Severe COVID-19 Disease Research Articles

Myocardial Injury by COVID-19 Infection Assessed by Cardiovascular Magnetic Resonance Imaging - A Prospective Multicenter Study.

This prospective multicenter study assessed the prevalence of myocardial injury in patients with COVID-19 using cardiac magnetic resonance imaging (CMR). We prospectively screened 505 patients with moderate to severe COVID-19 disease from 7 hospitals in Japan. Of these patients, 31 (mean [±SD] age 63.5±10.4 years, 23 [74%] male) suspected of myocardial injury, based on elevated serum troponin or B-type natriuretic peptide concentrations either upon admission or 3 months after discharge, underwent CMR 3 months after discharge. The primary endpoint was the presence of myocardial injury, defined by any of the following: (1) contrast enhancement in the left or right ventricle myocardium on late gadolinium enhancement CMR; (2) left or right ventricular dysfunction (defined as <50% and <45%, respectively); and (3) pericardial thickening on contrast enhancement. The mean (±SD) duration between diagnosis and CMR was 117±16 days. The primary endpoint was observed in 13 of 31 individuals (42%), with 8 (26%) satisfying the modified Lake Louise Criteria for the diagnosis of acute myocarditis. This study revealed a high incidence of myocardial injury identified by CMR in patients with moderate to severe COVID-19 and abnormal findings for cardiac biomarkers.

Use of tobacco during COVID-19: A qualitative study among medically underserved individuals.

The COVID-19 pandemic produced stress for people around the world. The perception that tobacco can be a coping tool for stress relief suggests that the conditions during the COVID-19 pandemic can provide insight into the relationship between stress and tobacco use patterns, particularly among those most at risk for severe COVID-19 disease. The goal was to identify the impacts of the COVID-19 pandemic on tobacco use and preparedness for smoking cessation among individuals who smoke and are older and medically underserved. We conducted in-depth interviews with 39 patients to learn about individuals' smoking behavior during the COVID-19 pandemic. We used a modified grounded theory approach to code and analyze all qualitative data. We conducted thematic analysis to identify key factors associated with smoking behaviors during COVID-19. Our results indicated that increases in perceived stress and social isolation may have been associated with increased tobacco use during the COVID-19 pandemic. Pandemic-related social isolation contributed to increases in smoking, despite respondents being concerned about the severity of COVID-19. While many respondents felt that smoking relieved their stress from the pandemic, they appeared unaware of the stress-inducing properties of tobacco use. Our findings indicate that pandemic-related stress impacted smoking behavior among older, medically underserved smokers. Results may assist clinicians in addressing the role of tobacco use in response to highly stressful events. Smoking cessation strategies should consider the implications of stress on smoking behavior, including smoking relapse in response to highly stressful events-particularly for medically underserved populations.

SARS-CoV-2 seroepidemiology in Cape Town, South Africa, and implications for future outbreaks in low-income communities.

In low- and middle-income countries where SARS-CoV-2 testing is limited, seroprevalence studies can help describe and characterise the extent of the pandemic, as well as elucidate protection conferred by prior exposure. We conducted repeated cross-sectional serosurveys (July 2020 -November 2021) using residual samples from patients from Cape Town, South Africa, sent for routine laboratory studies for non-COVID-19 conditions. SARS-CoV-2 anti-nucleocapsid antibodies and linked clinical information were used to investigate: (1) seroprevalence over time and risk factors associated with seropositivity, (2) ecological comparison of seroprevalence between subdistricts, (3) case ascertainment rates, and (4) the relative protection against COVID-19 associated with seropositivity and vaccination statuses. Among the subset sampled, seroprevalence of SARS-CoV-2 in Cape Town increased from 39.19% (95% confidence interval [CI] 37.23-41.19) in July 2020 to 67.8% (95%CI 66.31-69.25) in November 2021. Poorer communities had both higher seroprevalence and COVID-19 mortality. Only 10% of seropositive individuals had a recorded positive SARS-CoV-2 test. Using COVID-19 hospital admission and death data at the Provincial Health Data Centre, antibody positivity before the start of the Omicron BA.1 wave (28 November 2021) was strongly protective for severe disease (adjusted odds ratio [aOR] 0.15; 95%CI 0.05-0.46), with additional benefit in those who were also vaccinated (aOR 0.07, 95%CI 0.01-0.35). The high population seroprevalence in Cape Town was attained at the cost of substantial COVID-19 mortality. At the individual level, seropositivity was highly protective against subsequent infections and severe COVID-19 disease. In low-income communities, where diagnostic testing capacity is often limited, surveillance systems dependent on them will underestimate the true extent of an outbreak. Rapidly conducted seroprevalence studies can play an important role in addressing this.

Incidence and risk factors of SARS-CoV-2 breakthrough infection in the early Omicron variant era among vaccinated and boosted individuals in Chicago.

