Machine learning enabled detection of COVID-19 pneumonia using exhaled breath analysis: a proof-of-concept study.

Detection of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) relies on real-time-reverse-transcriptase polymerase chain reaction (RT-PCR) on nasopharyngeal swabs. The false-negative rate of RT-PCR can be high when viral burden and infection is localized distally in the lower airways and lung parenchyma. An alternate safe, simple and accessible method for sampling the lower airways is needed to aid in the early and rapid diagnosis of COVID-19 pneumonia. In a prospective unblinded observational study, patients admitted with a positive RT-PCR and symptoms of SARS-CoV-2 infection were enrolled from three hospitals in Ontario, Canada. Healthy individuals or hospitalized patients with negative RT-PCR and without respiratory symptoms were enrolled into the control group. Breath samples were collected and analyzed by laser absorption spectroscopy (LAS) for volatile organic compounds (VOCs) and classified by machine learning (ML) approaches to identify unique LAS-spectra patterns (breathprints) for SARS-CoV-2. Of the 135 patients enrolled, 115 patients provided analyzable breath samples. Using LAS-breathprints to train ML classifier models resulted in an accuracy of 72.2%-81.7% in differentiating between SARS-CoV2 positive and negative groups. The performance was consistent across subgroups of different age, sex, body mass index, SARS-CoV-2 variants, time of disease onset and oxygen requirement. The overall performance was higher than compared to VOC-trained classifier model, which had an accuracy of 63%-74.7%. This study demonstrates that a ML-based breathprint model using LAS analysis of exhaled breath may be a valuable non-invasive method for studying the lower airways and detecting SARS-CoV-2 and other respiratory pathogens. The technology and the ML approach can be easily deployed in any setting with minimal training. This will greatly improve access and scalability to meet surge capacity; allow early and rapid detection to inform therapy; and offers great versatility in developing new classifier models quickly for future outbreaks.

A retroviral link to vertebrate myelination through retrotransposon-RNA-mediated control of myelin gene expression.

Myelin, the insulating sheath that surrounds neuronal axons, is produced by oligodendrocytes in the central nervous system (CNS). This evolutionary innovation, which first appears in jawed vertebrates, enabled rapid transmission of nerve impulses, more complex brains, and greater morphological diversity. Here, we report that RNA-level expression of RNLTR12-int, a retrotransposon of retroviral origin, is essential for myelination. We show that RNLTR12-int-encoded RNA binds to the transcription factor SOX10 to regulate transcription of myelin basic protein (Mbp, the major constituent of myelin) in rodents. RNLTR12-int-like sequences (which we name RetroMyelin) are found in all jawed vertebrates, and we further demonstrate their function in regulating myelination in two different vertebrate classes (zebrafish and frogs). Our study therefore suggests that retroviral endogenization played a prominent role in the emergence of vertebrate myelin.

Repurposing an endogenous degradation domain for antibody-mediated disposal of cell-surface proteins.

The exquisite specificity of antibodies can be harnessed to effect targeted degradation of membrane proteins. Here, we demonstrate targeted protein removal utilising a protein degradation domain derived from the endogenous human protein Proprotein Convertase Subtilisin/Kexin type 9 (PCSK9). Recombinant antibodies genetically fused to this domain drive the degradation of membrane proteins that undergo constitutive internalisation and recycling, including the transferrin receptor and the human cytomegalovirus latency-associated protein US28. We term this approach PACTAC (PCSK9-Antibody Clearance-Targeting Chimeras).

In vitro modeling of the post-ingestion mobilization and bioaccessibility of pesticides sorbed to soil and house dust.

