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Abstract Background In the initial phase of the SARS-CoV-2 pandemic, masking has been widely accepted in healthcare institutions to mitigate the risk of healthcare-associated infection. Evidence, however, is still scant and the role of masks in preventing healthcare-associated SARS-CoV-2 acquisition remains unclear.We investigated the association of variation in institutional mask policies with healthcare-associated SARS-CoV-2 infections in acute care hospitals in Switzerland during the BA.4/5 2022 wave. Methods SARS-CoV-2 infections in hospitalized patients between June 1 and September 5, 2022, were obtained from the “Hospital-based surveillance of COVID-19 in Switzerland”-database and classified as healthcare- or community-associated based on time of disease onset. Institutions provided information regarding institutional masking policies for healthcare workers and other prevention policies. The percentage of healthcare-associated SARS-CoV-2 infections was calculated per institution and per type of mask policy. The association of healthcare-associated SARS-CoV-2 infections with mask policies was tested using a negative binominal mixed-effect model. Results We included 2’980 SARS-CoV-2 infections from 13 institutions, 444 (15%) were classified as healthcare-associated. Between June 20 and June 30, 2022, six (46%) institutions switched to a more stringent mask policy. The percentage of healthcare-associated infections subsequently declined in institutions with policy switch but not in the others. In particular, the switch from situative masking (standard precautions) to general masking of HCW in contact with patients was followed by a strong reduction of healthcare-associated infections (rate ratio 0.39, 95% CI 0.30–0.49). In contrast, when compared across hospitals, the percentage of health-care associated infections was not related to mask policies. Conclusions Our findings suggest switching to a more stringent mask policy may be beneficial during increases of healthcare-associated SARS-CoV-2 infections at an institutional level.

BACKGROUND: The COVID-19 pandemic has placed unprecedented pressure on hospitals worldwide. In such a context of tension in healthcare systems, efficiently allocating hospital resources is a crucial aspect of crisis management. The aim of this study was to describe the clinical characteristics of readmitted patients and to determine risk factors for hospital readmission using data from the Swiss COVID-19 Hospital-Based Surveillance system (CH-SUR). METHODS: We investigated hospital readmissions within 60 days after discharge of patients from the CH-SUR surveillance system with a first hospitalisation between 1 December 2020 and 1 December 2021. Only community-acquired cases were considered. We compared the baseline characteristics of readmitted and non-readmitted patients. We performed univariable and multivariable logistic regression analyses to investigate the risk factors for hospital readmission. FINDINGS: Of the 8039 eligible patients, 239 (3.0%, 95% confidence interval [CI] 2.6–3.3%) were readmitted to hospital within 60 days of discharge, with no significant variations observed over the study period; 80% of all readmissions occurred within 10 days of discharge of the index hospital stay. Based on our multivariable logistic regression models, factors increasing the odds of hospital readmission were age ≥65 years (odds ratio [OR] 1.63, 95% CI 1.24–2.15), male sex (OR 1.47, 95% CI 1.12–1.93), being discharged to home after first hospitalisation (OR 1.77, 95% CI 1.19–2.62), having oncological pathology (OR 1.82, 95% CI 1.27–2.61) and being immunosuppressed (OR 2.34, 95% CI 1.67–3.29). INTERPRETATIONS: Age, sex, cardiovascular diseases, oncological pathologies and immunosuppression were the main risk factors identified for hospital readmission.

Abstract Background In 2021, an Ebola virus disease (EVD) outbreak was declared in Guinea, linked to persistent virus from the 2014–2016 West Africa Epidemic. This paper analyzes factors associated with contact tracing reliability (defined as completion of a 21-day daily follow-up) during the 2021 outbreak, and transitively, provides recommendations for enhancing contact tracing reliability in future. Methods We conducted a descriptive and analytical cross-sectional study using multivariate regression analysis of contact tracing data from 1071 EVD contacts of 23 EVD cases (16 confirmed and 7 probable). Results Findings revealed statistically significant factors affecting contact tracing reliability. Unmarried contacts were 12.76× more likely to miss follow-up than those married (OR = 12.76; 95% CI [3.39–48.05]; p

INTRODUCTION: With the emergence of newer SARS-CoV-2 variants and their substantial effects on the levels and duration of protection against infection, an understanding of these characteristics of the protection conferred by humoral and cellular immunity can aid in the proper development and implementation of vaccine and safety guidelines. METHODS: We conducted a rapid literature review and searched five electronic databases weekly from 1 November 2021 to 30 September 2022. Studies that assessed the humoral or cellular immunity conferred by infection, vaccination or a hybrid (combination of both) in adults and risk groups (immunocompromised and older populations) were identified. Studies were eligible when they reported data on immunological assays of COVID-19 (related to vaccination and/or infection) or the effectiveness of protection (related to the effectiveness of vaccination and/or infection). RESULTS: We screened 5103 studies and included 205 studies, of which 70 provided data on the duration of protection against SARS-CoV-2 infection. The duration of protection of adaptive immunity was greatly impacted by Omicron and its subvariants: levels of protection were low by 3–6 months from exposure to infection/vaccination. Although more durable, cellular immunity also showed signs of waning by 6 months. First and second mRNA vaccine booster doses increased the levels of protection against infection and severe disease from Omicron and its subvariants but continued to demonstrate a high degree of waning over time. CONCLUSION: All humoral immunities (infection-acquired, vaccine-acquired and hybrid) waned by 3–6 months. Cellular immunity was more durable but showed signs of waning by 6 months. Hybrid immunity had the highest magnitude of protection against SARS-CoV-2 infection. Boosting may be recommended as early as 3–4 months after the last dose, especially in risk groups.

Background Chronic obstructive pulmonary disease (COPD) and tuberculosis (TB) impose a substantial economic burden globally. This systematic review summarised the evidence on the costs of COPD, including post-TB diseases in low- and middle-income countries.Methods A systematic review was conducted and studies published between 1 January 2013 and 28 March 2022 (the date of the search) were identified using various electronic databases without language restrictions. Titles, abstracts and full texts were screened in duplicate and data were extracted and verified by reviewers. Eligible studies were categorised as cost analysis and/or economic burden studies, and costs were converted to 2021 United State dollar. Meta-analysis was conducted on the costs of hospitalisations, medication and outpatient visits.Results 128 cost studies and 65 economic burden studies were included in this review. The data collected are presented in the Cost Database of COPD and Post-TB (CD-CPTB). The majority of studies were from Asia, Eastern Europe and Latin America, with a few from other middle-income countries. There were extremely limited data on the costs of post-TB sequelae and only a few studies were from Africa (n=6) and low-income (n=5) countries. The direct medical costs of COPD ranged from $26 per hospitalisation in India to $2694 per year per patient with severe disease in Mexico, while the costs of acute exacerbation of COPD ranged from $137 to $4207 per exacerbation with both the minimum and maximum costs occurring in Turkey. The costs were lower in lower middle-income countries compared with upper middle-income countries. Finally, considerable economic burden was attributable to smoking and air pollution.Conclusion The review and the CD-CPTB database give a thorough snapshot of the current evidence of the costs and economic burden of COPD and post-TB diseases. Future research is needed to investigate the economic impact after TB treatment and should be prioritised in Africa and low-income countries where there has been a lack of data collection.Protocol registration number CRD42022326609.

