Detailed analysis of in-hospital transmission of SARS-CoV-2 using whole genome sequencing.

BACKGROUND: Hospital transmission of SARS-CoV-2 has proved difficult to control, with healthcare-associated infections troublesome throughout. AIM: To understand factors contributing to hospital transmission of infections, which is necessary for containing spread. METHODS: An outbreak of 56 staff and patient cases of COVID-19 over a 31-day period in a tertiary referral unit is presented, with at least a further 29 cases identified outside of the unit and the hospital by whole genome sequencing (WGS). FINDINGS: Transmission is documented from staff to staff, staff to patients, and patients to staff, showing disruption of a tertiary referral service, despite implementation of nationally recommended control measures, superior ventilation, and use of personal protective equipment. There was extensive spread from the index case, despite this patient spending only 10 h bed bound on the ward in strict cubicle isolation and with an initial single target low level (CT = 32) polymerase chain reaction test. CONCLUSION: This investigation highlights how effectively and rapidly SARS-CoV-2 can spread in certain circumstances. It raises questions about infection control measures in place at the time and calls into question the premise that transmissibility can be reliably detected by using lower sensitivity rapid antigen lateral flow tests. We also highlight the value of early intervention in reducing impact as well as the value of WGS in understanding outbreaks.

Detecting COVID-19 from Red Blood Cells Using Digital Holographic Microscopy: an Overview

We overview our previously reported systems for detection of COVID-19 infection from digital holographic reconstructed red blood cells. The overviewed systems use time-varying information of the samples to classify specimens at the cellular level. © 2022 The Author(s)

OUTCOMES OF COVID-19 IN LUNG TRANSPLANT RECIPIENTS: A SINGLE CENTER REVIEW

SESSION TITLE: Lung Transplantation: New Issues in 2022 SESSION TYPE: Rapid Fire Original Inv PRESENTED ON: 10/19/2022 11:15 am - 12:15 pm PURPOSE: Currently the sequelae of COVID pneumonia in lung transplant recipients (LTR) is poorly described and the long-term effects are largely unknown. LTRs encompass a unique patient population with anatomic and immunological changes that pose a huge challenge in the management of COVID pneumonia compared to the general population. This project looks to further delineate risk factors, prognostication, and long-term sequelae of COVID pneumonia in LTRs. METHODS: A retrospective analysis was performed in a single large lung transplant center in Chicago from January 2020 to June 2021. Impact of COVID-19 based on patient demographics, management strategies, level of care, mortality, and pre- and post-COVID spirometry changes were analyzed based on follow-up visits after infection in survivors. RESULTS: There was an overall mortality of 21% with 68% requiring hospital admission. Of the patients admitted, there was a 62% mortality risk associated with ICU admission. Pre-existing chronic lung allograft dysfunction (CLAD) was present in 10 patients of which 50% were admitted to the ICU. Baseline FEV1 was 1.95 L with an average post covid FEV1 of 1.89 L (3.7% decline) for survivors. Pre-existing CLAD, lower baseline FEV1, and increased time since transplant were predictors of ICU admission. CONCLUSIONS: COVID-19 continues to remain a dangerous, life-threatening disease, particularly for LTRs. While there were no patients that developed CLAD post infection, there was an overall decrease in lung function. The long term trajectory of graft function post-covid remains unclear, however pre-existing allograft dysfunction appears to provide prognostic value. CLINICAL IMPLICATIONS: Further study needs to be done on COVID-19 and the long-term implications of allograft function in the LTR population. DISCLOSURES: Speaker/Speaker's Bureau relationship with boehringer ingelheim Please note: $5001 - $20000 by Brad Bemiss, value=Travel and payment for lecture No relevant relationships by Timothy O'Connor No relevant relationships by Love Patel

Getting to the Heart of In-hospital Transmission of SARS-CoV-2 with the Help of Whole Genome Sequencing

We present an outbreak of 56 staff and patient cases of COVID-19 over a 31 day period in a tertiary referral unit, with at least a further 29 cases identified outside of the unit and the hospital by whole genome sequencing (WGS). We document transmission from staff-to-staff, staff-to-patients and patients-to-staff and show disruption of a tertiary referral service, despite implementation of nationally recommended control measures, superior ventilation and use of PPE. We demonstrate extensive spread from the index case, despite them spending only 10 hours bed bound on the ward in strict cubicle isolation and with an initial single target low level (CT=32) PCR test. This investigation highlights critical issues including how effectively and explosively SARS-CoV-2 can spread in certain circumstances. It raises questions about infection control measures in place at the time and calls into question the premise that transmissibility can be reliably detected using lower sensitivity rapid antigen lateral flow tests. We also highlight the value of early intervention in reducing impact as well as the value of WGS in understanding outbreaks.

