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Ethics of Identifying Individuals Involved in HIV Transmission Events by Phylogenetics in Molecular Surveillance
ABSTRACTMolecular HIV surveillance, involving the collection and analysis of HIV genome sequences, has become an integral part of public health programmes in high‐income countries. By employing phylogenetic analysis, molecular HIV surveillance can identify individuals and their positions within networks of HIV transmission. While the primary aim of molecular surveillance is to yield public health benefits, such as linking people to care and reducing transmission, it also poses risks and potential infringements on individual privacy and liberty. This paper examines the ethical implications of using phylogenetics to identify individuals involved in multiple transmission events in high‐income countries. Although public health responses tailored to such individuals can significantly reduce further transmission, these individuals often face multiple intersecting vulnerabilities and bear the greatest risks associated with molecular surveillance. We analyze the risks related to privacy, stigma, mistrust, criminalization, and liberty infringements, alongside the benefits of preventing further transmission and increasing healthcare engagement for people living with HIV. We conclude by outlining plausible and ethically acceptable policy options for molecular surveillance practice.
Validity of Clinical Severity Scores for Respiratory Syncytial Virus: A Systematic Review.
BackgroundRespiratory syncytial virus (RSV) is a widespread respiratory pathogen, and RSV-related acute lower respiratory tract infections are the most common cause of respiratory hospitalization in children <2 years of age. Over the last 2 decades, a number of severity scores have been proposed to quantify disease severity for RSV in children, yet there remains no overall consensus on the most clinically useful score.MethodsWe conducted a systematic review of English-language publications in peer-reviewed journals published since January 2000 assessing the validity of severity scores for children (≤24 months of age) with RSV and/or bronchiolitis, and identified the most promising scores. For included articles, (1) validity data were extracted, (2) quality of reporting was assessed using the Transparent Reporting of a multivariable prediction model for Individual Prognosis Or Diagnosis checklist (TRIPOD), and (3) quality was assessed using the Prediction Model Risk Of Bias Assessment Tool (PROBAST). To guide the assessment of the validity data, standardized cutoffs were employed, and an explicit definition of what we required to determine a score was sufficiently validated.ResultsOur searches identified 8541 results, of which 1779 were excluded as duplicates. After title and abstract screening, 6670 references were excluded. Following full-text screening and snowballing, 32 articles, including 31 scores, were included. The most frequently assessed scores were the modified Tal score and the Wang Bronchiolitis Severity Score; none of the scores were found to be sufficiently validated according to our definition. The reporting and/or design of all the included studies was poor. The best validated score was the Bronchiolitis Score of Sant Joan de Déu, and a number of other promising scores were identified.ConclusionsNo scores were found to be sufficiently validated. Further work is warranted to validate the existing scores, ideally in much larger datasets.
Underreporting and Misclassification of Respiratory Syncytial Virus-Coded Hospitalization Among Adults in Denmark Between 2015-2016 and 2017-2018.
BackgroundLow awareness and lack of routine testing for respiratory syncytial virus (RSV) infections among adults has led to underreporting in hospital records. This study aimed to assess the underreporting and misclassification of RSV infections among adults hospitalized with an respiratory tract infection (RTI)-coded hospitalization.MethodsThis study is an observational cohort study of RSV-associated hospitalizations among Danish adults (≥18 years old) conducted, between 2015 to 2018. Data were extracted from the Danish National Patient Registry (DNPR) and the Danish Microbiology Database. We identified RSV-positive hospitalizations by linking RTI-coded hospitalizations with a positive RSV test.ResultsUsing hospital admission registries, we identified 440 RSV-coded hospitalizations, of whom 420 (95%) had a positive RSV test registered. By linking patients with RTI-coded hospital admissions to RSV test result, we found 570 additional episodes of RSV-positive hospitalizations without an RSV-coded diagnosis.ConclusionsOur study of national register data showed that RSV is underreported among Danish adults. The study showed that the reliability of hospitalization data to estimate the burden of RSV among adults is questionable and are sensitive to changes in practice over time, even with complete nationwide healthcare data. Healthcare data can be useful to observe seasonality but to estimate the disease burden, prospective surveillance is recommended.
Airway and Blood Monocyte Transcriptomic Profiling Reveals an Antiviral Phenotype in Infants With Severe Respiratory Syncytial Virus Infection.