Soils and dusts can act as sinks for semivolatile lipophilic organic compounds and children ingest relatively large amounts of both soils and dusts. Following intake, sorbed chemicals may desorb (mobilize) and become available for intestinal absorption (bioaccessible). When chemicals are not degraded in the digestive tract, mobilization can approximate bioaccessibility. Alternatively, when gastrointestinal degradation of mobilized chemicals does occur, it can be useful to separate mobilization from bioaccessibility. In this study we used synthetic digestive fluids in a sequential, three-compartment (saliva, gastric, and intestinal) in vitro assay to construct mobilization and bioaccessibility models for 16 pesticides (log Kow 2.5-6.8) sorbed to 32 characterized soils and house dusts. To address the potential loss of mobilized pesticides due to absorption, the assays were repeated using a solid phase sorbent (tenax) added to the digestive fluid immediately after addition of the intestinal fluid components. We found that pesticide mobilization was predicted by pesticide log Kow and the carbon content of the soils and dusts. Pesticide loss measurably reduced the bioaccessibility of most pesticides, and bioaccessibility was largely predicted by log Kow and pesticide loss rate constants. Introduction of the sink increased mobilization by x̄ = 4 ± 6% (soil) and x̄ = 9 ± 7% (dust) while bioaccessibility increases were x̄ = 41 ± 21% (soil) and x̄ = 24 ± 12% (dust). The physicochemical properties of the soils, dusts, and pesticides used in this study successfully predicted the in vitro mobilization and bioaccessibility of the pesticides. This suggests that modeling of pesticide mobilization and bioaccessibility could reduce uncertainty in exposure and risk assessments.

Pre-extensively Drug-Resistant Congenital Tuberculosis in an Extremely Premature Baby.

We describe a case of congenital tuberculosis in an extremely premature baby, with rapid molecular detection of a pre-extensively drug-resistant (XDR) pattern of drug resistance. The baby was treated successfully with a regimen including bedaquline and delamanid, drugs not previously described in the treatment of congenital tuberculosis (TB).

Diagnostic accuracy of a three-gene Mycobacterium tuberculosis host response cartridge using fingerstick blood for childhood tuberculosis: a multicentre prospective study in low-income and middle-income countries.

BACKGROUND: Childhood tuberculosis remains a major cause of morbidity and mortality in part due to missed diagnosis. Diagnostic methods with enhanced sensitivity using easy-to-obtain specimens are needed. We aimed to assess the diagnostic accuracy of the Cepheid Mycobacterium tuberculosis Host Response prototype cartridge (MTB-HR), a candidate test measuring a three-gene transcriptomic signature from fingerstick blood, in children with presumptive tuberculosis disease. METHODS: RaPaed-TB was a prospective diagnostic accuracy study conducted at four sites in African countries (Malawi, Mozambique, South Africa, and Tanzania) and one site in India. Children younger than 15 years with presumptive pulmonary or extrapulmonary tuberculosis were enrolled between Jan 21, 2019, and June 30, 2021. MTB-HR was performed at baseline and at 1 month in all children and was repeated at 3 months and 6 months in children on tuberculosis treatment. Accuracy was compared with tuberculosis status based on standardised microbiological, radiological, and clinical data. FINDINGS: 5313 potentially eligible children were screened, of whom 975 were eligible. 784 children had MTB-HR test results, of whom 639 had a diagnostic classification and were included in the analysis. MTB-HR differentiated children with culture-confirmed tuberculosis from those with unlikely tuberculosis with a sensitivity of 59·8% (95% CI 50·8-68·4). Using any microbiological confirmation (culture, Xpert MTB/RIF Ultra, or both), sensitivity was 41·6% (34·7-48·7), and using a composite clinical reference standard, sensitivity was 29·6% (25·4-34·2). Specificity for all three reference standards was 90·3% (95% CI 85·5-94·0). Performance was similar in different age groups and by malnutrition status. Among children living with HIV, accuracy against the strict reference standard tended to be lower (sensitivity 50·0%, 15·7-84·3) compared with those without HIV (61·0%, 51·6-69·9), although the difference did not reach statistical significance. Combining baseline MTB-HR result with one Ultra result identified 71·2% of children with microbiologically confirmed tuberculosis. INTERPRETATION: MTB-HR showed promising diagnostic accuracy for culture-confirmed tuberculosis in this large, geographically diverse, paediatric cohort and hard-to-diagnose subgroups. FUNDING: European and Developing Countries Clinical Trials Partnership, UK Medical Research Council, Swedish International Development Cooperation Agency, Bundesministerium für Bildung und Forschung; German Center for Infection Research (DZIF).