Abstract Background Persons with disability may have a higher HIV prevalence and be less likely than persons without disability to know their HIV-positive status, access antiretroviral therapy (ART), and suppress their HIV viral load (HIV care cascade). However, studies examining differences between persons with and without disability in HIV prevalence and the HIV care cascade are lacking. Using the Tanzania HIV Impact Survey (THIS) data collected between October 2016 and August 2017, we assessed differences in HIV prevalence and progress towards achieving the 2020 HIV care cascade target between persons with and without disability. Methods Using the Washington Group Short Set (WG-SS) Questions on Disability, we defined disability as having a functional difficulty in any of the six life domains (seeing, hearing, walking/climbing, remembering/ concentrating, self-care, and communicating). We classified respondents as disabled if they responded having either “Some Difficulty”, “A lot of difficulties” or “Unable to” in any of the WG-SS Questions. We presented the sample characteristics by disability status and analyzed the achievement of the cascade target by disability status, and sex. We used multivariable logistic regressions, and adjusted for age, sex, rural-urban residence, education, and wealth quintile. Results A total of 31,579 respondents aged 15 years and older had HIV test results. Of these 1,831 tested HIV-positive, corresponding to an estimated HIV prevalence of 4.9% (CI: 4.5 — 5.2%) among the adult population in Tanzania. The median age of respondents who tested HIV-positive was 32 years (with IQR of 21—45 years). HIV prevalence was higher (5.7%, 95% CI: 5.3—7.4%) among persons with disability than persons without disability (4.3%, 95% CI: 4.0 — 4.6%). Before adjustment, compared to women without disability, more women with disability were aware of their HIV-positive status (n = 101, 79.0%, 95% CI: 68.0—87.0% versus n = 703, 63.0%, 95% CI: 59.1—66.7%) and accessed ART more frequently (n = 98, 98.7%, 95% CI: 95.3—99.7% versus n = 661, 94.7%, 95% CI: 92.6—96.3%). After adjusting for socio-demographic characteristics, the odds of having HIV and of accessing ART did not differ between persons with and without disability. However, PLHIV with disability had higher odds of being aware of their HIV-positive status (aOR 1.69, 95% 1.05—2.71) than PLHIV without disability. Men living with HIV and with disability had lower odds (aOR = 0.23, 95% CI: 0.06—0.86) to suppress HIV viral loads than their counterparts without disability. Conclusion We found no significant differences in the odds of having HIV and of accessing ART between persons with and without disability in Tanzania. While PLHIV and disability, were often aware of their HIV-positive status than their non-disabled counterparts, men living with HIV and with disability may have been disadvantaged in having suppressed HIV viral loads. These differences are correctable with disability-inclusive HIV programming. HIV surveys around the world should include questions on disability to measure potential differences in HIV prevalence and in attaining the 2025 HIV care cascade target between persons with and without disability.

We assessed socioeconomic inequalities in social protection coverage among the public, men and women living with the human immunodeficiency virus (MLHIV, WLHIV), and adolescent girls and young women (AGYW). We used population-based data from Cameroon, Côte d'Ivoire, Ethiopia, Eswatini, Kenya, Lesotho, Malawi, Namibia, Rwanda, Tanzania, Uganda, Zambia, and Zimbabwe. We constructed concentration curves (CC) and computed concentration indices (CIX) for each country and population group. A CC represents the cumulative percentage of social protection coverage plotted on the y-axis against the cumulative proportion of the population-ranked by socioeconomic status from the poorest to the richest-on the x-axis. The CIX quantifies the concentration of social protection coverage among the poor or the rich. The sample size ranged from 10,197 in Eswatini to 29,577 in Tanzania. Social protection coverage among the public varied from 5.2% (95% Confidence Interval 4.5%-6.0%) in Ethiopia to 39.9% (37.0%-42.8%) in Eswatini. It ranged from 6.9% (5.7%-8.4%) MLHIV in Zambia to 45.0% (41.2-49.0) among WLHIV in Namibia. Among AGYW, it varied from 4.4% (3.6-5.3) in Ethiopia to 44.6% (40.8-48.5) in Eswatini. Socioeconomic inequalities in social protection coverage favored the poor in 11/13 countries surveyed. It favored the rich in Cameroon and was undefined in Côte d'Ivoire. The CIX in these 11 countries ranged from -0.080 (p = 0.002) among the public in Malawi to -0.372 (p< 0.001) among WLHIV in Zimbabwe. In 8 of these 11 countries, ≥15% of people from the poorest households reported receiving social protection. Only in countries with higher levels of social protection coverage did most people from the poorest households achieve high coverage. Social protection coverage was low and favored the poor. Pro-poor social protection is insufficient to reach the poor. Research is required to reach the poorest households with social protection in Africa.

BackgroundFemale sex workers (FSWs) are at high risk for HIV infection and face unique barriers to receiving and adhering to testing and treatment. Early viral suppression and consistent viral load testing are critical to optimizing health and reducing transmission in this population. However, the factors associated with testing and successful viral suppression among FSWs are poorly understood, especially in Sub-Saharan Africa. Our study aimed to examine factors, including social, demographic, and clinical characteristics, associated with viral load testing and suppression among female sex workers initiating antiretroviral therapy in Nigeria.MethodsIn this retrospective study, we analyzed routine programmatic data from FSWs enrolled in the National HIV Key Populations (KP) program in Nigeria. We included FSWs who were newly diagnosed with HIV and registered between January 2016 and January 2022. Primary outcomes of interest were a), receiving a viral load test at any point after treatment initiation and b), viral suppression (FindingsOut of 34,976 FSWs, 97.1% (n = 33,945) received at least one viral load test, with 94.5% (n = 32,092) indicating viral suppression. The odds of receiving at least one viral load test were higher for those who entered treatment in more recent years, those with formal education and those with advanced HIV stages at baseline (adjusted odds ratios [aOR]: 1.17 [1.14-1.19] for those who entered treatment in 2020 vs. 2016; 1.02 [1.01-1.03] for post-secondary vs. no education; and 1.05 [1.01-1.10] for WHO clinical stage 3/4 vs. stage 1 respectively). The odds of successful viral suppression were higher for those who entered treatment in more recent years, but lower for those with advanced HIV stages at baseline (aOR: 1.13 [1.09-1.18] for 2022 vs. 2016; and 0.92 [0.87-0.98] for WHO clinical stage 3/4 vs. stage 1 respectively).ConclusionsThe study underscored the relevance of timely diagnosis and ART initiation for optimal outcomes among HIV-positive FSWs in Nigeria. We also observed significant improvements in the likelihood of early viral load testing and suppression over the study period, reflecting advancements in the KP program. Further research should clarify factors driving these trends to further strengthen the HIV care pipeline for female sex workers.

Whilst it is now widely recognised that routine immunisation (RI) was disrupted by the COVID-19 pandemic in 2020, and further so in 2021, the extent of continued interruptions in 2022 and/or rebounds to previous trends remains unclear.We modelled country-specific RI trends using validated estimates of national coverage from the World Health Organisation and United Nation Children’s Fund for 182 countries (accounting for > 97% of children globally), to project expected diphtheria, tetanus, and pertussis-containing vaccine first-dose (DTP1), third-dose (DTP3) and measles-containing vaccine first-dose (MCV1) coverage for 2020–2022 based on pre-pandemic trends (from 2000 to 2019).We provide further evidence of peak pandemic immunisation disruption in 2021, followed by tentative recovery in 2022. We report a 3.4% (95 %CI: [2.5%; 4.4%]) decline in global DTP3 coverage in 2021 compared to 2000–2019 trends, from an expected 89.8% to reported 86.4%. This coverage gap reduced to a 2.7% (95 %CI: [1.8%; 3.6%]) decline in 2022, with reported coverage rising to 87.2%. Similar results were seen for DTP1 and MCV1. Whilst partial rebounds are encouraging, global coverage decline translates to a 17-year setback in RI to 2005 levels, and the majority of countries retain coverage at or lower than pre-pandemic levels. The Americas, Africa, and Asia were the most impacted regions; and low- and middle-income countries the most affected income groups.The number of annual Zero Dose (ZD) children – indicating those receiving no immunisations – increased from 12.1 million (M) globally in 2019 to a peak of 16.7 M in 2021, then reduced to 13.1 M in 2022. Overall, we estimate an excess of 8.8 M ZD children cumulatively in 2020–2022 compared to pre-pandemic levels.This work can be used as an objective baseline to inform future interventions to prioritise and target interventions, and facilitate catch-up of growing populations of under- and un-immunised children.

