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Abstract Previous studies have linked the evolution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic variants to persistent infections in people with immunocompromising conditions, but the processes responsible for these observations are incompletely understood. Here we use high-throughput, single-genome amplification and sequencing (HT-SGS) to sequence SARS-CoV-2 spike genes from people with HIV (PWH, n = 22) and people without HIV (PWOH, n = 25). In PWOH and PWH with CD4 T cell counts (i.e., CD4 counts) ≥ 200 cells/μL, we find that most SARS-CoV-2 genomes sampled in each person share one spike sequence. By contrast, in people with advanced HIV infection (i.e., CD4 counts

IntroductionTight junctions (TJs) serve as permeability filters between the internal and external cellular environment. A large number of proteins have been identified to be localized at the TJs. Due to limitations in tissue collection, TJs in the male genital tract have been understudied.MethodsWe analysed the transcriptomics of 132 TJ genes in foreskin tissue of men requesting voluntary medical male circumcision (VMMC) and enrolled in the Combined HIV Adolescent Prevention Study (CHAPS) trial conducted in South Africa and Uganda (NCT03986970). The trial evaluated the dose requirements for event-driven HIV pre-exposure prophylaxis (PrEP) with emtricitabine-tenofovir (FTC-TDF) or emtricitabine-tenofovir alafenamide (FTC-TAF) during insertive sex. A total of 144 participants were randomized to either control arm or one of 8 PrEP arms (n=16/arm), receiving oral FTC-TDF or FTC-TAF over one or two days. Following in vivo oral PrEP dosing and VMMC, the expression level of three important TJ proteins (CLDN-1, OCN and ZO-1) was measured ex vivo in foreskin tissue by Western blot. The expression of cytokine genes implicated in TJ regulation was determined. Non-parametric Kruskal-Wallis tests were used to compare TJ gene expression and protein levels by type of PrEP received, and Spearman’s correlation coefficients were calculated to assess whether TJ gene expression levels were related to cytokine gene levels or to PrEP drug concentrations and their active intracellularly phosphorylated metabolites.ResultsA high level of expression in foreskin tissue was found for 118 (of 132) TJ genes analysed; this finding contributed to create a map of TJ components within the male genital tract. Importantly, PrEP regimens tested in the CHAPS trial did not affect the expression of TJ genes and the analysed proteins in the foreskin; thus, further supporting the safety of this prevention strategy against HIV-1 transmission during insertive sex. Additionally, we identified the level of several cytokines’ genes to be correlated to TJ gene expression: among them, IL-18, IL-33 and VEGF.DiscussionTJs can limit viral entry into target cells; to affect this biological function viruses can reduce the expression of TJ proteins. Our study, on the expression and regulation of TJs in the foreskin, contribute important knowledge for PrEP safety and further design of HIV-1 prophylaxis.

Abstract Background Data on the characteristics of individuals with mild and asymptomatic infections with different SARS-CoV-2 variants are limited. We therefore compared the characteristics of individuals infected with ancestral, Beta and Delta SARS-CoV-2 variants in South Africa. Methods We conducted a prospective cohort study in a rural and an urban site during July 2020-August 2021. Mid-turbinate nasal swabs were collected twice-weekly from household members irrespective of symptoms and tested for SARS-CoV-2 using real-time reverse transcription polymerase chain reaction (rRT-PCR). Differences in demographic and clinical characteristics, shedding and cycle threshold (Ct) value of infection episodes by variant were evaluated using multinomial regression. Overall and age-specific incidence rates of infection were compared by variant. Results We included 1200 individuals from 222 households and 648 rRT-PCR-confirmed infection episodes (66, 10% ancestral, 260, 40% Beta, 322, 50% Delta). Symptomatic proportion was similar for ancestral (7, 11%), Beta (44, 17%), and Delta (46, 14%) infections (p=0.4). After accounting for previous infection, peak incidence shifted to younger age groups in successive waves (40-59 years ancestral, 19-39 years Beta, 13-18 years Delta). On multivariable analysis, compared to ancestral, Beta infection was more common in individuals aged 5-12 years (vs 19-39)(adjusted odds ratio (aOR) 2.6, 95% confidence interval (CI)1.1-6.6) and PCR cycle threshold (Ct) value 35)(aOR 3.2, 95%CI 1.3-7.9), while Delta was more common in individuals aged 35). Conclusions Consecutive SARS-CoV-2 waves with Beta and Delta variants were associated with a shift to younger individuals. Beta and Delta infections were associated with higher peak viral loads, potentially increasing infectiousness.

Abstract Data on respiratory syncytial virus (RSV) incidence and household transmission are limited. To describe RSV incidence and transmission, we conducted a prospective cohort study in rural and urban communities in South Africa over two seasons during 2017-2018. Nasopharyngeal swabs were collected twice-weekly for 10 months annually and tested for RSV using PCR. We tested 81,430 samples from 1,116 participants in 225 households (follow-up 90%). 32% (359/1116) of individuals had ≥1 RSV infection; 10% (37/359) had repeat infection during the same season, 33% (132/396) of infections were symptomatic, and 2% (9/396) sought medical care. Incidence was 47.2 infections/100 person-years and highest in children 10 days were more likely to transmit; household contacts aged 1-4 years vs. ≥65 years were more likely to acquire infection. Within two South African communities, RSV attack rate was high, and most infections asymptomatic. Young children were more likely to introduce RSV into the home, and to be infected. Future studies should examine whether vaccines targeting children aged

Abstract Background Large-scale prevention of respiratory syncytial virus (RSV) infection may have ecological consequences for co-circulating pathogens, including influenza. We assessed if and for how long RSV infection alters the risk for subsequent influenza infection. Methods We analysed a prospective longitudinal cohort study conducted in South Africa between 2016 and 2018. For participating households, nasopharyngeal samples were taken twice weekly, irrespective of symptoms, across three respiratory virus seasons, and real-time polymerase chain reaction (PCR) was used to identify infection with RSV and/or influenza. We fitted an individual-level hidden Markov transmission model in order to estimate RSV and influenza infection rates and their interdependence. Results Of a total of 122,113 samples collected, 1265 (1.0%) were positive for influenza and 1002 (0.8%) positive for RSV, with 15 (0.01%) samples from 12 individuals positive for both influenza and RSV. We observed a 2.25-fold higher incidence of co-infection than expected if assuming infections were unrelated. We estimated that infection with influenza is 2.13 (95% CI 0.97–4.69) times more likely when already infected with, and for a week following, RSV infection, adjusted for age. This equates to 1.4% of influenza infections that may be attributable to RSV in this population. Due to the local seasonality (RSV season precedes the influenza season), we were unable to estimate changes in RSV infection risk following influenza infection. Conclusions We find no evidence to suggest that RSV was associated with a subsequent reduced risk of influenza infection. Instead, we observed an increased risk for influenza infection for a short period after infection. However, the impact on population-level transmission dynamics of this individual-level synergistic effect was not measurable in this setting.

Abstract Background Antiretroviral therapy (ART) through universal test and treat (UTT) and HIV pre-exposure prophylaxis (PrEP) substantially reduces HIV-related mortality and incidence. Effective ART based prevention has not translated into population-level impact in southern Africa due to sub-optimal coverage among youth. We aim to investigate the effectiveness, implementation and cost effectiveness of peer-led social mobilisation into decentralised integrated HIV and sexual reproductive health (SRH) services amongst adolescents and young adults in KwaZulu-Natal (KZN). Methods We are conducting a type 1a hybrid effectiveness/implementation study, with a cluster randomized stepped-wedge trial (SWT) to assess effectiveness and a realist process evaluation to assess implementation outcomes. The SWT will be conducted in 40 clusters in rural KZN over 45 months. Clusters will be randomly allocated to receive the intervention in period 1 (early) or period 2 (delayed). 1) Intervention arm: Resident peer navigators in each cluster will approach young men and women aged 15–30 years living in their cluster to conduct health, social and educational needs assessment and tailor psychosocial support and health promotion, peer mentorship, and facilitate referrals into nurse led mobile clinics that visit each cluster regularly to deliver integrated SRH and differentiated HIV prevention (HIV testing, UTT for those positive, and PrEP for those eligible and negative). Standard of Care is UTT and PrEP delivered to 15–30 year olds from control clusters through primary health clinics. There are 3 co-primary outcomes measured amongst cross sectional surveys of 15–30 year olds: 1) effectiveness of the intervention in reducing the prevalence of sexually transmissible HIV; 2) uptake of universal risk informed HIV prevention intervention; 3) cost of transmissible HIV infection averted. We will use a realist process evaluation to interrogate the extent to which the intervention components support demand, uptake, and retention in risk-differentiated biomedical HIV prevention. Discussion The findings of this trial will be used by policy makers to optimize delivery of universal differentiated HIV prevention, including HIV pre-exposure prophylaxis through peer-led mobilisation into community-based integrated adolescent and youth friendly HIV and sexual and reproductive health care. Trial registration ClinicalTrials.gov Identifier—NCT05405582. Registered: 6th June 2022.

