Epigenetic and transcriptomic reprogramming in monocytes of severe COVID-19 patients reflects alterations in myeloid differentiation and the influence of inflammatory cytokines (preprint)

COVID-19 manifests with a wide spectrum of clinical phenotypes, ranging from asymptomatic and mild to severe and critical. Severe and critical COVID-19 patients are characterized by marked changes in the myeloid compartment, especially monocytes. However, little is known about the epigenetic alterations that occur in these cells during hyperinflammatory responses in severe COVID-19 patients. In this study, we obtained the DNA methylome and transcriptome of peripheral blood monocytes from severe COVID-19 patients. DNA samples extracted from CD14+CD15- monocytes of 48 severe COVID-19 patients and 11 healthy controls were hybridized on MethylationEPIC BeadChip arrays. In parallel, single-cell transcriptomics of 10 severe COVID-19 patients were generated. CellPhoneDB was used to infer changes in the crosstalk between monocytes and other immune cell types. We observed DNA methylation changes in CpG sites associated with interferon-related genes and genes associated with antigen presentation, concordant with gene expression changes. These changes significantly overlapped with those occurring in bacterial sepsis, although specific DNA methylation alterations in genes specific to viral infection were also identified. We also found these alterations to comprise some of the DNA methylation changes occurring during myeloid differentiation and under the influence of inflammatory cytokines. A progression of DNA methylation alterations in relation to the Sequential Organ Failure Assessment (SOFA) score was found to be related to interferon-related genes and T-helper 1 cell cytokine production. CellPhoneDB analysis of the single-cell transcriptomes of other immune cell types suggested the existence of altered crosstalk between monocytes and other cell types like NK cells and regulatory T cells. Our findings show the occurrence of an epigenetic and transcriptional reprogramming of peripheral blood monocytes, which could be associated with the release of aberrant immature monocytes, increased systemic levels of pro-inflammatory cytokines, and changes in immune cell crosstalk in these patients.

ICU-Acquired Pneumonia is a Risk Factor of a Poor Health Post-Covid-19 Syndrome (preprint)

Background: . Some patients who had previously presented with COVID-19 have been reported to develop persistent COVID-19 symptoms. Whilst this information has been adequately recognised and extensively published with respect to non-critically ill patients, less is known about the prevalence and risk factors and characteristics of persistent COVID_19 . On other hand these patients have very often intensive care unit-acquired pneumonia (ICUAP). A second infectious hit after COVID increases the length of ICU stay and mechanical ventilation and could have an influence in the poor health post-Covid 19 syndrome in ICU discharged patients Methods: This prospective, multicentre and observational study was done across 40 selected ICUs in Spain. Consecutive patients with COVID-19 requiring ICU admission were recruited and evaluated three months after hospital discharge. Results: A total of 1,255 ICU patients were scheduled to be followed up at 3 months; however, the final cohort comprised 991 (78.9%) patients. A total of 315 patients developed ICUAP (97% of them had ventilated ICUAP) Patients requiring invasive mechanical ventilation had persistent, post-COVID-19 symptoms than those who did not require mechanical ventilation. Female sex, duration of ICU stay, and development of ICUAP were independent risk factors for persistent poor health post-COVID-19. Conclusions: : Persistent, post-COVID-19 symptoms occurred in more than two-thirds of patients. Female sex, duration of ICU stay and the onset of ICUAP comprised all independent risk factors for persistent poor health post-COVID-19. Prevention of ICUAP could have beneficial effects in poor health post-Covid 19

New susceptibility loci for severe COVID-19 by detailed GWAS analysis in European populations (preprint)

Due to the highly variable clinical phenotype of Coronavirus disease 2019 (COVID-19), deepening the host genetic contribution to severe COVID-19 may further improve our understanding about underlying disease mechanisms. Here, we describe an extended GWAS meta-analysis of 3,260 COVID-19 patients with respiratory failure and 12,483 population controls from Italy, Spain, Norway and Germany, as well as hypothesis-driven targeted analysis of the human leukocyte antigen (HLA) region and chromosome Y haplotypes. We include detailed stratified analyses based on age, sex and disease severity. In addition to already established risk loci, our data identify and replicate two genome-wide significant loci at 17q21.31 and 19q13.33 associated with severe COVID-19 with respiratory failure. These associations implicate a highly pleiotropic ~0.9-Mb 17q21.31 inversion polymorphism, which affects lung function and immune and blood cell counts, and the NAPSA gene, involved in lung surfactant protein production, in COVID-19 pathogenesis.

