-constructing evidence among community stakeholders in safe spaces for dialogue and cooperative action-learning built collective capabilities. The authorities embraced the platform as a space to safely engage with communities and the process was taken up in the district health system. Responding to COVID-19, the process was collectively re-designed to include a training package for community health workers (CHWs) in rapid PAR. New skills and competencies, new community and facility-based alliances and explicit recognition of CHW roles, value, and contribution at higher levels of the system were reported following the adaptations. The process was subsequently scaled across the sub-district. CONCLUSIONS: Community power-building in rural PHC was multidimensional, non-linear, and deeply relational. Collective mindsets and capabilities for joint action and learning were built through a pragmatic, cooperative, adaptive process, creating spaces where people could produce and use evidence to make decisions. Impacts were seen in demand for implementation outside the study setting. We offer a practice framework to expand community power in PHC: (1) prioritising community capability-building, (2) navigating social and institutional contexts, and (3) developing and sustaining authentic learning spaces.

Quality of routine health data at the onset of the COVID-19 pandemic in Ethiopia, Haiti, Laos, Nepal, and South Africa.

BACKGROUND: During the COVID-19 pandemic, governments and researchers have used routine health data to estimate potential declines in the delivery and uptake of essential health services. This research relies on the data being high quality and, crucially, on the data quality not changing because of the pandemic. In this paper, we investigated those assumptions and assessed data quality before and during COVID-19. METHODS: We obtained routine health data from the DHIS2 platforms in Ethiopia, Haiti, Lao People's Democratic Republic, Nepal, and South Africa (KwaZulu-Natal province) for a range of 40 indicators on essential health services and institutional deaths. We extracted data over 24 months (January 2019-December 2020) including pre-pandemic data and the first 9 months of the pandemic. We assessed four dimensions of data quality: reporting completeness, presence of outliers, internal consistency, and external consistency. RESULTS: We found high reporting completeness across countries and services and few declines in reporting at the onset of the pandemic. Positive outliers represented fewer than 1% of facility-month observations across services. Assessment of internal consistency across vaccine indicators found similar reporting of vaccines in all countries. Comparing cesarean section rates in the HMIS to those from population-representative surveys, we found high external consistency in all countries analyzed. CONCLUSIONS: While efforts remain to improve the quality of these data, our results show that several indicators in the HMIS can be reliably used to monitor service provision over time in these five countries.