Forecasting local hospital bed demand for COVID-19 using on-request simulations (preprint)

For hospitals, realistic forecasting of bed demand during impending epidemics of infectious diseases is essential to avoid being overwhelmed by a potential sudden increase in the number of admitted patients. Short-term forecasting can aid hospitals in adjusting their planning and freeing up beds in time. We created an easy-to-use online on-request tool based on local data to forecast COVID-19 bed demand for individual hospitals. The tool is flexible and adaptable to different settings. It is based on a stochastic compartmental model for estimating the epidemic dynamics and coupled with an exponential smoothing model for forecasting. The models are written in R and Julia and implemented as an R-shiny dashboard. The model is parameterized using COVID-19 incidence, vaccination, and bed occupancy data at customizable geographical resolutions, loaded from official online sources or uploaded manually. Users can select their hospital's catchment area and adjust the number of COVID-19 occupied beds at the start of the simulation. The tool provides short-term forecasts of disease incidence and past and forecasted estimation of the epidemic reproductive number at the chosen geographical level. These quantities are then used to estimate the bed occupancy in both general wards and intensive care unit beds. The platform has proven efficient, providing results within seconds while coping with many concurrent users. By providing ad-hoc, local data informed forecasts, this platform allows decision-makers to evaluate realistic scenarios for allocating scarce resources, such as ICU beds, at various geographic levels.

Allocation of scarce critical care resources during public health emergencies: which ethical principles support decision making.

Aim: To investigate whether and how ten ethical principles are mentioned within documents on critical care resources allocation during public health emergencies. Materials and Methods: We conducted a search of documents con-cerning critical resources allocation during public emergencies publicly available from Google and two specific international websites, up to November 2020. Each document was analyzed by two independent reviewers to assess whether a reference to any of the 10 key ethical principles indicated by the Northern Italy Ethical Committee could be found in the documents. Cohen's K statistic was used. Results: We obtained 34 documents, of which 19 were allocation frameworks, 15 crisis standards of care, 4 clinical triage protocol, 3 clinical guidelines and 2 public health emergency response plans. The principles most frequently mentioned as important for decision-making was "number of lives saved", followed by "transparency", "equity", "respect of person and their autonomy". The most cited tiebreakers were "younger first/life cycle" and "lottery". Conclusions: All documents aim to protect the life and health of the largest number of people and should be objective, ethical, transparent, applied equitably, and be publicly disclosed. It is plausible that short- and long-term prognostic tools can help allocate critical resources, but it remains strong that the decision-making process must be guided by a multi-principle ethical model that is not always easy to apply.

Detection of Covid-19 in CXR: A Low Sample Size Deep Convolutional Neural Network Training Data Approach

Infectious illness Covid-19 is highly contagious and has claimed the lives of numerous individuals. To assist prevent the virus's transmission, it's critical to identify and isolate those who have been infected with the infection. The purpose of the study is to aid in the detection of Covid-19 alongside with RT-PCR test by utilizing a deep learning algorithm, specifically YOLOv3 as the technique to be used for it uses CNN, which then implements deep learning technique. The study has a promising detection to detect if the person's CXR has Covid-19, normal or viral pneumonia, obtaining an mAP value of 95.27% from model 14, which is the highest among the 12 models created. © 2022 IEEE.

RESPIRABLE POWDER CONTAINING CYCLOSPORINE A LOADED LIPOSOMES AS IMMUNOSUPPRESSIVE AGENT SUITABLE FOR LUNG TRANSPLANT REJECTION AND THE CONTAINMENT OF SEVERE LUNG INFLAMMATION