Label-Free Plasmonic Biosensor for Rapid, Quantitative, and Highly Sensitive COVID-19 Serology: Implementation and Clinical Validation (preprint)

Serological tests are essential for the control and management of COVID-19 pandemic, not only for current and historical diagnostics but especially for surveillance, epidemiological, and acquired immunity studies. Clinical COVID-19 serology is routinely performed by enzymatic or chemiluminescence immunoassays (i.e., ELISA or CLIA), which provide good sensitivities at the expense of relatively long turnaround times and specialized laboratory settings. Rapid serological tests, based on lateral flow assays, have also been developed and widely commercialized, but they suffer from limited reliability due to relatively low sensitivity and specificity. We have developed and validated a direct serological biosensor assay employing proprietary technology based on Surface Plasmon Resonance (SPR). The biosensor offers a rapid -less than 15 min- identification and quantification of SARS-CoV-2 antibodies directly in clinical samples, without the need of any signal amplification. The portable plasmonic biosensor device employs a custom-designed multi-antigen sensor biochip, combining the two main viral antigens (RBD peptide and N protein), for simultaneous detection of human antibodies targeting both antigens. The SPR serology assay reaches detection limits in the low ng mL-1 range employing polyclonal antibodies as standard, which are well below the commonly detected antibody levels in COVID-19 patients. The assay has also been implemented employing the first WHO approved anti-SARS-CoV-2 immunoglobulin standard. We have carried out a clinical validation with COVID-19 positive and negative samples (n=120) that demonstrates the excellent diagnostic sensitivity (99%) and specificity (100%). This positions our biosensor device as an accurate, robust, and easy-to-use diagnostics tool for rapid and reliable COVID-19 serology to be employed both at laboratory and decentralized settings for the management of COVID-19 patients and for the evaluation of immunological status during vaccination, treatment or in front of emerging variants.

Cytokine Hemoadsorption As Rescue Therapy for Critically Ill Patients with SARS-CoV-2 Pneumonia with Severe Respiratory Failure and Hypercytokinemia (preprint)

Background : A dysregulated inflammatory response, known as “cytokine storm”, plays an important role in the pathophysiology of coronavirus 2019 disease (COVID-19). There is a subgroup of patients who develop a hyperinflammatory response with severe respiratory failure and organ dysfunction with high mortality. Identifying these patients is outstanding as they could benefit from specific therapies, such as cytokine removal by hemoadsorption. Methods: Single-center, observational and prospective study of critically ill patients with SARS-CoV-2 pneumonia, severe acute respiratory failure and hypercytokinemia. All patients received cytokine hemoadsorption using Cytosorb® (Cytosorbents Europe, Berlin, Germany). The indication for treatment was acute respiratory failure, inadequate prone response, and hypercytokinemia. Results : A total of 343 patients were admitted to the ICU due to SARS-Cov-2 infection between March 3, 2020, to June 22, 2020. Of these, six patients [5 (83.3%) men; mean age 57 (10.5) years; SOFA 5 (1.4); mean Acute Physiology And Chronic Health Evaluation (APACHE) II score 19.5 (6)] underwent hemoadsorption with Cytosorb®. All patients fulfilled the Berlin criteria for severe acute respiratory distress syndrome (ARDS), underwent prone positioning, and were on mechanical ventilation for 15.2 (7.2) days. One session of 16 (9.0) hours duration was performed. IL-6 levels were significantly reduced [(pre- hemoadsorption levels 17.367 (4.539– 22.532) pg/ml; post-hemoadsorption levels 2.403 (917 – 3.724) pg/ml, p = 0.043], and improvements in oxygenation were observed [pre-hemoadsorption PaO 2 /FiO 2 ratio was 103 (18.4), post- hemoadsorption PaO2/FiO2 ratio was 222 (20.9), p = 0.029]. We documented the clinical improvement and rapid reversal of organ dysfunction [pre-hemoadsorption Sequential Organ Failure Assessment (SOFA) score 9 (4.7); post- hemoadsorption SOFA score 7.7 (5.4), p = 0.046]. Inflammatory markers (C-reactive protein, D-dimer, and ferritin) also improved significantly. Mean ICU stay was 17.2 (8.0) days. ICU and in-hospital mortality was 33.7%. Conclusions : In our cohort, patients with SARS-CoV-2 pneumonia and severe acute respiratory failure and hypercytokinemia who received cytokine hemoadsorption, an important reduction in IL-6 levels and improvements in oxygenation and SOFA score were observed.

