Blood RNA alternative splicing events as diagnostic biomarkers for infectious disease

Summary Assays detecting blood transcriptome changes are studied for infectious disease diagnosis. Blood-based RNA alternative splicing (AS) events, which have not been well characterized in pathogen infection, have potential normalization and assay platform stability advantages over gene expression for diagnosis. Here, we present a computational framework for developing AS diagnostic biomarkers. Leveraging a large prospective cohort of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and whole-blood RNA sequencing (RNA-seq) data, we identify a major functional AS program switch upon viral infection. Using an independent cohort, we demonstrate the improved accuracy of AS biomarkers for SARS-CoV-2 diagnosis compared with six reported transcriptome signatures. We then optimize a subset of AS-based biomarkers to develop microfluidic PCR diagnostic assays. This assay achieves nearly perfect test accuracy (61/62 = 98.4%) using a naive principal component classifier, significantly more accurate than a gene expression PCR assay in the same cohort. Therefore, our RNA splicing computational framework enables a promising avenue for host-response diagnosis of infection. Graphical abstract Highlights • We present a computational framework for alternative splicing (AS) diagnostic markers• Our AS biomarkers outperform gene-expression biomarkers in COVID-19 detection• Microfluidic PCR diagnostic assay of AS biomarkers achieves greater than 98% accuracy• We interpret the biological importance of identified AS biomarkers Motivation Host-based response assays (HRAs) can often diagnose infectious disease earlier and more precisely than pathogen-based tests. However, the role of RNA alternative splicing (AS) in HRAs remains unexplored, as existing HRAs are restricted to gene expression signatures. We report a computational framework for the identification, optimization, and evaluation of blood AS-based diagnostic assay development for infectious disease. Using SARS-CoV-2 infection as a case study, we demonstrate the improved accuracy of AS biomarkers for COVID-19 diagnosis when compared against six reported transcriptome signatures and when implemented as a microfluidic PCR diagnostic assay. Host-based response assays can diagnose infectious disease earlier and more precisely than pathogen-based tests. However, the role of RNA alternative splicing (AS) remains unexplored. Zhang et al. present a computational framework for AS diagnostic biomarkers. Using SARS-CoV-2 as a case study, they demonstrate the improved accuracy of AS biomarkers for COVID-19 diagnosis.

Blood RNA alternative splicing events as diagnostic biomarkers for infectious disease.

Assays detecting blood transcriptome changes are studied for infectious disease diagnosis. Blood-based RNA alternative splicing (AS) events, which have not been well characterized in pathogen infection, have potential normalization and assay platform stability advantages over gene expression for diagnosis. Here, we present a computational framework for developing AS diagnostic biomarkers. Leveraging a large prospective cohort of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and whole-blood RNA sequencing (RNA-seq) data, we identify a major functional AS program switch upon viral infection. Using an independent cohort, we demonstrate the improved accuracy of AS biomarkers for SARS-CoV-2 diagnosis compared with six reported transcriptome signatures. We then optimize a subset of AS-based biomarkers to develop microfluidic PCR diagnostic assays. This assay achieves nearly perfect test accuracy (61/62 = 98.4%) using a naive principal component classifier, significantly more accurate than a gene expression PCR assay in the same cohort. Therefore, our RNA splicing computational framework enables a promising avenue for host-response diagnosis of infection.

Viral infections and persistent cough: Evidence for treatment options.

BACKGROUND: Upper respiratory tract infections (URTIs) are one of the most common presentations to Australian general practitioners. Patients often present hoping to be cured, but most URTIs are caused by viral infections, so the task of management is predominantly symptomatic. Patients may be impatient to recover from cough because of concerns from others regarding infectivity from potential SARS-CoV-2 infection. Unfortunately, the effectiveness of interventions is poorly understood and lacking a robust evidence base. As a result, URTIs are a common presentation leading to unnecessary use of antibiotics or ineffectual treatments. OBJECTIVE: The aim of this article is to improve the management of acute cough, a common reason for consulting a general practitioner. Understanding the pathophysiology and time course of this symptom informs selection of evidence-based treatment options and supports better antibiotic stewardship. DISCUSSION: URTI presentations provide fertile ground for educating patients about infections, self-management options, dealing with uncertainty and responsible use of medicines.

Virological and Serological Assessment of US Army Trainees Isolated for Coronavirus Disease 2019.