Introduction We consider an analytical problem of characterising patterns and identifying discrepancies between database systems for longitudinal aggregated healthcare data involving multiple facilities.Methods We used routinely collected data on the registered number of people living with HIV who initiated antiretroviral treatment (ART) in 69 South African facilities in 2019; reported in the Three Interlinked Electronic register (Tier.net) and the District Health Information System. A Bayesian multiplicative interaction model quantified the average time effect as realised through the heterogeneous facility-specific slopes and quantified discrepancies between the two database sources.Results The estimated average trends showed a slight dip in June and a large dip in December. The estimated slopes identified clusters of facilities based on their ranges of fluctuations over time. The differences in average monthly ART initiations between the two database sources had a median of 1.6 (IQR 0.8–3.3), while 3 outlying facilities differed by at least 10 ART initiations between the 2 sources.Conclusion Multiplicative interaction models are a powerful tool for quantifying average trends over time and for evaluating discrepancies between reporting systems for multiple facilities with heterogeneous time slopes. The Bayesian framework enables efficient estimation for a very large number of parameters.

The penile epithelial microbiome remains underexplored. We sequenced human RNA and a segment of the bacterial 16S rRNA gene from the foreskin tissue of 144 adolescents from South Africa and Uganda collected during penile circumcision after receipt of 1–2 doses of placebo, emtricitabine + tenofovir disoproxil fumarate, or emtricitabine + tenofovir alafenamide to investigate the microbiome of foreskin tissue and its potential changes with antiretroviral use. We identified a large number of anaerobic species, including Corynebacterium acnes, which was detected more frequently in participants from South Africa than Uganda. Bacterial populations did not differ by treatment received, and no differentially abundant taxa were identified between placebo versus active drug recipients. The relative abundance of specific bacterial taxa was negatively correlated with expression of genes downstream of the innate immune response to bacteria and regulation of inflammation. Our results show no difference in the tissue microbiome of the foreskin with short-course antiretroviral use but that bacterial taxa were largely inversely correlated with inflammatory gene expression, consistent with commensal colonization.

We conducted 3 prospective cohort studies (2016–2018), enrolling persons from 2 communities in South Africa. Nasopharyngeal swab specimens were collected twice a week from participants. Factors associated with Bordetella pertussis incidence, episode duration, and household transmission were determined by using Poisson regression, Weibull accelerated time-failure, and logistic regression hierarchical models, respectively. Among 1,684 participants, 118 episodes of infection were detected in 107 participants (incidence 0.21, 95% CI 0.17–0.25 infections/100 person-weeks). Children 7 days infection duration. In both communities, there was high incidence of B. pertussis infection and most cases were colonized.

Emergence of the Omicron BA.1/2 SARS-CoV-2 subvariants led to a wave of infection South Africa. Here, the authors use serological data from a prospective household study to characterise infection rates in the context of diverse immune histories following vaccination and exposure to different variants.

Background: Non-communicable diseases (NCDs) are an emerging global public health problem. Objectives: To assess the prevalence of NCDs and their risk factors among adults on antiretroviral therapy (ART). Method: This was a cross-sectional study (July 2019 – January 2020) in Limpopo, South Africa. Patients were enrolled if they were ≥ 40 years, HIV-positive, and virologically suppressed on ART. Data were analysed descriptively, and a binomial regression model was used to identify risk factors for NCDs. Results: The majority of participants (65%; 319/488) were women. Most (83%; 405/488) were aged 40–59 years; 60% (285/472) were overweight or obese. Based on self-report, 22% (107/488) were currently smokers. Almost half (44%) 213/488) reported daily consumption of vegetables and 65% (319/488) exercised regularly and 39% (190/488) reported treatment for another chronic disease. The leading comorbid conditions were hypertension (32%; 158/488) and diabetes mellitus (5%; 24/488). Risk factors for hypertension included age 60 years and older (relative risk [RR]: 1.72; 95% confidence interval [CI]: 1.29–2.30) diabetes (RR: 1.42; 95% CI: 1.08–1.87), overweight (RR: 1.32; 95% CI: 1.03–1.69) and obesity (RR: 1.69; 95% CI: 1.32–2.17). Conclusion: There is a high prevalence, both of risk factors for NCDs and multimorbidity ( 1 chronic disease) in patients who are ≥ 40 years and virologically suppressed on ART.

BackgroundThe 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 findingsSixty-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.ConclusionsOur 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 registrationSouth African National Clinical Trials Registry DOH-27-092021-4901.

By November 2021, after the third wave of severe acute respiratory syndrome coronavirus 2 infections in South Africa, seroprevalence was 60% in a rural community and 70% in an urban community. High seroprevalence before the Omicron variant emerged may have contributed to reduced illness severity observed in the fourth wave.

With the onset of COVID-19, the development of ex vivo laboratory models became an urgent priority to study host-pathogen interactions in response to the pandemic. In this study, we aimed to establish an ex vivo mucosal tissue explant challenge model for studying SARS-CoV-2 infection and replication. Nasal or oral tissue samples were collected from eligible participants and explants generated from the tissue were infected with various SARS-CoV-2 strains, including IC19 (lineage B.1.13), Beta (lineage B.1.351) and Delta (lineage B.1.617.2). A qRT-PCR assay used to measure viral replication in the tissue explants over a 15-day period, demonstrated no replication for any viral strains tested. Based on this, the ex vivo challenge protocol was modified by reducing the viral infection time and duration of sampling. Despite these changes, viral infectivity of the nasal and oral mucosa was not improved. Since 67% of the enrolled participants were already vaccinated against SARS-CoV-2, it is possible that neutralizing antibodies in explant tissue may have prevented the establishment of infection. However, we were unable to optimize plaque assays aimed at titrating the virus in supernatants from both infected and uninfected tissue, due to limited volume of culture supernatant available at the various collection time points. Currently, the reasons for the inability of these mucosal tissue samples to support replication of SARS-CoV-2 ex vivo remains unclear and requires further investigation.

Healthcare utilization surveys contextualize facility-based surveillance data for burden estimates. We describe healthcare utilization in the catchment areas for sentinel site healthcare facilities during the first year of the COVID-19 pandemic. We conducted a cross-sectional healthcare utilization survey in households in three communities from three provinces (KwaZulu-Natal, Western Cape and North West). Field workers administered structured questionnaires electronically with the household members reporting influenza-like illness (ILI) in the past 30 days or severe respiratory illness (SRI) since March 2020. Multivariable logistic regression was used to identify factors associated with healthcare utilization among individuals that reported illness. From November 2020 through April 2021, we enrolled 5804 households and 23,003 individuals. Any respiratory illness was reported by 1.6% of individuals; 0.7% reported ILI only, 0.8% reported SRI only, and 0.1% reported both ILI and SRI. Any form of medical care was sought by 40.8% (95% CI 32.9% - 49.6%) and 71.3% (95% CI 63.2% - 78.6%) of individuals with ILI and SRI, respectively. On multivariable analysis, respiratory illness was more likely to be medically attended for individuals at the Pietermaritzburg site (aOR 3.2, 95% CI 1.1-9.5, compared to Klerksdorp), that were underweight (aOR 11.5, 95% CI 1.5-90.2, compared to normal weight), with underlying illness (aOR 3.2, 95%CI 1.2-8.5), that experienced severe illness (aOR 4.8, 95% CI 1.6-14.3) and those with symptom duration of ≥10 days (aOR 7.9, 95% CI 2.1-30.2, compared to

