The Prothrombotic State Associated with SARS-CoV-2 Infection: Pathophysiological Aspects

Experimental and analytical pipeline for sub-genomic RNA landscape of coronavirus by Nanopore sequencer

Coronaviruses (CoVs), including severe acute respiratory syndrome coronavirus 2, can infect a variety of mammalian and avian hosts with significant medical and economic consequences. During the life cycle of CoV, a coordinated series of subgenomic RNAs, including canonical subgenomic messenger RNA and non-canonical defective viral genomes (DVGs), are generated with different biological implications. Studies that adopted the Nanopore sequencer (ONT) to investigate the landscape and dynamics of viral RNA subgenomic transcriptomes applied arbitrary bioinformatics parameters without justification or experimental validation. The current study used bovine coronavirus (BCoV), which can be performed under biosafety level 2 for library construction and experimental validation using traditional colony polymerase chain reaction and Sanger sequencing. Four different ONT protocols, including RNA direct and cDNA direct sequencing with or without exonuclease treatment, were used to generate RNA transcriptomic libraries from BCoV-infected cell lysates. Through rigorously examining the k-mer, gap size, segment size, and bin size, the optimal cutoffs for the bioinformatic pipeline were determined to remove the sequence noise while keeping the informative DVG reads. The sensitivity and specificity of identifying DVG reads using the proposed pipeline can reach 82.6% and 99.6% under the k-mer size cutoff of 15. Exonuclease treatment reduced the abundance of RNA transcripts; however, it was not necessary for future library preparation. Additional recovery of clipped BCoV nucleotide sequences with experimental validation expands the landscape of the CoV discontinuous RNA transcriptome, whose biological function requires future investigation. The results of this study provide the benchmarks for library construction and bioinformatic parameters for studying the discontinuous CoV RNA transcriptome.IMPORTANCEFunctional defective viral genomic RNA, containing all the cis-acting elements required for translation or replication, may play different roles in triggering cell innate immune signaling, interfering with the canonical subgenomic messenger RNA transcription/translation or assisting in establishing persistence infection. This study does not only provide benchmarks for library construction and bioinformatic parameters for studying the discontinuous coronavirus RNA transcriptome but also reveals the complexity of the bovine coronavirus transcriptome, whose functional assays will be critical in future studies.

Modulations of Homeostatic ACE2, CD147, GRP78 Pathways Correlate with Vascular and Endothelial Performance Markers during Pulmonary SARS-CoV-2 Infection

The pathologic consequences of Coronavirus Disease-2019 (COVID-19) include elevated inflammation and dysregulated vascular functions associated with thrombosis. In general, disruption of vascular homeostasis and ensuing prothrombotic events are driven by activated platelets, monocytes, and macrophages, which form aggregates (thrombi) attached to the endothelium lining of vessel walls. However, molecular pathways underpinning the pathological interactions between myeloid cells and endothelium during COVID-19 remain undefined. Here, we tested the hypothesis that modulations in the expression of cellular receptors angiotensin-converting enzyme 2 (ACE2), CD147, and glucose-regulated protein 78 (GRP78), which are involved in homeostasis and endothelial performance, are the hallmark responses induced by SARS-CoV-2 infection. Cultured macrophages and lungs of hamster model systems were used to test this hypothesis. The results indicate that while macrophages and endothelial cells are less likely to support SARS-CoV-2 proliferation, these cells may readily respond to inflammatory stimuli generated by the infected lung epithelium. SARS-CoV-2 induced modulations of tested cellular receptors correlated with corresponding changes in the mRNA expression of coagulation cascade regulators and endothelial integrity components in infected hamster lungs. Among these markers, tissue factor (TF) had the best correlation for prothrombotic events during SARS-CoV-2 infection. Furthermore, the single-molecule fluorescence in situ hybridization (smFISH) method alone was sufficient to determine the peak and resolution phases of SARS-CoV-2 infection and enabled screening for cellular markers co-expressed with the virus. These findings suggest possible molecular pathways for exploration of novel drugs capable of blocking the prothrombotic shift events that exacerbate COVID-19 pathophysiology and control the disease.