The work led to the formulation of a powder of calcium phosphate coated liposomes containing cyclosporine A (CsA). The formulation was designed to reduce the dose of CsA to be administered following lung transplantation. Potentially this formulation can be used also to contain the inflammatory process due to SARS-CoV-2. Calcium phosphate (CaP) is a material found in bones and teeth and considered non-toxic and biocompatible and this coating could reduce the recognition by alveolar macrophages and increase the cell uptake. Moreover, CaP is insoluble at physiological pH (7.4), while it solubilizes easily at pH below 5. This could favor drug release in the cell after pinocytosis and in inflamed tissues, while reducing drug release at physiological pH [1]. The liposomes produced were evaluated in terms of size, surface charge and drug loading. The presence of the CaP coating was verified by calcium titration, variation of the zeta potential and by cryogenic transmission electron microscopy (cryo-TEM). The highest loading was obtained in the formulation containing CsA at 7% (w/w). Cholesterol was added to liposomes at two different concentrations in order to improve the stability of the nanostructure and reduce the drug leakage. However, cholesterol did not bring any improvement to the formulation. The inhalation powder produced by spray drying with the best aerosolization performance (fine particle fraction of coated liposomes powder 33.69 - 1.6% and 50.50- 0.6% for the uncoated liposomes powder) was obtained using a 1:3 weight ratio between liposomes and excipients using mannitol as bulking agent and 15% L-leucine. Key Message: This work aimed to develop a respirable dry powder for inhalation containing CsA for the local treatment of lung immune diseases. CsA was efficiently loaded into CaP-coated liposomes and transformed into a respirable powder by spray-drying. The inhaled immunosuppressive product would offer multiple advantages related to drug deposition at the target site. Furthermore, the coating of the liposomes governs the release of the drug which will occur only at only at biological acidic conditions.

Cross-talk between red blood cells and plasma influences blood flow and omics phenotypes in severe COVID-19 (preprint)

Coronavirus disease 2019 (COVID-19) is caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and can affect multiple organs, among which is the circulatory system. Inflammation and mortality risk markers were previously detected in COVID-19 plasma and red blood cells (RBCs) metabolic and proteomic profiles. Additionally, biophysical properties, such as deformability, were found to be changed during the infection. Based on such data, we aim to better characterize RBC functions in COVID-19. We evaluate the flow properties of RBCs in severe COVID-19 patients admitted to the intensive care unit by using in vitro microfluidic techniques and automated methods, including artificial neural networks, for an unbiased RBC analysis. We find strong flow and RBC shape impairment in COVID-19 samples and demonstrate that such changes are reversible upon suspension of COVID-19 RBCs in healthy plasma. Vice versa, healthy RBCs immediately resemble COVID-19 RBCs when suspended in COVID-19 plasma. Proteomics and metabolomics analyses allow us to detect the effect of plasma exchanges on both plasma and RBCs and demonstrate a new role of RBCs in maintaining plasma equilibria at the expense of their flow properties. Our findings provide a framework for further investigations of clinical relevance for therapies against COVID-19 and possibly other infectious diseases.

SARS-CoV-2 Infection Breakthrough among the non-vaccinated and vaccinated: a Real World Evidence study based on Big Data (preprint)

ABSTRACT Background: SARS-CoV-2 infection after vaccination can occur because COVID-19 vaccines do not offer 100% protection. The aim of this study was to assess vaccination coverage among people nasopharyngeal swabs, disease symptoms and type of hospitalisation (Intensive Care Unit) between the non-vaccinated and the effective dose vaccinated and to evaluate vaccination trend over time. Methods: A retrospective cohort study was carried out among people tested positive for COVID-19 in Campania Region using collected information from Health Information System of Campania Region (Sinfonia). The status of vaccination was assess according to the following timetable: non-vaccinated; Ineffective dose vaccination; Effective dose vaccination. Univariate and multivariate logistic regression models were conducted to evaluate the association between Intensive Care Unit (ICU) to COVID-19 and gender, age groups and vaccine. To determine vaccine coverage in subjects who received an effective dose, trend changes over time were investigated using segmented linear regression models and breakpoints estimations. Vaccination coverage was assessed by analysing the trend in the percentage of covid 19 positive subjects in the 9 months after vaccination with an effective dose stratified by age group and type of vaccine. Statistical analyses were performed using R platform Results: A significant association with the risk of hospitalisation in Intensive Care Unit was the vaccination status of the subjects: subjects with ineffective dose (adjusted OR: 3.68) and subjects no-vaccination (adjusted OR: 7.14) were at three- and seven-times higher risk of hospitalisation in Intensive Care Unit, respectively, than subjects with an effective dose. Regarding subjects with an effective dose of vaccine, the vaccine's ability to protect against infection in the months following vaccination decreased. The first breakpoints is evident five months after vaccination ({beta} =1.441, p<0.001). This increase was most evident after the seventh month after vaccination ({beta} =3.110, p<0.001). Conclusions: COVID19 vaccines protect from symptomatic infection by significantly reducing the risk of ICU hospitalization for severe disease. However, it seems they have trend to decrease their fully protection against SARS-COV-2 after five months regardless age, sex or type of vaccine. Therefore it seems clear that those not undergoing vaccine had higher risk to develop clinically significant disease and being at risk of ICU stay. Thus, considering highest percentage of asymptomatic patients and that few data about their capacity to transmit SARS-CoV-2, third dose vaccination should be introduced as soon as possible, Finally, a surveillance approach based on the use of integrated BIG Data system to match all clinical conditions too, offer a precise and real analysis with low incidence of errors in the categorization of subjects.