Background: The prevalence of HIV varies greatly between and within countries. We aimed to build a comprehensive mathematical modelling tool capable of exploring the reasons of this heterogeneity and test its applicability by simulating the Malawian HIV epidemic. Methods: We developed a flexible individual-based mathematical model for HIV transmission that comprises a spatial representation and individual-level determinants. We tested this model by calibrating it to the HIV epidemic in Malawi and exploring whether the heterogeneity in HIV prevalence could be reproduced. We ran the model for 1975–2030 with five alternative realizations of the geographical structure and mobility: (I) no geographical structure; 28 administrative districts including (II) only permanent inter-district relocations, (III) inter-district permanent relocations and casual sexual relationships, or (IV) permanent relocations between districts and to/from abroad and inter-district casual sex; and (V) a grid of 10 × 10km2 cells, with permanent relocations and between-cell casual relationships. We assumed HIV was present in 1975 in the districts with >10 % prevalence in 2010. We calibrated the models to national and district-level prevalence estimates. Results: Reaching the national prevalence required all adults to have at least 22 casual sex acts/year until 1990. Models II, III and V reproduced the geographical heterogeneity in prevalence in 2010 to some extent if between-district relationships were excluded (Model II; 4.9 %–21.1 %). Long-distance casual partnership mixing mitigated the differences in prevalence substantially (range across districts 4.1%–18.9 % in 2010 in Model III; 4.0%–17.6 % in Model V); with international migration the differences disappeared (Model IV; range across districts 6.9%–13.3 % in 2010). National prevalence decreased to 5 % by 2030. Conclusion: Earlier introduction of HIV into the Southern part of Malawi may cause some level of heterogeneity in HIV prevalence. Other factors such as sociobehavioural characteristics are likely to have a major impact and need investigation.

BackgroundLiterature reviews (LRs) identify, evaluate, and synthesize relevant papers to a particular research question to advance understanding and support decision-making. However, LRs, especially traditional systematic reviews, are slow, resource-intensive, and become outdated quickly. ObjectiveLiteRev is an advanced and enhanced version of an existing automation tool designed to assist researchers in conducting LRs through the implementation of cutting-edge technologies such as natural language processing and machine learning techniques. In this paper, we present a comprehensive explanation of LiteRev’s capabilities, its methodology, and an evaluation of its accuracy and efficiency to a manual LR, highlighting the benefits of using LiteRev. MethodsBased on the user’s query, LiteRev performs an automated search on a wide range of open-access databases and retrieves relevant metadata on the resulting papers, including abstracts or full texts when available. These abstracts (or full texts) are text processed and represented as a term frequency-inverse document frequency matrix. Using dimensionality reduction (pairwise controlled manifold approximation) and clustering (hierarchical density-based spatial clustering of applications with noise) techniques, the corpus is divided into different topics described by a list of the most important keywords. The user can then select one or several topics of interest, enter additional keywords to refine its search, or provide key papers to the research question. Based on these inputs, LiteRev performs a k-nearest neighbor (k-NN) search and suggests a list of potentially interesting papers. By tagging the relevant ones, the user triggers new k-NN searches until no additional paper is suggested for screening. To assess the performance of LiteRev, we ran it in parallel to a manual LR on the burden and care for acute and early HIV infection in sub-Saharan Africa. We assessed the performance of LiteRev using true and false predictive values, recall, and work saved over sampling. ResultsLiteRev extracted, processed, and transformed text into a term frequency-inverse document frequency matrix of 631 unique papers from PubMed. The topic modeling module identified 16 topics and highlighted 2 topics of interest to the research question. Based on 18 key papers, the k-NNs module suggested 193 papers for screening out of 613 papers in total (31.5% of the whole corpus) and correctly identified 64 relevant papers out of the 87 papers found by the manual abstract screening (recall rate of 73.6%). Compared to the manual full text screening, LiteRev identified 42 relevant papers out of the 48 papers found manually (recall rate of 87.5%). This represents a total work saved over sampling of 56%. ConclusionsWe presented the features and functionalities of LiteRev, an automation tool that uses natural language processing and machine learning methods to streamline and accelerate LRs and support researchers in getting quick and in-depth overviews on any topic of interest.

Abstract Here we present the design and results of an analytical pipeline for COVID-19 data for Switzerland. It is applied to openly available data from the beginning of the epidemic in 2020 to the present day (august 2022). We analyzed the spatio-temporal patterns of the spread of SARS-CoV2 throughout the country, applying Bayesian inference to estimate population prevalence and hospitalization ratio. We also developed forecasting models to characterize the transmission dynamics for all the country’s cantons taking into account their spatial correlations in COVID incidence. The two-week forecasts of new daily hospitalizations showed good accuracy, as reported herein. These analyses’ raw data and live results are available on the open-source EpiGraphHub platform to support further studies.

AIMS OF THE STUDY: Remdesivir has shown benefits against COVID-19. However, it remains unclear whether, to what extent, and among whom remdesivir can reduce COVID-19-related mortality. We explored whether the treatment response to remdesivir differed by patient characteristics. METHODS: We analysed data collected from a hospital surveillance study conducted in 21 referral hospitals in Switzerland between 2020 and 2022. We applied model-based recursive partitioning to group patients by the association between treatment levels and mortality. We included either treatment (levels: none, remdesivir within 7 days of symptom onset, remdesivir after 7 days, or another treatment), age and sex, or treatment only as regression variables. Candidate partitioning variables included a range of risk factors and comorbidities (and age and sex unless included in regression). We repeated the analyses using local centring to correct the results for the propensity to receive treatment. RESULTS: Overall (n = 21,790 patients), remdesivir within 7 days was associated with increased mortality (adjusted hazard ratios 1.28–1.54 versus no treatment). The CURB-65 score caused the most instability in the regression parameters of the model. When adjusted for age and sex, patients receiving remdesivir within 7 days of onset had higher mortality than those not treated in all identified eight patient groups. When age and sex were included as partitioning variables instead, the number of groups increased to 19–20; in five to six of those branches, mortality was lower among patients who received early remdesivir. Factors determining the groups where remdesivir was potentially beneficial included the presence of oncological comorbidities, male sex, and high age. CONCLUSIONS: Some subgroups of patients, such as individuals with oncological comorbidities or elderly males, may benefit from remdesivir.

Objectives We examined age, residence, education and wealth inequalities and their combinations on cervical precancer screening probabilities for women. We hypothesised that inequalities in screening favoured women who were older, lived in urban areas, were more educated and wealthier.Design Cross-sectional study using Population-Based HIV Impact Assessment data.Setting Ethiopia, Malawi, Rwanda, Tanzania, Zambia and Zimbabwe. Differences in screening rates were analysed using multivariable logistic regressions, controlling for age, residence, education and wealth. Inequalities in screening probability were estimated using marginal effects models.Participants Women aged 25–49 years, reporting screening.Outcome measures Self-reported screening rates, and their inequalities in percentage points, with differences of 20%+ defined as high inequality, 5%–20% as medium, 0%–5% as low.Results The sample size of participants ranged from 5882 in Ethiopia to 9186 in Tanzania. The screening rates were low in the surveyed countries, ranging from 3.5% (95% CI 3.1% to 4.0%) in Rwanda to 17.1% (95% CI 15.8% to 18.5%) and 17.4% (95% CI 16.1% to 18.8%) in Zambia and Zimbabwe. Inequalities in screening rates were low based on covariates. Combining the inequalities led to significant inequalities in screening probabilities between women living in rural areas aged 25–34 years, with a primary education level, from the lowest wealth quintile, and women living in urban areas aged 35–49 years, with the highest education level, from the highest wealth quintile, ranging from 4.4% in Rwanda to 44.6% in Zimbabwe.Conclusions Cervical precancer screening rates were inequitable and low. No country surveyed achieved one-third of the WHO’s target of screening 70% of eligible women by 2030. Combining inequalities led to high inequalities, preventing women who were younger, lived in rural areas, were uneducated, and from the lowest wealth quintile from screening. Governments should include and monitor equity in their cervical precancer screening programmes.