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections may be underestimated because of limited access to testing. We measured SARS-CoV-2 seroprevalence in South Africa every 2 months during July 2020–March 2021 in randomly selected household cohorts in 2 communities. We compared seroprevalence to reported laboratory-confirmed infections, hospitalizations, and deaths to calculate infection–case, infection–hospitalization, and infection–fatality ratios in 2 waves of infection. Post–second wave seroprevalence ranged from 18% in the rural community children

Whilst short-term oral pre-exposure prophylaxis (PrEP) with antiretroviral drugs in men who have sex with men has shown protection against HIV-1 infection, the impact of this regimen on the in vivo foreskin transcriptome is unknown. We collected foreskin tissue after voluntary medical male circumcision from 144 young men (72 from Uganda and 72 from South Africa) randomized to one to two doses of either oral tenofovir (TFV) disoproxil fumarate (FTC-TDF) or tenofovir alafenamide (FTC-TAF) or no drug (untreated controls). This novel approach allowed us to examine the impact of short-term oral PrEP on transcriptome of the male genital tract. A single dose of FTC-TDF did not affect the foreskin transcriptome in relation to control arm, however one dose of FTC-TAF induced upregulation of four genes AKAP8, KIAA0141, HSCB and METTL17. Following two doses of either FTC-TDF or FTC-TAF, there was an increase in 34 differentially expressed genes for FTC-TDF and 15 for FTC-TAF, with nine DEGs in common: KIAA0141, SAFB2, CACTIN, FXR2, AKAP8, HSCB, CLNS1A, DDX27 and DCAF15. Functional analysis of differentially expressed genes revealed modulation of biological processes related to mitochondrial stress (KIAA0141, HSCB and METTL17), anti-viral and anti-inflammatory pathways (CACTIN and AKAP8). Our results show that short-course on-demand oral PrEP in men modulates genes in foreskin tissue which are likely unfavorable to HIV acquisition and replication. We also describe an upregulated expression of genes involved in diverse mitochondria biology which may potentially result in worsened mitochondria-related. These results warrant further studies to assess the role of short-course and prolonged oral PrEP on biological processes of the foreskin mucosa.

HIV-1 pre-exposure prophylaxis (PrEP) relies on inhibition of HIV-1 replication steps. To understand how PrEP modulates the immunological environment, we derived the plasma proteomic profile of men receiving emtricitabine-tenofovir (FTC-TDF) or emtricitabine-tenofovir alafenamide (FTC-TAF) during the CHAPS trial in South Africa and Uganda (NCT03986970). The CHAPS trial randomized 144 participants to one control and 8 PrEP arms, differing by drug type, number of PrEP doses and timing from final PrEP dose to sampling. Blood was collected pre- and post-PrEP. The inflammatory profile of plasma samples was analyzed using Olink (N=92 proteins) and Luminex (N=33) and associated with plasma drug concentrations using mass spectrometry. The proteins whose levels changed most significantly from pre- to post-PrEP were CCL4, CCL3 and TNF-α; CCL4 was the key discriminator between pre- and post-PrEP samples. CCL4 and CCL3 levels were significantly increased in post-PrEP samples compared to control specimens. CCL4 was significantly correlated with FTC drug levels in plasma. Production of inflammatory chemokines CCL4 and CCL3 in response to short-term PrEP indicates the mobilization of ligands which potentially block virus attachment to CCR5 HIV-1 co-receptor. The significant correlation between CCL4 and FTC levels suggests that CCL4 increase is modulated as an inflammatory response to PrEP.

Abstract Background Describing contact patterns is crucial to understanding infectious disease transmission dynamics and guiding targeted transmission mitigation interventions. Data on contact patterns in Africa, especially South Africa, are limited. We measured and compared contact patterns in a rural and urban community, South Africa. We assessed participant and contact characteristics associated with differences in contact rates. Methods We conducted a cross-sectional study nested in a prospective household cohort study. We interviewed participants to collect information on persons in contact with for one day. We described self-reported contact rates as median number people contacted per day, assessed differences in contact rates based on participant characteristics using quantile regression, and used a Poisson model to assess differences in contact rates based on contact characteristics within age groups. We also calculated cumulative person hours in contact within age groups at different locations. Results We conducted 535 interviews (269 rural, 266 urban), with 17,252 contacts reported. The overall contact rate was 14 (interquartile range (IQR) 9–33) contacts per day. Those ≤18 years had higher contact rates at the rural site (coefficient 17, 95% confidence interval (95%CI) 10–23) compared to the urban site, for those aged 14–18 years (13, 95%CI 3–23) compared to

Abstract Background Pulmonary tuberculosis (TB) in people living with HIV (PLH) frequently presents as sputum smear-negative. However, clinical trials of TB in adults often use smear-positive individuals to ensure measurable bacterial responses following initiation of treatment, thereby excluding HIV-infected patients from trials. Methods In this prospective case cohort study, 118 HIV-seropositive TB patients were assessed prior to initiation of standard four-drug TB therapy and at several time points through 35 days. Sputum bacillary load, as a marker of treatment response, was determined serially by: smear microscopy, Xpert MTB/RIF, liquid culture, and colony counts on agar medium. Results By all four measures, patients who were baseline smear-positive had higher bacterial loads than those presenting as smear-negative, until day 35. However, most smear-negative PLH had significant bacillary load at enrolment and their mycobacteria were cleared more rapidly than smear-positive patients. Smear-negative patients’ decline in bacillary load, determined by colony counts, was linear to day 7 suggesting measurable bactericidal activity. Moreover, the decrease in bacterial counts was comparable to smear-positive individuals. Increasing cycle threshold values (Ct) on the Xpert assay in smear-positive patients to day 14 implied decreasing bacterial load. Conclusion Our data suggest that smear-negative PLH can be included in clinical trials of novel treatment regimens as they contain sufficient viable bacteria, but allowances for late exclusions would have to be made in sample size estimations. We also show that increases in Ct in smear-positive patients to day 14 reflect treatment responses and the Xpert MTB/RIF assay could be used as biomarker for early treatment response.

Abstract Background Chronic care models like the Integrated Chronic Disease Management (ICDM) model strive to improve the efficiency and quality of care for patients with chronic diseases. However, there is a dearth of studies assessing the moderating factors of fidelity during the implementation of the ICDM model. The aim of this study is to assess moderating factors of implementation fidelity of the ICDM model. Methods This was a cross-sectional mixed method study conducted in two health districts in South Africa. The process evaluation and implementation fidelity frameworks were used to guide the assessment of moderating factors influencing implementation fidelity of the ICDM model. We interviewed 30 purposively selected healthcare workers from four facilities (15 from each of the two facilities with lower and higher levels of implementation fidelity of the ICDM model). Data on facility characteristics were collected by observation and interviews. Linear regression and descriptive statistics were used to analyse quantitative data while qualitative data were analysed thematically. Results The median age of participants was 36.5 (IQR: 30.8–45.5) years, and they had been in their roles for a median of 4.0 (IQR: 1.0–7.3) years. The moderating factors of implementation fidelity of the ICDM model were the existence of facilitation strategies (training and clinical mentorship); intervention complexity (healthcare worker, time and space integration); and participant responsiveness (observing operational efficiencies, compliance of patients and staff attitudes). One feature of the ICDM model that seemingly compromised fidelity was the inclusion of tuberculosis patients in the same stream (waiting areas, consultation rooms) as other patients with non-communicable diseases and those with HIV/AIDS with no clear infection control guidelines. Participants also suggested that poor adherence to any one component of the ICDM model affected the implementation of the other components. Contextual factors that affected fidelity included supply chain management, infrastructure, adequate staff, and balanced patient caseloads. Conclusion There are multiple (context, participant responsiveness, intervention complexity and facilitation strategies) interrelated moderating factors influencing implementation fidelity of the ICDM model. Augmenting facilitation strategies (training and clinical mentorship) could further improve the degree of fidelity during the implementation of the ICDM model.