The Role of the Kinin System and the Effect of Des-Arginine9-Bradykinin on Coagulation and Platelet Function in Critically Ill COVID-19 Patients: A Secondary Analysis of a Prospective Observational Study

The effect of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on the coagulation system is not fully understood. SARS-CoV-2 penetrates cells through angiotensin-converting enzyme 2 (ACE2) receptors, leading to its downregulation. Des-arginine9-bradykinin (DA9B) is degraded by ACE2 and causes vasodilation and increased vascular permeability. Furthermore, DA9B is associated with impaired platelet function. Therefore, the aim of this study was to evaluate the effects of DA9B on platelet function and coagulopathy in critically ill coronavirus disease 2019 (COVID-19) patients. In total, 29 polymerase-positive SARS-CoV-2 patients admitted to the intensive care unit of the University Hospital of Giessen and 29 healthy controls were included. Blood samples were taken, and platelet impedance aggregometry and rotational thromboelastometry were performed. Enzyme-linked immunosorbent assays measured the concentrations of DA9B, bradykinin, and angiotensin 2. Significantly increased concentrations of DA9B and angiotensin 2 were found in the COVID-19 patients. A negative effect of DA9B on platelet function and intrinsic coagulation was also found. A sub-analysis of moderate and severe acute respiratory distress syndrome patients revealed a negative association between DA9B and platelet counts and fibrinogen levels. DA9B provokes inhibitory effects on the intrinsic coagulation system in COVID-19 patients. This negative feedback seems reasonable as bradykinin, which is transformed to DA9B, is released after contact activation. Nevertheless, further studies are needed to confirm our findings.

Thrombocytopenia Secondary to COVID-19: Outcomes Analysis in Terms of Thrombotic Microangiopathy, Acute Kidney Injury, and Mortality

Background: COVID-19 usually complicates respiratory failure; microvascular, macrovascular, and renal complications are common. Both micro and macrovascular complications are associated with multi-organ dysfunction and in-hospital mortality. Thrombotic microangiopathy (TMA) causes microvascular thromboses associated with organ failure, including acute kidney injury (AKI). Materials and Methods: This Retrospective Cohort study included 100 COVID-19 patients with thrombocytopenia, followed up in a university hospital's intensive care unit (ICU). The primary endpoints were in-hospital mortality or discharge from the hospital and assessing the occurrence of TMA and AKI during the hospitalization. The effect of thrombotic microangiopathy and acute kidney injury on mortality was investigated using logistic regression models in Stata software version 12.1. Results: The TMA and AKI were associated with in-hospital mortality in COVID-19 patients presenting with thrombocytopenia in multivariate regression analysis, adjusted for other variables. The effect of AKI on mortality was obtained (adjusted OR 4.09, 95% CI: 1.33-12.53, p = 0.01). Moreover, the odds of mortality due to TMA were ten-fold higher in the patients who had TMA than those who did not (adjusted OR 10.26, 95% CI: 1.26-83.76, p = 0.03). Conclusion: We outlined TMA in COVID-19 patients, which could be responsible for kidney injury and mortality in critically COVID-19 patients.

Adoption of a National Prophylactic Anticoagulation Guideline for Hospitalized Pregnant Women With COVID-19: Retrospective Cohort Study

BACKGROUND

Both COVID-19 and pregnancy are associated with hypercoagulability. Due to the increased risk for thrombosis, the United States National Institute of Health's recommendation for prophylactic anticoagulant use for pregnant patients has expanded from patients hospitalized for severe COVID-19 manifestation to all patients hospitalized for the manifestation of COVID-19 (no guideline: before December 26, 2020; first update: December 27, 2022; second update: February 24, 2022-present). However, no study has evaluated this recommendation.

OBJECTIVE

The objective of this study was to characterize prophylactic anticoagulant use among hospitalized pregnant people with COVID-19 from March 20, 2020, to October 19, 2022.

METHODS

This was a retrospective cohort study in large US health care systems across 7 states. The cohort of interest was pregnant patients who were hospitalized with COVID-19, without previous coagulopathy or contraindication to anticoagulants (n=2767). The treatment group consisted of patients prescribed prophylactic dose anticoagulation between 2 days before and 14 days after COVID-19 treatment onset (n=191). The control group was patients with no anticoagulant exposure between 14 days before and 60 days after COVID-19 treatment onset (n=2534). We ascertained the use of prophylactic anticoagulants with attention to the updates in guidelines and emerging SARS-CoV-2 variants. We propensity score matched the treatment and control group 1:1 on the most important features contributing to the prophylactic anticoagulant administration status classification. Outcome measures included coagulopathy, bleeding, COVID-19-related complications, and maternal-fetal health outcomes. Additionally, the inpatient anticoagulant administration rate was validated in a nationwide population from Truveta, a collective of 700 hospitals across the United States.

RESULTS

The overall administration rate of prophylactic anticoagulants was 7% (191/2725). It was lowest after the second guideline update (no guideline: 27/262, 10%; first update: 145/1663, 8.72%; second update: 19/811, 2.3%; P<.001) and during the omicron-dominant period (Wild type: 45/549, 8.2%; Alpha: 18/129, 14%; Delta: 81/507, 16%; and Omicron: 47/1551, 3%; P<.001). Models developed on retrospective data showed that the variable most associated with the administration of inpatient prophylactic anticoagulant was comorbidities prior to SARS-CoV-2 infection. The patients who were administered prophylactic anticoagulant were also more likely to receive supplementary oxygen (57/191, 30% vs 9/188, 5%; P<.001). There was no statistical difference in a new diagnosis of coagulopathy, bleeding, or maternal-fetal health outcomes between those who received treatment and the matched control group.