Early Diffusion of SARS-CoV-2 Infection in the Inner Area of the Italian Sardinia Island.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been responsible for the coronavirus disease 2019 (COVID-19) pandemic, which started as a severe pneumonia outbreak in Wuhan, China, in December 2019. Italy has been the first European country affected by the pandemic, registering a total of 300,363 cases and 35,741 deaths until September 24, 2020. The geographical distribution of SARS-CoV-2 in Italy during early 2020 has not been homogeneous, including regions severely affected as well as administrative areas being only slightly interested by the infection. Among the latter, Sardinia represents one of the lowest incidence areas likely due to its insular nature. METHODS: Next-generation sequencing of a small number of complete viral genomes from clinical samples and their virologic and phylogenetic characterization was performed. RESULTS: We provide a first overview of the SARS-CoV-2 genomic diversity in Sardinia in the early phase of the March-May 2020 pandemic based on viral genomes isolated in the most inner regional hospital of the island. Our analysis revealed a remarkable genetic diversity in local SARS-CoV-2 viral genomes, showing the presence of at least four different clusters that can be distinguished by specific amino acid substitutions. Based on epidemiological information, these sequences can be linked to at least eight different clusters of infection, four of which likely originates from imported cases. In addition, the presence of amino acid substitutions that were not previously reported in Italian patients has been observed, asking for further investigations in a wider population to assess their prevalence and dynamics of emergence during the pandemic. CONCLUSION: The present study provides a snapshot of the initial phases of the SARS-CoV-2 infection in inner area of the Sardinia Island, showing an unexpected genomic diversity.

Private Struggles in Public Spaces: Documenting COVID-19 Material Culture and Landscapes

The COVID-19 pandemic has disrupted nearly every facet of our world, including some of the most fundamental forms of human behavior and our conception of the social. Everyday activities now pose a risk to individuals and to society as a whole. This radical shift in how we live has produced a wide array of material responses across the globe. This photo essay seeks to open up dialogue and ask questions about the numerous forms of COVID-19 materiality and altered landscapes that the authors have chronicled, witnessed, documented and cataloged in their communities, using archaeological and ethnographic methods. This materiality includes chalk art, graffiti, painted rocks and signage placed in both public and private spaces within the project authors' commu- nities. In framing our questions, we draw upon theoretical frameworks in the fields of cultural trauma studies, cultural anthropology and contemporary archaeology.

Specialized interferon ligand action in COVID19 (preprint)

The impacts of IFN signaling on COVID19 pathology are multiple, with protective and harmful effects being documented. We report here a multi-omics investigation of IFN signaling in hospitalized COVID19 patients, defining the biosignatures associated with varying levels of 12 different IFN ligands. Previously we showed that seroconversion associates with decreased production of select IFN ligands (Galbraith et al, 2021). We show now that the antiviral transcriptional response in circulating immune cells is strongly associated with a specific subset of ligands, most prominently IFNA2 and IFNG. In contrast, proteomics signatures indicative of endothelial damage associate with levels of IFNB and IFNA6. Differential IFN ligand production is linked to distinct constellations of circulating immune cells. Lastly, IFN ligands associate differentially with activation of the kynurenine pathway, dysregulated fatty acid metabolism, and altered central carbon metabolism. Altogether, these results reveal specialized IFN ligand action in COVID19, with potential diagnostic and therapeutic implications.