BACKGROUND: Laboratory screening for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a key mitigation measure to avoid the spread of infection among recruits starting basic combat training in a congregate setting. Because viral nucleic acid can be detected persistently after recovery, we evaluated other laboratory markers to distinguish recruits who could proceed with training from those who were infected. METHODS: Recruits isolated for coronavirus disease 2019 (COVID-19) were serially tested for SARS-CoV-2 subgenomic ribonucleic acid (sgRNA), and viral load (VL) by reverse-transcriptase polymerase chain reaction (RT-PCR), and for anti- SARS-CoV-2. Cluster and quadratic discriminant analyses of results were performed. RESULTS: Among 229 recruits isolated for COVID-19, those with a RT-PCR cycle threshold >30.49 (sensitivity 95%, specificity 96%) or having sgRNA log10 RNA copies/mL <3.09 (sensitivity and specificity 96%) at entry into isolation were likely SARS-CoV-2 uninfected. Viral load >4.58 log10 RNA copies/mL or anti-SARS-CoV-2 signal-to-cutoff ratio <1.38 (VL: sensitivity and specificity 93%; anti-SARS-CoV-2: sensitivity 83%, specificity 79%) had comparatively lower sensitivity and specificity when used alone for discrimination of infected from uninfected. CONCLUSIONS: Orthogonal laboratory assays used in combination with RT-PCR may have utility in determining SARS-CoV-2 infection status for decisions regarding isolation.

Establishing an In Vitro System to Assess How Specific Antibodies Drive the Evolution of Foot-and-Mouth Disease Virus.

Viruses can evolve to respond to immune pressures conferred by specific antibodies generated after vaccination and/or infection. In this study, an in vitro system was developed to investigate the impact of serum-neutralising antibodies upon the evolution of a foot-and-mouth disease virus (FMDV) isolate. The presence of sub-neutralising dilutions of specific antisera delayed the onset of virus-induced cytopathic effect (CPE) by up to 44 h compared to the untreated control cultures. Continued virus passage with sub-neutralising dilutions of these sera resulted in a decrease in time to complete CPE, suggesting that FMDV in these cultures adapted to escape immune pressure. These phenotypic changes were associated with three separate consensus-level non-synonymous mutations that accrued in the viral RNA-encoding amino acids at positions VP266, VP280 and VP1155, corresponding to known epitope sites. High-throughput sequencing also identified further nucleotide substitutions within the regions encoding the leader (Lpro), VP4, VP2 and VP3 proteins. While association of the later mutations with the adaptation to immune pressure must be further verified, these results highlight the multiple routes by which FMDV populations can escape neutralising antibodies and support the application of a simple in vitro approach to assess the impact of the humoral immune system on the evolution of FMDV and potentially other viruses.

Severe Acute Respiratory Syndrome Coronavirus 2 Is Detected in the Gastrointestinal Tract of Asymptomatic Endoscopy Patients but Is Unlikely to Pose a Significant Risk to Healthcare Personnel.

Background and Aims: Recent evidence suggests that the gut is an additional target for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. However, whether SARS-CoV-2 spreads via gastrointestinal secretions remains unclear. To determine the prevalence of gastrointestinal SARS-CoV-2 infection in asymptomatic subjects, we analyzed gastrointestinal biopsy and liquid samples from endoscopy patients for the presence of SARS-CoV-2. Methods: We enrolled 100 endoscopic patients without known SARS-CoV-2 infection (cohort A) and 12 patients with a previous COVID-19 diagnosis (cohort B) in a cohort study performed at a regional hospital. Gastrointestinal biopsies and fluids were screened for SARS-CoV-2 by polymerase chain reaction (PCR), immunohistochemistry, and virus isolation assay, and the stability of SARS-CoV-2 in gastrointestinal liquids in vitro was analyzed. Results: SARS-CoV-2 ribonucleic acid was detected by PCR in the colonic tissue of 1/100 patients in cohort A. In cohort B, 3 colonic liquid samples tested positive for SARS-CoV-2 by PCR and viral nucleocapsid protein was detected in the epithelium of the respective biopsy samples. However, no infectious virions were recovered from any samples. In vitro exposure of SARS-CoV-2 to colonic liquid led to a 4-log-fold reduction of infectious SARS-CoV-2 within 1 hour (P ≤ .05). Conclusion: Overall, the persistent detection of SARS-CoV-2 in endoscopy samples after resolution of COVID-19 points to the gut as a long-term reservoir for SARS-CoV-2. Since no infectious virions were recovered and SARS-CoV-2 was rapidly inactivated in the presence of colon liquids, it is unlikely that performing endoscopic procedures is associated with a significant infection risk due to undiagnosed asymptomatic or persistent gastrointestinal SARS-CoV-2 infections.