Effectiveness of a community-based approach for the investigation and management of children with household tuberculosis contact in Cameroon and Uganda: a cluster-randomised trial.

BACKGROUND: Globally, the uptake of tuberculosis-preventive treatment (TPT) among children with household tuberculosis contact remains low, partly due to the necessity of bringing children to health facilities for investigations. This study aimed to evaluate the effect on TPT initiation and completion of community-based approaches to tuberculosis contact investigations in Cameroon and Uganda. METHODS: We did a parallel, cluster-randomised, controlled trial across 20 clusters (consisting of 25 district hospitals and primary health centres) in Cameroon and Uganda, which were randomised (1:1) to receive a community-based approach (intervention group) or standard-of-care facility-based approach to contact screening and management (control group). The community-based approach consisted of symptom-based tuberculosis screening of all household contacts by community health workers at the household, with referral of symptomatic contacts to local facilities for investigations. Initiation of TPT (3-month course of rifampicin-isoniazid) was done by a nurse in the household, and home visits for TPT follow-up were done by community health workers. Index patients were people aged 15 years or older with bacteriologically confirmed, drug-susceptible, pulmonary tuberculosis diagnosed less than 1 month before inclusion and who declared at least one child or young adolescent (aged 0-14 years) household contact. The primary endpoint was the proportion of declared child contacts in the TPT target group (those aged <5 years irrespective of HIV status, and children aged 5-14 years living with HIV) who commenced and completed TPT, assessed in the modified intention-to-treat population (excluding enrolled index patients and their contacts who did not fit the eligibility criteria). Descriptive cascade of care assessment and generalised linear mixed modelling were used for comparison. This study is registered with ClinicalTrials.gov (NCT03832023). FINDINGS: The study included nine clusters in the intervention group (after excluding one cluster that did not enrol any index patients for >2 months) and ten in the control group. Between Oct 14, 2019 and Jan 13, 2022, 2894 child contacts were declared by 899 index patients with bacteriologically confirmed tuberculosis. Among all child contacts declared, 1548 (81·9%) of 1889 in the intervention group and 475 (47·3%) of 1005 in the control group were screened for tuberculosis. 1400 (48·4%) child contacts were considered to be in the TPT target group: 941 (49·8%) of 1889 in the intervention group and 459 (45·7%) of 1005 in the control group. In the TPT target group, TPT was commenced and completed in 752 (79·9%) of 941 child contacts in the intervention group and 283 (61·7%) of 459 in the control group (odds ratio 3·06 [95% CI 1·24-7·53]). INTERPRETATION: A community-based approach using community health workers can significantly increase contact investigation coverage and TPT completion among eligible child contacts in a tuberculosis-endemic setting. FUNDING: Unitaid. TRANSLATION: For the French translation of the abstract see Supplementary Materials section.

In vitro modeling of the post-ingestion bioaccessibility of per- and polyfluoroalkyl substances sorbed to soil and house dust.

Per- and polyfluoroalkyl substances (PFAS) are regularly found in soils and dusts, both of which can be consumed by children at relatively high amounts. However, there is little data available to model the bioaccessibility of PFAS in soils and dusts when consumed or to describe how the physiochemical properties of PFAS and soils/dusts might affect bioaccessibility of these chemicals. Because bioaccessibility is an important consideration in estimating absorbed dose for exposure and risk assessments, in the current study, in vitro assays were used to determine bioaccessibility of 14 PFAS in 33 sets of soils and dusts. Bioaccessibility assays were conducted with and without a sink, which was used to account for the removal of PFAS due to their movement across the human intestine. Multiple linear regression with backward elimination showed that a segmented model using PFAS chain length, number of branches, and percent total organic carbon explained 78.0%-88.9% of the variability in PFAS bioaccessibility. In general, PFAS had significantly greater bioaccessibility in soils relative to dusts and the addition of a sink increased bioaccessibility in the test system by as much as 10.8% for soils and 20.3% for dusts. The results from this study indicate that PFAS bioaccessibility in soils and dusts can be predicted using a limited set of physical chemical characteristics and could be used to inform risk assessment models.