SARS-CoV-2 vaccines are safe and effective against infection and severe COVID-19 disease worldwide. Certain co-morbid conditions cause immune dysfunction and may reduce immune response to vaccination. In contrast, those with co-morbidities may practice infection prevention strategies. Thus, the real-world clinical impact of co-morbidities on SARS-CoV-2 infection in the recent post-vaccination period is not well established. This study was performed to understand the epidemiology of Omicron breakthrough infection and evaluate associations with number of comorbidities in a vaccinated and boosted population. A retrospective clinical cohort study was performed utilizing the Northwestern Medicine Enterprise Data Warehouse. Our study population was identified as fully vaccinated adults with at least one booster. The primary risk factor of interest was the number of co-morbidities. The primary outcome was the incidence and time to the first positive SARS-CoV-2 molecular test in the Omicron predominant era. Multivariable Cox modeling analyses to determine the hazard of SARS-CoV-2 infection were stratified by calendar time (Period 1: January 1 -June 30, 2022; Period 2: July 1 -December 31, 2022) due to violations in the proportional hazards assumption. In total, 133,191 patients were analyzed. During Period 1, having 3+ comorbidities was associated with increased hazard for breakthrough (HR = 1.16 CI 1.08-1.26). During Period 2 of the study, having 2 comorbidities (HR = 1.45 95% CI 1.26-1.67) and having 3+ comorbidities (HR 1.73, 95% CI 1.51-1.97) were associated with increased hazard for Omicron breakthrough. Older age was associated with decreased hazard in Period 1 of follow-up. Interaction terms for calendar time indicated significant changes in hazard for many factors between the first and second halves of the follow-up period. Omicron breakthrough is common with significantly higher risk for our most vulnerable patients with multiple co-morbidities. Age plays an important role in breakthrough infection with the highest incidence among young adults, which may be due to age-related behavioral factors. These findings reflect real-world differences in immunity and exposure risk behaviors for populations vulnerable to COVID-19.

Pediatric COVID-19 in Lesotho and Post-pandemic Implications on Lower Respiratory Infections in Children.

Background The United States Agency for International Development (USAID) Reaching Impact, Saturation, and Epidemic Control (RISE) program funded Jhpiego to support the Government of Lesotho's COVID-19 response, including two national COVID-19 treatment centers. To evaluate the status of post-pandemic pediatric respiratory care in Lesotho, we analyzed pediatric treatment center data and healthcare worker (HCW) performance on pediatric COVID-19 training offered to HCWs at COVID-19 treatment centers. Methods We conducted a retrospective cohort study of patients 15 years of age or less hospitalized at two COVID-19 treatment centers in Lesotho from May 1, 2020, to April 30, 2022. Patient data were extracted from hospital files. We used the independent sample t-test, Mann-Whitney U test, or Fisher's exact test to evaluate associations between exposure variables and death. We also assessed differences between pre- and post-training examination scores of three one-day HCW training on pediatric COVID-19 using paired t-tests. Results Overall, <15-year-olds comprised 18/1,448 (1.2%) hospitalizations. Twenty-two percent (4/18) of children were hypoxemic (oxyhemoglobin saturation <94%) within the first 24 hours and 44% (8/18) at any point in the hospitalization. Oxygen utilization increased over the two-year period (p=0.004) and all eight children with hypoxemia received oxygen (p<0.001). Four of 18 (22%) patients died. For HCW training, pre- and post-training examinations were completed by 76/82 (92.7%) participants. The overall mean pretraining score was 44.6% (standard deviation (SD) 15.7%). Mean scores improved by an average of 32.2% (95% confidence interval (CI) 27.7%, 36.6%, p<0.001) on the same day post-training examination. Conclusions National COVID-19 treatment center data indicate a low burden of severe pediatric COVID-19 disease in Lesotho. However, recognized HCW knowledge gaps suggest deficiencies in identifying and referring severely ill children, which may detrimentally impact the ongoing post-pandemic care of children with severe lower respiratory infections.

Nirmatrelvir/Ritonavir (Paxlovid) Use Among Individuals at Risk of Severe COVID-19: An Analysis of the National COVID Cohort Collaborative (N3C).