Patients surviving COVID-19 had increased risk for adverse mental health outcomes vs. persons without COVID-19.

SOURCE CITATION: Xie Y, Xu E, Al-Aly Z. Risks of mental health outcomes in people with covid-19: cohort study. BMJ. 2022;376:e068993. 35172971.

Planning for the Next Pandemic: Trauma Injuries Require Pre-COVID-19 Levels of High-Intensity Resources.

As hospital systems plan for health care utilization surges and stress, understanding the necessary resources of a trauma system is essential for planning capacity. We aimed to describe trends in high-intensity resource utilization (operating room [OR] usage and intensive care unit [ICU] admissions) for trauma care during the initial months of the COVID-19 pandemic. Trauma registry data (2019 pre-COVID-19 and 2020 COVID-19) were collected retrospectively from 4 level I trauma centers. Direct emergency department (ED) disposition to the OR or ICU was used as a proxy for high-intensity resource utilization. No change in the incidence of direct ED to ICU or ED to OR utilization was observed (2019: 24%, 2020 23%; P = .62 and 2019: 11%, 2020 10%; P = .71, respectively). These results suggest the need for continued access to ICU space and OR theaters for traumatic injury during national health emergencies, even when levels of trauma appear to be decreasing.

Adherence to Recommended Preventive Behaviors During the COVID-19 Pandemic: The Role of Empathy and Perceived Health Threat.

BACKGROUND: Coping via empathic responding may play a role in preventive behavior engagement during the COVID-19 pandemic, and unlike trait empathy, is a potentially alterable target for changing health behavior. PURPOSE: Our goal was to examine the role of empathic responding in preventive behavior engagement during the COVID-19 pandemic, independent of trait empathy and perceived threat of COVID-19. METHODS: Participants (N = 2,841) completed a baseline survey early in the pandemic, and a follow-up survey approximately 2 weeks later (M = 13.50 days, SD = 5.61). Preventive health behaviors, including physical distancing and hygiene practices, were assessed at both timepoints. Hierarchical linear regression examined the contributions of trait empathy, perceived threat of COVID-19, and empathic responding at baseline to preventive behaviors at follow-up. RESULTS: Controlling for baseline levels of preventive behaviors and demographic covariates, trait empathy and threat of COVID-19 at baseline were each independently associated with preventive behaviors at follow-up. An interaction between perceived threat and empathic responding indicated that those perceiving high threat of COVID-19 at baseline tended to report engaging in preventive behaviors at follow-up regardless of their levels of empathic responding, whereas for those reporting low levels of perceived threat, higher levels of empathic responding were associated with higher engagement in preventive behavior. CONCLUSIONS: When perceived threat of COVID-19 was low, higher empathic responding was associated with increased engagement in preventive behaviors regardless of trait empathy, suggesting that empathic responding can serve as an actionable target for intervention to promote preventive behavior during the pandemic.

Bowel Ischemia in COVID-19 Infection: One-Year Surgical Experience.

BACKGROUND: COVID-19 is a deadly multisystemic disease, and bowel ischemia, the most consequential gastrointestinal manifestation, remains poorly described. Our goal is to describe our institution's surgical experience with management of bowel ischemia due to COVID-19 infection over a one-year period. METHODS: All patients admitted to our institution between March 2020 and March 2021 for treatment of COVID-19 infection and who underwent exploratory laparotomy with intra-operative confirmation of bowel ischemia were included. Data from the medical records were analyzed. RESULTS: Twenty patients were included. Eighty percent had a new or increasing vasopressor requirement, 70% had abdominal distension, and 50% had increased gastric residuals. Intra-operatively, ischemia affected the large bowel in 80% of cases, the small bowel in 60%, and both in 40%. Sixty five percent had an initial damage control laparotomy. Most of the resected bowel specimens had a characteristic appearance at the time of surgery, with a yellow discoloration, small areas of antimesenteric necrosis, and very sharp borders. Histologically, the bowel specimens frequently have fibrin thrombi in the small submucosal and mucosal blood vessels in areas of mucosal necrosis. Overall mortality in this cohort was 33%. Forty percent of patients had a thromboembolic complication overall with 88% of these developing a thromboembolic phenomenon despite being on prophylactic pre-operative anticoagulation. CONCLUSION: Bowel ischemia is a potentially lethal complication of COVID-19 infection with typical gross and histologic characteristics. Suspicious clinical features that should trigger surgical evaluation include a new or increasing vasopressor requirement, abdominal distension, and intolerance of gastric feeds.

