Multiple early factors anticipate post-acute COVID-19 sequelae

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Computer modeling of a potential agent against SARS-Cov-2 (COVID-19) protease

We have modeled modifications of a known ligand to the SARS-CoV-2 (COVID-19) protease, that can form a covalent adduct, plus additional ligand-protein hydrogen bonds.     

A blood atlas of COVID-19 defines hallmarks of disease severity and specificity

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Integrated analysis of multimodal single-cell data

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Sex differences in immune responses to SARS-CoV-2 in patients with COVID-19

Millions of people infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been diagnosed with coronavirus infectious disease 2019 (COVID-19). The prevalence and severity of COVID-19 differ between sexes. To explain these differences, we analyzed clinical features and laboratory values in male and female COVID-19 patients. The present study included a cohort of 111 people, i.e. 36 COVID-19 patients, 54 sex- and age-matched common viral community-acquired pneumonia (CAP) patients, and 21 healthy controls. Monocyte counts, lymphocyte subset counts, and alanine aminotransferase (ALT), aspartate aminotransferase (AST), and C-reactive protein (CRP) levels in the peripheral blood were analyzed. Higher Acute Physiology and Chronic Health Evaluation II (APACHE II) scores, monocyte counts, and CRP and ALT levels were found in male COVID-19 patients. Decreased lymphocyte subset counts and proportions were observed in COVID-19 patients, except for the CD3⁺ and CD8⁺ T cell proportions. The lower CD4⁺ T cell proportions and higher CD8⁺ T cell proportions were observed in male and severe COVID-19 patients and the differences were independent of estrogen level. The CD4⁺ T cell proportion was negatively associated with the CD8⁺ T cell proportion in male COVID-19 patients; this correlation was non-significant in females. Our work demonstrates differences between sexes in circulating monocyte counts and CD4⁺ T cell and CD8⁺ T cell proportions in COVID-19 patients, independent of estrogen levels, are associated with the clinical manifestations in COVID-19 patients with high specificity.     

Humoral and cellular immune memory to four COVID-19 vaccines

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Transient plasma cell dyscrasia in COVID-19 patients linked to IL-6 triggering

An unusual clonal gammopathy was reported in COVID-19 patient but whether this anomaly is related or not to the disease has not yet been clarified. To this aim, we selected a cohort of 35 COVID-19 patients swab positive and investigated serological levels of IL-6, immune response to major viral antigens and electrophoretic profile. Elevated levels of IL-6 were accompanied by a significative humoral response to viral Spike protein, revealing an altered electrophoretic profile in the gamma region. We can conclude that elevated levels of IL-6 triggers humoral response inducing a transient plasma cell dyscrasia in severe COVID-19 patients.     

Functional SARS-CoV-2-Specific Immune Memory Persists after Mild COVID-19

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Does the compromised sleep and circadian disruption of night and shiftworkers make them highly vulnerable to 2019 coronavirus disease (COVID-19)?

ABSTRACT

Rotating and permanent night shiftwork schedules typically result in acute and sometimes chronic sleep deprivation plus acute and sometimes chronic disruption of the circadian time structure. Immune system processes and functionalities are organized as circadian rhythms, and they are also strongly influenced by sleep status. Sleep is a vital behavioral state of living beings and a modulator of immune function and responsiveness. Shiftworkers show increased risk for developing viral infections due to possible compromise of both innate and acquired immunity responses. Short sleep and sleep loss, common consequences of shiftwork, are associated with altered integrity of the immune system. We discuss the possible excess risk for COVID-19 infection in the context of the common conditions among shiftworkers, including nurses, doctors, and first responders, among others of high exposure to the contagion, of sleep imbalance and circadian disruption.     

The immune landscape in tuberculosis reveals populations linked to disease and latency

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Cytokine storm in COVID-19: from viral infection to immune responses,diagnosis and therapy

The COVID-19 outbreak is emerging as a significant public health challenge. Excessive production of proinflammatory cytokines, also known as cytokine storm, is a severe clinical syndrome known to develop as a complication of infectious or inflammatory diseases. Clinical evidence suggests that the occurrence of cytokine storm in severe acute respiratory syndrome secondary to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is closely associated with the rapid deterioration and high mortality of severe cases. In this review, we aim to summarize the mechanism of SARS-CoV-2 infection and the subsequent immunological events related to excessive cytokine production and inflammatory responses associated with ACE2-AngII signaling. An overview of the diagnosis and an update on current therapeutic regimens and vaccinations is also provided.     

COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas

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Immunoinformatic analysis of the SARS-CoV-2 envelope protein as a strategy to assess cross-protection against COVID-19

Envelope protein of coronaviruses is a structural protein existing in both monomeric and homo-pentameric form. It has been related to a multitude of roles including virus infection, replication, dissemination and immune response stimulation. In the present study, we employed an immunoinformatic approach to investigate the major immunogenic domains of the SARS-CoV-2 envelope protein and map them among the homologue proteins of coronaviruses with tropism for animal species that are closely inter-related with the human beings population all over the world. Also, when not available, we predicted the envelope protein structural folding and mapped SARS-CoV-2 epitopes. Envelope sequences alignment provides evidence of high sequence homology for some of the investigated virus specimens; while the structural mapping of epitopes resulted in the interesting maintenance of the structural folding and epitope sequence localization also in the envelope proteins scoring a lower alignment score. In line with the One-Health approach, our evidences provide a molecular structural rationale for a potential role of taxonomically related coronaviruses in conferring protection from SARS-CoV-2 infection and identifying potential candidates for the development of diagnostic tools and prophylactic-oriented strategies.     

Mesenchymal stromal cell delivery as a potential therapeutic strategy against COVID-19: Promising evidence from in vitro results

BACKGROUNDSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the coronavirus disease 2019 (COVID-19) pandemic, which was initiated in December 2019. COVID-19 is characterized by a low mortality rate (< 6%); however, this percentage is higher in elderly people and patients with underlying disorders. COVID-19 is characterized by mild to severe outcomes. Currently, several therapeutic strategies are evaluated, such as the use of anti-viral drugs, prophylactic treatment, monoclonal antibodies, and vaccination. Advanced cellular therapies are also investigated, thus representing an additional therapeutic tool for clinicians. Mesenchymal stromal cells (MSCs), which are known for their immunoregulatory properties, may halt the induced cytokine release syndrome mediated by SARS-CoV-2, and can be considered as a potential stem cell therapy.AIMTo evaluate the immunoregulatory properties of MSCs, upon stimulation with COVID-19 patient serum. METHODSMSCs derived from the human Wharton’s Jelly (WJ) tissue and bone marrow (BM) were isolated, cryopreserved, expanded, and defined according to the criteria outlined by the International Society for Cellular Therapies. Then, WJ and BM-MSCs were stimulated with a culture medium containing 15% COVID-19 patient serum, 1% penicillin-streptomycin, and 1% L-glutamine for 48 h. The quantification of interleukin (IL)-1 receptor a (Ra), IL-6, IL-10, IL-13, transforming growth factor (TGF)-β1, vascular endothelial growth factor (VEGF)-a, fibroblast growth factor (FGF), platelet-derived growth factor (PDGF), and indoleamine-2,3-dioxygenase (IDO) was performed using commercial ELISA kits. The expression of HLA-G1, G5, and G7 was evaluated in unstimulated and stimulated WJ and BM-MSCs. Finally, the interactions between MSCs and patients’ macrophages were established using co-culture experiments.RESULTSThawed WJ and BM-MSCs exhibited a spindle-shaped morphology, successfully differentiated to “osteocytes”, “adipocytes”, and “chondrocytes”, and in flow cytometric analysis were characterized by positivity for CD73, CD90, and CD105 (> 95%) and negativity for CD34, CD45, and HLA-DR (< 2%). Moreover, stimulated WJ and BM-MSCs were characterized by increased cytoplasmic granulation, in comparison to unstimulated cells. The HLA-G isoforms (G1, G5, and G7) were successfully expressed by the unstimulated and stimulated WJ-MSCs. On the other hand, only weak expression of HLA-G1 was identified in BM-MSCs. Stimulated MSCs secreted high levels of IL-1Ra, IL-6, IL-10, IL-13, TGF-β1, FGF, VEGF, PDGF, and IDO in comparison to unstimulated cells (P < 0.05) after 12 and 24 h. Finally, macrophages derived from COVID-19 patients successfully adapted the M2 phenotype after co-culturing with stimulated WJ and BM-MSCs.CONCLUSIONWJ and BM-MSCs successfully produced high levels of immunoregulatory agents, which may efficiently modulate the over-activated immune responses of critically ill COVID-19 patients.     