BackgroundRespiratory syncytial virus (RSV) infection is the primary cause of lower respiratory tract infections in children <5 years of age. Monocytes, especially in the respiratory tract, are suggested to contribute to RSV pathology, but their role is incompletely understood. With transcriptomic profiling of blood and airway monocytes, we describe the role of monocytes in severe RSV infection.MethodsTracheobronchial aspirates and blood samples were collected from control patients (n = 9) and those infected with RSV (n = 14) who were admitted to the pediatric intensive care unit. Monocytes (CD14+) were sorted and analyzed by RNA sequencing for transcriptomic profiling.ResultsPeripheral blood and airway monocytes of patients with RSV demonstrated increased expression of antiviral and interferon-responsive genes as compared with controls. Cytokine signaling showed a shared response between blood and airway monocytes while displaying responses that were more pronounced according to the tissue of origin. Airway monocytes upregulated additional genes related to migration and inflammation.ConclusionsWe found that the RSV-induced interferon response extends from the airways to the peripheral blood. Moreover, RSV induces a migration-promoting transcriptional program in monocytes. Unraveling the monocytic response and its role in the immune response to RSV infection could help the development of therapeutics to prevent severe disease.
Respiratory viral detection in children hospitalized with pneumonia during periods of major population disruptions in Nepal, 2014-2018.
BackgroundRespiratory viruses commonly cause pneumonia in children. We aimed to identify respiratory viral nucleic acids in the nasopharynx of children admitted with pneumonia from 2014 to 2018, a period including a major earthquake (April 2015), PCV10 introduction (August 2015), and a fuel shortage (October 2015 to March 2016).MethodsChildren 2 months to 14 years admitted to Patan Hospital between March 2014 and February 2018 with a clinical diagnosis of pneumonia had nasopharyngeal swabs collected and tested with a multiplex panel for the presence of genetic material from 23 respiratory pathogens.ResultsOf 1343 children with pneumonia, 974 (72.5%) had the nucleic acids of at least one respiratory virus in the nasopharynx. The median age of children with any viral genetic material detected was lower than those without (1.18, IQR: 0.59-2.39 years; versus 2.01 years, IQR: 0.81-4.34 years; p<0.001). Commonly detected viral nucleic acids included those of RSV (21.0%), rhino/enterovirus (30.8%), and parainfluenza (7.4%). The odds of detecting any respiratory viral genetic material in children with pneumonia increased by 1.88 (95% confidence interval: 1.15, 3.06) in the year after the earthquake, when there were several aftershocks and a fuel crisis, relative to other periods and accounting for other potential confounding factors.ConclusionsThese findings highlight the importance of viral diagnostics in pediatric pneumonia and suggest that public health measures addressing environmental conditions during disasters might help reduce respiratory infections.
Age differences in immunity to human seasonal coronaviruses and the immunogenicity of ChAdOx1 nCoV-19 (AZD1222).
BackgroundChAdOx1 nCoV-19 (AZD1222) vaccine was widely deployed to protect against severe COVID-19 in adults, but the relationship between pre-existing immunity to human seasonal coronaviruses (HCoVs) and vaccine-induced SARS-CoV-2 (SCoV2) response across age groups remains unclear.MethodsWe analysed SCoV2 and HCoVs antibody profiles in UK volunteers (aged 6-≥70), assessing antibody levels, avidity, and FcγR binding after receiving one or two doses of ChAdOx1 nCoV-19. Adult cohorts from trials in Brazil and Kenya were also included to evaluate geographical impacts on baseline HCoVs and SCoV2 induced response.FindingsIn the UK cohort, younger individuals had higher SCoV2 IgG, avidity, FcγR binding and cross-reactivity, particularly towards OC43 and HKU1. The greatest differences were seen after the first dose of ChAdOx1 nCoV-19, but these effects diminished after the second dose. Although baseline HCoVs IgG varied geographically, similar trends were observed across adult cohorts with younger adults showing higher SCoV2 IgG compared to older adults (UK and Brazil).InterpretationThese findings contribute to a better understanding of the immunogenicity of ChAdOx1-based vaccines in various age groups. Determining whether this applies across other vaccines using same platform is essential for evaluating the viability of one-dose regimens in outbreak responses.FundingThe clinical trials COV002, COV003, COV004, and COV006 were made possible by funding from Astra Zeneca, the NIHR and the University of Oxford, UK Department of Health and Social Care, through the UK National Institute for Health and Care Research, the Wellcome Trust (220991), and Innovate UK (project 971614).