Introduction Despite tremendous progress in the development of diagnostics, vaccines and therapeutics for Ebola virus disease (EVD), challenges remain in the implementation of holistic strategies to rapidly curtail outbreaks. We investigated the effectiveness of a community-based contact isolation strategy to limit the spread of the disease in the Democratic Republic of Congo (DRC).Methods We did a quasi-experimental comparison study. Eligible participants were EVD contacts registered from 12 June 2019 to 18 May 2020 in Beni and Mabalako Health Zones. Intervention group participants were isolated to specific community sites for the duration of their follow-up. Comparison group participants underwent contact tracing without isolation. The primary outcome was measured as the reproduction number (R) in the two groups. Secondary outcomes were the delay from symptom onset to isolation and case management, case fatality rate (CFR) and vaccination uptake.Results 27 324 EVD contacts were included in the study; 585 in the intervention group and 26 739 in the comparison group. The intervention group generated 32 confirmed cases (5.5%) in the first generation, while the comparison group generated 87 (0.3%). However, the 32 confirmed cases arising from the intervention contacts did not generate any additional transmission (R=0.00), whereas the 87 confirmed cases arising from the comparison group generated 99 secondary cases (R=1.14). The average delay between symptom onset and case isolation was shorter (1.3 vs 4.8 days; p

BackgroundGuaranteeing durability, provenance, accessibility, and trust in open data sets can be challenging for researchers and organizations that rely on public repositories of data critical for epidemiology and other health analytics. The required data repositories are often difficult to locate and may require conversion to a standard data format. Data-hosting websites may also change or become unavailable without warning. A single change to the rules in one repository can hinder updating a public dashboard reliant on data pulled from external sources. These concerns are particularly challenging at the international level, because policies on systems aimed at harmonizing health and related data are typically dictated by national governments to serve their individual needs. ObjectiveIn this paper, we introduce a comprehensive public health data platform, EpiGraphHub, that aims to provide a single interoperable repository for open health and related data. MethodsThe platform, curated by the international research community, allows secure local integration of sensitive data while facilitating the development of data-driven applications and reports for decision-makers. Its main components include centrally managed databases with fine-grained access control to data, fully automated and documented data collection and transformation, and a powerful web-based data exploration and visualization tool. ResultsEpiGraphHub is already being used for hosting a growing collection of open data sets and for automating epidemiological analyses based on them. The project has also released an open-source software library with the analytical methods used in the platform. ConclusionsThe platform is fully open source and open to external users. It is in active development with the goal of maximizing its value for large-scale public health studies.

Abstract Emerging infectious diseases are a growing threat in sub-Saharan African countries, but the human and technical capacity to quickly respond to outbreaks remains limited. Here, we describe the experience and lessons learned from a joint project with the WHO Regional Office for Africa (WHO AFRO) to support the sub-Saharan African COVID-19 response. In June 2020, WHO AFRO contracted a number of consultants to reinforce the COVID-19 response in member states by providing actionable epidemiological analysis. Given the urgency of the situation and the magnitude of work required, we recruited a worldwide network of field experts, academics and students in the areas of public health, data science and social science to support the effort. Most analyses were performed on a merged line list of COVID-19 cases using a reverse engineering model (line listing built using data extracted from national situation reports shared by countries with the Regional Office for Africa as per the IHR (2005) obligations). The data analysis platform The Renku Project ( https://renkulab.io ) provided secure data storage and permitted collaborative coding. Over a period of 6 months, 63 contributors from 32 nations (including 17 African countries) participated in the project. A total of 45 in-depth country-specific epidemiological reports and data quality reports were prepared for 28 countries. Spatial transmission and mortality risk indices were developed for 23 countries. Text and video-based training modules were developed to integrate and mentor new members. The team also began to develop EpiGraph Hub, a web application that automates the generation of reports similar to those we created, and includes more advanced data analyses features (e.g. mathematical models, geospatial analyses) to deliver real-time, actionable results to decision-makers. Within a short period, we implemented a global collaborative approach to health data management and analyses to advance national responses to health emergencies and outbreaks. The interdisciplinary team, the hands-on training and mentoring, and the participation of local researchers were key to the success of this initiative.

Non-pharmaceutical interventions remain key in mitigating the spread of SARS-CoV-2. We sought to assess COVID-19 preventive, social-behavioural practices, and SARS-CoV-2 exposure through IgG rapid tests. This was a cross-sectional survey among 971 respondents residing in 180 households within the "Cite Verte" health district of Yaounde-Cameroon, from October-November 2020. Using a structured questionnaire, data on SARS-CoV-2 preventive and social behavioural practices were collected, while exposure to SARS-CoV-2 was determined by IgG profiling. p

The 10th and largest Ebola virus disease epidemic in the Democratic Republic of the Congo (DRC) was declared in North Kivu Province in August 2018 and ended in June 2020. We describe and evaluate an Early Warning, Alert and Response System (EWARS) implemented in the Beni health zone of DRC during August 5, 2018–June 30, 2020. During this period, 194,768 alerts were received, of which 30,728 (15.8%) were validated as suspected cases. From these, 801 confirmed and 3 probable cases were detected. EWARS showed an overall good performance: sensitivity and specificity >80%, nearly all (97%) of alerts investigated within 2 hours of notification, and good demographic representativeness. The average cost of the system was US $438/case detected and US $1.8/alert received. The system was stable, despite occasional disruptions caused by political insecurity. Our results demonstrate that EWARS was a cost-effective component of the Ebola surveillance strategy in this setting.

Despite its critical role in containing outbreaks, the efficacy of contact tracing, measured as the sensitivity of case detection, remains an elusive metric. We estimated the sensitivity of contact tracing by applying unilist capture-recapture methods on data from the 2018–2020 outbreak of Ebola virus disease in the Democratic Republic of the Congo. To compute sensitivity, we applied different distributional assumptions to the zero-truncated count data to estimate the number of unobserved case-patients with any contacts and infected contacts. Geometric distributions were the best-fitting models. Our results indicate that contact tracing efforts identified almost all (n = 792, 99%) of case-patients with any contacts but only half (n = 207, 48%) of case-patients with infected contacts, suggesting that contact tracing efforts performed well at identifying contacts during the listing stage but performed poorly during the contact follow-up stage. We discuss extensions to our work and potential applications for the ongoing coronavirus pandemic.

Many African countries have reported relatively low numbers of COVID-19 cases but the true scale of the epidemic is unclear. Here, the authors conduct a population-based survey in a province of Cameroon and estimate 29% seroprevlance, >300 fold higher than the nationwide attack rate implied by case counts.

Introduction: Few data on the COVID-19 epidemiological characteristics among the pediatric population in Africa exists. This paper examines the age and sex distribution of the morbidity and mortality rate in children with COVID-19 and compares it to the adult population in 15 Sub-Saharan African countries. Methods: A merge line listing dataset shared by countries within the Regional Office for Africa was analyzed. Patients diagnosed within 1 March and 1 September 2020 with a confirmed positive RT-PCR test for SARS-CoV-2 were analyzed. Children's data were stratified into three age groups: 0-4 years, 5-11 years, and 12-17 years, while adults were combined. The cumulative incidence of cases, its medians, and 95% confidence intervals were calculated. Results: 9% of the total confirmed cases and 2.4% of the reported deaths were pediatric cases. The 12-17 age group in all 15 countries showed the highest cumulative incidence proportion in children. Adults had a higher case incidence per 100,000 people than children. Conclusion: The cases and deaths within the children's population were smaller than the adult population. These differences may reflect biases in COVID-19 testing protocols and reporting implemented by countries, highlighting the need for more extensive investigation and focus on the effects of COVID-19 in children.

Summary: Background: Inequalities undermine efforts to end AIDS by 2030. We examined socioeconomic inequalities in the 90–90–90 target among people living with HIV (PLHIV) —men (MLHIV), women (WLHIV) and adolescents (ALHIV). Methods: We analysed the available Population HIV Impact Assessment (PHIA) survey data for each of the 12 sub-Saharan African countries, collected between 2015 and 2018 to estimate the attainment of each step of the 90–90–90 target by wealth quintiles. We constructed concentration curves, computed concentration indices (CIX) —a negative (positive) CIX indicated pro-poor (pro-rich) inequalities— and identified factors associated with, and contributing to inequality. Findings: Socioeconomic inequalities in achieving the 90–90–90 target components among PLHIV were noted in 11 of the 12 countries surveyed: not in Rwanda. Awareness of HIV positive status was pro-rich in 5/12 countries (Côte d'Ivoire, Tanzania, Uganda, Malawi, and Zambia) ranging from CIX=0·085 (p< 0·05) in Tanzania for PLHIV, to CIX = 0·378 (p

