Hybrid Immunization In COVID-19: Time Matters (preprint)

Purpose: SARS-CoV-2 reinfections have been frequent, even among those vaccinated. The aim of this study is to know if hybrid immunity (infection+vaccination) is affected by the moment of vaccination and the number of doses received. Methods: We conducted a retrospective study in 745 patients with a history of COVID-19 reinfection and recovered the dates of infection and reinfection and vaccination status (date and number of doses). To assess differences in the time to reinfection(tRI) between unvaccinated, vaccinated before 6 months and later, and comparing one, two or three doses(incomplete, complete and booster regime) we performed  the log-rank test of the cumulative incidence calculated as 1 minus the Kaplan-Meier estimator. Results: The tRI was significantly higher in those vaccinated vs. non-vaccinated (q<0.001). However, an early incomplete regime(1 dose) protects similar time than not receiving a vaccine. Vaccination before 6 months after infection showed a lower tRI compared to those vaccinated later with the same regime(q<0.001). Actually, early vaccination with complete(2 doses) and booster regimes(3 doses) provided lower length of protection compared to vaccinating later with incomplete(1 dose) and complete regime(2 doses), respectively.  Vaccination with complete and booster regimes significantly increases the tRI(q<0.001). Conclusion: Vaccination increases the time it takes for a person to become reinfected with SARS-CoV-2. Increasing the time from infection to vaccination increases the time in which a person could be reinfected. Booster doses increase the time to reinfection. Those results emphasize the role of vaccines and boosters during the pandemic and can guide strategies on future vaccination policy.

A Differential Therapeutic consideration for use of Corticosteroids according to Established COVID-19 Clinical Phenotypes in Critically ill Patients.

OBJECTIVE: To determine if the use of corticosteroids was associated with Intensive Care Unit (ICU) mortality among whole population and pre-specified clinical phenotypes. DESIGN: A secondary analysis derived from multicenter, observational studySetting: Critical Care UnitsPatients: Adult critically ill patients with confirmed COVID-19 disease admitted to 63 ICUs in Spain. INTERVENTIONS: corticosteroids vs no corticosteroidsMain variables of interest: Three phenotypes were derived by non-supervised clustering analysis from whole population and classified as (A: severe, B: critical and C: life-threatening). We performed a Multivariate analysis after propensity optimal full matching (PS) for whole population and weighted Cox regression (HR) 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. No effect of corticosteroids on ICU mortality was observed when HR was performed (0.72[0.49-1.05]). Finally, 535/857(62.4%) patients in "C" phenotype received corticosteroids. In this phenotype HR (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 dose. Only patients with the highest inflammatory levels could benefit from steroid treatment.

Adaptation of practical classes of clinical subjects in the COVID-19 era

Abstract Pharmaceutical Care is a subject within the Pharmacy Degree that is taught using theoretical and practical classes. When COVID-19 appeared, Faculty of Pharmacy had to change its way of teaching and learning to online classes. Our aim is to assess the impact of COVID-19 situation on practical classes in Pharmaceutical Care. A prospective study was performed by undergraduate students from Pharmaceutical Care subject. Students attended to 2-day practical classes and were assessed through an evaluative workbook. Undergraduate students (n=390) obtained a score of 8.4±0.8 in practical classes, being higher in face-to-face sessions than online sessions, but not significant differences among both methodologies. The higher score was for the session of minor ailment services (9.3±1.3) and the lower for Personalized Medication Dosage (7.0±1.6) and similar in both scenarios. 59% of students obtained more than 8 score in the global punctuation, being higher in in-face-to-face practical classes. This study showed that learning in health care can be guided and evaluated through an online method. Adapt to new technologies, prevent vulnerable students from being left behind, as well as working on cross-cutting skills at a distance, are some of the challenges of higher education in times of COVID-19.

Elevated plasma Complement Factor H Regulating Protein 5 is associated with venous thromboembolism and COVID-19 severity (preprint)

Venous thromboembolism (VTE), comprising both deep vein thrombosis (DVT) and pulmonary embolism (PE) is a common, multi-causal disease with potentially serious short- and long-term complications. In clinical practice, there is a need for improved plasma biomarker-based tools for VTE diagnosis and risk prediction. We used multiplex proteomics profiling to screen plasma from patients with suspected acute VTE, and a case-control study of patients followed up after ending anticoagulant treatment for a first VTE. With replication in 5 independent studies, together totalling 1137 patients and 1272 controls, we identify Complement Factor H Related Protein (CFHR5), a regulator of the alternative pathway of complement activation, as a novel VTE associated plasma biomarker. Using GWAS analysis of 2967 individuals we identified a genome-wide significant pQTL signal on chr1q31.3 associated with CFHR5 levels. We showed that higher CFHR5 levels are associated with increased thrombin generation in patient plasma and that recombinant CFHR5 enhances platelet activation in vitro. Thrombotic complications are a frequent feature of COVID-19; in hospitalised patients we found CFHR5 levels at baseline were associated with short-time prognosis of disease severity, defined as maximum level of respiratory support needed during hospital stay. Our results indicate a clinically important role for regulation of the alternative pathway of complement activation in the pathogenesis of VTE and pulmonary complications in acute COVID-19. Thus, CFHR5 is a potential diagnostic and/or risk predictive plasma biomarker reflecting underlying pathology in VTE and acute COVID-19.