Paxlovid is effective in reducing COVID-19 hospitalization and mortality. This study characterized Paxlovid use and evaluated racial/ethnic disparities over time among community-dwelling adults at high risk of progression to severe COVID-19 disease. This retrospective cohort study used the National COVID Cohort Collaborative (N3C) data and included individuals aged 18 years or older diagnosed with COVID-19 between January 2022 and December 2023. The study cohort included nonhospitalized individuals who were at high risk of COVID-19 progression, and selected the first COVID-19 episode in each quarter, including reinfection episodes. Paxlovid use was defined as receiving Paxlovid within ±5 days of a COVID-19 diagnosis. We used descriptive statistics to characterize Paxlovid use overall and by calendar quarter and race/ethnicity. We used a generalized estimating equations (GEE) models to quantify the association of race/ethnicity with Paxlovid use controlling for age, gender, and clinical characteristics. Among 1 264 215 individuals at high risk of disease progression (1 404 607 episodes), Paxlovid use increased from 1.2% in January-March 2022 to 35.1% in October-December 2023. Paxlovid use was more common among non-Hispanic White individuals (23.9%) than non-Hispanic Black (16.5%) and Latinx/e (16.7%) patients. After adjusting age, gender, and clinical characteristics, Paxlovid use was less likely among non-Hispanic Black (odds ratio [OR] 0.69, 95% confidence interval [CI] 0.68-0.70) and Latinx/e (OR 0.72, CI 0.71-0.73) patients than non-Hispanic White patients. Among a large, diverse cohort of community-dwelling individuals with COVID-19, nearly two out of three eligible individuals did not receive Paxlovid, and minoritized racial/ethnic groups were less likely to use Paxlovid than their non-Hispanic White individuals.

Killer-cell immunoglobulin-like receptor polymorphism is associated with COVID-19 outcome: Results of a pilot observational study.

The pathogenesis of COVID-19 warrants unravelling. Genetic polymorphism analysis may help answer the variability in disease outcome. To determine the role of KIR and HLA polymorphisms in susceptibility, progression, and severity of SARS-CoV-2 infection, 458 patients and 667 controls enrolled in this retrospective observational study from April to December 2020. Mild/moderate and severe/death study groups were established. HLA-A, -B, -C, and KIR genotyping were performed using the Lifecodes® HLA-SSO and KIR-SSO kits on the Luminex® 200™ xMAP fluoroanalyser. A probability score using multivariate binary logistic regression analysis was calculated to estimate the likelihood of severe COVID-19. ROC analysis was used to calculate the best cut-off point for predicting a worse clinical outcome with high sensitivity and specificity. A p ≤ 0.05 was considered statistically significant. KIR AA genotype protected positively against severity/death from COVID-19. Furthermore, KIR3DL1, KIR2DL3 and KIR2DS4 genes protected patients from severe forms of COVID-19. KIR Bx genotype, as well as KIR2DL2, KIR2DS2, KIR2DS3 and KIR3DS1 were identified as biomarkers of severe COVID-19. Our logistic regression model, which included clinical and KIR/HLA variables, categorised our cohort of patients as high/low risk for severe COVID-19 disease with high sensitivity and specificity (Se = 94.29%, 95% CI [80.84-99.30]; Sp = 84.55%, 95% CI [79.26-88.94]; OR = 47.58, 95%CI [11.73-193.12], p < 0.0001). These results illustrate an association between KIR/HLA ligand polymorphism and different COVID-19 outcomes and remarks the possibility of use them as a surrogate biomarkers to detect severe patients in possible future infectious outbreaks.

Before Low Serum Cortisol Can Be Attributed to SARS-Cov-2 Infection, Alternative Causes Must Be Ruled Out

We read with interest Banu et al.,’s article about a cross-sectional study of adrenal function using blood levels of cortisol and adrenocorticotropic hormone (ACTH) in 91 patients with acute SARS-CoV-2 infection. It was found that 27% of patients with severe COVID-19, 26% with mild COVID-19 and 4% with moderate COVID-19 had adrenal insufficiency. Decreased cortisol reserve was found in 6.6% of all patients. It was concluded that the adrenocortical response was impaired in a significant number of non-critically ill COVID-19 patients, with the percentage being highest in patients with severe COVID-19 disease.1 The study is impressive, but some points should be discussed. The major limitation of the study is that imaging of the pituitary gland and hypothalamus was not performed. To rule out pituitary adenoma, hypophysitis, pituitary apoplexy, pituitary abscess, sellar tuberculoma, or hypothalamic stroke or bleeding, magnetic resonance imaging (MRI) of the pituitary gland and the hypothalamus with contrast agent must be performed. Like any other infection, SARS-CoV-2 infection can trigger the appearance of symptoms of a pituitary pathology.2 A second limitation is that imaging of the suprarenal glands was not performed. To assess whether there was adrenal atrophy, adenoma, ischemia, bleeding, or carcinoma, adrenal imaging is mandatory. 3 A third limitation is that current medication was not reported. Several medications are known to affect serum cortisol levels, making it imperative to know all medications regularly taken by the included patients. Ketoconazole, isilodrostat, vitamin D and omega-3 fatty acids in particular are known to be able to reduce cortisol levels in the blood.4 A fourth limitation is that no ACTH stimulation test was performed to determine whether primary or secondary suprarenal insufficiency was present. Determining cortisol levels alone without ACTH stimulation testing is not reliable with regard to cortical adrenal function. A fifth limitation is that serum dehydroepiandrosterone (DHEA) levels were not measured. Since DHEA is the antagonist of cortisol and decreases with age, it is conceivable that high levels of DHEA promoted the reduction of serum cortisol.5 Since low thyroxine levels may be associated with low cortisol levels,6 it would also be desirable to know whether thyroid function was normal or abnormal in the included patients. In summary, the excellent study has limitations that should be addressed before drawing final conclusions. Clarifying the weaknesses would strengthen the conclusions and could improve the study. Serum cortisol levels may be low not only due to SARS-CoV-2 infection but also due to several other causes. Before adrenal insufficiency can be attributed solely to inadequate cortical cortisol production, the entire hypothalamic-pituitary-adrenal axis must be thoroughly examined.