The clinical presentation and detection of tuberculosis during pregnancy and in the postpartum period in low- and middle-income countries: A systematic review and meta-analysis.

For women infected with Mycobacterium tuberculosis, pregnancy is associated with an increased risk of developing or worsening TB disease. TB in pregnancy increases the risk of adverse maternal and neonatal outcomes, however the detection of TB in pregnancy is challenging. We aimed to identify and summarise the findings of studies regarding the clinical presentation and diagnosis of TB during pregnancy and the postpartum period (within 6 months of birth) in low-and middle-income countries (LMICs). A systematic review was conducted searching Ovid MEDLINE, Embase, CINAHL and Global Index Medicus databases. We included any primary research study of women diagnosed with TB during pregnancy or the postpartum period in LMICs that described the clinical presentation or method of diagnosis. Meta-analysis was used to determine pooled prevalence of TB clinical features and health outcomes, as well as detection method yield. Eighty-seven studies of 2,965 women from 27 countries were included. 70.4% of women were from South Africa or India and 44.7% were known to be HIV positive. For 1,833 women where TB type was reported, pulmonary TB was most common (79.6%). Most studies did not report the prevalence of presenting clinical features. Where reported, the most common were sputum production (73%) and cough (68%). Having a recent TB contact was found in 45% of women. Only six studies screened for TB using diagnostic testing for asymptomatic antenatal women and included mainly HIV-positive women ‒ 58% of women with bacteriologically confirmed TB did not report symptoms and only two were in HIV-negative women. Chest X-ray had the highest screening yield; 60% abnormal results of 3036 women tested. Screening pregnant women for TB-related symptoms and risk factors is important but detection yields are limited. Chest radiography and bacteriological detection methods can improve this, but procedures for optimal utilisation remain uncertain in this at-risk population. Trial registration: Prospero registration number: CRD42020202493.

Prevalence, clinical presentation and factors associated with chronic lung disease among children and adolescents living with HIV in Kenya.

INTRODUCTION: Children and adolescents with HIV (CAHIV) may experience recurrent and severe respiratory disease and are at risk of residual lung sequelae, and long-term morbidity from chronically damaged lungs. With improved survival due to increased access to effective antiretroviral therapy there is an increasing population of CAHIV who require optimal life-long care. Chronic lung disease in CAHIV is an under-recognised problem in African settings. We sought to determine the prevalence, clinical presentation and factors associated with chronic lung disease (CLD) among CAHIV in Kenya. METHODS: CAHIV aged ≤19 years in care at a public hospital in Nairobi were enrolled into a longitudinal cohort study. Sociodemographic and clinical information were obtained through interview, medical record review, physical examination and six-minute walk test. CD4 counts and viral load were determined. Enrolment data was analysed to determine baseline sociodemographic and clinical characteristics. Prevalence of CLD defined as presence of ≥2 respiratory symptoms or signs at enrolment was computed. Logistic regression analysis was performed to evaluate for association between various factors and presence or absence of CLD. RESULTS: We enrolled 320 CAHIV of median age 13 (IQR 10-16) years, 80 (25%) were <10 years, 46% were female, 31% lived in a one-room house and 51% used polluting cooking fuel. Antiretroviral therapy (ART) was initiated after age five years in 56%, 43% had prior pneumonia or tuberculosis, 11% had low CD4 count and 79% were virologically suppressed. Common respiratory symptoms and signs were exertional breathlessness (40%), chronic cough (23%), chest problems in the preceding year (24%), tachypnoea (52%), finger clubbing (6%), exercise limitation (59%) and oxygen desaturation during exercise (7%). CLD was present in 82 (26%) participants, and adding the six-minute walk distance <70% of predicted (exercise limitation) identified an additional 28 (9%) CAHIV with CLD. CLD was more common among older teenagers (odds ratio (OR) 1.95), those who had prior TB or pneumonia (OR 2.04), delayed initiation of ART (OR 2.60), cotrimoxazole prophylaxis (OR 3.35) or TB preventive therapy (OR 2.81). CLD was associated with viraemia (OR 2.7), lower quality of life (OR 12.7), small houses (OR 2.05), caregiver having fewer years of education (OR 2.46), outdoor pollution exposure (OR 3.31) and lower use of polluting cooking fuel indoors (OR 0.26). Adjusted analysis revealed CLD to be associated with prior tuberculosis or pneumonia (adjusted OR (aOR) [95%CI] 2.15 [1.18-3.91]), small house (aOR 1.95 [1.02-3.73]), lower use of polluting cooking fuel (aOR 0.35 [0.13-0.94]) and negative impact on health-related quality of life (aOR 6.91 [3.66-13.03]). CONCLUSIONS: CLD is highly prevalent across the age spectrum of CAHIV, and most are symptomatic with cough or exertional breathlessness. CLD is associated with prior tuberculosis or pneumonia, socio-environmental factors, and lower quality of life. Structured interventions are needed to provide optimal care specific to their needs.