The mucosal environment of the upper respiratory tract is the first barrier of protection against SARS-CoV-2 transmission. However, the mucosal factors involved in viral transmission and potentially modulating the capacity to prevent such transmission have not fully been identified. In this pilot proteomics study, we compared mucosal and systemic compartments in a South African cohort of vaccinated and unvaccinated individuals undergoing maxillofacial surgery with previous history of COVID-19 or not. Inflammatory profiles were analyzed in plasma, nasopharyngeal swabs, and nasal and oral tissue explant cultures, using Olink and Luminex technologies. SARS-CoV-2-specific antibody levels were measured in serum and tissue explants. An increased pro-inflammatory proteomic profile was measured in the nasal compartment compared to plasma. However, IP-10 and MIG levels were higher in secretions than in nasal tissue, and the opposite was observed for TGF-β. Nasal anti-SARS-CoV-2 spike IgG correlated with mucosal MIG expression for all participants. A further positive correlation was found with IP-10 in BioNTech/Pfizer-vaccinated individuals. Systemic levels of anti-SARS-CoV-2 spike IgG elicited by this vaccine correlated with plasma IL-10, IL-6 and HBD4. Proteomic profiles measured in mucosal tissues and secretions using combined technologies could reveal correlates of protection at the mucosal portals of viral entry.

Background: Human-to-animal transmission of M. tuberculosis (Mtb) is reported in South Africa but there is a paucity of epidemiological data. The aim of this One Health manuscript is to describe zooanthroponotic exposure of domestic animals to TB patients, virtually all of whom had laboratory confirmed pulmonary Mtb disease. Methods: This cross-sectional study was nested within two TB contact tracing studies and collected data from 2017 to 2019. TB index patients and their households in three provinces of South Africa were recruited. A questionnaire was administered to households, assessing type and number of animals owned, degree of exposure of animals to humans, and veterinary consultations. For this analysis, we compared descriptive variables by animal-keeping status (animal-keeping vs non-animal keeping households), calculated the chi square and respective p-values. Results: We visited 1766 households with at least one confirmed case of TB, 33% (587/1766) had livestock or companion animals. Of non-animal-owning households, 2% (27/1161) cared for other community members' livestock. Few (16%, 92/587) households kept animals in their dwelling overnight, while 45% (266/587) kept animals outside the home, but within 10 m of where people slept and ate. Most (81%, 478/587) of people in animal-owning households were willing for their animal/s to have a TB skin test, but

Summary: Background: Data on influenza community burden and transmission are important to plan interventions especially in resource-limited settings. However, data are limited, particularly from low-income and middle-income countries. We aimed to evaluate the community burden and transmission of influenza in a rural and an urban setting in South Africa. Methods: In this prospective cohort study approximately 50 households were selected sequentially from both a rural setting (Agincourt, Mpumalanga Province, South Africa; with a health and sociodemographic surveillance system) and an urban setting (Klerksdorp, Northwest Province, South Africa; using global positioning system data), enrolled, and followed up for 10 months in 2017 and 2018. Different households were enrolled in each year. Households of more than two individuals in which 80% or more of the occupants agreed to participate were included in the study. Nasopharyngeal swabs were collected twice per week from participating household members irrespective of symptoms and tested for influenza using real-time RT-PCR. The primary outcome was the incidence of influenza infection, defined as the number of real-time RT-PCR-positive episodes divided by the person-time under observation. Household cumulative infection risk (HCIR) was defined as the number of subsequent infections within a household following influenza introduction. Findings: 81 430 nasopharyngeal samples were collected from 1116 participants in 225 households (follow-up rate 88%). 917 (1%) tested positive for influenza; 178 (79%) of 225 households had one or more influenza-positive individual. The incidence of influenza infection was 43·6 (95% CI 39·8–47·7) per 100 person-seasons. 69 (17%) of 408 individuals who had one influenza infection had a repeat influenza infection during the same season. The incidence (67·4 per 100 person-seasons) and proportion with repeat infections (22 [23%] of 97 children) were highest in children younger than 5 years and decreased with increasing age (p

Abstract Background The Integrated Chronic Disease Management (ICDM) model has been implemented in South Africa to enhance quality of clinical services in Primary Healthcare (PHC) clinics in a context of a high prevalence of chronic conditions and multi-morbidity. This study aimed to assess the implementation fidelity (adherence to guidelines) of the ICDM model. Methods A cross-sectional study in 16 PHC clinics in two health districts in South Africa: Dr. Kenneth Kaunda (DKK) and West Rand (WR). A fidelity assessment tool with 89 activities and maximum score of 158 was developed from the four interrelated ICDM model components: facility re-organization, clinical supportive management, assisted self-management and strengthening of support systems. Value stream mapping of patient flow was conducted to analyse waiting time and identify operational inefficiencies. ICDM items were scored based on structured observations, facility document reviews and structured questionnaires completed by healthcare workers. Fidelity scores were summarized using medians and proportions and compared by facilities and districts using Chi-Square and Kruskal Wallis test. Results The monthly patient headcount over a six-month period in these 16 PHC clinics was a median of 2430 (IQR: 1685–2942) individuals over 20 years. The DKK district had more newly diagnosed TB patients per month [median 5.5 (IQR: 4.00–9.33) vs 2.0 (IQR: 1.67–2.92)], and fewer medical officers per clinic [median 1 (IQR: 1–1) vs 3.5 (IQR:2–4.5)] compared to WR district. The median fidelity scores in both districts for facility re-organization, clinical supportive management, assisted self-management and strengthening of support systems were 78% [29/37, IQR: 27–31)]; 77% [30/39 (IQR: 27–34)]; 77% [30/39 (IQR: 28–34)]; and 80% [35/44 (IQR: 30–37)], respectively. The overall median implementation fidelity of the ICDM model was 79% (125/158, IQR, 117–132); WR was 80% (126/158, IQR, 123–132) while DKK was 74% (117/158, IQR, 106–130), p = 0.1409. The lowest clinic fidelity score was 66% (104/158), while the highest was 86% (136/158). A patient flow analysis showed long (2–5 h) waiting times and one stream of care for acute and chronic services. Conclusion There was some variability of scores on components of the ICDM model by PHC clinics. More research is needed on contextual adaptations of the model.

Abstract Background Household contact tracing of index TB cases has been advocated as a key part of TB control for many years, but has not been widely implemented in many low-resource setting because of the current dearth of high quality evidence for effectiveness. Innovative strategies for earlier, more effective treatment are particularly important in contexts with hyper-endemic levels of HIV, where levels of TB infection remain extremely high. Methods We present the design of a household cluster-randomised controlled trial of interventions aimed at improving TB-free survival and reducing childhood prevalence of Mycobacterium tuberculosis infection among household contacts of index TB cases diagnosed in two provinces of South Africa. Households of index TB cases will be randomly allocated in a 1:1 ratio to receive either an intensified home screening and linkage for TB and HIV intervention, or enhanced standard of care. The primary outcome will compare between groups the TB-free survival of household contacts over 15 months. All participants, or their next-of-kin, will provide written informed consent to participate. Discussion Evidence from randomised trials is required to identify cost-effective approaches to TB case-finding that can be applied at scale in sub-Saharan Africa. Trial registration ISRCTN16006202 (01/02/2017: retrospectively registered) and NHREC4399 (11/04/2016: prospectively registered). Protocol version: 4.0 (date: 18th January 2018).

Abstract Background The past four years has seen a rapid roll-out of male medical circumcision services in South Africa in response to clinical trials showing circumcision prevents HIV acquisition in heterosexual men. Clinics conduct substantial numbers of circumcisions per day. We report three cases of glans amputation in adolescents attending high volume clinics where modified Models of Optimising Volume and Efficiency (MOVE) are implemented. Case presentations Three cases of glans amputation in young healthy men that presented for voluntary medical male circumcision. The procedures were performed by highly experienced medical officers in two cases. All these cases shared characteristics: younger males with immature genitalia, forceps guided circumcision, and likely operator fatigue. Voluntary male medical circumcision programs should include regular monitoring and evaluation and training of operators to ensure high quality surgical techniques such as working in clean areas and taking frequent breaks. Conclusion Circumcision is a relatively simple medical procedure, however regular training and quality control in high volume Male Medical Circumcision sites is essential to prevent rare catastrophic adverse events.