Background Although 1·3 million women with HIV give birth annually, care and outcomes for HIV-exposed infants remain incompletely understood. We analyzed programmatic and health indicators in a large, multidecade global dataset of linked mother–infant records from clinics and programs associated with the International epidemiology Databases to Evaluate AIDS (IeDEA) consortium. Methods and findings HIV-exposed infants were eligible for this retrospective cohort analysis if enrolled at Conclusions While there was marked regional and temporal heterogeneity in clinical and programmatic outcomes, infant LTFU was high across all regions and time periods. Further efforts are needed to keep HIV-exposed infants in care to receive essential services to reduce HIV infection and mortality. Author summary Why was this study done? Clinical and programmatic outcomes among HIV-exposed infants are poorly documented, with gaps in information on receipt of antiretrovirals by infants and their mothers, early infant diagnosis and definitive diagnostic testing, anthropometric and developmental measures, and susceptibilities to mortality and loss to follow-up (LTFU). Previous evidence from both observational studies and clinical trials is largely limited to single-program or single-country reports with small sample sizes, lack of mother–infant linkages, or restricted geographical or temporal breadth. What did the researchers do and find? Pooling data from the International epidemiology Databases to Evaluate AIDS consortium (sub-Saharan Africa and Brazil) and the Umoyo+ project (Malawi) to create the largest global dataset of HIV-exposed infants to date, our study features >82,000 HIV-exposed infants, with >90% linked to maternal records, born over a 25-year period at 198 clinics providing routine HIV services in 10 countries—including 6 UNAIDS high HIV burden focus countries. Results from this retrospective cohort analysis provide robust, geographically broad insights on key clinical and programmatic outcomes across 5 regions, including the cumulative incidences of DNA PCR testing, LTFU, HIV diagnosis, and death through 24 months of age, accounting for relevant competing risks, while also utilizing mother–infant linkages to examine associations between these outcomes and maternal and infant characteristics. Notably, we found that while mortality and HIV diagnosis decreased over time globally, infant retention at 2 years did not exceed 60% in any period in any region. What do these findings mean? Although real-world service delivery data limitations include potential misclassification of outcomes and nonrepresentativeness of contributing sites, this study generated novel information on clinical characteristics and programmatic outcomes among HIV-exposed infants. While elucidating deficiencies in care that must be mitigated to deliver the package of medications and support necessary to assure that all such children remain uninfected, survive, and thrive, our analysis corroborated prior studies in highlighting unacceptably poor retention among those initially engaged in care. Our finding of widespread and persistent LTFU across disparate settings should motivate changes in policy and practice to improve patient retention, as maintaining infants in care will facilitate not only HIV testing and prevention, but also the provision of other services (primary care, nutrition, immunizations, etc.) essential for the achievement of long-term health.

BACKGROUND: Indoor aerosol transmission of SARS-CoV-2 has been widely recognised, especially in schools where children remain in closed indoor spaces and largely unvaccinated. Measures such as strategic natural ventilation and high efficiency particulate air (HEPA) filtration remain poorly implemented and mask mandates are often progressively lifted as vaccination rollout is enhanced. METHODS: We adapted a previously developed aerosol transmission model to study the effect of interventions (natural ventilation, face masks, HEPA filtration and their combinations) on the concentration of virus particles in a classroom of 160 m3 containing one infectious individual. The cumulative dose of viruses absorbed by exposed occupants was calculated. RESULTS: In the absence of interventions, the cumulative dose absorbed was 1.5 times higher in winter than in spring/summer, increasing chances of indoor airborne transmission in winter. However, natural ventilation was more effective in winter, leading to up to a 20-fold decrease in cumulative dose when six windows were fully open at all times. In winter, partly opening two windows all day or fully opening six windows at the end of each class was effective as well (2.7- to 3-fold decrease). In summer, good ventilation levels could be achieved through the opening of windows all day long (2- to 7-fold decrease depending on the number of windows open). Opening windows only during yard and lunch breaks had minimal effect (≤1.5-fold decrease). One HEPA filter was as effective as two windows partly open all day in winter (3-fold decrease) whereas two filters were more effective (5-fold decrease). Surgical face masks were very effective independently of the season (8-fold decrease). Combined interventions (i.e., natural ventilation, masks, and HEPA filtration) were the most effective (≥25-fold decrease) and remained highly effective in the presence of a super-spreader. INTERPRETATION: Natural ventilation, face masks, and HEPA filtration are effective interventions to reduce SARS-CoV-2 aerosol transmission. These measures should be combined and complemented by additional interventions (e.g., physical distancing, hygiene, testing, contact tracing and vaccination) to maximise benefit.

Abstract Background Male partners are rarely present during PMTCT (Prevention-Mother-To-Child-Transmission) services in Sub-Saharan Africa (SSA). Male involvement is increasingly recognised as an important element of women’s access to care. This study aims to identify the socio-demographic characteristics, HIV-Knowledge, Attitude and Practice (KAP) among women accompanied and not accompanied by their male partners. Methods We included pregnant women enrolled in PMTCT programme between August 2018 and November 2019 in the Southern Region of Malawi. Eligible women were aged 18 years or older, living with a male partner, enrolled for the first time in one of the four selected facilities. We provided a KAP survey to women and their partners attending the facilities. Our primary objective was to assess and analyse the proportion of women who were accompanied by their partner at least once. We applied descriptive statistics and logistic regressions to study the association between being accompanied and explanatory variables. Results We enrolled 128 HIV-positive women: 82 (64.1%) were accompanied by their male partners and 46 (35.9%) were alone. In the multivariable model, women’s unemployment and owning a means of transport are negatively associated with male attendance (respectively adjusted OR 0.32 [95% CI, 0.11–0.82] and 0.23 [95% CI, 0.07–0.77]), whereas, in the univariable model, high women’s level of knowledge of HIV is positively associated with male attendance (OR 2.17 [95% CI, 1.03–4.58]). Level of attitude and practice toward HIV were not significantly associated to our study variable. Conclusions Our study shows a high male attendance in Malawi compared to other studies performed in SSA. This study highlights that women’s level of knowledge on HIV and their economic condition (employment and owning a means of transport) affects male attendance. Moreover, the study points out that gender power relationships and stringent gender norms play a crucial role thus they should be considered to enhance male involvement.

Large-scale protracted outbreaks can be prevented through early detection, notification, and rapid control. We assessed trends in timeliness of detecting and responding to outbreaks in the African Region reported to the World Health Organization during 2017–2019. We computed the median time to each outbreak milestone and assessed the rates of change over time using univariable and multivariable Cox proportional hazard regression analyses. We selected 296 outbreaks from 348 public reported health events and evaluated 184 for time to detection, 232 for time to notification, and 201 for time to end. Time to detection and end decreased over time, whereas time to notification increased. Multiple factors can account for these findings, including scaling up support to member states after the World Health Organization established its Health Emergencies Programme and support given to countries from donors and partners to strengthen their core capacities for meeting International Health Regulations.

Objectives: We examined associations between accelerators (interventions impacting ≥2 SDG targets) and SDG-aligned well-being indicators among adolescents 16–24 years old in Zambia.Methods: We surveyed adults from 1,800 randomly sampled households receiving social cash transfers. We examined associations between accelerators (social cash transfers, life-long learning, mobile phone access) and seven well-being indicators among adolescents using multivariate logistic regressions.Results: The sample comprised 1,725 adolescents, 881 (51.1%) girls. Mobile phone access was associated with no poverty (adjusted Odds Ratio [aOR] 2.08, p < 0.001), informal cash transfers (aOR 1.82, p = 0.004), and seeking mental health support (aOR 1.61, p = 0.020). Social cash transfers were associated with no disability-related health restrictions (aOR 2.56, p = 0.004) and lesser odds of seeking mental health support (aOR 0.53, p = 0.029). Life-long learning was associated with informal cash transfers (aOR 3.49, p < 0.001) and lower school enrollment (aOR 0.70, p = 0.004). Adolescents with disabled head-of-household reported worse poverty, good health but less suicidal ideation.Conclusions: Social cash transfers, life-long learning, and mobile phone access were positively associated with well-being indicators. Adolescents living with disabled head-of-household benefited less. Governments should implement policies to correct disability-related inequalities.