Longitudinal kinetics of the viral infection biomarker 3'-deoxy-3',4'-didehydro-cytidine in SARS-CoV-2, influenza A virus and RSV human challenge models.
3'-deoxy-3',4'-didehydro-cytidine (ddhC) is a recently discovered host biomarker for viral infections, though its temporal kinetics remain unclear. This study tests the hypothesis that ddhC is an acute phase reactant, rising shortly after viral infection and subsequently falling to baseline. We leveraged the precise monitoring facilitated by human challenge studies to investigate healthy participants inoculated with SARS-CoV-2, influenza A virus (H3N2), or respiratory syncytial virus (RSV). Using targeted liquid chromatography-tandem mass spectrometry, we quantified ddhC concentrations in serial plasma samples collected pre- and post-inoculation. In SARS-CoV-2 and H3N2 influenza A virus infection, but not RSV, ddhC levels peaked at 3-7 days post inoculation and declined to baseline by days 10-14. This pattern was also observed in asymptomatic or paucisymptomatic participants. A comparison of ddhC concentrations with matched timepoint whole blood gene expression revealed a correlation with interferon-related genes, including viperin and CMPK2-enzymes implicated in its upstream biosynthesis. Our results suggest that ddhC is a biomarker of the acute phase of viral infection, with potential to guide early interventions that reduce antimicrobial resistance and strengthen pandemic preparedness. Future work should explore ddhC dynamics in natural and experimental infections across varying severities and assess its utility in diverse populations and healthcare settings.
Mpox stigma in the UK and implications for future outbreak control: a cross-sectional mixed methods study.
BACKGROUND: Stigma emerged as a prominent public health challenge in the global mpox outbreak that began in 2022, impeding outbreak control efforts and the well-being of affected individuals. Addressing stigma is important for improving infection prevention and control. Despite frequent mention in public and policy discourse, robust assessment of mpox stigma is lacking. This study investigated the causes, manifestations, and impacts of mpox-related stigma in the UK, focusing on anticipated stigma among directly and indirectly affected communities. METHODS: We conducted an online, mixed-methods cross-sectional survey to assess mpox stigma. We developed and content validated a new tool, the Stigma Survey and Community-based Assessment for New and Re-emerging outbreaks (Stigma-SCANR) for this purpose. Through quota sampling, the survey targeted populations most affected by mpox at the time of data collection (March-July 2024), including gay, bisexual, and other men who have sex with men (GBMSM), and healthcare workers. The survey primarily explored anticipated stigma. Respondents with previous mpox diagnoses were asked about personal experiences of stigma. RESULTS: Of 479 respondents who initiated the survey, 437 (91%) were included in analyses. In modules related to drivers of stigma, pre-existing prejudices towards associated groups such as GBMSM and migrants were emphasised, alongside fear and misinformation. On average, respondents anticipated higher levels of negative judgement and unwarranted avoidance compared to other forms of social stigma, particularly from casual partners and the public. Among the 13 respondents who reported a previous mpox diagnosis, 11 (85%) had experienced mpox-related stigma. Nearly a quarter of respondents (24%) said they would not, or were unlikely to, tell a recent sexual partner about an mpox diagnosis. Feelings of shame were considered the most common barrier to care-seeking (299 respondents, 68%). CONCLUSIONS: This analysis of mpox stigma in the UK offers insights for international outbreak response, particularly in countries with similarly affected communities. Lessons learnt may also be transferable to other disease outbreaks. We propose practical recommendations for reducing stigma in future outbreaks, including peer support initiatives, distributing accessible information about safe timelines for returning to socialising and work or school, and co-designing public communications and contact tracing programmes with affected community members.