Abstract Background HIV diagnosis is a critical step in linking HIV-infected individuals to care and treatment and linking HIV-uninfected persons to prevention services. However, the uptake of HIV testing remains low in many countries. HIV self-screening (HIVSS) is acceptable to adults, but there is limited data on HIVSS feasibility in community programmes. This study aimed to evaluate the feasibility of HIVSS in South Africa. Methods We conducted a prospective study that enrolled participants through mobile site, homebased, workplace and sex worker programmes in two townships from May to November 2017. Following an information session on HIVSS, interested participants were offered one of three methods of HIVSS testing: supervised, semi-supervised, and unsupervised. Participants who opted for unsupervised testing and those who tested HIV positive after semi- or supervised HIVSS were followed up telephonically or with a home visit one week after receipt of the test kit to confirm results and linkages to care. Follow-up visits were concluded when the participant indicated that they had used the kit or had accessed a confirmatory HIV test. Results Of the 2061 people approached, 88.2% (1818/2061) received HIV testing information. Of this group, 89% (1618/1818) were enrolled in the study and 70.0% (1133/1618) were tested for HIV with the kit. The median age was 28 (IQR:23–33) years with an even gender distribution. Of those enrolled, 43.0% (696/1618) were identified through homebased outreach, 42.5% (687/1618) through mobile sites, 7.3% (118/1618) at their workplace and 7.2% (117/1618) from sex worker programmes. A total of 68.7% (1110/1616) selected unsupervised HIVSS, whereas 6.3% (101/1616) opted for semi-supervised and 25.0% ((405/1616) chose supervised HIVSS. Overall, the HIV prevalence using the HIVSS test was 8.2% (93/1129). Of those newly diagnosed with HIV, 16% (12/75) were initiated on ART. Almost half (48.0%; 543/1131) of those tested were linked to a primary HIV test as follows: supervised (85.2%; 336/394); semi-supervised (93.8%; 91/97) and unsupervised (18.1%; 116/640). Conclusion Unsupervised HIVSS was by far the most selected and utilised HIVSS method. Linkages to primary and confirmatory testing for the unsupervised HIVSS and further care were low, despite home visits and telephonic reminders.

Background: HIV-1 pre-exposure prophylaxis (PrEP) has focused predominantly on protective efficacy in receptive sex, with limited research on the dosing requirements for insertive sex. We pre-clinically assessed the ex vivo pharmacokinetic–pharmacodynamic (PK–PD) profile of tenofovir (TFV) and tenofovir alafenamide (TAF) in foreskin tissue. Methods: Inner and outer foreskin explants were exposed to serial dilutions of TFV or TAF prior to addition of HIV-1BaL at a high (HVT) or a low viral titer (LVT). Infection was assessed by measurement of p24 in foreskin culture supernatants. TFV, TAF and TFV–diphosphate (TFV–DP) concentrations were measured in tissues, culture supernatants and dosing and washing solutions. Results: Dose–response curves were obtained for both drugs, with greater potency observed against LVT. Inhibitory equivalency mimicking oral dosing was defined between 1 mg/mL of TFV and 15 µg/mL of TAF against HVT challenge. Concentrations of TFV–DP in foreskin explants were approximately six-fold higher after ex vivo dosing with TAF than with TFV. Statistically significant negative linear correlations were observed between explant levels of TFV or TFV–DP and p24 concentrations following HVT. Conclusions: Pre-clinical evaluation of TAF in foreskin explants revealed greater potency than TFV against penile HIV transmission. Clinical evaluation is underway to support this finding.

BackgroundIn highly resource-limited settings, many clinics lack same-day microbiological testing for active tuberculosis (TB). In these contexts, risk of pretreatment loss to follow-up is high, and a simple, easy-to-use clinical risk score could be useful.Methods and findingsWe analyzed data from adults tested for TB with Xpert MTB/RIF across 28 primary health clinics in rural South Africa (between July 2016 and January 2018). We used least absolute shrinkage and selection operator regression to identify characteristics associated with Xpert-confirmed TB and converted coefficients into a simple score. We assessed discrimination using receiver operating characteristic (ROC) curves, calibration using Cox linear logistic regression, and clinical utility using decision curves. We validated the score externally in a population of adults tested for TB across 4 primary health clinics in urban Uganda (between May 2018 and December 2019). Model development was repeated de novo with the Ugandan population to compare clinical scores. The South African and Ugandan cohorts included 701 and 106 individuals who tested positive for TB, respectively, and 686 and 281 randomly selected individuals who tested negative. Compared to the Ugandan cohort, the South African cohort was older (41% versus 19% aged 45 years or older), had similar breakdown of biological sex (48% versus 50% female), and had higher HIV prevalence (45% versus 34%). The final prediction model, scored from 0 to 10, included 6 characteristics: age, sex, HIV (2 points), diabetes, number of classical TB symptoms (cough, fever, weight loss, and night sweats; 1 point each), and >14-day symptom duration. Discrimination was moderate in the derivation (c-statistic = 0.82, 95% CI = 0.81 to 0.82) and validation (c-statistic = 0.75, 95% CI = 0.69 to 0.80) populations. A patient with 10% pretest probability of TB would have a posttest probability of 4% with a score of 3/10 versus 43% with a score of 7/10. The de novo Ugandan model contained similar characteristics and performed equally well. Our study may be subject to spectrum bias as we only included a random sample of people without TB from each cohort. This score is only meant to guide management while awaiting microbiological results, not intended as a community-based triage test (i.e., to identify individuals who should receive further testing).ConclusionsIn this study, we observed that a simple clinical risk score reasonably distinguished individuals with and without TB among those submitting sputum for diagnosis. Subject to prospective validation, this score might be useful in settings with constrained diagnostic resources where concern for pretreatment loss to follow-up is high.

Objective To assess whether organisational culture influences the fidelity of implementation of the Integrated Chronic Disease Management (ICDM) model at primary healthcare (PHC) clinics.Design A cross-sectional study.Setting The ICDM model was introduced in South African clinics to strengthen delivery of care and improve clinical outcomes for patients with chronic conditions, but the determinants of its implementation have not been assessed.Participants The abbreviated Denison organisational culture (DOC) survey tool was administered to 90 staff members to assess three cultural traits: involvement, consistency and adaptability of six PHC clinics in Dr. Kenneth Kaunda and West Rand (WR) health districts.Primary and secondary outcome measures Each cultural trait has three indices with five items, giving a total of 45 items. The items were scored on a Likert scale ranging from one (strongly disagree) to five (strongly agree), and mean scores were calculated for each item, cultural traits and indices. Descriptive statistics were used to describe participants and clinics, and Pearson correlation coefficient to asses association between fidelity and culture.Results Participants’ mean age was 38.8 (SD=10.35) years, and 54.4% (49/90) were nurses. The overall mean score for the DOC was 3.63 (SD=0.58). The involvement (team orientation, empowerment and capability development) cultural trait had the highest (3.71; SD=0.72) mean score, followed by adaptability (external focus) (3.62; SD=0.56) and consistency (3.56; SD=0.63). There were no statistically significant differences in cultural scores between PHC clinics. However, culture scores for all three traits were significantly higher in WR (involvement 3.39 vs 3.84, p=0.011; adaptability 3.40 vs 3.73, p=0.007; consistency 3.34 vs 3.68, p=0.034).Conclusion Leadership intervention is required to purposefully enhance adaptability and consistency cultural traits of clinics to enhance the ICDM model’s principles of coordinated, integrated, patient-centred care.