CONCLUSIONS

Most hospitalized pregnant patients with COVID-19 did not receive prophylactic anticoagulants across health care systems as recommended by guidelines. Guideline-recommended treatment was administered more frequently to patients with greater COVID-19 illness severity. Given the low rate of administration and differences between treated and untreated cohorts, efficacy could not be assessed.

Status of major hemostatic components in the setting of COVID-19: the effect on endothelium, platelets, coagulation factors, fibrinolytic system, and complement

The coagulation, fibrinolytic, anticoagulation, and complement systems are in delicate balance with the vessel wall endothelium ensuring appropriate hemostasis. Coagulopathy in coronavirus disease 2019 (COVID-19) is not a simple disorder of one hemostatic component but a complicated process affecting most of the hemostasis system. COVID-19 disturbs the balance between the procoagulant systems and the regulatory mechanisms. Here, we investigate the effect of COVID-19 on key hemostatic components, including platelets, endothelial cells, coagulation factors, fibrinolytic system, anticoagulant protein system, and complement system, to improve our understanding of the pathophysiological processes underlying COVID-19 coagulopathy based on evidence.

Sex differences in D-dimer and critical illness in patients with COVID-19: A systematic review and meta-analysis

Background

Observed sex differences in COVID-19 outcomes suggest that men are more likely to experience critical illness and mortality. Thrombosis is common in severe COVID-19, and D-dimer is a significant marker for COVID-19 severity and mortality. It is unclear whether D-dimer levels differ between men and women, and the effect of D-dimer levels on disease outcomes remains under investigation.

Objectives

We aimed to evaluate the sex difference in the D-dimer level among hospitalized patients with COVID-19 and the effect of sex and D-dimer level on disease outcomes.

Methods

We meta-analyzed articles reporting D-dimer levels in men and women hospitalized for COVID-19, until October 2021, using random effects. Primary outcomes were mortality, critical illness, and thrombotic complications.

Results

In total, 11,682 patients from 10 studies were analyzed (N = 5606 men (55.7%), N = 5176 women (44.3%)). Men had significantly higher odds of experiencing mortality (odds ratios (OR) = 1.41, 95% CI: [1.25, 1.59], P ≤ .001, I² = 0%) and critical illness (OR = 1.76, 95% CI: [1.43, 2.18], P ≤ .001, I² = 61%). The mean D-dimer level was not significantly different between men and women (MD = 0.08, 95% CI: [-0.23, 0.40], P = .61, I² = 52%). In the subgroup analysis, men had significantly higher odds of experiencing critical illness compared with women in both the "higher" (P = .006) and "lower" (P = .001) D-dimer subgroups.

Conclusion

Men have significantly increased odds of experiencing poor COVID-19 outcomes compared with women. No sex difference was found in the D-dimer level between men and women with COVID-19. The diversity in D-dimer reporting impacts data interpretation and requires further attention.

The Dual Pandemics of COVID-19 and Obesity: Bidirectional Impact

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19 pandemic, has been shown to disrupt many organ systems in the human body. Though several medical disorders have been affected by this infection, a few illnesses in addition may also play a role in determining the outcome of COVID-19. Obesity is one such disease which is not only affected by the occurrence of COVID-19 but can also result in a worse clinical outcome of COVID-19 infection. This manuscript summarizes the most recent evidence supporting the bidirectional impact of COVID-19 and obesity. It highlights how the presence of obesity can be detrimental to the outcome of COVID-19 in a given patient because of the mechanical limitations in lung compliance and also by the activation of several thrombo-inflammatory pathways. The sociodemographic changes brought about by the pandemic in turn have facilitated the already increasing prevalence of obesity. This manuscript highlights the importance of recognizing these pathways which may further help in policy changes that facilitate appropriate measures to prevent the further worsening of these two pandemics.

Symptomatic, clinical and biomarker associations for mortality in hospitalized COVID-19 patients enriched for African Americans

BACKGROUND AND AIMS

Initial reports on US COVID-19 showed different outcomes in different races. In this study we use a diverse large cohort of hospitalized COVID-19 patients to determine predictors of mortality.

METHODS

We analyzed data from hospitalized COVID-19 patients (n = 5852) between March 2020- August 2020 from 8 hospitals across the US. Demographics, comorbidities, symptoms and laboratory data were collected.