Clinical algorithm reduces antibiotic use among children presenting with respiratory symptoms to hospital in central Vietnam.

OBJECTIVE: To assess the safety and utility of a pragmatic clinical algorithm to guide rational antibiotic use in children presenting with respiratory infection. METHODS: The effect of an algorithm to guide the management of young (< 5 years) children presenting with respiratory symptoms to the Da Nang Hospital for Women and Children, Vietnam, was evaluated in a before-after intervention analysis. The main outcome was reduction in antibiotic use, with monitoring of potential harm resulting from reduced antibiotic use. The intervention comprised a single training session of physicians in the use of an algorithm informed by local evidence; developed during a previous prospective observational study. The evaluation was performed one month after the training. RESULTS: Of the 1290 children evaluated before the intervention, 102 (7.9%) were admitted to hospital and 556/1188 (46.8%) were sent home with antibiotics. Due to COVID-19, only 166 children were evaluated after the intervention of whom 14 (8.4%) were admitted to hospital and 54/152 (35.5%) were sent home with antibiotics. Antibiotic use was reduced (from 46.8% to 35.5%; p = 0.009) after clinician training, but adequate comparison was compromised. The reduction was most pronounced in children with wheeze or runny nose and no fever, or a normal chest radiograph, where antibiotic use declined from 46.7% to 28.8% (p < 0.0001). The frequency of repeat presentation to hospital was similar between the two study periods (141/1188; 11.9% before and 10/152; 6.6% after; p = 0.10). No child represented with serious disease after being sent home without antibiotics. CONCLUSIONS: We observed a reduction in antibiotic use in young children with a respiratory infection after physician training in the use of a simple evidence-based management algorithm. However, the study was severely impacted by COVID-19 restrictions, requiring further evaluation to confirm the observed effect.

Attenuation hotspots in neurotropic human astroviruses.

During the last decade, the detection of neurotropic astroviruses has increased dramatically. The MLB genogroup of astroviruses represents a genetically distinct group of zoonotic astroviruses associated with gastroenteritis and severe neurological complications in young children, the immunocompromised, and the elderly. Using different virus evolution approaches, we identified dispensable regions in the 3' end of the capsid-coding region responsible for attenuation of MLB astroviruses in susceptible cell lines. To create recombinant viruses with identified deletions, MLB reverse genetics (RG) and replicon systems were developed. Recombinant truncated MLB viruses resulted in imbalanced RNA synthesis and strong attenuation in iPSC-derived neuronal cultures confirming the location of neurotropism determinants. This approach can be used for the development of vaccine candidates using attenuated astroviruses that infect humans, livestock animals, and poultry.