BackgroundA cost analysis of implementation of interventions informs budgeting and economic evaluations.ObjectiveTo estimate the cost of implementing the integrated chronic disease management (ICDM) model in primary healthcare (PHC) clinics in South Africa.MethodsCost data from the provider's perspective were collected in 2019 from four PHC clinics with comparable patient caseloads (except for one). We estimated the costs of implementing the ICDM model current activities for three (facility reorganization, clinical supportive management and assisted self-management) components and additional costs of implementing with enhanced fidelity. Costs were estimated based on budget reviews, interviews with management teams, and other published data. The standard of care activities such as medication were not included in the costing. One-way sensitivity analyses were carried out for key parameters by varying patient caseloads, required infrastructure and staff. Annual ICDM model implementation costs per PHC clinic and per patient per visit are presented in 2019 US dollars.ResultsThe overall mean annual cost of implementing the ICDM model was $148 446.00 (SD: $65 125.00) per clinic. Current ICDM model activities cost accounted for 84% ($124 345.00) of the annual mean cost, while additional costs for higher fidelity were 16% ($24 102.00). The mean cost per patient per visit was $6.00 (SD:$0.77); $4.94 (SD:0.70) for current cost and $1.06 (SD:0.33) for additional cost to enhance ICDM model fidelity. For the additional cost, 49% was for facility reorganization, 31% for adherence clubs and 20% for training of nursing staff. In the sensitivity analyses, the major cost drivers were the proportion of effort of assisted self-management staff and the number of patients with chronic diseases receiving care at the clinic.ConclusionMinimal additional cost are required to implement the ICDM model with higher fidelity. Further research on the cost-effectiveness of the ICDM model in middle-income countries is required.

IntroductionHousehold contacts of patients with active pulmonary tuberculosis (TB) often have latent TB infection, and are at risk of progression to disease. We set out to investigate whether index TB case HIV status was linked to a higher probability of latent TB infection among household contacts.Materials and methodsData were collected prospectively from participants in the intervention arm of a household cluster-randomised trial in two South Africa provinces (Mangaung, Free State, and Capricorn, Limpopo). In intervention group households, TB contacts underwent HIV testing and tuberculin skin testing (TST). TST induration was estimated at two cut-offs (≥5mm, ≥10mm). Multilevel Bayesian regression models estimated posterior distributions of the percentage of household contacts with TST induration ≥5mm and ≥10mm by age group, and compared the odds of latent TB infection by key risk factors including HIV status index case age and study province.ResultsA total of 2,985 household contacts of 924 index cases were assessed, with most 2,725 (91.3%) undergoing TST. HIV prevalence in household contacts was 14% and 10% in Mangaung and Capricorn respectively. Overall, 16.8% (458/2,725) had TST induration of ≥5mm and 13.1% (359/2,725) ≥10mm. In Mangaung, children aged 0-4 years had a high TST positivity prevalence compared to their peers in Capricorn (22.0% vs. 7.6%, and 20.5% vs. 2.3%, using TST thresholds of ≥5mm and ≥10mm respectively). Compared to contacts from Capricorn, household contacts living in Mangaung were more likely to have TST induration ≥5mm (odds ratio [OR]: 3.08, 95% credibility interval [CI]: 2.13-4.58) and ≥10mm (OR: 4.52, 95% CI: 3.03-6.97). There was a 90% and 92% posterior probability that the odds of TST induration ≥5mm (OR: 0.79, 95% CI: 0.56-1.14) and ≥10mm (OR: 0.77, 95% CI: 0.53-1.10) respectively were lower in household contacts of HIV-positive compared to HIV-negative index cases.ConclusionsHigh TST induration positivity, especially among young children and people living in Mangaung indicates considerable TB transmission despite high antiretroviral therapy coverage. Household contact of HIV-positive index TB cases were less likely to have evidence of latent TB infection than contacts of HIV-negative index cases.

Abstract Background Tuberculosis (TB) is the leading cause of mortality among people living with HIV (PLHIV), despite the availability of effective preventive therapy. The TEKO trial is assessing the impact of using a blood test, Quantiferon-TB Gold In-Tube Test (QGIT), to screen for latent TB compared to the Tuberculin Screening Test (TST) among PLHIV in South Africa. Methods Fifty-six qualitative interviews were conducted with PLHIV and clinical providers participating in the TEKO trial. We explored TB screening, diagnosis, and treatment guidelines and processes and the use of the QGIT to screen for latent TB infection at the time of CD4 blood draw. Thematic content analysis was conducted. Results Considerable variability in TB screening procedures was documented due to lack of personnel and clarity regarding current national TB guidelines for PLHIV. Few clinics had started using the TST per national guidelines and many patients had never heard of isoniazid preventive therapy (IPT). Nearly all participants supported the idea of latent TB screening using routine blood drawn for CD4 counts. Conclusions Findings indicate that screening for latent TB infection using QGIT from blood drawn for CD4 counts among PLHIV is an acceptable approach to increase latent TB detection given the challenges associated with ensuring systematic latent TB screening in overburdened public clinics. Trial registration The results presented here were from formative research related to the TEKO trial (Identifier NCT02119130, registered 10 April 2014).

Abstract Objectives Secondhand tobacco smoke (SHS), use of solid fuels, and kerosene may play an important role in perpetuating the tuberculosis (TB) epidemic. The purpose of this study was to explore the prevalence of household air pollution (HAP) from these sources in homes of someone with TB in a high HIV-prevalence setting. A convenience sample of homes and household members participating in an ongoing active case-finding study in Matlosana district townships surrounding Klerksdorp, South Africa were included. Results We found a high prevalence of air pollution from SHS, solid fuels, and kerosene among individuals in homes with a case of prevalent active TB disease in Klerksdorp, South Africa. Adults in 40% of homes reported a daily smoker in the home, and 70% of homes had detectable air nicotine. In homes with a history of previous TB (prior to but not including the index case) as compared to those without previous TB, both SHS (83% vs. 65%, respectively) and solid/kerosene fuel use for more than 1 h/day (27% vs. 21%, respectively) were more prevalent. Larger studies are needed to estimate the risk of TB from these types of air pollution in HIV infected individuals and settings with high HIV prevalence.

Abstract Background Tuberculosis (TB) is the leading infectious killer worldwide, with approximately 1.8 million deaths in 2015. While effective treatment exists, implementation of active case finding (ACF) methods to identify persons with active TB in a timely and cost-effective manner continues to be a major challenge in resource-constrained settings. Limited qualitative work has been conducted to gain an in-depth understanding of implementation barriers. Methods Qualitative research was conducted to inform the development of three ACF strategies for TB to be evaluated as part of the Kharitode cluster-randomised trial being conducted in a rural province of South Africa. This included 25 semi-structured in-depth interviews among 8 TB patients, 7 of their household members and 10 clinic health workers, as well as 4 focus group discussions (2 rural and 2 main town locations) with 6–8 participants each (n = 27). Interviews and focus group discussions explored the context, advantages and limitations, as well as the implications of three ACF methods. Content analysis was utilised to document salient themes regarding their feasibility, acceptability and potential effectiveness. Results Study participants (TB patients and community members) reported difficulty identifying TB symptoms and seeking care in a timely fashion. In turn, all stakeholder groups felt that more proactive case finding strategies would be beneficial. Clinic-based strategies (including screening all patients regardless of visit purpose) were seen as the most acceptable method based on participants’ preference ranking of the ACF strategies. However, given the resource constraints experienced by the public healthcare system in South Africa, many participants doubted whether it would be the most effective strategy. Household outreach and incentive-based strategies were described as promising, but participants reported some concerns (e.g. stigma in case of household-based and ethical concerns in the case of incentives). Participants offered insights into how to optimise each strategy, tailoring implementation to community needs (low TB knowledge) and realities (financial constraints, transport, time off from work). Conclusions Findings suggest different methods of TB ACF are likely to engage different populations, highlighting the utility of a comprehensive approach. Trial registration Clinicaltrials.gov ( NCT02808507 ). Registered June 1, 2016. The participants in this formative study are not trial participants.