Becoming a Doctor During a Pandemic: Impact on Medical Student Social Identity Formation.

The COVID-19 pandemic required modifications to undergraduate medical education that likely affected medical students' social identity formation (SIF). SIF is shaped by experiences throughout the medical education continuum. This commentary explores factors potentially affecting medical student SIF during the COVID-19 pandemic focusing on students' perceptions of being part of the healthcare team, their role in medicine, and their engagement during the pandemic. Based on such considerations, we propose that educators should aim to design effective learning environments to support a full educational experience that encompasses acquiring medical knowledge and building strong social identities even during a pandemic.

An ethical analysis of clinical triage protocols and decision-making frameworks: what do the principles of justice, freedom, and a disability rights approach demand of us?

BACKGROUND: The expectation of pandemic-induced severe resource shortages has prompted authorities to draft and update frameworks to guide clinical decision-making and patient triage. While these documents differ in scope, they share a utilitarian focus on the maximization of benefit. This utilitarian view necessarily marginalizes certain groups, in particular individuals with increased medical needs. MAIN BODY: Here, we posit that engagement with the disability critique demands that we broaden our understandings of justice and fairness in clinical decision-making and patient triage. We propose the capabilities theory, which recognizes that justice requires a range of positive capabilities/freedoms conducive to the achievement of meaningful life goals, as a means to do so. Informed by a disability rights critique of the clinical response to the pandemic, we offer direction for the construction of future clinical triage protocols which will avoid ableist biases by incorporating a broader apprehension of what it means to be human. CONCLUSION: The clinical pandemic response, codified across triage protocols, should embrace a form of justice which incorporates a vision of pluralistic human capabilities and a valuing of positive freedoms.

Guidelines for the use of the Attend Anywhere Platform for Telecommunications within the Pain Service

Introduction Remote consultation is of growing in importance and gaining popularity in both primary and secondary healthcare settings. Reduced necessity for a physical presence of the patient within the healthcare setting is of particular benefit in the current COVID-19 era. It is also of benefit to a diverse group of patients, for example: those who are geographically distant from the base hospital, those suffering from mobility issues or chronic illness, those who require chaperoning as well as those with limited access to transport. We have developed guidelines for the use of the medical telecommunications platform, Attend Anywhere, which has been utilised across the English and Scottish National Health Services, as well as with the Australian Health service, and is now available in Health Service Executive (HSE) settings. Herein we describe and recommend a process that we have found helpful, and we propose guidelines on how a Health Care Worker (HCW) might consider approaching a virtual consultation when initiating and safely executing a patient encounter on Attend Anywhere, in a secure and efficient manner. The guidelines were created following review of the literature on previous experience by others with this software, as well as recent guidance published by the Irish Medical Council. A proportion of this guidance is transferable to other platforms. Methods We also undertook a short survey of our patients and physicians in Sligo University Hospital, who used Attend Anywhere over a six-week period to gauge their satisfaction levels with the experience., We estimated distance that our patients would have travelled for their appointment had the traditional face-to-face consultation been carried out. We noted whether we considered the medium appropriate for the patient consultations. Results 53 patients took part and satisfaction was rated from satisfied to very satisfied on a 3-point scale for all stakeholders. In addition, we found that remote consultation, when compared to face-to-face consultation, alleviated an average of 144km of unnecessary travel per appointment. Remote consultation was deemed appropriate in all cases and no rescheduled face-to-face appointments were required due to failure of the consultation due to difficulties encountered. Conclusion The authors recommend the implementation of the described guidance, with suggested Checklist, Information leaflet and Consent form, as a means of ensuring the confidentiality of the consultation and to ensure that processes are adhered to that optimise protection for both the patient and the clinician, while reducing the burden of attendance to the healthcare location.

Metacoupled tourism and wildlife translocations affect synergies and trade-offs among sustainable development goals across spillover systems

Synergies and trade-offs among the United Nations Sustainable Development Goals (SDGs) have been hotly debated. Although the world is increasingly metacoupled (socioeconomic-environmental interactions within and across adjacent or distant systems), there is little understanding of the impacts of globally widespread and important flows on enhancing or compromising sustainability in different systems. Here, we used a new integrated framework to guide SDG synergy and trade-off analysis within and across systems, as influenced by cross-boundary tourism and wildlife translocations. The world's terrestrial protected areas alone receive approximately 8 billion visits per year, generating a direct economic impact of US $600 billion. Globally, more than 5000 animal species and 29,000 plant species are traded across country borders, and the wildlife trade has arguably contributed to zoonotic disease worldwide, such as the ongoing COVID-19 pandemic. We synthesized 22 cases of tourism and wildlife translocations across six continents and found 33 synergies and 14 trade-offs among 10 SDGs within focal systems and across spillover systems. Our study provides an empirical demonstration of SDG interactions across spillover systems and insights for holistic sustainability governance, contributing to fostering synergies and reducing trade-offs to achieve global sustainable development in the metacoupled Anthropocene.