Biological and Clinical Factors contributing to the Metabolic Heterogeneity of Hospitalized Patients with and without COVID-19 (preprint)

The Corona Virus Disease 2019 (COVID-19) pandemic represents an ongoing worldwide challenge. Exploratory studies evaluating the impact of COVID-19 infection on the plasma metabolome have been performed, often with small numbers of patients, and with or without relevant control data; however, determining the impact of biological and clinical variables remains critical to understanding potential markers of disease severity and progression. The present large study, including relevant controls, sought to understand independent and overlapping metabolic features of samples from acutely ill patients (n = 831), testing positive (n = 543) or negative (n = 288) for COVID-19. High-throughput metabolomics analyses were complemented with antigen and enzymatic activity assays on 831 plasma samples from acutely ill patients while in the emergency department, at admission, and during hospitalization. We then performed additional lipidomics analyses of the 60 subjects with the lowest and highest body mass index, either COVID-19 positive or negative. Omics data were correlated to detailed data on patient characteristics and clinical laboratory assays measuring coagulation, hematology and chemistry analytes. Significant changes in arginine/proline/citrulline, tryptophan/indole/kynurenine, fatty acid and acyl-carnitine metabolism emerged as highly relevant markers of disease severity, progression and prognosis as a function of biological and clinical variables in these patients. Further, machine learning models were trained by entering all metabolomics and clinical data from half of the COVID-19 patient cohort and then tested on the other half yielding ~ 78% prediction accuracy. Finally, the extensive amount of information accumulated in this large, prospective, observational study provides a foundation for follow-up mechanistic studies and data sharing opportunities, which will advance our understanding of the characteristics of the plasma metabolism in COVID-19 and other acute critical illnesses.

The COVIDome Explorer Researcher Portal (preprint)

COVID-19 pathology involves dysregulation of diverse molecular, cellular, and physiological processes. In order to expedite integrated and collaborative COVID-19 research, we completed multi-omics analysis of hospitalized COVID-19 patients including matched analysis of the whole blood transcriptome, plasma proteomics with two complementary platforms, cytokine profiling, plasma and red blood cell metabolomics, deep immune cell phenotyping by mass cytometry, and clinical data annotation. We refer to this multidimensional dataset as the COVIDome. We then created the COVIDome Explorer, an online researcher portal where the data can be analyzed and visualized in real time. We illustrate here the use of the COVIDome dataset through a multi-omics analysis of biosignatures associated with C-reactive protein (CRP), an established marker of poor prognosis in COVID-19, revealing associations between CRP levels and damage-associated molecular patterns, depletion of protective serpins, and mitochondrial metabolism dysregulation. We expect that the COVIDome Explorer will rapidly accelerate data sharing, hypothesis testing, and discoveries worldwide.Funding: This work was supported by NIH grants R01AI150305, 3R01AI150305-01S1, R01AI145988, UL1TR002535, 3UL1TR002535-03S2, R01HL146442, R01HL149714, R01HL148151, R21HL150032, P30CA046934, R35GM124939 and RM1GM131968, as well as grants from the Boettcher Foundation and Fast Grants. Additional support was received from Chancellor’s Discovery Innovation Fund at the CU Anschutz Medical Campus, the Global Down Syndrome Foundation, the Anna and John J. Sie Foundation, and Lyda Hill Philanthropies.Conflict of Interest: KDS and JME are co-inventors on two patents related to JAK inhibition in COVID-19; JME serves in the COVID Development Advisory Board for Elly Lilly and has provided consulting services to Gilead Sciences Inc. JME serves on the Cell Reports Advisory Board.

The COVIDome Explorer Researcher Portal (preprint)

SUMMARY COVID-19 pathology involves dysregulation of diverse molecular, cellular, and physiological processes. In order to expedite integrated and collaborative COVID-19 research, we completed multi-omics analysis of hospitalized COVID-19 patients including matched analysis of the whole blood transcriptome, plasma proteomics with two complementary platforms, cytokine profiling, plasma and red blood cell metabolomics, deep immune cell phenotyping by mass cytometry, and clinical data annotation. We refer to this multidimensional dataset as the COVIDome. We then created the COVIDome Explorer, an online researcher portal where the data can be analyzed and visualized in real time. We illustrate here the use of the COVIDome dataset through a multi-omics analysis of biosignatures associated with C-reactive protein (CRP), an established marker of poor prognosis in COVID-19, revealing associations between CRP levels and damage-associated molecular patterns, depletion of protective serpins, and mitochondrial metabolism dysregulation. We expect that the COVIDome Explorer will rapidly accelerate data sharing, hypothesis testing, and discoveries worldwide.