IntroductionThe South African Department of Health has developed and implemented the Integrated Chronic Disease Management (ICDM) model to respond to the increased utilisation of primary healthcare services due to a surge of non-communicable diseases coexisting with a high prevalence of communicable diseases. However, some of the expected outcomes on implementing the ICDM model have not been achieved. The aims of this study are to assess if the observed suboptimal outcomes of the ICDM model implementation are due to lack of fidelity to the ICDM model, to examine the contextual factors associated with the implementation fidelity and to calculate implementation costs.Methods and analysisA process evaluation, mixed methods study in 16 pilot clinics from two health districts to assess the degree of fidelity to four major components of the ICDM model. Activity scores will be summed per component and overall fidelity score will be calculated by summing the various component scores and compared between components, facilities and districts. The association between contextual factors and the degree of fidelity will be asseseed by multivariate analysis, individual and team characteristics, facility features and organisational culture indicators will be included in the regression. Health system financial and economic costs of implementing the four components of the ICDM model will be calculated using an ingredient approach. The unit of implementation costs will be by activity of each of the major components of the ICDM model. Sensitivity analysis will be carried out using clinic size, degree of fidelity and different inflation situations.Ethics and disseminationThe protocol has been approved by the University of Cape Town and University of the Witwatersrand Human Research ethics committees. The results of the study will be shared with the Department of Health, participating health facilities and through scientific publications and conference presentations.

BackgroundThere is a dearth of comparative effectiveness research examining the implementation of different strategies for active tuberculosis (TB) case finding, particularly in rural settings, which represent 60% of the population of sub-Saharan Africa.Methods and findingsWe conducted a pragmatic, cluster-randomized comparative effectiveness trial of two TB case finding strategies (facility-based screening and contact tracing) in 56 public primary care clinics in two largely rural districts of Limpopo Province, South Africa. In the facility-based screening arm, sputum Xpert MTB/RIF was performed on all patients presenting (for any reason) with TB symptoms to 28 study clinics, and no contact tracing was performed. In the contact-tracing arm, contacts of patients with active TB were identified (via household tracing in 14 clinics and using small monetary incentives in the other 14 clinics), screened for TB symptoms, and offered Xpert MTB/RIF testing. The primary outcome was the number of newly identified patients with TB started on treatment. The analysis used multivariable Poisson regression adjusted for historical clinic-level TB case volumes and district. The trial was registered with ClinicalTrials.gov (NCT02808507). From July 18, 2017, to January 17, 2019, a total of 3,755 individuals started TB treatment across 56 study clinics in the 18-month period. Clinic characteristics and clinic-level averages of patient characteristics were similar across the two arms: 40/56 (71%) clinics were in a rural location, 2,136/3,655 (58%) patients were male, and 2,243 (61%) were HIV positive. The treatment initiation ratio comparing the yield of TB patients started on treatment in the facility-based arm compared to that from the contact-tracing arm was 1.04 (95% confidence interval [CI] 0.83-1.30, p = 0. 73). In the contact-tracing arm, 1,677 contacts of 788 new TB index patients were screened, yielding 12 new patients with TB. Prespecified subgroup analyses resulted in similar results, with estimated treatment initiation ratios of 0.96 (95% CI 0.64-1.27; p = 0.78) and 1.23 (95% CI 0.87-1.59; p = 0.29) among historically smaller and historically larger clinics, respectively. This ratio was 1.02 (95% CI 0.66-1.37; p = 0.93) and 1.08 (95% CI 0.74-1.42; p = 0.68) in the Vhembe and Waterberg districts, respectively. The estimated treatment initiation ratio was unchanged in sensitivity analyses excluding 24 records whose TB registration numbers could not be verified (1.03, 95% CI 0.82-1.29; p = 0.78) and excluding transfers-in (1.02, 95% CI 0.80-1.29; p = 0.71). Study limitations include the possibility of imbalance on cluster size owing to changes in catchment population over time and the inability to distinguish the independent effects of the two contact investigation strategies.ConclusionsContact tracing based on symptom screening and Xpert MTB/RIF testing did not increase the rate of treatment initiation for TB relative to the less resource-intensive approach of facility-based screening in this rural sub-Saharan setting.Trial registrationClinicalTrials.gov NCT02808507.

Objectives The use of tobacco by youth constitutes a major public health problem globally as well as in South Africa. Early onset of smoking increases the risk of contracting a wide range of potentially fatal diseases. Therefore, the aim was to assess the prevalence and risk factors of tobacco smoking in youth. Methods Cross-sectional study across five medical male circumcision (MMC) sites in three provinces in South Africa among young healthy men aged 10-18 years. Data were collected on demographics, tobacco (positive urine cotinine test) and dagga smoking, risky behaviour, and alcohol consumption. A CO breathalyser test was done to categorise smokers as either mild, moderate or severe. Multivariable logistic regression was used to determine risk factors of tobacco smoking. Results Of the 1109 participants, 68.9% were aged 10-14 years, 93.3% were in school/studying, 17.7% and 41.0% had mothers and fathers who smoke, 10% (105/1088) of participants were tobacco smokers with 51.7% being severe smokers. Participants aged 15-18 years were more likely to have anyone smoking indoors in the past 30 days (32.0% vs. 19.8%, p

Background Dry nasal snuff is a fine powdered smokeless tobacco product inhaled through the nose. People living with HIV (PLWH) in South Africa have a higher prevalence of smoking than their sero-negative peers, however little is known about the prevalence of snuff use or its health effects. Methods A cross-sectional survey was conducted among randomly selected adults with HIV infection attending 3 HIV treatment clinics in Klerksdorp, South Africa from April 2012 to August 2013. A questionnaire was administered to participants to assess snuff use and current smoking status, and urine for cotinine analysis was collected from each participant. Results We enrolled 1,130 HIV-infected adults, of whom 705 (62%) were women. At the time of interview, 304 (43%) women and 11 (3%) men self-reported snuff use. Only 10 (3%) women who used snuff also smoked cigarettes, thus we limited our analysis to the n = 606 non-smoking women. Nearly all participants were receiving ART, and their median (IQR) CD4 count and BMI were 390 cells/mL (236 - 564 cells/mL) and 25 kg/m 2 (21 - 30 kg/m 2 ), respectively. Adjusted analysis showed odds of snuff use were lower among women completing grade 12 or higher (OR 0.3; 95% CI: 0.2, 0.6). Odds of snuff use were higher among women who had ever had tuberculosis (TB) (OR 1.4; 95% CI 1.0 - 2.1). A subset of participants was asked about alcohol use, which was positively associated with snuff use (OR 2.8; 95% CI: 1.3 - 6.0). In the model including alcohol, association with TB lost statistical significance. Conclusions An extremely high proportion of women with HIV use snuff. Snuff prevention and cessation strategies are needed and should not be overlooked by tobacco control efforts, especially for women, in this population. Drivers of snuff use and the health consequences, particularly regarding TB, need further elucidation.

Background Despite public health intervention, exposure to secondhand smoke, specifically in the home, remains high. Secondhand smoke has been linked to several health outcomes however there is limited information on how secondhand smoke impacts on severity of smoking. Methods We report interim results of a cross-sectional study among young men (10-34 years) attending five Voluntary Medical Male Circumcision (VMMC) clinics in South Africa. Data were collected on participant and parental smoking status; exposure to secondhand smoking and alcohol consumption. A qualitative urine test for cotinine and a breathalyser test for Carbon monoxide measured in parts per million (COppm) were administered. COppm scores were classified into two categories: moderate/mild and severe. Secondhand smoking was defined as exposure to indoor and family members smoking. Logistic regression was used to determine risk factors associated with severe smoking. Results Of the 2465 participants, median age 20 (IQR: 13-27) years, 32.5% (785/2418) tested positive for urine cotinine of which 98.6% (774/785) had a COppm result. COppm result showed 53.2% (412/774) were severe smokers, 46.8% (362/774) were moderate/mild smokers. A total of 46.3% (189/408) of severe smokers reported often having someone smoking in their home of whom 27.8% (72/259) reported that their mother and 59.9% (100/167) report that their father smokes. Overall, 80.3% (330/411) of severe smokers self-reported drinking alcohol. Multivariate analysis adjusting for age and alcohol use showed that severe smoking was associated with often exposure to indoor smoking at home (OR: 1.612 95%CI: 1.195-2.173) and to family members that smoke (OR: 3.495 95%CI: 1.413-8.646). Conclusions Family members who smoke and alcohol use put young men at risk of severe smoking. Rules and social norms must encourage smokers to smoke outside of their houses. Policy interventions should focus on highlighting the risks and reducing the prevalence of secondhand smoking.