Association of chronic opioid therapy and opioid use disorder with COVID-19-related hospitalization and mortality: Evidence from three health systems in the United States

ObjectiveChronic opioid use can lead to detrimental effects on the immune and various organ systems that put individuals prescribed chronic opioid therapy (COT) for pain and those with an opioid use disorder (OUD) at risk for severe COVID-19 disease. We assessed the association of COT and OUD with COVID-19-related hospitalization and death to inform targeted interventions to improve clinical outcomes in COVID-19 patients who use opioids. MethodsWe conducted a retrospective cohort study of adults ages ≥ 18 with laboratory-confirmed SARS-CoV-2 infection in 2020 and 2021 from three US health systems. We used Cox proportional hazards regression to estimate the 30-day risk of COVID-19-related hospitalization and death associated with two opioid exposures (COT and OUD) following an infection. ResultsThe study cohort included 53,123 patients with SARS-CoV-2 infection and a mean (SD) age of 45.1 (16.5), of whom 1,059 (2.0 %) were exposed to COT and 269 (0.5 %) had an OUD diagnosis in the year prior to infection. There were 2,270 observed COVID-19-related hospitalizations or deaths (1.6 per 1,000 person-days, 95 % CI 1.5–1.7). In the fully adjusted model, COT was not associated with increased risk (HR 1.19; 95 % CI, 0.98–1.43), while past-year OUD was independently associated with severe COVID-19 disease (HR 1.82; 95 % CI, 1.18–2.80). Past-year OUD remained associated with increased risk in post-hoc analysis with COVID-19-related hospitalization alone as the outcome (HR 2.00; 95 % CI, 1.30–3.08). ConclusionsPast-year OUD is a potential independent risk factor for severe COVID-19 disease that warrants monitoring to improve the prognosis of patients with COVID-19.

Sample-to-Answer Detection of SARS-CoV-2 Viremia Using Thermally Responsive Alkane Partitions.

The diagnosis of bloodborne viral infections (viremia) is currently relegated to central laboratories because of the complex procedures required to detect viruses in blood samples. The development of point-of-care diagnostics for viremia would enable patients to receive a diagnosis and begin treatment immediately instead of waiting days for results. Point-of-care systems for viremia have been limited by the challenges of integrating multiple precise steps into a fully automated (i.e., sample-to-answer), compact, low-cost system. We recently reported the development of thermally responsive alkane partitions (TRAPs), which enable the complete automation of diagnostic assays with complex samples. Here we report the use of TRAPs for the sample-to-answer detection of viruses in blood using a low-cost portable device and easily manufacturable cassettes. Specifically, we demonstrate the detection of SARS-CoV-2 in spiked blood samples, and we show that our system detects viremia in COVID-19 patient samples with good agreement to conventional RT-qPCR. We anticipate that our sample-to-answer system can be used to rapidly diagnose SARS-CoV-2 viremia at the point of care, leading to better health outcomes for patients with severe COVID-19 disease, and that our system can be applied to the diagnosis of other life-threatening bloodborne viral diseases, including Hepatitis C and HIV.

Proprotein Convertase Subtilisin/Kexin Type 9 Induction in COVID-19 Is Poorly Associated with Disease Severity and Cholesterol Levels.

SARS-CoV-2 infection was shown to induce proprotein convertase subtilisin/kexin type 9 (PCSK9) plasma levels in sepsis. Here, we investigate the association between serum PCSK9 levels and disease severity. PCSK9 was measured in serum of 55 controls, 40 patients with moderate and 60 patients with severe COVID-19 disease. Serum PCSK9 was elevated in moderate COVID-19 compared to controls and further increased in severe cases. PCSK9 levels were not associated with C-reactive protein, bacterial superinfections, interventions, or survival in patients with severe COVID-19. PCSK9 regulates circulating cholesterol levels, and 15 cholesteryl ester (CE) species and free cholesterol (FC) were quantified by direct flow injection analysis using a high-resolution hybrid quadrupole-Orbitrap mass spectrometer. Most CE species with shorter fatty acid chains were decreased in severe compared to moderate COVID-19, and none of the CE species were correlated with PCSK9 in patients with severe COVID-19. Levels of all CE species negatively correlated with C-reactive protein in severe COVID-19 patients. Notably, FC was induced in severe compared to moderate COVID-19. The FC/CE ratio correlated positively with inflammatory markers and was associated with non-survival. The current study suggests that the imbalance between CE and FC levels is associated with disease severity and mortality in patients with COVID-19.