IntroductionHigh yield HIV testing strategies are critical to reach epidemic control in high prevalence and low-resource settings such as East and Southern Africa. In this study, we aimed to predict the HIV status of individuals living in Angola, Burundi, Ethiopia, Lesotho, Malawi, Mozambique, Namibia, Rwanda, Zambia and Zimbabwe with the highest precision and sensitivity for different policy targets and constraints based on a minimal set of socio-behavioural characteristics.MethodsWe analysed the most recent Demographic and Health Survey from these 10 countries to predict individual's HIV status using four different algorithms (a penalized logistic regression, a generalized additive model, a support vector machine, and a gradient boosting trees). The algorithms were trained and validated on 80% of the data, and tested on the remaining 20%. We compared the predictions based on the F1 score, the harmonic mean of sensitivity and positive predictive value (PPV), and we assessed the generalization of our models by testing them against an independent left-out country. The best performing algorithm was trained on a minimal subset of variables which were identified as the most predictive, and used to 1) identify 95% of people living with HIV (PLHIV) while maximising precision and 2) identify groups of individuals by adjusting the probability threshold of being HIV positive (90% in our scenario) for achieving specific testing strategies.ResultsOverall 55,151 males and 69,626 females were included in the analysis. The gradient boosting trees algorithm performed best in predicting HIV status with a mean F1 score of 76.8% [95% confidence interval (CI) 76.0%-77.6%] for males (vs [CI 67.8%-70.6%] for SVM) and 78.8% [CI 78.2%-79.4%] for females (vs [CI 73.4%-75.8%] for SVM). Among the ten most predictive variables for each sex, nine were identical: longitude, latitude and, altitude of place of residence, current age, age of most recent partner, total lifetime number of sexual partners, years lived in current place of residence, condom use during last intercourse and, wealth index. Only age at first sex for male (ranked 10th) and Rohrer's index for female (ranked 6th) were not similar for both sexes. Our large-scale scenario, which consisted in identifying 95% of all PLHIV, would have required testing 49.4% of males and 48.1% of females while achieving a precision of 15.4% for males and 22.7% for females. For the second scenario, only 4.6% of males and 6.0% of females would have had to be tested to find 55.7% of all males and 50.5% of all females living with HIV.ConclusionsWe trained a gradient boosting trees algorithm to find 95% of PLHIV with a precision twice higher than with general population testing by using only a limited number of socio-behavioural characteristics. We also successfully identified people at high risk of infection who may be offered pre-exposure prophylaxis or voluntary medical male circumcision. These findings can inform the implementation of new high-yield HIV tests and help develop very precise strategies based on low-resource settings constraints.

BackgroundWhile many countries including Kenya transitioned from sentinel surveillance to the use of routine antenatal care (ANC) data to estimate the burden of HIV, countries in Sub Saharan Africa reported several challenges of this transition, including low uptake of HIV testing and sub national / site-level differences in HIV prevalence estimates. In Kenya voluntary HIV testing is offered to all 1st ANC clients. However, some women may decline testing. We aim to predict the HIV positivity (as a proxy of prevalence) at ANC assuming 100% uptake of HIV testing and compare this to the observed positivity.MethodsUsing a cross sectional study design, we examine routine data on HIV testing among all women attending ANC in Kwale County, Kenya, for the period January 2015 to December 2019.We used a generalized estimating equation with binomial distribution to model the observed HIV prevalence as explained by HIV status ascertainment. We then used marginal standardization to predict the HIV prevalence at 100% HIV status ascertainment and make recommendations to improve the utility of ANC routine data for HIV surveillance.ResultsHIV testing at ANC was at 91.3%, slightly above the global target of 90%. If there was 100% HIV status ascertainment at ANC, the HIV prevalence would be 2.7% (95% CI 2.3-3.2). This was 0.3% lower than the observed prevalence. Across the yearly predictions, there was no difference between the observed and predicted values except for 2018 where the HIV prevalence was underestimated with an absolute bias of -0.2 percent. This implies missed opportunities for identifying new HIV infections in the year 2018.ConclusionsImperfect HIV status ascertainment at ANC overestimates HIV prevalence among women attending ANC in Kwale County. However, the use of ANC routine data may underestimate the true population prevalence. There is need to address both community level and health facility level barriers to the uptake of ANC services.

Summary: Background: The HIV epidemic in Nigeria is concentrated in Key Populations (KP), people who inject drugs (PWID), men who have sex with men (MSM), female sex workers (FSW), and partners of people living with HIV. Due to stigma and discrimination, these groups have low access to HIV testing services (HTS) and linkage to treatment is challenging. To address this gap, index partner testing, targeting sexual contacts and injecting partners of KP index clients, was introduced in 2017. Methods: The study was a retrospective analysis of community-led HIV index partner testing-involving review of secondary data from partner notification services registers. Between October 1, 2018, and September 30, 2019, HIV testing as part of index partner testing services was offered at nightclubs, hotels, and community-based ART clinics in the states of Akwa Ibom, Cross River, and Lagos. Index testing was assisted by peer navigators. We used provider and passive Partner Notification (PN) methods. In-person and social network methods were used to recruit partners of KP. We described the implementation of index partner testing services as part of the national KP program, analyzed PN delivery models, and calculated HIV seropositivity among persons who underwent Index Partner Testing. One-Way ANOVA and Tukey-HSD test were performed to determine whether the differences in mean HIV seropositivity between partners are statistically significant. Findings: PN was predominantly done through provider referral 5,159 (68.3%) and passive/client referral 2,278 (30.1%). A total of 3,119 index partners; 1,322 FSW (42.4%), 1,255 MSM (40.2%) and 542 PWID (17.4%) identified 8,989 sexual and injecting partners (index partner ratio 1:2.9). Among the partners, 7,556 (84.1%) were first-time testers, and 79.4% (5,999) of male partners tested. Of the 3,753 (49.7%) partners who tested HIV-positive, 3,492 (93.0%) were enrolled in HIV care. HIV seropositivity rate was 65.5% (1,021/1,557) among females and 45.5% (2,732/5,999) among males and was disproportionately higher among PWID injecting partners 99.1% (581/586), PWID sexual partners 98.9% (433/438) and MSM sexual partners 95.6% (605/633) in Cross river compared with 71.4% (575/805) in FSW sexual partners. Interpretations: Including index partner testing as part of a community-led HTS can help improve HIV case-finding approach for KP, particularly for reaching first-time testers, male KP, and persons not yet diagnosed with HIV. Scale-up of index partner testing within community-led HTS is essential for achieving the United Nations 95–95–95 goals. Funding: This research received no specific grant from any funding agency in the public, commercial or not-for-profit sectors.

BACKGROUND: When the periods of time during and after the first wave of the ongoing SARS-CoV-2/COVID-19 pandemic in Europe are compared, the associated COVID-19 mortality seems to have decreased substantially. Various factors could explain this trend, including changes in demographic characteristics of infected persons and the improvement of case management. To date, no study has been performed to investigate the evolution of COVID-19 in-hospital mortality in Switzerland, while also accounting for risk factors. METHODS: We investigated the trends in COVID-19-related mortality (in-hospital and in-intermediate/intensive-care) over time in Switzerland, from February 2020 to June 2021, comparing in particular the first and the second wave. We used data from the COVID-19 Hospital-based Surveillance (CH-SUR) database. We performed survival analyses adjusting for well-known risk factors of COVID-19 mortality (age, sex and comorbidities) and accounting for competing risk. RESULTS: Our analysis included 16,984 patients recorded in CH-SUR, with 2201 reported deaths due to COVID-19 (13.0%). We found that overall in-hospital mortality was lower during the second wave of COVID-19 than in the first wave (hazard ratio [HR] 0.70, 95% confidence interval [CI] 0.63– 0.78; p

Objective During the first COVID-19 wave in Switzerland, relative mortality was at least eight times higher compared with the uninfected general population. We aimed to assess sex-specific and age-specific relative mortality associated with a SARS-CoV-2 diagnosis during the second wave.Design Prospective population-based study.Setting Individuals testing positive for SARS-CoV-2 after the start of the second wave on 1 October 2020 were followed up until death or administrative censoring on 31 December 2020.Participants 5 179 740 inhabitants of Switzerland in fall 2018 aged 35–95 years (without COVID-19) and 257 288 persons tested positive for SARS-CoV-2 by PCR or antigen testing during the second wave.Primary and secondary outcome measures The planned outcome measure was time to death from any cause, measured from the date of a SARS-CoV-2 diagnosis or 1 October in the general population. Information on confirmed SARS-CoV-2 diagnoses and deaths was matched by calendar time with the all-cause mortality of the general Swiss population of 2018. Proportional hazards models were used to estimate sex-specific and age-specific mortality rates and probabilities of death within 60 days.Results The risk of death for individuals tested positive for SARS-CoV-2 in the second wave in Switzerland increased at least sixfold compared with the general population. HRs, reflecting the risk attributable to a SARS-CoV-2 infection, were higher for men (1.40, 95% CI 1.29 to 1.52) and increased for each additional year of age (1.01, 95% CI 1.01 to 1.02). COVID-19 mortality was reduced by at least 20% compared with the first wave in spring 2020.Conclusion General mortality patterns, increased for men and older persons, were similar in spring and in fall. Absolute and relative COVID-19 mortality was smaller in fall.Trial registration The protocol for this study was registered on 3 December 2020 at https://osf.io/gbd6r.