Impact of the COVID-19 pandemic on exposure and response prevention outcomes in adults and youth with obsessive-compulsive disorder.

The COVID-19 pandemic has created novel mental health challenges for those with pre-existing problems including obsessive-compulsive disorder (OCD). Our study reports on clinician perceptions regarding the effect of the COVID-19 pandemic on patients with OCD receiving exposure and response prevention treatment (ERP) prior to and during the pandemic. Participating clinicians completed a survey which included questions adapted from National Institute of Mental Health-Global Obsessive-Compulsive Scale (NIMH-GOCS) and Yale-Brown Obsessive-Compulsive Scale (Y-BOCS). Clinicians rated clinical features at treatment initiation, just prior to the pandemic, and mid-pandemic (July/August, 2020). Findings suggest that the COVID-19 pandemic was associated with attenuation of ERP progress from expected rates in most patients during first several months of the pandemic; clinicians estimated that 38% of their patients had symptoms worsen during the pandemic and 47% estimated that symptoms remained unchanged despite participating in ERP. Those who endured financial distress or were medically at-risk for severe COVID-19 disease had worse ERP course. Adults also had a worse ERP course during than pandemic than youth. Further research is needed to better understand the effect of the COVID-19 pandemic on OCD symptomatology and treatment trajectory post-pandemic.

The Impact of Infectious Disease-Related Public Health Emergencies on Suicide, Suicidal Behavior, and Suicidal Thoughts.

Background: Infectious disease-related public health emergencies (epidemics) may increase suicide risk, and high-quality evidence is needed to guide an international response. Aims: We investigated the potential impacts of epidemics on suicide-related outcomes. Method: We searched MEDLINE, EMBASE, PsycInfo, CINAHL, Scopus, Web of Science, PsyArXiv, medRxiv, and bioRxiv from inception to May 13-16, 2020. Inclusion criteria: primary studies, reviews, and meta-analyses; reporting the impact of epidemics; with a primary outcome of suicide, suicidal behavior, suicidal ideation, and/or self-harm. Exclusion criteria: not concerned with suicide-related outcomes; not suitable for data extraction. PROSPERO registration: #CRD42020187013. Results: Eight primary papers were included, examining the effects of five epidemics on suicide-related outcomes. There was evidence of increased suicide rates among older adults during SARS and in the year following the epidemic (possibly motivated by social disconnectedness, fears of virus infection, and concern about burdening others) and associations between SARS/Ebola exposure and increased suicide attempts. A preprint study reported associations between COVID-19 distress and past-month suicidal ideation. Limitations: Few studies have investigated the topic; these are of relatively low methodological quality. Conclusion: Findings support an association between previous epidemics and increased risk of suicide-related outcomes. Research is needed to investigate the impact of COVID-19 on suicide outcomes.

Repurposing TREC-COVID Annotations to Answer the Key Questions of CORD-19 (preprint)

The novel coronavirus disease 2019 (COVID-19) began in Wuhan, China in late 2019 and to date has infected over 14M people worldwide, resulting in over 750,000 deaths. On March 10, 2020 the World Health Organization (WHO) declared the outbreak a global pandemic. Many academics and researchers, not restricted to the medical domain, began publishing papers describing new discoveries. However, with the large influx of publications, it was hard for these individuals to sift through the large amount of data and make sense of the findings. The White House and a group of industry research labs, lead by the Allen Institute for AI, aggregated over 200,000 journal articles related to a variety of coronaviruses and tasked the community with answering key questions related to the corpus, releasing the dataset as CORD-19. The information retrieval (IR) community repurposed the journal articles within CORD-19 to more closely resemble a classic TREC-style competition, dubbed TREC-COVID, with human annotators providing relevancy judgements at the end of each round of competition. Seeing the related endeavors, we set out to repurpose the relevancy annotations for TREC-COVID tasks to identify journal articles in CORD-19 which are relevant to the key questions posed by CORD-19. A BioBERT model trained on this repurposed dataset prescribes relevancy annotations for CORD-19 tasks that have an overall agreement of 0.4430 with majority human annotations in terms of Cohen's kappa. We present the methodology used to construct the new dataset and describe the decision process used throughout.