Severe Acute Respiratory Syndrome Coronavirus 2 Testing Trends Among Persons Aged <18 Years in an Outpatient Pediatric Practice - Metropolitan Atlanta, Georgia, May-December 2020.

PURPOSE: The purpose of this study was to analyze trends in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing and test positivity among persons aged <18 years in a three-site outpatient pediatric practice in Atlanta, Georgia, serving approximately 35,000 pediatric patients. METHODS: Using electronic medical records, weekly trends in SARS-CoV-2 tests performed and the 14-day moving average of test positivity were examined, overall and by age group, during May 24-December 5, 2020. RESULTS: Among 4,995 patients who received at least 1 SARS-CoV-2 test, 6,813 total tests were completed. Overall test positivity was 5.4% and was higher among older pediatric patients (<5 years: 3.3%; 5-11 years: 4.1%; 12-17 years: 8.6%). The number of tests and test positivity increased after holidays and school breaks. CONCLUSIONS: Families might benefit from communication focused on reducing SARS-CoV-2 transmission during holidays. In addition, given higher test positivity in children aged 12-17 years, tailoring public health messaging to older adolescents could help limit SARS-CoV-2 transmission risk in this population.

Migrants’ Vulnerabilities and Their Responses to the COVID-19 Pandemic: A Case Study of Mobile Shoe Shine Boys in the Cape Coast Metropolis (preprint)

Covid-19 pandemic has impacted socio-economic activities in sub-Saharan Africa and Ghana for that matter. Occupations in the informal sector such as shoe-shine business have been affected by the disease outbreak. This paper focuses on migrant vulnerabilities and their responses to Covid-19 with a specific focus on shoe-shine boys in Cape Coast Metropolis. The study is guided by the IOM determinants of migrant vulnerability model, empirical review on the shoe-shine business and conceptual framework on shoe-shine business within the informal sector. Using an interview guide, ten shoe-shine boys were interviewed in the Cape Coast Metropolis. Their responses were transcribed and a content analysis was employed to analyze the data. The main challenges caused by Covid-19 were the reduction in income, decrease in customer base and changes in the nature of work. The study concluded that the irregular nature of the shoe-shine business exacerbated the impact of the covid-19 on the occupation but individual coping strategies were key in ensuring the sustainability of the occupation.

Who Decides? Toward a Typology of Transit Governance

This article describes a typology for formal governance structures of public transit in the United States to support inquiry into how organizational structures influence policy making processes, organizational capacity and policy outcomes. Scholarship of public transit has largely explored outcome-based research while paying less attention to how decisions are made. Despite some transport scholarship that shows how institutional characteristics influence financing, power arrangements and public discourse, there has been little recent analysis of governance within public transit systems beyond the regional role of Metropolitan Planning Organizations (MPOs). Using data from multiple sources, we assembled a database of governance structure of transit systems in the largest 40 cities in the United States. We show that the structure of transit decision making has substantial variance across and within cities, and is far from limited to MPOs. The variety of governance models and growth of local and sub-local models suggest that local context is critical for better understanding transit priorities and decision-making processes.

Multisystem outcomes and predictors of mortality in critically ill patients with COVID-19: Demographics and disease acuity matter more than comorbidities or treatment modalities.