RESULTS

The cohort contained 3,662 (61.7%) African Americans (AA), 286 (5%) American Latinx (LAT), 1,407 (23.9%), European Americans (EA), and 93 (1.5%) American Asians (AS). Survivors and non-survivors mean ages in years were 58 and 68 for AA, 58 and 77 for EA, 44 and 61 for LAT, and 51 and 63 for AS. Mortality rates for AA, LAT, EA and AS were 14.8, 7.3, 16.3 and 2.2%. Mortality increased among patients with the following characteristics: age, male gender, New York region, cardiac disease, COPD, diabetes mellitus, hypertension, history of cancer, immunosuppression, elevated lymphocytes, CRP, ferritin, D-Dimer, creatinine, troponin, and procalcitonin. Use of mechanical ventilation (p = 0.001), shortness of breath (SOB) (p < 0.01), fatigue (p = 0.04), diarrhea (p = 0.02), and increased AST (p < 0.01), significantly correlated with death in multivariate analysis. Male sex and EA and AA race/ethnicity had higher frequency of death. Diarrhea was among the most common GI symptom amongst AAs (6.8%). When adjusting for comorbidities, significant variables among the demographics of study population were age (over 45 years old), male sex, EA, and patients hospitalized in New York. When adjusting for disease severity, significant variables were age over 65 years old, male sex, EA as well as having SOB, elevated CRP and D-dimer. Glucocorticoid usage was associated with an increased risk of COVID-19 death in our cohort.

CONCLUSION

Among this large cohort of hospitalized COVID-19 patients enriched for African Americans, our study findings may reflect the extent of systemic organ involvement by SARS-CoV-2 and subsequent progression to multi-system organ failure. High mortality in AA in comparison with LAT is likely related to high frequency of comorbidities and older age among AA. Glucocorticoids should be used carefully considering the poor outcomes associated with it. Special focus in treating patients with elevated liver enzymes and other inflammatory biomarkers such as CRP, troponin, ferritin, procalcitonin, and D-dimer are required to prevent poor outcomes.

Longitudinal Analysis of Biologic Correlates of COVID-19 Resolution: Case Report

While the biomarkers of COVID-19 severity have been thoroughly investigated, the key biological dynamics associated with COVID-19 resolution are still insufficiently understood. We report a case of full resolution of severe COVID-19 due to convalescent plasma transfusion. Following transfusion, the patient showed fever remission, improved respiratory status, and rapidly decreased viral burden in respiratory fluids and SARS-CoV-2 RNAemia. Longitudinal unbiased proteomic analysis of plasma and single-cell transcriptomics of peripheral blood cells conducted prior to and at multiple times after convalescent plasma transfusion identified the key biological processes associated with the transition from severe disease to disease-free state. These included (i) temporally ordered upward and downward changes in plasma proteins reestablishing homeostasis and (ii) post-transfusion disappearance of a subset of monocytes characterized by hyperactivated Interferon responses and decreased TNF-α signaling. Monitoring specific dysfunctional myeloid cell subsets in peripheral blood may provide prognostic keys in COVID-19.

Antibody-Based Affinity Capture Combined with LC-MS Analysis for Identification of COVID-19 Disease Serum Biomarkers

Blood serum or plasma proteins are potentially useful in COVID-19 research as biomarkers for risk prediction, diagnosis, stratification, and treatment monitoring. However, serum protein-based biomarker identification and validation is complicated due to the wide concentration range of these proteins, which spans more than ten orders of magnitude. Here we present a combined affinity purification-liquid chromatography mass spectrometry approach which allows identification and quantitation of the most abundant serum proteins along with the nonspecifically bound and interaction proteins. This led to the reproducible identification of more than 100 proteins that were not specifically targeted by the affinity column. Many of these have already been implicated in COVID-19 disease.

Home pharmacological therapy in early COVID-19 to prevent hospitalization and reduce mortality: Time for a suitable proposal

The COVID‐19 pandemic is a highly dramatic concern for mankind. In Italy, the pandemic exerted its major impact throughout the period of February to June 2020. To date, the awkward amount of more than 134,000 deaths has been reported. Yet, post‐mortem autopsy was performed on a very modest number of patients who died from COVID‐19 infection, leading to a first confirmation of an immune‐thrombosis of the lungs as the major COVID‐19 pathogenesis, likewise for SARS. Since then (June–August 2020), no targeted early therapy considering this pathogenetic issue was approached. The patients treated with early anti‐inflammatory, anti‐platelet, anticoagulant and antibiotic therapy confirmed that COVID‐19 was an endothelial inflammation with immuno‐thrombosis. Patients not treated or scarcely treated with the most proper and appropriate therapy and in the earliest, increased the hospitalization rate in the intensive care units and also mortality, due to immune‐thrombosis from the pulmonary capillary district and alveoli. The disease causes widespread endothelial inflammation, which can induce damage to various organs and systems. Therapy must be targeted in this consideration, and in this review, we demonstrate how early anti‐inflammatory therapy may treat endothelia inflammation and immune‐thrombosis caused by COVID‐19, by using drugs we are going to recommend in this paper.