BACKGROUND: There has been much discussion about coronavirus disease 2019 (COVID-19) and the virus that causes it, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in children and adolescents, since the pandemic was recognised in early 2020. Understanding their role in this pandemic is important for the development of appropriate prevention measures. OBJECTIVE: To summarise evidence about three aspects of SARS-CoV-2 and COVID-19 in children and adolescents: (1) severity of SARS-CoV-2 presentation, (2) risk of SARS-CoV-2 infection and (3) risk of transmitting SARS-CoV-2. METHODS: We searched PubMed and MedRxiv for studies on SARS-CoV-2 and COVID-19 in children and adolescents from January 2020 to 21 January 2021. The electronic search was supplemented by papers found in a manual search or suggested by experts up to 29 March 2021. We included case reports, cross-sectional studies, cohort studies, narrative reviews or viewpoints, systematic reviews and modelling studies. We synthesised the information descriptively and attempted to report findings separately for: infants and small children (0–5 years) who are mostly pre-school; school children (6–12 years) broadly covering primary school years; and adolescents (13–17 years). RESULTS: Of 2778 screened articles, we included 63 (20 case reports, 18 cross-sectional studies, 8 cohort studies, 6 narrative reviews or viewpoints, 10 systematic reviews and 1 modelling study). Children (≤12 years of age) and adolescents (13–17 years of age) usually present with mild disease, with few requiring intensive care treatment. A minority of children of all ages (

Background The cost and complexity of the polymerase chain reaction (PCR) test are barriers to diagnosis and treatment of hepatitis C virus (HCV) infection. We investigated the cost-effectiveness of testing strategies using antigen instead of PCR testing. Methods We developed a mathematical model for HCV to estimate the number of diagnoses and cases of liver disease. We compared the following testing strategies: antibody test followed by PCR in case of positive antibody (baseline strategy); antibody test followed by HCV-antigen test (antibody-antigen); antigen test alone; PCR test alone. We conducted cost-effectiveness analyses considering either the costs of HCV testing of infected and uninfected individuals alone (A1), HCV testing and liver-related complications (A2), or all costs including HCV treatment (A3). The model was parameterized for the country of Georgia. We conducted several sensitivity analyses. Results The baseline scenario could detect 89% of infected individuals. Antibody-antigen detected 86% and antigen alone 88% of infected individuals. PCR testing alone detected 91% of the infected individuals: the remaining 9% either died or spontaneously recovered before testing. In analysis A1, the baseline strategy was not essentially more expensive than antibody-antigen. In analysis A2, strategies using PCR became cheaper than antigen-based strategies. In analysis A3, antibody-antigen was again the cheapest strategy, followed by the baseline strategy, and PCR testing alone. Conclusions Antigen testing, either following a positive antibody test or alone, performed almost as well as the current practice of HCV testing. The cost-effectiveness of these strategies depends on the inclusion of treatment costs.

BACKGROUND As clinical signs of COVID-19 differ widely among individuals, from mild to severe, the definition of risk groups has important consequences for recommendations to the public, control measures and patient management, and needs to be reviewed regularly. AIM The aim of this study was to explore risk factors for in-hospital mortality and intensive care unit (ICU) admission for hospitalised COVID-19 patients during the first epidemic wave in Switzerland, as an example of a country that coped well during the first wave of the pandemic. METHODS This study included all (n = 3590) adult polymerase chain reaction (PCR)-confirmed hospitalised patients in 17 hospitals from the hospital-based surveillance of COVID-19 (CH-Sur) by 1 September 2020. We calculated univariable and multivariable (adjusted) (1) proportional hazards (Fine and Gray) survival regression models and (2) logistic regression models for in-hospital mortality and admission to ICU, to evaluate the most common comorbidities as potential risk factors. RESULTS AND DISCUSSION We found that old age was the strongest factor for in-hospital mortality after having adjusted for gender and the considered comorbidities (hazard ratio [HR] 2.46, 95% confidence interval [CI] 2.33−2.59 and HR 5.6 95% CI 5.23−6 for ages 65 and 80 years, respectively). In addition, male gender remained an important risk factor in the multivariable models (HR 1.47, 95% CI 1.41−1.53). Of all comorbidities, renal disease, oncological pathologies, chronic respiratory disease, cardiovascular disease (but not hypertension) and dementia were also risk factors for in-hospital mortality. With respect to ICU admission risk, the pattern was different, as patients with higher chances of survival might have been admitted more often to ICU. Male gender (OR 1.91, 95% CI 1.58−2.31), hypertension (OR 1.3, 95% CI 1.07−1.59) and age 55–79 years (OR 1.15, 95% CI 1.06−1.26) are risk factors for ICU admission. Patients aged 80+ years, as well as patients with dementia or with liver disease were admitted less often to ICU. CONCLUSION We conclude that increasing age is the most important risk factor for in-hospital mortality of hospitalised COVID-19 patients in Switzerland, along with male gender and followed by the presence of comorbidities such as renal diseases, chronic respiratory or cardiovascular disease, oncological malignancies and dementia. Male gender, hypertension and age between 55 and 79 years are, however, risk factors for ICU admission. Mortality and ICU admission need to be considered as separate outcomes when investigating risk factors for pandemic control measures and for hospital resources planning.

Background: We aimed to estimate the disease burden of Tuberculosis (TB) and return on investment of TB care in selected high-burden countries of the Western Pacific Region (WPR) until 2030. Methods: We projected the TB epidemic in Viet Nam and Lao People's Democratic Republic (PDR) 2020–2030 using a mathematical model under various scenarios: counterfactual (no TB care); baseline (TB care continues at current levels); and 12 different diagnosis and treatment interventions. We retrieved previous modeling results for China and the Philippines. We pooled the new and existing information on incidence and deaths in the four countries, covering >80% of the TB burden in WPR. We estimated the return on investment of TB care and interventions in Viet Nam and Lao PDR using a Solow model. Findings: In the baseline scenario, TB incidence in the four countries decreased from 97•0/100,000/year (2019) to 90•1/100,000/year (2030), and TB deaths from 83,300/year (2019) to 71,100/year (2030). Active case finding (ACF) strategies (screening people not seeking care for respiratory symptoms) were the most effective single interventions. Return on investment (2020–2030) for TB care in Viet Nam and Lao PDR ranged US$4-US$49/dollar spent; additional interventions brought up to US$2•7/dollar spent. Interpretation: In the modeled countries, TB incidence will only modestly decrease without additional interventions. Interventions that include ACF can reduce TB burden but achieving the End TB incidence and mortality targets will be difficult without new transformational tools (e.g. vaccine, new diagnostic tools, shorter treatment). However, TB care, even at its current level, can bring a multiple-fold return on investment. Funding: World Health Organization Western Pacific Regional Office; Swiss National Science Foundation Grant 163878.

Objective: Hepatitis C virus (HCV) infection is a major cause of liver disease. Since symptoms of chronic liver disease usually appear only late in the course of the disease, infected individuals may remain undiagnosed until advanced disease has developed. We aimed to investigate which screening strategies would be most effective to detect individuals unaware of their infection. Methods: We developed a mathematical model for HCV disease progression and compared the current practice of HCV testing in Switzerland with the following screening strategies: intensive screening of active injection drug users (IDU), screening of former IDU, screening of individuals originating from countries with high HCV prevalence, screening of individuals born 1951–1985 (birth-cohort) and universal screening. All screening interventions were considered in addition to a baseline scenario that reflected the current practice of HCV testing. Results: Within the first 4 years (2018–2021), every year, on average 650 cases were diagnosed in the baseline scenario, 660 with intensified IDU screening, 760 with former IDU screening, 830 with origin-based screening, 1420 with birth-cohort screening and 1940 with universal screening. No difference in liver-related mortality and incidence of end-stage liver disease between the screening scenarios was observed. Conclusion: Our results suggest that only large-scale screening of the general population could substantially accelerate the rate of HCV diagnosis and treatment in Switzerland and other countries with similar epidemics. However, this implies screening of a large population with low prevalence, and may trigger considerable numbers of false-positive and borderline test results.