LISTEN: lived experiences of Long COVID: a social media analysis of mental health and supplement use
IntroductionLong COVID, or Post-Acute Sequelae of SARS-CoV-2 infection (PASC), is a complex condition characterized by a wide range of persistent symptoms that can significantly impact an individual's quality of life and mental health. This study explores public perspectives on the mental health impact of Long COVID and the use of dietary supplements for recovery, drawing on social media content. It uniquely addresses how individuals with Long COVID discuss supplement use in the absence of public health recommendations.MethodsThe study employs the LISTEN method (“Collaborative and Digital Analysis of Big Qual Data in Time Sensitive Contexts”), an interdisciplinary approach that combines human insight and digital analysis software. Social media data related to Long COVID, mental health, and supplement use were collected using the Pulsar Platform. Data were analyzed using the free-text discourse analysis tool Infranodus and collaborative qualitative analysis methods.ResultsThe findings reveal key themes, including the impact of Long COVID on mental health, occupational health, and the use of food supplements. Analysis of attitudes toward supplement use highlights the prevalence of negative emotions and experiences among Long COVID patients. The study also identifies the need for evidence-based recommendations and patient education regarding supplement use.DiscussionThe findings contribute to a better understanding of the complex nature of Long COVID and inform the development of comprehensive, patient-centered care strategies addressing both physical and mental health needs.
Immunogenicity and Safety of ChAdOx1 nCoV-19 (AZD1222) as a Homologous Fourth-Dose Booster: A Substudy of the Phase 3 COV003 Trial in Brazil
Objective: To address that, despite widespread use of ChAdOx1 nCoV-19 (AZD1222) as a COVID-2019 booster, fourth-dose clinical outcomes data are limited. We report immunogenicity and safety for ChAdOx1 nCoV-19 as a homologous fourth-dose booster. Participants and Methods: Participants (aged ≥18 years) who had received 2 doses of ChAdOx1 nCoV-19 in phase 3 COV003 trial in Brazil were offered a third dose after a planned dose interval from 11 to 13 months and a fourth dose after a planned interval from 6 to 15 months (both 5 × 1010 viral particles). All fourth doses were administered to substudy participants between August 18 and October 28, 2022. The data cutoff was December 9, 2022. The primary immunogenicity outcome was noninferiority of ancestral severe acute respiratory syndrome coronavirus (SARS-CoV)-2–neutralizing antibody responses 28 days after dose 4 versus dose 3. Solicited and unsolicited adverse events were recorded 7 and 28 days postdose 4, respectively. Results: 172 participants received a fourth dose (median interval postthird dose, 10.7 months). Ancestral SARS-CoV-2–neutralizing antibody titers postdose 4 were noninferior to those postdose 3; geometric mean fold rise was 1.9 (95% CI, 1.6-2.4; n=112). Immunogenicity results were consistent across all variants analyzed. Local and systemic solicited adverse events were reported in 60.3% (n=35/58) and 43.1% (n=25/58) of participants, respectively. Conclusion: Immune responses after a fourth dose of ChAdOx1 nCoV-19 were noninferior to those after a third dose across SARS-CoV-2 variants. The fourth dose was well tolerated with no emergent safety concerns, supporting the continued development of the ChAdOx1 platform in preparation for future pandemics. Trial Registration: clinicaltrials.gov Identifier: NCT04536051
SPIKELLM: SCALING UP SPIKING NEURAL NETWORK TO LARGE LANGUAGE MODELS VIA SALIENCY-BASED SPIKING
Recent advancements in large language models (LLMs) with billions of parameters have improved performance in various applications, but their inference processes demand significant energy and computational resources. In contrast, the human brain, with approximately 86 billion neurons, is much more energy-efficient than LLMs with similar parameters. Inspired by this, we redesign 7∼70 billion parameter LLMs using bio-plausible spiking mechanisms, emulating the efficient behavior of the human brain. We propose the first spiking large language model, SpikeLLM. Coupled with the proposed model, two essential approaches are proposed to improve spike training efficiency: Generalized Integrate-and-Fire (GIF) neurons to compress spike length from T to TL log2 L bits, and an Optimal Brain Spiking framework to divide outlier channels and allocate different T for GIF neurons, which further compresses spike length to approximate log2T bits. The necessity of spike-driven LLM is proved by comparison with quantized LLMs with similar operations. In the OmniQuant pipeline, SpikeLLM reduces 11.01% WikiText2 perplexity and improves 2.55% accuracy of common scene reasoning on a LLAMA-7B W4A4 model. In the GPTQ pipeline, SpikeLLM achieves direct additive in linear layers, significantly exceeding PB-LLMs. Our code is publicly available at https://github.com/Xingrun-Xing2/SpikeLLM.