Seroconversion stages COVID19 into distinct pathophysiological states (preprint)

COVID19 is a heterogeneous medical condition involving a suite of underlying pathophysiological processes including hyperinflammation, endothelial damage, thrombotic microangiopathy, and end-organ damage. Limited knowledge about the molecular mechanisms driving these processes and lack of staging biomarkers hamper the ability to stratify patients for targeted therapeutics. We report here the results of a cross-sectional multi-omics analysis of hospitalized COVID19 patients revealing that seroconversion status associates with distinct underlying pathophysiological states. Seronegative COVID19 patients harbor hyperactive T cells and NK cells, high levels of IFN alpha, gamma and lambda ligands, markers of systemic complement activation, neutropenia, lymphopenia and thrombocytopenia. In seropositive patients, all of these processes are attenuated, observing instead increases in B cell subsets, emergency hematopoiesis, increased markers of platelet activation, and hypoalbuminemia. We propose that seroconversion status could potentially be used as a biosignature to stratify patients for therapeutic intervention and to inform analysis of clinical trial results in heterogenous patient populations.

ANALYSIS OF SARS-COV-2 GENOME SEQUENCES FROM THE PHILIPPINES: GENETIC SURVEILLANCE AND TRANSMISSION DYNAMICS (preprint)

The spread of the corona virus around the world has spurred travel restrictions and community lockdowns to manage the transmission of infection. In the Philippines, with a large population of overseas Filipino contract workers (OFWs), as well as foreign workers in the local online gaming industry and visitors from nearby countries, the first reported cases were from a Chinese couple visiting the country in mid-January 2020. Three months on, by mid-March, the COVID-19 cases in the Philippines had reached its first 100, before it exploded to the present 178,022 cases (as of August 20, 2020). Here, we report a genomic survey of six (6) whole genomes of the SARS-CoV-2 virus collected from COVID-19 patients seen at the Philippine General Hospital, the major referral hospital for COVID-19 cases in Metro Manila at about the time the Philippines had over a hundred cases. Analysis of commonly observed variants did not reveal a clear pattern of the virus evolving towards a more infectious and severe strain. When combined with other available viral sequences from the Philippines and from GISAID, phylogenomic analysis reveal that the sequenced Philippine isolates can be classified into three primary groups based on collection dates and possible infection sources: (1) January samples collected in the early phases of the pandemic that are closely associated with isolates from Wuhan, China; (2) March samples that are mainly linked to the M/V Diamond Princess Cruise Ship outbreak; and (3) June samples that clustered with European isolates, one of which already harbor the globally prevalent D614G mutation which initially circulated in Europe. The presence of community-acquired viral transmission amidst compulsory and strict quarantine protocols, particularly for repatriated Filipino workers, highlights the need for a refinement of the quarantine, testing, and tracing strategies currently being implemented to adapt to the current pandemic situation.

Evidence for structural protein damage and membrane lipid remodeling in red blood cells from COVID-19 patients (preprint)

The SARS-CoV-2 beta coronavirus is the etiological driver of COVID-19 disease, which is primarily characterized by shortness of breath, persistent dry cough, and fever. Because they transport oxygen, red blood cells (RBCs) may play a role in the severity of hypoxemia in COVID-19 patients. The present study combines state-of-the-art metabolomics, proteomics, and lipidomics approaches to investigate the impact of COVID-19 on RBCs from 23 healthy subjects and 29 molecularly-diagnosed COVID-19 patients. RBCs from COVID-19 patients had increased levels of glycolytic intermediates, accompanied by oxidation and fragmentation of ankyrin, spectrin beta, and the N-terminal cytosolic domain of band 3 (AE1). Significantly altered lipid metabolism was also observed, especially short and medium chain saturated fatty acids, acyl-carnitines, and sphingolipids. Nonetheless, there were no alterations of clinical hematological parameters, such as RBC count, hematocrit, and mean corpuscular hemoglobin concentration, with only minor increases in mean corpuscular volume. Taken together, these results suggest a significant impact of SARS-CoV-2 infection on RBC structural membrane homeostasis at the protein and lipid levels. Increases in RBC glycolytic metabolites are consistent with a theoretically improved capacity of hemoglobin to off-load oxygen as a function of allosteric modulation by high-energy phosphate compounds, perhaps to counteract COVID-19-induced hypoxia. Conversely, because the N-terminus of AE1 stabilizes deoxyhemoglobin and finely tunes oxygen off-loading, RBCs from COVID-19 patients may be incapable of responding to environmental variations in hemoglobin oxygen saturation when traveling from the lungs to peripheral capillaries and, as such, may have a compromised capacity to transport and deliver oxygen. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/20142703v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@16db0d2org.highwire.dtl.DTLVardef@73b808org.highwire.dtl.DTLVardef@1374ee5org.highwire.dtl.DTLVardef@1cbbc8_HPS_FORMAT_FIGEXP M_FIG C_FIG Key PointsO_LICOVID-19 promotes oxidation and fragmentation of membrane proteins, including the N-term of band 3 C_LIO_LIRBCs from COVID-19 patients are characterized by increases in glycolysis and altered lipidomes C_LIO_LICOVID-19 impacts two critical mechanisms that finely tune red cell membranes and hemoglobin oxygen affinity C_LI