Genomic Landscape of Susceptibility to Severe COVID-19 in the Slovenian Population.

Determining the genetic contribution of susceptibility to severe SARS-CoV-2 infection outcomes is important for public health measures and individualized treatment. Through intense research on this topic, several hundred genes have been implicated as possibly contributing to the severe infection phenotype(s); however, the findings are complex and appear to be population-dependent. We aimed to determine the contribution of human rare genetic variants associated with a severe outcome of SARS-CoV-2 infections and their burden in the Slovenian population. A panel of 517 genes associated with severe SARS-CoV-2 infection were obtained by combining an extensive review of the literature, target genes identified by the COVID-19 Host Genetic Initiative, and the curated Research COVID-19 associated genes from PanelApp, England Genomics. Whole genome sequencing was performed using PCR-free WGS on DNA from 60 patients hospitalized due to severe COVID-19 disease, and the identified rare genomic variants were analyzed and classified according to the ACMG criteria. Background prevalence in the general Slovenian population was determined by comparison with sequencing data from 8025 individuals included in the Slovenian genomic database (SGDB). Results show that several rare pathogenic/likely pathogenic genomic variants in genes CFTR, MASP2, MEFV, TNFRSF13B, and RNASEL likely contribute to the severe infection outcomes in our patient cohort. These results represent an insight into the Slovenian genomic diversity associated with a severe COVID-19 outcome.

A Retrospective Case Series Analysis of Pregnancy and COVID-19 Based on a Global Postmarketing COVID-19 Surveillance Program

PurposeTo document and characterize COVID-19 cases involving pregnancy in the context of exposure to pharmaceutical products. MethodsThis retrospective case series analysis leveraged the Pfizer safety database containing worldwide adverse event data related to use of Pfizer products between October 1, 2019 and November 3, 2022. Selected Medical Dictionary for Drug Regulatory Activities (Version 25.0) Preferred Terms and subsequent clinical review were used to identify COVID-19 cases involving female patients who received Pfizer products during pregnancy and infants with intrauterine exposure to Pfizer products. FindingsAs of November 3, 2022, 504 pregnancy cases (426 maternal; 78 infants) were identified. Most maternal cases reported COVID-19 during the third trimester, and (when known) 52% of cases involved presentation or progression of severe COVID-19 with associated complications requiring hospitalization, and often intensive management (eg, mechanical ventilation, oxygen support) and emergent delivery. Twenty-three maternal cases were fatal; patients developed severe COVID-19 disease involving multisystem deterioration (eg, cardiopulmonary injury/decompensation, coagulopathies, septic/hemorrhagic shock) and frequently required risk-benefit decisions regarding maintaining/prolonging pregnancies to improve fetal viability while attempting to improve or stabilize maternal conditions or electing to either terminate pregnancies or induce emergent deliveries. Approximately 40% of maternal cases reported medical history involving at least one underlying condition (eg, diabetes, respiratory disorders, renal/hepatic disease, cardiac disease, obesity, autoimmune conditions) considered potentially associated with susceptibility to infection/adverse outcome of infection, or twin/triplet pregnancy, which may further complicate COVID-19 disease. Most cases with known fetal outcomes reported normal newborns including preterm/low birth weight infants, which occurred in many cases involving emergent preterm delivery due to deteriorating maternal conditions. The remaining smaller proportion of cases involved abnormal newborn/perinatal/postperinatal complications (eg, premature births, respiratory distress, alveolar damage, meconium aspiration with hypoxic-ischemic encephalopathy), intrauterine/neonatal death (due to multiple concurrent complications such as neonatal sepsis, hypoxemia/acute respiratory distress, potential cardiac damage, mucormycosis) and congenital anomaly (eg, intrauterine growth restriction in association with contracting COVID-19). Among infants tested within our dataset, 28 cases involved reference to infants who tested positive for COVID-19 infection at birth or shortly thereafter, with vertical transmission suspected only in 2 infants. ImplicationThis large retrospective case series provides additional perspectives regarding potential impact of COVID-19 on pregnancy outcomes, and its characterization of this case volume may contribute to the current information landscape related to COVID-19 in pregnancy. Further studies may be warranted to confirm the generalizability of our findings to the general pregnant patient population infected with COVID-19.

How international guidelines recommend treating children who have severe COVID-19 or risk disease progression.