Antimicrobial stewardship in the era of the COVID-19 pandemic: A systematic review protocol on the opportunities and challenges for Sub-Saharan Africa.

BACKGROUND: Antimicrobial resistance (AMR) remains one of the leading threats to global public health and this may increase following COVID-19 pandemic. This is particularly the case in Africa where regulations on antimicrobial usage are weak. This protocol outlines the steps to undertake a systematic review to synthesize evidence on drivers of AMR and evaluate existing approaches to strengthening antimicrobial stewardship (AMS) programs in Sub-Saharan Africa (SSA). On the basis of the evidence generated from the evidence synthesis, the overarching goal of this work is to provide recommendations to support best practices in AMS implementation in SSA. METHODS: A systematic search will be conducted using the following databases: Global Health Library, PubMed, Cumulative Index to Nursing and Allied Health Literature, Scopus, Google Scholar, Global Health, Embase, African Journals Online Library, Web of Science, antimicrobial databases (WHO COVID-19, TrACSS, NDARO, and JPIAMR), and the Cochrane databases for systematic reviews. Studies will be included if they assess AMR and AMS in SSA from January 2000 to January 31, 2023. RESULTS: The primary outcomes will include the drivers of AMR and approaches to AMS implementation in SSA. The Preferred Reporting Items for Systematic Reviews and Meta-analyses will guide the reporting of this systematic review. CONCLUSIONS: The findings are expected to provide evidence on best practices and resource sharing for policy consideration to healthcare providers and other stakeholders both at the local and international levels. Additionally, the study seeks to establish drivers specific to AMR during the COVID-19 era in the SSA, for example, with the observed increasing trend of antimicrobial misuse during the first or second year of the pandemic may provide valuable insights for policy recommendation in preparedness and response measures to future pandemics. PROSPERO REGISTRATION NUMBER: CRD42022368853.

Altered plasma membrane abundance of the sulfatide-binding protein NF155 links glycosphingolipid imbalances to demyelination.

Myelin is a multilayered membrane that tightly wraps neuronal axons, enabling efficient, high-speed signal propagation. The axon and myelin sheath form tight contacts, mediated by specific plasma membrane proteins and lipids, and disruption of these contacts causes devastating demyelinating diseases. Using two cell-based models of demyelinating sphingolipidoses, we demonstrate that altered lipid metabolism changes the abundance of specific plasma membrane proteins. These altered membrane proteins have known roles in cell adhesion and signaling, with several implicated in neurological diseases. The cell surface abundance of the adhesion molecule neurofascin (NFASC), a protein critical for the maintenance of myelin-axon contacts, changes following disruption to sphingolipid metabolism. This provides a direct molecular link between altered lipid abundance and myelin stability. We show that the NFASC isoform NF155, but not NF186, interacts directly and specifically with the sphingolipid sulfatide via multiple binding sites and that this interaction requires the full-length extracellular domain of NF155. We demonstrate that NF155 adopts an S-shaped conformation and preferentially binds sulfatide-containing membranes in cis, with important implications for protein arrangement in the tight axon-myelin space. Our work links glycosphingolipid imbalances to disturbance of membrane protein abundance and demonstrates how this may be driven by direct protein-lipid interactions, providing a mechanistic framework to understand the pathogenesis of galactosphingolipidoses.

Development of treatment-decision algorithms for children evaluated for pulmonary tuberculosis: an individual participant data meta-analysis.