BACKGROUND: We sought to describe characteristics, multisystem outcomes, and predictors of mortality of the critically ill COVID-19 patients in the largest hospital in Massachusetts. METHODS: This is a prospective cohort study. All patients admitted to the intensive care unit (ICU) with reverse-transcriptase-polymerase chain reaction-confirmed severe acute respiratory syndrome coronavirus 2 infection between March 14, 2020, and April 28, 2020, were included; hospital and multisystem outcomes were evaluated. Data were collected from electronic records. Acute respiratory distress syndrome (ARDS) was defined as PaO2/FiO2 ratio of ≤300 during admission and bilateral radiographic pulmonary opacities. Multivariable logistic regression analyses adjusting for available confounders were performed to identify predictors of mortality. RESULTS: A total of 235 patients were included. The median (interquartile range [IQR]) Sequential Organ Failure Assessment score was 5 (3-8), and the median (IQR) PaO2/FiO2 was 208 (146-300) with 86.4% of patients meeting criteria for ARDS. The median (IQR) follow-up was 92 (86-99) days, and the median ICU length of stay was 16 (8-25) days; 62.1% of patients were proned, 49.8% required neuromuscular blockade, and 3.4% required extracorporeal membrane oxygenation. The most common complications were shock (88.9%), acute kidney injury (AKI) (69.8%), secondary bacterial pneumonia (70.6%), and pressure ulcers (51.1%). As of July 8, 2020, 175 patients (74.5%) were discharged alive (61.7% to skilled nursing or rehabilitation facility), 58 (24.7%) died in the hospital, and only 2 patients were still hospitalized, but out of the ICU. Age (odds ratio [OR], 1.08; 95% confidence interval [CI], 1.04-1.12), higher median Sequential Organ Failure Assessment score at ICU admission (OR, 1.24; 95% CI, 1.06-1.43), elevated creatine kinase of ≥1,000 U/L at hospital admission (OR, 6.64; 95% CI, 1.51-29.17), and severe ARDS (OR, 5.24; 95% CI, 1.18-23.29) independently predicted hospital mortality.Comorbidities, steroids, and hydroxychloroquine treatment did not predict mortality. CONCLUSION: We present here the outcomes of critically ill patients with COVID-19. Age, acuity of disease, and severe ARDS predicted mortality rather than comorbidities. LEVEL OF EVIDENCE: Prognostic, level III.

Visioning transport futures through windows of opportunity: changing streets and humanscaled networks

The COVID-19 pandemic helped reveal much-needed insights about how people view cities and interact with public space. City leaders, planners and even the public realized how much space in streets is devoted to moving automobiles at the expense of walking and bicycling. Responses to the pandemic, furthermore, helped people become aware of how the character of streets can change quickly. Here, King and Krizek argue that there is an urgency to act now, being on the brink of a once-in-a-century occurrence where street use is changing potentially at the same time as new vehicle types. They view the condition of the pandemic as one capable of spurring rapid change to fix long-standing problems with urban transport.

Baseline results of a living systematic review for COVID-19 clinical trial registrations.

Background: Since the coronavirus disease 2019 (COVID-19) outbreak was first reported in December 2019, many independent trials have been planned that aim to answer similar questions. Tools allowing researchers to review studies already underway can facilitate collaboration, cooperation and harmonisation. The Infectious Diseases Data Observatory (IDDO) has undertaken a living systematic review (LSR) to provide an open, accessible and frequently updated resource summarising characteristics of COVID-19 study registrations. Methods: Review of all eligible trial records identified by systematic searches as of 3 April 2020 and initial synthesis of clinical study characteristics were conducted. In partnership with Exaptive, an open access, cloud-based knowledge graph has been created using the results.  Results: There were 728 study registrations which met eligibility criteria and were still active. Median (25 th, 75 th percentile) sample size was 130 (60, 400) for all studies and 134 (70, 300) for RCTs. Eight lower middle and low income countries were represented among the planned recruitment sites. Overall 109 pharmacological interventions or advanced therapy medicinal products covering 23 drug categories were studied. Majority (57%, 62/109) of them were planned only in one study arm, either alone or in combination with other interventions. There were 49 distinct combinations studied with 90% (44/49) of them administered in only one or two study arms. The data and interactive platform are available at https://iddo.cognitive.city/. Conclusions:  Baseline review highlighted that the majority of investigations in the first three months of the outbreak were small studies with unique treatment arms, likely to be unpowered to provide solid evidence.  The continued work of this LSR will allow a more dependable overview of interventions tested, predict the likely strength of evidence generated, allow fast and informative filtering of relevant trials for specific user groups and provide the rapid guidance needed by investigators and funders to avoid duplication of efforts.