This study reviewed the current knowledge and guidelines on managing COVID-19 in children and proposed a practical approach to drug treatment. We analysed international guidelines from four prominent scientific bodies on treating COVID-19 in children. These were the UK National Institute for Health and Care Excellence, the American National Institutes of Health, the Infectious Diseases Society of America and the Australian National Clinical Evidence Taskforce COVID-19. Most paediatric patients with COVID-19 only require symptomatic treatment. There was limited evidence on treatment recommendations for children with severe COVID-19 or at risk of disease progression. However, several drugs are available for children and we have summarised the guidelines, in order to provide a concise, practical format for clinicians. All the guidelines agree that nirmatrelvir plus ritonavir or remdesivir can be used as prophylaxis for severe COVID-19 in high-risk patients. Remdesivir can also be used for severe COVID-19 cases. Glucocorticosteroids are recommended, particularly in patients requiring oxygen therapy. Tocilizumab or baricitinib should be reserved for patients with progressive disease and/or signs of systemic inflammation. The guidelines provide useful advice and a degree of consensus on specific drug treatment for children with severe COVID-19 or at risk of progression.

Network-based integrative multi-omics approach reveals biosignatures specific to COVID-19 disease phases.

COVID-19 disease is characterized by a spectrum of disease phases (mild, moderate, and severe). Each disease phase is marked by changes in omics profiles with corresponding changes in the expression of features (biosignatures). However, integrative analysis of multiple omics data from different experiments across studies to investigate biosignatures at various disease phases is limited. Exploring an integrative multi-omics profile analysis through a network approach could be used to determine biosignatures associated with specific disease phases and enable the examination of the relationships between the biosignatures. To identify and characterize biosignatures underlying various COVID-19 disease phases in an integrative multi-omics data analysis. We leveraged a multi-omics network-based approach to integrate transcriptomics, metabolomics, proteomics, and lipidomics data. The World Health Organization Ordinal Scale WHO Ordinal Scale was used as a disease severity reference to harmonize COVID-19 patient metadata across two studies with independent data. A unified COVID-19 knowledge graph was constructed by assembling a disease-specific interactome from the literature and databases. Disease-state specific omics-graphs were constructed by integrating multi-omics data with the unified COVID-19 knowledge graph. We expanded on the network layers of multiXrank, a random walk with restart on multilayer network algorithm, to explore disease state omics-specific graphs and perform enrichment analysis. Network analysis revealed the biosignatures involved in inducing chemokines and inflammatory responses as hubs in the severe and moderate disease phases. We observed distinct biosignatures between severe and moderate disease phases as compared to mild-moderate and mild-severe disease phases. Mild COVID-19 cases were characterized by a unique biosignature comprising C-C Motif Chemokine Ligand 4 (CCL4), and Interferon Regulatory Factor 1 (IRF1). Hepatocyte Growth Factor (HGF), Matrix Metallopeptidase 12 (MMP12), Interleukin 10 (IL10), Nuclear Factor Kappa B Subunit 1 (NFKB1), and suberoylcarnitine form hubs in the omics network that characterizes the moderate disease state. The severe cases were marked by biosignatures such as Signal Transducer and Activator of Transcription 1 (STAT1), Superoxide Dismutase 2 (SOD2), HGF, taurine, lysophosphatidylcholine, diacylglycerol, triglycerides, and sphingomyelin that characterize the disease state. This study identified both biosignatures of different omics types enriched in disease-related pathways and their associated interactions (such as protein-protein, protein-transcript, protein-metabolite, transcript-metabolite, and lipid-lipid interactions) that are unique to mild, moderate, and severe COVID-19 disease states. These biosignatures include molecular features that underlie the observed clinical heterogeneity of COVID-19 and emphasize the need for disease-phase-specific treatment strategies. The approach implemented here can be used to find associations between transcripts, proteins, lipids, and metabolites in other diseases.

Network-based Multi-omics Disease–Drug Associations Reveal Drug Repurposing Candidates for Covid-19 Disease Phases

Background The development and rollout of vaccines and the use of various drugs have contributed to controlling the coronavirus disease 2019 (Covid-19) pandemic. Nevertheless, challenges such as the inequitable distribution of vaccines, the influence of emerging viral lineages and immunoevasive variants on vaccine efficacy, and the inadequate immune defense in subgroups of the population continue to motivate the development of new drugs to combat the disease. Aim In this study, we sought to identify, prioritize, and characterize drug repurposing candidates appropriate for treating mild, moderate, or severe Covid-19 using a network-based integrative approach that systematically integrates drug-related data and multi-omics datasets. Methods We leveraged drug data and multi-omics data and used a random walk with restart algorithm to explore an integrated knowledge graph comprising three subgraphs: (i) a Covid-19 knowledge graph, (ii) a drug repurposing knowledge graph, and (iii) a Covid-19 disease state-specific omics graph. Results We prioritized 20 US Food and Drug Administration-approved agents as potential candidate drugs for mild, moderate, and severe Covid-19 disease phases. Specifically, drugs that could stimulate immune cell recruitment and activation including histamine, curcumin, and paclitaxel have potential utility in mild disease states to mitigate disease progression. Drugs like omacetaxine, crizotinib, and vorinostat that exhibit antiviral properties and have the potential to inhibit viral replication can be considered for mild to moderate Covid-19 disease states. Also, given the association between antioxidant deficiency and high inflammatory factors that trigger cytokine storms, antioxidants like glutathione can be considered for moderate disease states. Drugs that exhibit potent anti-inflammatory effects like (i) anti-inflammatory drugs (sarilumab and tocilizumab), (ii) corticosteroids (dexamethasone and hydrocortisone), and (iii) immunosuppressives (sirolimus and cyclosporine) are potential candidates for moderate to severe disease states that trigger a hyperinflammatory cascade of Covid-19. Conclusion Our study demonstrates that the multi-omics data-driven integrative analysis within the drug data enables prioritizing drug candidates for Covid-19 disease phases, offering a comprehensive basis for therapeutic strategies that can be brought to market quickly given their established safety profiles. Importantly, the multi-omics data-driven integrative analysis within the drug data approach implemented here can be used to prioritize drug repurposing candidates appropriate for other diseases.