BACKGROUND: Many children with pulmonary tuberculosis remain undiagnosed and untreated with related high morbidity and mortality. Recent advances in childhood tuberculosis algorithm development have incorporated prediction modelling, but studies so far have been small and localised, with limited generalisability. We aimed to evaluate the performance of currently used diagnostic algorithms and to use prediction modelling to develop evidence-based algorithms to assist in tuberculosis treatment decision making for children presenting to primary health-care centres. METHODS: For this meta-analysis, we identified individual participant data from a WHO public call for data on the management of tuberculosis in children and adolescents and referral from childhood tuberculosis experts. We included studies that prospectively recruited consecutive participants younger than 10 years attending health-care centres in countries with a high tuberculosis incidence for clinical evaluation of pulmonary tuberculosis. We collated individual participant data including clinical, bacteriological, and radiological information and a standardised reference classification of pulmonary tuberculosis. Using this dataset, we first retrospectively evaluated the performance of several existing treatment-decision algorithms. We then used the data to develop two multivariable prediction models that included features used in clinical evaluation of pulmonary tuberculosis-one with chest x-ray features and one without-and we investigated each model's generalisability using internal-external cross-validation. The parameter coefficient estimates of the two models were scaled into two scoring systems to classify tuberculosis with a prespecified sensitivity target. The two scoring systems were used to develop two pragmatic, treatment-decision algorithms for use in primary health-care settings. FINDINGS: Of 4718 children from 13 studies from 12 countries, 1811 (38·4%) were classified as having pulmonary tuberculosis: 541 (29·9%) bacteriologically confirmed and 1270 (70·1%) unconfirmed. Existing treatment-decision algorithms had highly variable diagnostic performance. The scoring system derived from the prediction model that included clinical features and features from chest x-ray had a combined sensitivity of 0·86 [95% CI 0·68-0·94] and specificity of 0·37 [0·15-0·66] against a composite reference standard. The scoring system derived from the model that included only clinical features had a combined sensitivity of 0·84 [95% CI 0·66-0·93] and specificity of 0·30 [0·13-0·56] against a composite reference standard. The scoring system from each model was placed after triage steps, including assessment of illness acuity and risk of poor tuberculosis-related outcomes, to develop treatment-decision algorithms. INTERPRETATION: We adopted an evidence-based approach to develop pragmatic algorithms to guide tuberculosis treatment decisions in children, irrespective of the resources locally available. This approach will empower health workers in primary health-care settings with high tuberculosis incidence and limited resources to initiate tuberculosis treatment in children to improve access to care and reduce tuberculosis-related mortality. These algorithms have been included in the operational handbook accompanying the latest WHO guidelines on the management of tuberculosis in children and adolescents. Future prospective evaluation of algorithms, including those developed in this work, is necessary to investigate clinical performance. FUNDING: WHO, US National Institutes of Health.

Beyond patient delay, navigating structural health system barriers to timely care and treatment in a high burden TB setting in Papua New Guinea.

Tuberculosis (TB) is a major public health issue in Papua New Guinea, with incidence rates particularly high in the South Fly District of Western Province. We present three case studies, along with additional vignettes, that were derived from interviews and focus groups carried out between July 2019 and July 2020 of people living in rural areas of the remote South Fly District depicting their challenges accessing timely TB diagnosis and care; most services within the district are only offered offshore on Daru Island. The findings detail that rather than 'patient delay' attributed to poor health seeking behaviours and inadequate knowledge of TB symptoms, many people were actively trying to navigate structural barriers hindering access to and utilisation of limited local TB services. The findings highlight a fragile and fragmented health system, a lack of attention given to primary health services, and undue financial burdens placed on people living in rural and remote areas associated with costly transportation to access functioning health services. We conclude that a person-centred and effective decentralised model of TB care as outlined in health policies is imperative for equitable access to essential health care services in Papua New Guinea.

A scoping review of lung function in children and adolescents living with HIV in the era of antiretroviral treatment.