A Differential Therapeutic Consideration for use of Corticosteroids According to Established COVID-19 Clinical Phenotypes in Critically Ill Patients (preprint)

Background: The steroids are currently used as standard treatment for severe COVID-19. However, the evidence is weak. Our aim is to determine if the use of corticosteroids was associated with Intensive Care Unit (ICU) mortality among whole population and pre-specified clinical phenotypes.Methods: A secondary analysis derived from multicenter, observational study of adult critically ill patients with confirmed COVID-19 disease admitted to 63 ICUs in Spain. Three phenotypes were derived by non-supervised clustering analysis from whole population and classified as (A: severe, B: critical and C: life-threatening). The primary outcome was ICU mortality. We performed a Multivariate analysis after propensity score full matching (PS), Cox proportional hazards (CPH), Cox covariate time interaction (TIR), Weighted Cox Regression (WCR) and Fine-Gray analysis(sHR) to assess the impact of corticosteroids on ICU mortality according to the whole population and distinctive patient clinical phenotypes. Results:  A total of 2,017 patients were analyzed, 1171(58%) with corticosteroids. After PS, corticosteroids were shown not to be associated with ICU mortality (OR:1.0,95%CI:0.98-1.15). Corticosteroids were administered in 298/537(55.5%) patients of “A” phenotype and their use was not associated with ICU mortality (HR=0.85[0.55-1.33]). A total of 338/623(54.2%) patients in “B” phenotype received corticosteroids. The CPH (HR =0.65 [0.46-0.91]) and TIR regression (1- 25 day tHR=0.56[0.39-0.82] and >25 days tHR=1.53[1.03-7.12]) showed a biphasic effect of corticosteroids due to proportional assumption violation. No effect of corticosteroids on ICU mortality was observed when WCR was performed (wHR=0.72[0.49-1.05]). Finally, 535/857(62.4%) patients in “C” phenotype received corticosteroids. The CPH (HR=0.73[0.63-0.98]) and TIR regression (1- 25 day tHR=0.69[ 0.53-0.89] and >25 days tHR=1.30[ 1.14-3.25]) showed a biphasic effect of corticosteroids and proportional assumption violation. However, wHR (0.75[0.58-0.98]) and sHR (0.79[0.63-0.98]) suggest a protective effect of corticosteroids on ICU mortality.     Conclusion: Our finding warns against the widespread use of corticosteroids in all critically ill patients with COVID-19 at moderate-high dose. Only patients with the highest severity could benefit from steroid treatment although this effect on clinical outcome was minimized during ICU stay. 

Absent or insufficient anti-SARS-CoV-2 S antibodies at ICU admission are associated to higher viral loads in plasma, antigenemia and mortality in COVID-19 patients (preprint)

Purposeto evaluate the association between anti-SARS-CoV-2 S IgM and IgG antibodies with viral RNA load in plasma, the frequency of antigenemia and with the risk of mortality in critically ill patients with COVID-19. Methodsanti-SARS-CoV-2 S antibodies levels, viral RNA load and antigenemia were profiled in plasma of 92 adult patients in the first 24 hours following ICU admission. The impact of these variables on 30-day mortality was assessed by using Kaplan-Meier curves and multivariate Cox regression analysis. Resultsnon survivors showed more frequently absence of anti-SARS-CoV-2 S IgG and IgM antibodies than survivors (26.3% vs 5.6% for IgM and 18.4% vs 5.6% for IgG), and a higher frequency of antigenemia (47.4% vs 22.2%) (p <0.05). Non survivors showed lower concentrations of anti-S IgG and IgM and higher viral RNA loads in plasma, which were associated to increased 30-day mortality and decreased survival mean time. [Adjusted HR (CI95%), p]: [S IgM (AUC [≥]60): 0.48 (0.24; 0.97), 0.040]; [S IgG (AUC [≥]237): 0.47 (0.23; 0.97), 0.042]; [Antigenemia (+): 2.45 (1.27; 4.71), 0.007]; [N1 viral load ([≥] 2.156 copies/mL): 2.21 (1.11; 4.39),0.024]; [N2 viral load ([≥] 3.035 copies/mL): 2.32 (1.16; 4.63), 0.017]. Frequency of antigenemia was >2.5-fold higher in patients with absence of antibodies. Levels of anti-SARS-CoV-2 S antibodies correlated inversely with viral RNA load. Conclusionabsence / insufficient levels of anti-SARS-CoV-2 S antibodies following ICU admission is associated to poor viral control, evidenced by increased viral RNA loads in plasma, higher frequency of antigenemia, and also to increased 30-day mortality. Take-home messageabsent or low levels of antibodies against the S protein of SARS-CoV- 2 at ICU admission is associated to an increased risk of mortality, higher frequency of antigenemia and higher viral RNA loads in plasma. Profiling anti-SARS-CoV-2 s antibodies at ICU admission could help to predict outcome and to better identify those patients potentially deserving replacement treatment with monoclonal or polyclonal antibodies.