Chatbot, as Educational and Inclusive Tool for People with Intellectual Disabilities

In the current health crisis due to COVID-19, people with intellectual disabilities have especially suffered. The development of their social abilities has been restricted, first with the lockdown and then with the current limitation of social life. They have lost some of these abilities or are having difficulty practicing them. CapacitaBOT, our use case, is a mobile application based on a chatbot, which allows people with intellectual disabilities to work and train their social skills. A chatbot is a software tool that allows to maintain a conversation in automatic way between the user and the machine, the mobile application. CapacitaBOT can be considered by its features, an educational ICT tool that introduces innovation, inclusion and quality in order to be integrated into education for people with intellectual disabilities. The tool trains these people for real-life situations and can also be considered a resource that allows the application of active methodologies since it makes easy the learning of social skills. In addition, all the contributions of the tool are aligned with the objectives of sustainable development because it is a tool that facilities the accessibility of people with disabilities, who more than ever have been affected by social isolation caused by the COVID-19 crisis.

High efficacy of therapeutic equine hyperimmune antibodies against SARS CoV-2 variants of concern (preprint)

SARS-CoV-2 variants of concern (VoC) show reduced neutralization by vaccine-induced and therapeutic monoclonal antibodies. We tested therapeutic equine polyclonal antibodies (pAbs) against four VoC (alpha, beta, epsilon and gamma). We show that equine pAbs efficiently neutralize VoC, suggesting they are an effective, broad coverage, low-cost and a scalable COVID-19 treatment.

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. 

Development and pre-clinical characterization of two therapeutic equine formulations towards SARS-CoV-2 proteins for the potential treatment of COVID-19 (preprint)

In the current global emergency due to SARS-CoV-2 outbreak, passive immunotherapy emerges as a promising treatment for COVID-19. Among animal-derived products, equine formulations are still the cornerstone therapy for treating envenomations due to animal bites and stings. Therefore, drawing upon decades of experience in manufacturing snake antivenom, we developed and preclinically evaluated two anti-SARS-CoV-2 polyclonal equine formulations as potential alternative therapy for COVID-19. We immunized two groups of horses with either S1 (anti-S1) or a mixture of S1, N, and SEM mosaic (anti-Mix) viral recombinant proteins. Horses reached a maximum anti-viral antibody level at 7 weeks following priming, and showed no major adverse acute or chronic clinical alterations. Two whole-IgG formulations were prepared via hyperimmune plasma precipitation with caprylic acid and then formulated for parenteral use. Both preparations had similar physicochemical and microbiological quality and showed ELISA immunoreactivity towards S1 protein and the receptor binding domain (RBD). The anti-Mix formulation also presented immunoreactivity against N protein. Due to high anti-S1 and anti-RBD antibody content, final products exhibited high in vitro neutralizing capacity of SARS-CoV-2 infection, 80 times higher than a pool of human convalescent plasma. Pre-clinical quality profiles were similar among both products, but clinical efficacy and safety must be tested in clinical trials. The technological strategy we describe here can be adapted by other producers, particularly in low- and middle-income countries.

A novel viral protein translation mechanism reveals mitochondria as a target for antiviral drug development (preprint)

The ongoing Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) pandemic has acutely highlighted the need to identify new treatment strategies for viral infections. Here we present a pivotal molecular mechanism of viral protein translation that relies on the mitochondrial translation machinery. We found that rare codons such as Leu-TTA are highly enriched in many viruses, including SARS-CoV-2, and these codons are essential for the regulation of viral protein expression. SARS-CoV-2 controls the translation of its spike gene by hijacking host mitochondria through 5' leader and 3'UTR sequences that contain mitochondrial localization signals and activate the EGR1 pathway. Mitochondrial-targeted drugs such as lonidamine and polydatin significantly repress rare codon-driven gene expression and viral replication. This study identifies an unreported viral protein translation mechanism and opens up a novel avenue for developing antiviral drugs.

On Classification and Taxonomy of Coronaviruses (Riboviria, Nidovirales, Coronaviridae) with the special focus on severe acute respiratory syndrome-related coronavirus 2 (SARS-Cov-2) (preprint)

Coronaviruses are highly pathogenic and therefore important human and veterinary pathogens viruses worldwide. Members of family Coronaviridae have previously been analysed phylogenetically, resulting in proposals of virus interrelationships. However, available Coronavirus phylogenies remain unrooted, based on limited sampling, and normally depend on a single method. The main subjects of this study are the taxonomy and systematics of coronaviruses and our goal is to build the first natural classification of Coronaviridae using several methods of cladistic analyses, Maximum Likelihood method, as well as rigorous taxonomic sampling, making the most accurate representation of Coronaviridae s relationships to date. Nomenclature recommendations to help effectively incorporate principles of binary nomenclature into Coronaviridae taxonomy are provided. We have stressed that no member of Sarbecovirus clade is an ancestor of SARS Cov 2, and humans are the only known host.