BACKGROUND: Human immunodeficiency virus (HIV) in children and adolescents remains an important health challenge in many countries and is commonly associated with lung disease. The introduction of antiretroviral therapy (ART) has greatly improved survival but chronic lung disease is a common ongoing challenge. We conducted a scoping review of studies that have reported lung function in school-aged children and adolescents living with HIV. METHODS: A systematic literature search was performed by searching Medline, Embase, and PubMed databases, limited to articles published between 2011 and 2021 in English language. Inclusion criteria were studies involving participants living with HIV aged 5-18 years and having spirometry data. The primary outcome was lung function as measured by spirometry. RESULTS: Twenty-one studies were included in the review. Most study participants were living in the sub-Saharan African region. The prevalence of reduced forced expiratory volume in 1 s (FEV1 ) ranged from 25.3% to 73% across studies, reduced forced vital capacity (FVC) ranged from 10% to 42% and reduced FEV1 /FVC ranged from 3% to 26%. The mean z-score of FEV1 ranged from -2.19 to -0.73, mean zFEV1 /FVC ranged from -0.74 to 0.2, and mean FVC ranged from -1.86 to -0.63. CONCLUSION: There is a high prevalence of lung function impairment in children and adolescents living with HIV, which persists in the ART era. Further studies are needed of interventions that might improve lung function in these vulnerable populations.

Rapid and Accurate Diagnosis of Pediatric Tuberculosis Disease: A Diagnostic Accuracy Study for Pediatric Tuberculosis.

INTRODUCTION: An estimated 1.2 million children develop tuberculosis (TB) every year with 240,000 dying because of missed diagnosis. Existing tools suffer from lack of accuracy and are often unavailable. Here, we describe the scientific and clinical methodology applied in RaPaed-TB, a diagnostic accuracy study. METHODS: This prospective diagnostic accuracy study evaluating several candidate tests for TB was set out to recruit 1000 children <15 years with presumptive TB in 5 countries (Malawi, Mozambique, South Africa, Tanzania, India). Assessments at baseline included documentation of TB signs and symptoms, TB history, radiography, tuberculin skin test, HIV testing and spirometry. Respiratory samples for reference standard testing (culture, Xpert Ultra) included sputum (induced/spontaneous) or gastric aspirate, and nasopharyngeal aspirate (if <5 years). For novel tests, blood, urine and stool were collected. All participants were followed up at months 1 and 3, and month 6 if on TB treatment or unwell. The primary endpoint followed NIH-consensus statements on categorization of TB disease status for each participant. The study was approved by the sponsor's and all relevant local ethics committees. DISCUSSION: As a diagnostic accuracy study for a disease with an imperfect reference standard, Rapid and Accurate Diagnosis of Pediatric Tuberculosis Disease (RaPaed-TB) was designed following a rigorous and complex methodology. This allows for the determination of diagnostic accuracy of novel assays and combination of testing strategies for optimal care for children, including high-risk groups (ie, very young, malnourished, children living with HIV). Being one of the largest of its kind, RaPaed-TB will inform the development of improved diagnostic approaches to increase case detection in pediatric TB.

Structure and neutralization mechanism of a human antibody targeting a complex Epitope on Zika virus.

We currently have an incomplete understanding of why only a fraction of human antibodies that bind to flaviviruses block infection of cells. Here we define the footprint of a strongly neutralizing human monoclonal antibody (mAb G9E) with Zika virus (ZIKV) by both X-ray crystallography and cryo-electron microscopy. Flavivirus envelope (E) glycoproteins are present as homodimers on the virion surface, and G9E bound to a quaternary structure epitope spanning both E protomers forming a homodimer. As G9E mainly neutralized ZIKV by blocking a step after viral attachment to cells, we tested if the neutralization mechanism of G9E was dependent on the mAb cross-linking E molecules and blocking low-pH triggered conformational changes required for viral membrane fusion. We introduced targeted mutations to the G9E paratope to create recombinant antibodies that bound to the ZIKV envelope without cross-linking E protomers. The G9E paratope mutants that bound to a restricted epitope on one protomer poorly neutralized ZIKV compared to the wild-type mAb, demonstrating that the neutralization mechanism depended on the ability of G9E to cross-link E proteins. In cell-free low pH triggered viral fusion assay, both wild-type G9E, and epitope restricted paratope mutant G9E bound to ZIKV but only the wild-type G9E blocked fusion. We propose that, beyond antibody binding strength, the ability of human antibodies to cross-link E-proteins is a critical determinant of flavivirus neutralization potency.