The PrePex medical male circumcision (MMC) device is relatively easy to place and remove with some training. PrePex has been evaluated in several countries to assess feasibility and acceptability. However, several studies have reported pain associated with removal.To assess safety of PrePex and whether analgesia administered prior to removal reduces pain experienced by participants.A multi-site non-randomized, prospective cohort study in which adult (18-45 years old) males requesting PrePex device male circumcision, were enrolled in six South African clinics from July 2014 to March 2015. Participants were routinely provided with analgesia shortly after the surveillance commenced following a protocol review. Analgesia regimen for device removal depended on medication availability at clinics.Of 1023 enrolled participants who had PrePex placed, 98% (1004) had the device removed at a study clinic. Their median age was 25 (IQR: 21-30) years. HIV sero-positivity was 3.6% (37/1023). Nurses placed and removed half of all devices. Adverse events were experienced by 2.4% (25/1023) of participants; 15 required surgical intervention: device displacement (5/14), early removals (3/14), self-removals (5/14) and insufficient skin removed (2/14). Majority (792: 79%) of participants received analgesia. Most received either paracetamol-codeine (33%), lidocaine (29%) or EMLA and Oral Combination (28%). A lower proportion of participants who received any analgesia (except for lidocaine) prior to PrePex removal experienced severe pain compared to those who received no analgesia (16.6% vs. 29%: p = 0.0001).Reported adverse events during this PrePex active surveillance were similar to previous reports and to those of surgical circumcision. Pain medication provided prior to removal is effective at decreasing severe pain during PrePex device removal.

Background: Several circumcision devices have been evaluated for a safe and simplified male circumcision among adults. The PrePex device was prequalified for voluntary male medical circumcision (VMMC) in May 2013 by the World Health Organization and is expected to simplify the procedure safely while reducing cost. South Africa is scaling up VMMC. Objective: To evaluate the overall unit cost of VMMC at a mixed site vs. a hypothetical PrePex-only site in South Africa. Design: We evaluated the overall unit cost of VMMC at a mixed site where PrePex VMMC procedure was added to routine forceps-guided scalpel-based VMMC in Soweto, South Africa. We abstracted costs and then modeled these costs for a hypothetical PrePex-only site, at which 9,600 PrePex circumcisions per year could be done. We examined cost drivers and modeled costs, varying the price of the PrePex device. The healthcare system perspective was used. Results: In both sites, the main contributors of cost were personnel and consumables. If 10% of all VMMC were by PrePex at the mixed site, the overall costs of the surgical method and PrePex were similar – US$59.62 and $59.53, respectively. At the hypothetical PrePex-only site, the unit cost was US$51.10 with PrePex circumcisions having markedly lower personnel and biohazardous waste management costs. In sensitivity analysis with the cost of PrePex kit reduced to US$10 and $2, the cost of VMMC was further reduced. Conclusions: Adding PrePex to an existing site did not necessarily reduce the overall costs of VMMC. However, starting a new PrePex-only site is feasible and may significantly reduce the overall cost by lowering both personnel and capital costs, thus being cost-effective in the long term. Achieving a lower cost for PrePex will be an important contributor to the scale-up of VMMC.

Medical device use is currently approved for males without preputial or major penile scrotal abnormalities for voluntary medical male circumcision (VMMC). We determined the prevalence of preputial abnormalities at a busy VMMC centre in Soweto, South Africa.This was a cross-sectional record review at a high-volume VMMC centre in South Africa. We collated pre-circumcision demographic and genital examination findings from clients 8 years and older who had undergone VMMC from 01 May 2013 to 30 April 2014. Logistic regression was used to determine factors associated with preputial abnormalities.During the review period, 6861 circumcisions were conducted and 37.1% (n = 2543) were 8-13 year olds. Median age was 15 years (IQR: 12-23 years). Fifteen percent (n = 1030) had preputial abnormalities or major penile scrotal abnormalities. Age-specific prevalence of preputial or major genital abnormalities were 27.3%, 10.6% and 6.0% in 8-13, 14-18 and > 18 year olds respectively. The odds of preputial or major penile scrotal abnormality were higher in younger clients aged 8-13 years (OR = 5.9; 95% CI = 4.8-7.1) and 14-18 years (OR = 1.9; 95% CI = 1.5-2.4) compared to older clients above18 years and in those testing for HIV outside our clinic network (OR = 1.9; 95% CI = 1.4-2.7).The high prevalence of preputial and penile scrotal abnormalities observed suggests a need for VMMC sites to provide for both open surgical and devices methods in the provision of VMMC services. This is especially so among young male subjects presenting themselves for VMMC services at the various sites being developed in sub Saharan African countries.

Introduction. Tuberculosis is a major cause of morbidity and mortality especially in high HIV burden settings. Active case finding is one strategy to potentially reduce TB disease burden. Xpert MTB/Rif has recently been recommended for diagnosis of TB. Methods. Pragmatic randomized trial to compare diagnosis rate and turnaround time for laboratory testing for Xpert MTB/Rif with TB microscopy and culture in household contacts of patients recently diagnosed with TB. Results. 2464 household contacts enrolled into the study from 768 active TB index cases. 1068 (44%) were unable to give sputum, but 24 of these were already on TB treatment. 863 (53%) participants sputum samples were tested with smear and culture and 2.7% (23/863; CI: 1.62–3.78) were diagnosed with active TB. Xpert MTB/Rif was used in 515 (21%) participants; active TB was diagnosed in 1.6% (8/515; CI: 0.52–2.68). Discussion and Conclusions. Additional 31 cases were diagnosed with contact tracing of household members. When Xpert MTB/Rif is compared with culture, there is no significant difference in diagnostic yield.

The World Health Organisation and the Joint United Nations Programme on HIV/AIDS have recommended the scale-up of Medical Male Circumcision (MMC) in countries with high HIV and low MMC prevalence. PrePex device circumcision is proposed as an alternate method for scaling up MMC.Evaluate safety and feasibility of PrePex in South Africa.A multisite prospective cohort PrePex study in adults and adolescents at three MMC clinics. Participants were followed-up 8 times, up to 56 days after PrePex placement.In total, 398 PrePex circumcisions were performed (315 adults and 83 adolescents) their median ages were 26 (IQR: 22-30) and 16 years (IQR: 15-17), respectively. The median time for device placement across both groups was 6 minutes (IQR: 5-9) with the leading PrePex sizes being B (30%) and C (35%) for adults (18-45 years), and A (31%) and B (38%) for adolescents (14-17 years). Additional sizes (size 12-20) were rarely used, even in the younger age group. Pain of device application was minimal but that of removal was severe. However, described pain abated rapidly and almost no pain was reported 1 hour after removal. The Adverse Events rate were experienced by 2.7% (11/398) of all participants, three of which were serious (2 displacements and 1 self-removal requiring prompt surgery). None of the Adverse Events required hospitalization. The majority of participants returned to work within a day of device placement.Our study shows that PrePex is a safe MMC method, for males 14 years and above. PrePex circumcision had a similar adverse event rate to that reported for surgical MMC, but device removal caused high levels of pain, which subsided rapidly.

To report the incidence rates of TB and HIV in household contacts of index patients diagnosed with TB.A prospective cohort study in the Matlosana sub-district of North West Province, South Africa.Contacts of index TB patients received TB and HIV testing after counseling at their first household visit and were then followed up a year later, in 2010. TB or HIV diagnoses that occurred during the period were determined.For 2,377 household contacts, the overall observed TB incidence rate was 1.3 per 100 person years (95% CI 0.9-1.9/100py) and TB incidence for individuals who were HIV-infected and HIV seronegative at baseline was 5.4/100py (95% CI 2.9-9.0/100py) and 0.7/100py (95% CI 0.3-1.4/100py), respectively. The overall HIV incidence rate was 2.2/100py (95% CI 1.3-8.4/100py).In the year following a household case finding visit when household contacts were tested for TB and HIV, the incidence rate of both active TB and HIV infection was found to be extremely high. Clearly, implementing proven strategies to prevent HIV acquisition and preventing TB transmission and progression to disease remains a priority in settings such as South Africa.