COVID-19: Variant screening, an important step towards precision epidemiology (preprint)

Precision epidemiology using genomic technologies allows for a more targeted approach to COVID-19 control and treatment at individual and population level, and is the urgent need of the day. It enables identification of patients who may be at higher risk than others to COVID-19-related mortality, due to their genetic architecture, or who might respond better to a COVID-19 treatment. The COVID-19 virus, similar to SARS-CoV, uses the ACE2 receptor for cell entry and employs the cellular serine protease TMPRSS2 for viral S protein priming. This study aspires to present a multi-omics view of how variations in the ACE2 and TMPRSS2 genes affect COVID-19 infection and disease progression in affected individuals. It reports, for both genes, several variant and gene expression analysis findings, through (i) comparison analysis over single nucleotide polymorphisms (SNPs), that may account for the difference of COVID-19 manifestations among global sub-populations; (ii) calculating prevalence of structural variations (copy number variations (CNVs) / insertions), amongst populations; and (iii) studying expression patterns stratified by gender and age, over all human tissues. This work is a good first step to be followed by additional studies and functional assays towards informed treatment decisions and improved control of the infection rate.

An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants (preprint)

The spike S of SARS-CoV-2 recognizes ACE2 on the host cell membrane to initiate entry. Soluble decoy receptors, in which the ACE2 ectodomain is engineered to block S with high affinity, potently neutralize infection and, due to close similarity with the natural receptor, hold out the promise of being broadly active against virus variants without opportunity for escape. Here, we directly test this hypothesis. We find an engineered decoy receptor, sACE22.v2.4, tightly binds S of SARS-associated viruses from humans and bats, despite the ACE2-binding surface being a region of high diversity. Saturation mutagenesis of the receptor-binding domain followed by in vitro selection, with wild type ACE2 and the engineered decoy competing for binding sites, failed to find S mutants that discriminate in favor of the wild type receptor. We conclude that resistance to engineered decoys will be rare and that decoys may be active against future outbreaks of SARS-associated betacoronaviruses.

Single cell resolution of SARS-CoV-2 tropism, antiviral responses, and susceptibility to therapies in primary human airway epithelium (preprint)

The human airway epithelium is the initial site of SARS-CoV-2 infection. We used flow cytometry and single cell RNA-Sequencing to understand how the heterogeneity of this diverse cell population contributes to elements of viral tropism and pathogenesis, antiviral immunity, and treatment response to remdesivir. We found that, while a variety of cell types are susceptible to infection, ciliated cells are a predominant cell target for SARS-CoV-2. Remdesivir treatment effectively inhibited viral replication across cell types, and blunted hyperinflammatory responses. We also found that heavily infected epithelial cells demonstrate impaired IFN signaling and express abundant IL-6, a potential mediator of COVID-19 pathogenesis.

An In-Silico Analysis of Drugs Potentially Modulating the Cytokine Storm Triggered by SARS-CoV-2 Infection (preprint)

The ongoing COVID-19 pandemic is one of the biggest health and societal challenges of the recent decades. Among the causes of mortality triggered by SARS-CoV-2 infection, the presence of an inflammatory "cytokine storm" (CS) at later stages of the disease has been found to play a determinant role. Here, we used available transcriptomic data from the bronchoalveolar lavage fluid (BALF) of COVID-19 patients suffering from a CS to obtain gene-signatures associated to this pathological process. Using these signatures, we interrogated the Connectivity MAP (CMap) dataset that contains the effects of over 5,000 small molecules on the transcriptome of human cancer cell lines, and looked for molecules which effects on transcription mimic or oppose those associated to the CS. Consistent with their medical use, this analysis found a significant enrichment of glucocorticoids or inhibitors of the Janus Kinases (JAK) as drugs that could revert the CS. On the other hand, molecules that potentiate the immune response such as PKC activators are predicted to worsen the CS. Besides these expected findings, our analysis also reveals a potential effect of the antibiotic doxycycline or MAPK/RAF/MEK inhibitors in reverting the CS, or of topoisomerase inhibitors and the anti-alcohol abuse drug disulfiram in potentiating its effects. Finally, our analyses support that the gender-related differences in the severity of COVID-19 are related to the anti-inflammatory properties of female hormones. While acknowledging that this is an analysis based on limited available data, we decided to share it as a resource that might help others in the selection of drugs that could be tested in the context of experimental models of CS triggered by viral infections.

Managing Soils for Recovering from the COVID-19 Pandemic

The COVID-19 pandemic has disrupted the global food supply chain and exacerbated the problem of food and nutritional insecurity.