Hospitalisations and humoral COVID-19 vaccine response in vaccinated rituximab-treated multiple sclerosis patients

BackgroundPatients with multiple sclerosis (MS) treated with anti-CD20 therapies such as rituximab may have increased risk of severe COVID-19 disease. Vaccination induces protective immunity, but humoral vaccine response is known to be attenuated in rituximab-treated MS-patients-patients, which has indicated a need for real world data on severe morbidity and mortality from COVID-19 after vaccination. MethodsRituximab-treated patients treated at Haukeland University Hospital were identified through the National MS Registry and invited to participate in the study by giving a consent and providing a blood sample 3 weeks or later after ordinary COVID-19- vaccination, i.e. 2 doses given with a standard interval of 3 weeks. Blood samples were analysed with Enzyme-Linked Immunosorbent assay (ELISA) to evaluate humoral vaccine response with screening test against receptor-binding domain (RBD) and confirmatory Spike IgG-specific ELISA. A haemagglutination test (HAT) was performed as a marker of neutralizing antibodies. Patient serum concentration of rituximab were quantified using liquid chromatography tandem mass spectrometry (LC-MS/MS). Registry data from the Norwegian MS registry and information on hospitalization from patient records were collected and linked to laboratory results. Results111 patients were included in the study. A total of 7 (6.3%) were hospitalized due to COVID-19 disease during the observation period. No patient was admitted to ICU and there were no deaths. 34.2% did not have detectable titre of SARS CoV-2 Spike IgG antibodies, 72.1% did not have a detectable titre of SARS CoV-2 RBD antibodies, and 88.2% did not have a detectable HAT titre. There was a correlation between hospitalisation and the absence of SARS CoV-2 Spike IgG antibody titre, and between hospitalisation and MS disease duration, as well as between spike IgG antibody titre and CD19 B-cell count, time since last rituximab infusion, cumulative rituximab treatment time and total IgG level in the patients. ConclusionA substantial proportion of rituximab-treated MS-patients-patients did not have detectable humoral vaccine responses after 2 doses of COVID-19 vaccination. Despite this, the cumulative percentage of patients hospitalized with COVID-19 disease throughout the observation period of 22 months was low, and no patients required ICU treatment. The results support that vaccinated MS-patients treated with rituximab have a protective effect against serious Covid-19 infection.

The impact of COVID-19 vaccine spring boosters on COVID-19 hospital admissions in England 2022/23

In the spring of 2022 and 2023 COVID-19 vaccine boosters were recommended for those aged ≥75 years in England as well as those in an immunosuppression risk group. The aim was to reduce severe COVID-19 disease in these groups. The large difference in coverage between those above and below age 75 years was the basis for applying an age-discontinuity approach for measuring the impact of vaccination on COVID-19 hospitalisations in both spring 2022 and 2023. Hospitalisations in individuals positive by PCR for COVID-19 were obtained from the national secondary user service hospital dataset. The ratio of hospital counts by each year of age in 8-week periods after compared to before the roll out was modelled using negative binomial regression to estimate the discontinuity at age 75 years. A clear discontinuity was seen at age 75 years of 17.0% (95% CI: 6.1%-26.6%) in 2022 and 18.0% (3.3%-30.4%) in 2023. If applied to those aged ≥75 years this translates to 1302 and 418 averted hospitalisations in the 8-week period in 2022 and 2023, respectively. This study shows a clear impact of vaccination on preventing COVID-19 hospitalisations and compliments other epidemiological methods assessing the impact of COVID-19 vaccines. One way to see if the booster vaccines doses given to protect against COVID-19 disease are working is to compare hospital admissions in groups of people who were and were not eligible for the dose. In England the spring booster doses were recommended for those aged 75 years and above. We could therefore compare hospitalisations in those above this age to those just below (aged 65-74) and see if there is a step change in rates from age 74 to 75 in the time after the vaccine was given. The results showed hospitalisations were about 18% lower in the group that were eligible, which is evidence that the vaccine is protecting against severe COVID-19.