Objective Severity of the COVID-19 has been previously reported in terms of absolute mortality in SARS-CoV-2 positive cohorts. An assessment of mortality relative to mortality in the general population is presented.Design Retrospective population-based study.Setting Individual information on symptomatic confirmed SARS-CoV-2 patients and subsequent deaths from any cause were compared with the all-cause mortality in the Swiss population of 2018. Starting 23 February 2020, mortality in COVID-19 patients was monitored for 80 days and compared with the population mortality observed in the same time of year starting 23 February 2018.Participants 5 102 300 inhabitants of Switzerland aged 35–95 without COVID-19 (general population in spring 2018) and 20 769 persons tested positively for COVID-19 during the first wave in spring 2020.Measurements Sex-specific and age-specific mortality rates were estimated using Cox proportional hazards models. Absolute probabilities of death were predicted and risk was assessed in terms of relative mortality by taking the ratio between the sex-specific and age-specific absolute mortality in COVID-19 patients and the corresponding mortality in the 2018 general population.Results Absolute mortalities increased with age and were higher for males compared with females, both in the general population and in positively tested persons. A confirmed SARS-CoV-2 infection substantially increased the probability of death across all patient groups at least eightfold. The highest relative mortality risks were observed among males and younger patients. Male COVID-19 patients exceeded the population hazard for males (HR 1.21, 95% CI 1.02 to 1.44). An additional year of age increased the population hazard in COVID-19 patients only marginally (HR 1.00, 95% CI 1.00 to 1.01).Conclusions Healthcare professionals, decision-makers and societies are provided with an additional population-adjusted assessment of COVID-19 mortality risk. In combination with absolute measures of risk, the relative risks presented here help to develop a more comprehensive understanding of the actual impact of COVID-19.

The recent lifting of COVID-19 related restrictions in Switzerland causes uncertainty about the future of the epidemic. We developed a compartmental model for SARS-CoV-2 transmission in Switzerland and projected the course of the epidemic until the end of year 2020 under various scenarios. The model was age-structured with three categories: children (0-17), adults (18-64) and seniors (65- years). Lifting all restrictions according to the plans disclosed by the Swiss federal authorities by mid-May resulted in a rapid rebound in the epidemic, with the peak expected in July. Measures equivalent to at least 76% reduction in all contacts were able to eradicate the epidemic; a 54% reduction in contacts could keep the intensive care unit occupancy under the critical level and delay the next wave until October. In scenarios where strong contact reductions were only applied in selected age groups, the epidemic could not be suppressed, resulting in an increased risk of a rebound in July, and another stronger wave in September. Future interventions need to cover all age groups to keep the SARS-CoV-2 epidemic under control.

BACKGROUND SARS-CoV-2/COVID-19, which emerged in China in late 2019, rapidly spread across the world with several million victims in 213 countries. Switzerland was severely hit by the virus, with 43,000 confirmed cases as of 1 September 2020. AIM In cooperation with the Federal Office of Public Health, we set up a surveillance database in February 2020 to monitor hospitalised patients with COVID-19, in addition to their mandatory reporting system. METHODS Patients hospitalised for more than 24 hours with a positive polymerase chain-reaction test, from 20 Swiss hospitals, are included. Data were collected in a customised case report form based on World Health Organisation recommendations and adapted to local needs. Nosocomial infections were defined as infections for which the onset of symptoms was more than 5 days after the patient’s admission date. RESULTS As of 1 September 2020, 3645 patients were included. Most patients were male (2168, 59.5%), and aged between 50 and 89 years (2778, 76.2%), with a median age of 68 (interquartile range 54–79). Community infections dominated with 3249 (89.0%) reports. Comorbidities were frequently reported, with hypertension (1481, 61.7%), cardiovascular diseases (948, 39.5%) and diabetes (660, 27.5%) being the most frequent in adults; respiratory diseases and asthma (4, 21.1%), haematological and oncological diseases (3, 15.8%) were the most frequent in children. Complications occurred in 2679 (73.4%) episodes, mostly respiratory diseases (2470, 93.2% in adults; 16, 55.2% in children), and renal (681, 25.7%) and cardiac (631, 23.8%) complications for adults. The second and third most frequent complications in children affected the digestive system and the liver (7, 24.1%). A targeted treatment was given in 1299 (35.6%) episodes, mostly with hydroxychloroquine (989, 76.1%). Intensive care units stays were reported in 578 (15.8%) episodes. A total of 527 (14.5%) deaths were registered, all among adults. CONCLUSION The surveillance system has been successfully initiated and provides a robust set of data for Switzerland by including about 80% (compared with official statistics) of SARS-CoV-2/COVID-19 hospitalised patients, with similar age and comorbidity distributions. It adds detailed information on the epidemiology, risk factors and clinical course of these cases and, therefore, is a valuable addition to the existing mandatory reporting.

BackgroundThe WHO African region frequently experiences outbreaks and epidemics of infectious diseases often exacerbated by weak health systems and infrastructure, late detection, and ineffective outbreak response. To address this, the WHO Regional Office for Africa developed and began implementing the Integrated Disease Surveillance and Response strategy in 1998.ObjectivesThis systematic review aims to document the identified successes and challenges surrounding the implementation of IDSR in the region available in published literature to highlight areas for prioritization, further research, and to inform further strengthening of IDSR implementation.MethodsA systematic review of peer-reviewed literature published in English and French from 1 July 2012 to 13 November 2019 was conducted using PubMed and Web of Science. Included articles focused on the WHO African region and discussed the use of IDSR strategies and implementation, assessment of IDSR strategies, or surveillance of diseases covered in the IDSR framework. Data were analyzed descriptively using Microsoft Excel and Tableau Desktop 2019.ResultsThe number of peer-reviewed articles discussing IDSR remained low, with 47 included articles focused on 17 countries and regional level systems. Most commonly discussed topics were data reporting (n = 39) and challenges with IDSR implementation (n = 38). Barriers to effective implementation were identified across all IDSR core and support functions assessed in this review: priority disease detection; data reporting, management, and analysis; information dissemination; laboratory functionality; and staff training. Successful implementation was noted where existing surveillance systems and infrastructure were utilized and streamlined with efforts to increase access to healthcare.Conclusions and implications of findingsThese findings highlighted areas where IDSR is performing well and where implementation remains weak. While challenges related to IDSR implementation since the first edition of the technical guidelines were released are not novel, adequately addressing them requires sustained investments in stronger national public health capabilities, infrastructure, and surveillance processes.

BACKGROUND:In 2015, Zimbabwe introduced third-line antiretroviral therapy (ART) through four designated treatment centers; three government clinics in Harare and Bulawayo, and Newlands Clinic (NC), operated by a private voluntary organization in Harare. We describe characteristics of patients receiving third line ART and analyzed treatment outcomes in this national programme as of 31 December 2018. METHODS:We described the population using proportions for categorical variables, and medians and interquartile ranges for continuous variables. Patients from NC, where data were more complete, were followed from the date of starting third-line ART until death, transfer, loss to follow up or 31 December 2018. RESULTS:A total of 209 patients had ever received third-line ART: 124 at NC and 85 from the three government clinics. HIV genotype results were available for 89 (72%) patients at NC and fourteen (16.5%) patients in the government clinics. Median duration of third line ART (years) in the government clinics was 2.3 (IQR:0.6-3.4), 1.3 (IQR: 0.7-1.7) and 1 (0.6-1.9). Of the 67 patients who received third line ART in the government clinics for at least six months, 53 (79%) had most recent viral load (VL) < 1000 copies/ml. Data on other treatment outcomes from government clinics were incomplete. From NC: a total of 109 (88%) patients were still in care, 13 (10.5%) had died and 2 (1.5%) were transferred. Median duration of third-line ART was 1.4 years (IQR: 0.6-2.8). Among the 111 NC patients who had received third-line ART for at least 6 months, 83 (75%) had a VL