Serum proteomics in COVID-19 patients: Altered coagulation and complement status as a function of IL-6 level (preprint)

Over 5 million people around the world have tested positive for the beta coronavirus SARS-CoV-2 as of May 29, 2020, a third of which in the United States alone. These infections are associated with the development of a disease known as COVID-19, which is characterized by several symptoms, including persistent dry cough, shortness of breath, chills, muscle pain, headache, loss of taste or smell, and gastrointestinal distress. COVID-19 has been characterized by elevated mortality (over 100 thousand people have already died in the US alone), mostly due to thromboinflammatory complications that impair lung perfusion and systemic oxygenation in the most severe cases. While the levels of pro-inflammatory cytokines such as interleukin-6 (IL-6) have been associated with the severity of the disease, little is known about the impact of IL-6 levels on the proteome of COVID-19 patients. The present study provides the first proteomics analysis of sera from COVID-19 patients, stratified by circulating levels of IL-6, and correlated to markers of inflammation and renal function. As a function of IL-6 levels, we identified significant dysregulation in serum levels of various coagulation factors, accompanied by increased levels of anti-fibrinolytic components, including several serine protease inhibitors (SERPINs). These were accompanied by up-regulation of the complement cascade and antimicrobial enzymes, especially in subjects with the highest levels of IL-6, which is consistent with an exacerbation of the acute phase response in these subjects. Although our results are observational, they highlight a clear increase in the levels of inhibitory components of the fibrinolytic cascade in severe COVID-19 disease, providing potential clues related to the etiology of coagulopathic complications in COVID-19 and paving the way for potential therapeutic interventions, such as the use of pro-fibrinolytic agents.

COVID-19 infection results in alterations of the kynurenine pathway and fatty acid metabolism that correlate with IL-6 levels and renal status (preprint)

Previous studies suggest a role for systemic reprogramming of host metabolism during viral pathogenesis to fuel rapidly expanding viral proliferation, for example by providing free amino acids and fatty acids as building blocks. In addition, general alterations in metabolism can provide key understanding of pathogenesis. However, little is known about the specific metabolic effects of SARS-COV-2 infection. The present study evaluated the serum metabolism of COVID-19 patients (n=33), identified by a positive nucleic acid test of a nasopharyngeal swab, as compared to COVID-19-negative control patients (n=16). Targeted and untargeted metabolomics analyses specifically identified alterations in the metabolism of tryptophan into the kynurenine pathway, which is well-known to be involved in regulating inflammation and immunity. Indeed, the observed changes in tryptophan metabolism correlated with serum interleukin-6 (IL-6) levels. Metabolomics analysis also confirmed widespread dysregulation of nitrogen metabolism in infected patients, with decreased circulating levels of most amino acids, except for tryptophan metabolites in the kynurenine pathway, and increased markers of oxidant stress (e.g., methionine sulfoxide, cystine), proteolysis, and kidney dysfunction (e.g., creatine, creatinine, polyamines). Increased circulating levels of glucose and free fatty acids were also observed, consistent with altered carbon homeostasis in COVID-19 patients. Metabolite levels in these pathways correlated with clinical laboratory markers of inflammation and disease severity (i.e., IL-6 and C-reactive protein) and renal function (i.e., blood urea nitrogen). In conclusion, this initial observational study of the metabolic consequences of COVID-19 infection in a clinical cohort identified amino acid metabolism (especially kynurenine and cysteine/taurine) and fatty acid metabolism as correlates of COVID-19, providing mechanistic insights, potential markers of clinical severity, and potential therapeutic targets.