Humoral immunity to SARS-CoV-2 in kidney transplant recipients and dialysis patients: IgA and IgG patterns unraveled after SARS-CoV-2 infection and vaccination

BackgroundInfection with SARS-CoV-2 in high-risk groups such as kidney transplant and dialysis patients is shown to be associated with a more serious course of the disease. Four years after the start of the COVID-19 pandemic, crucial knowledge on the immune responses in these patient groups is still lacking. Therefore, this study aimed at investigating the humoral immune response after a SARS-CoV-2 infection compared to vaccination as well as the evolution of immunoglobulins over time.MethodsKidney transplant recipients, patients on haemodialysis or on peritoneal dialysis and healthy controls were included in this longitudinal multicenter study. SARS-CoV-2 anti-RBD, anti-NP and anti-S1S2 immunoglobulin G (IgG) and A (IgA) as well as the neutralizing antibody capacity were measured.ResultsKidney transplant recipients had a significantly better humoral response to SARS-CoV-2 after infection (86.4%) than after a two-dose mRNA vaccination (55.8%) while seroconversion was comparable in patients on haemodialysis after infection (95.8%) versus vaccination (89.4%). In individuals without prior COVID-19, the IgG levels after vaccination were significantly lower in kidney transplant recipients when compared to all other groups. However, the IgA titres remained the highest in this patient group at each time point, both after infection and vaccination. A history COVID-19 was associated with higher antibody levels after double-dose vaccination in all patient categories and, while decreasing, titres remained high six months after double-dose vaccination.ConclusionKidney transplant recipients had a more robust humoral response to SARS-CoV-2 following infection compared to a two-dose mRNA vaccination, while patients on haemodialysis exhibited comparable seroconversion rates. Notably, individuals with prior COVID-19 exhibited higher IgG levels in response to vaccination. Hybrid immunity is thus the best possible defence against severe COVID-19 disease and seems also to hold up for these populations. Next, it is not clear whether the higher IgA levels in the kidney transplant recipients is beneficial for neutralizing SARS-CoV-2 or if it is a sign of disease severity.

A Nationwide Cohort Study of Delta and Omicron SARS-CoV-2 Outcomes in Vaccinated Individuals With Chronic Lung Disease

BackgroundIndividuals with chronic-lung-disease (CLD) are more susceptible to respiratory viral infections; however, there is significant heterogeneity in the literature on CLD and COVID-19 outcomes. Data is lacking on outcomes with newer variants (eg. Omicron) and in vaccinated/boosted populations. Research QuestionWhat are the outcomes of SARS-CoV-2 infection in individuals with CLD during Delta and Omicron transmission, in a highly vaccinated/boosted population-based cohort? Study Design and MethodsOutcomes of Delta/Omicron SARS-CoV-2 infection in a highly vaccinated/boosted cohort of adult Singaporeans with CLD (including asthma, chronic-obstructive-pulmonary-disease [COPD], bronchiectasis and pulmonary fibrosis) were contrasted against matched population controls. Calendar time-scale Cox regressions were used to compare risk of infection, COVID-19-related hospitalizations and severe COVID-19 disease, adjusting for sociodemographic factors/comorbidities. ResultsOverall, 68,782 individual patients with CLD and 534,364 matched population controls were included. 92.7% of CLD patients were boosted by the end of the Omicron wave. Compared with controls, higher risk of SARS-CoV-2 infection, COVID-19-related hospitalization and severe COVID-19 was observed amongst patients with CLD during both Delta (infection: adjusted-hazards-ratio, aHR=1.22[1.17-1.28]; hospitalization: aHR=1.76[1.61-1.92]; severe-COVID-19: aHR=1.75[1.50-2.05]) and Omicron waves (infection: aHR=1.15[1.14-1.17]; hospitalization: aHR=1.82[1.74-1.91]; severe-COVID-19: aHR=2.39[2.18-2.63]). During Omicron, significantly higher risk of infection, hospitalization and severe-COVID-19 was observed amongst patients with asthma (severe-COVID-19: aHR=1.31[1.10-1.55]) and COPD (severe-COVID-19: aHR=1.36[1.12-1.66]) compared with controls. Severe exacerbation (requiring hospitalization) in the preceding year was associated with higher risk of poorer outcomes (Delta-severe-COVID-19: aHR=9.84[6.33-15.28]; Omicron-severe-COVID-19: aHR=19.22[15.35-24.06]). Risk was attenuated in the boosted group, with numerically lower HRs against hospitalization/severe-COVID-19 in the 4-dose group compared with the 3-dose group. InterpretationIncreased risk of COVID-19-related hospitalization and severe-COVID-19 was observed amongst patients with CLD compared with matched population controls, during Delta/Omicron predominance. Boosting attenuated serious COVID-19 outcomes.