Deploying unsupervised clustering analysis to derive clinical phenotypes and risk factors associated with mortality risk in 2,022 critically ill patients with COVID-19 in Spain (preprint)

Background: The identification of factors associated with Intensive Care Unit (ICU) mortality and derived clinical phenotypes in COVID-19 patients could help for a more tailored approach to clinical decision-making that improves prognostic outcomes. Methods: Prospective, multicenter, observational study of critically ill patients with confirmed COVID-19 disease and acute respiratory failure admitted from 63 Intensive Care Units(ICU) in Spain. The objective was to utilize an unsupervised clustering analysis to derive clinical COVID-19 phenotypes and to analyze patient’s factors associated with mortality risk. Patient features including demographics and clinical data at ICU admission were analyzed. Generalized linear models were used to determine ICU morality risk factors. The prognostic models were validated and their performance was measured using accuracy test, sensitivity, specificity and ROC curves. Results: : The database included a total of 2,022 patients (mean age 64[IQR5-71] years, 1423(70.4%) male, median APACHE II score (13[IQR10-17]) and SOFA score (5[IQR3-7]) points. The ICU mortality rate was 32.6%. Of the 3 derived phenotypes, the A(mild) phenotype (537;26.7%) included older age (<65 years), fewer abnormal laboratory values and less development of complications, B (moderate) phenotype (623,30.8%) had similar characteristics of A phenotype but were more likely to present shock. The C(severe) phenotype was the most common (857;42.5%) and was characterized by the interplay of older age (>65 years), high severity of illness and a higher likelihood of development shock. Crude ICU mortality was 20.3%, 25% and 45.4% for A, B and C phenotype respectively. The ICU mortality risk factors and model performance differed between whole population and phenotype classifications. Conclusion: The presented machine learning model identified three clinical phenotypes that significantly correlated with host-response patterns and ICU mortality. Different risk factors across the whole population and clinical phenotypes were observed which may limit the application of a “one-size-fits-all” model in practice .

Deploying Machine Learning to Validate Clinical Phenotypes and Factors Associated with Mortality Risk in 2,022 Critically Ill Patients with COVID-19 in Spain (preprint)

Background: The identification of factors associated with Intensive Care Unit (ICU) mortality and derived clinical phenotypes in COVID-19 patients could help for a more tailored approach to clinical decision-making that improves prognostic outcomes. The objective was to analyze patient’s factors associated with mortality risk and utilize a Machine Learning(ML) to derive clinical COVID-19 phenotypes.Methods: Prospective, multicenter, observational study of critically ill patients with confirmed COVID-19 disease and acute respiratory failure admitted from 63 Intensive Care Units(ICU) in Spain. Patient features including demographics and clinical data at ICU admission were analyzed. Generalized linear models were used to determine ICU morality risk factors. An unsupervised clustering analysis was applied to determine presence of phenotypes. The prognostic models were validated and their performance was measured using accuracy test, sensitivity, specificity and ROC curves.Findings: The database included a total of 2,022 patients (mean age 64[IQR5-71] years, 1423(70·4%) male, median APACHE II score (13[IQR10-17]) and SOFA score (5[IQR3-7]) points. The ICU mortality rate was 32·6%. Of the 3 derived phenotypes, the C(severe) phenotype was the most common (857;42·5%) and was characterized by the interplay of older age (>65 years), high severity of illness and a higher likelihood of development shock. The A(mild) phenotype (537;26·7%) included older age (>65 years), fewer abnormal laboratory values and less development of complications and B (moderate) phenotype (623,30·8%) had similar characteristics of A phenotype but were more likely to present shock. Crude ICU mortality was 45·4%, 25·0% and 20·3% for the C, B and A phenotype respectively. The ICU mortality risk factors and model performance differed between whole population and phenotype classifications.Interpretation: The presented ML model identified three clinical phenotypes that significantly correlated with host-response patterns and ICU mortality. Different risk factors across the whole population and clinical phenotypes were observed which may limit the application of a “one-size-fits-all” model in practice.Funding Statement: This study was supported by the Spanish Intensive Care Society(SEMICYUC) and Ricardo Barri Casanovas Foundation.Declaration of Interests: All authors declare that they have no conflicts of interest.Ethics Approval Statement: The study was approved by the reference institutional review board at Joan XXIII University Hospital (IRB# CEIM/066/2020) and each participating site with a waiver of informed consent. All data values were anonymized prior to the phenotyping which consisted of clustering clinical variables on their association with COVID-19 mortality.

SARS-CoV-2-RNA viremia is associated to hypercytokinemia and critical illness in COVID-19 (preprint)

BackgroundSevere COVID-19 is characterized by clinical and biological manifestations typically observed in sepsis. SARS-CoV-2 RNA is commonly detected in nasopharyngeal swabs, however viral RNA can be found also in peripheral blood and other tissues. Whether systemic spreading of the virus or viral components plays a role in the pathogenesis of the sepsis-like disease observed in severe COVID-19 is currently unknown. MethodsWe determined the association of plasma SARS-CoV-2 RNA with the biological responses and the clinical severity of patients with COVID-19. 250 patients with confirmed COVID-19 infection were recruited (50 outpatients, 100 hospitalised ward patients, and 100 critically ill). The association between plasma SARS-CoV-2 RNA and laboratory parameters was evaluated using multivariate GLM with a gamma distribution. The association between plasma SARS-CoV-2 RNA and severity was evaluated using multivariate ordinal logistic regression analysis and Generalized Linear Model (GLM) analysis with a binomial distribution. ResultsThe presence of SARS-CoV-2-RNA viremia was independently associated with a number of features consistently identified in sepsis: 1) high levels of cytokines (including CXCL10, CCL-2, IL-10, IL-1ra, IL-15, and G-CSF); 2) higher levels of ferritin and LDH; 3) low lymphocyte and monocyte counts 4) and low platelet counts. In hospitalised patients, the presence of SARS-CoV-2-RNA viremia was independently associated with critical illness: (adjusted OR= 8.30 [CI95%=4.21 - 16.34], p < 0.001). CXCL10 was the most accurate identifier of SARS-CoV-2-RNA viremia in plasma (area under the curve (AUC), [CI95%], p) = 0.85 [0.80 - 0.89), <0.001]), suggesting its potential role as a surrogate biomarker of viremia. The cytokine IL-15 most accurately differentiated clinical ward patients from ICU patients (AUC: 0.82 [0.76 - 0.88], <0.001). Conclusionssystemic dissemination of genomic material of SARS-CoV-2 is associated with a sepsis-like biological response and critical illness in patients with COVID-19. RNA viremia could represent an important link between SARS-CoV-2 infection, host response dysfunction and the transition from moderate illness to severe, sepsis-like COVID-19 disease.

Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients (preprint)

The SARS-CoV-2 spike (S) protein, the viral mediator for binding and entry into the host cell, has sparked great interest as a target for vaccine development and treatments with neutralizing antibodies. Initial data suggest that the virus has low mutation rates, but its large genome could facilitate recombination, insertions, and deletions, as has been described in other coronaviruses. Here, we deep-sequenced the complete SARS-CoV-2 S gene from 18 patients (10 with mild and 8 with severe COVID-19), and found that the virus accumulates deletions upstream and very close to the S1/S2 cleavage site, generating a frameshift with appearance of a stop codon. These deletions were found in a small percentage of the viral quasispecies (2.2%) in samples from all the mild and only half the severe COVID-19 patients. Our results suggest that the virus may generate free S1 protein released to the circulation. We propose that natural selection has favored a "Dont burn down the house" strategy, in which free S1 protein may compete with viral particles for the ACE2 receptor, thus reducing the severity of the infection and tissue damage without losing transmission capability.