Low serum calcium: a new,important indicator of COVID-19 patients from mild/moderate to severe/critical

Background: Coronavirus disease 2019 (COVID-19) virus is still spreading, finding out the initial hits of viral infection is important to minimize the mild/moderate population, prevent disease aggravation and organs dysfunction.Objective: We investigated COVID-19 patients with different serum calcium levels.Design: We checked the serum calcium level of the patients based on days after symptom onset as well as the severity of COVID-19. We also checked multiorgan injuries and immune cytokines level in their blood.Results: Both mild/moderate and severe critical cases we observed showed low calcium level in the early stage of viral infection, while the severe/critical cases showed significant lower calcium level than mild/moderate cases in the early stage. We also found that low calcium level related to severe/critical multiorgan injuries especially in the mild/moderate population. Proinflammatory cytokine IL-6 also correlated to calcium change in both mild/moderate and severe/critical cases.Conclusions: Our finding indicates that calcium balance is a primal hit of COVID-19 and a biomarker of clinical severity at the beginning of symptom onset. Calcium is closely associated with virus-associated multiple organ injuries and the increase in inflammatory cytokines. Our results provide a new, important indicator of COVID-19 patients from mild/moderate to severe/critical: serum calcium.     

Zinc levels of patients with a moderate to severe COVID-19 infection at hospital admission and after 4th days of ward hospitalization and their clinical outcome

BackgroundPrevious studies associate the disturbance of the Zinc (Zn) status with the severity of the disease and the inflammatory process in the critically ill patient. This decrease in Zn concentrations is an indicator of poor prognosis. Our aim was to evaluate Zn levels at admission and after four days, and to study if lower Zn levels at those days were related to a worse clinical outcome.Material and methodsObservational cohort study at a tertiary Hospital. Recruitment period: 09/04/2020–04/24/2021. Clinical information on hypertension, diabetes mellitus (DM), chronic obstructive pulmonary disease (COPD), or bronchial asthma was collected. Obesity was defined as BMI ≥ 30 Kg/m2. Blood extraction was performed at admission and after 4 days. Zn was measured by atomic absorption using a flame method. Worse clinical outcome was defined as death during admission, intensive critical care unit admission or receiving supplemental oxygen through noninvasive or invasive ventilator care.Results129 subjects were invited to participate but only 100 subjects completed the survey. According to ROC curve [AUC= 0.63 (95% CI 0.60–0.66)], Zn < 79 μg/dL showed the best performance to detect a worse outcome (Sn=0.85; Sp=0.36). Patients with Zn < 79 μg/dL were older (70 vs 61 y; p = 0.002) with no differences by sex. Most patients presented with fever, dysthermic symptoms and cough, without differences between groups. Pre-existing comorbid conditions did not differ significantly between groups. Less obese subjects were found in the Zn < 79 μg/dL group (21.4 vs 43.3%, p = 0.025). In the univariate analysis, Zn < 79 μg/dL at hospital admission was related to a worse outcome (p = 0.044), but after adjusting for age, C-reactive protein, and obesity there was no difference, but a tendency towards a worse prognosis [OR 2.20 (0.63–7.70), p = 0.215]. Zn levels increased in both groups after 4 days (66.6 vs 73.1 μg/dL at admission, and 72.2 vs 80.5 μg/dL at 4th day), with ns. difference (p = 0.214).ConclusionZn < 79 μg/dL at admission for a moderate to severe COVID-19 infection could be related to a worse outcome, although after adjustment for age, C-reactive protein levels and obesity, this Zn level threshold did not show statistically significant difference in the composite end point, but a tendency towards a worse prognosis. In addition, patients with the best clinical evolution showed higher serum Zn levels at 4th day after hospital admission than the patients with a worse prognosis.     

Improved binding of SARS-CoV-2 Envelope protein to tight junction-associated PALS1 could play a key role in COVID-19 pathogenesis

The Envelope (E) protein of SARS-CoV-2 is the most enigmatic protein among the four structural ones. Most of its current knowledge is based on the direct comparison to the SARS E protein, initially mistakenly undervalued and subsequently proved to be a key factor in the ER-Golgi localization and in tight junction disruption.We compared the genomic sequences of E protein of SARS-CoV-2, SARS-CoV and the closely related genomes of bats and pangolins obtained from the GISAID and GenBank databases. When compared to the known SARS E protein, we observed a significant difference in amino acid sequence in the C-terminal end of SARS-CoV-2 E protein.Subsequently, in silico modelling analyses of E proteins conformation and docking provide evidences of a strengthened binding of SARS-CoV-2 E protein with the tight junction-associated PALS1 protein. Based on our computational evidences and on data related to SARS-CoV, we believe that SARS-CoV-2 E protein interferes more stably with PALS1 leading to an enhanced epithelial barrier disruption, amplifying the inflammatory processes, and promoting tissue remodelling. These findings raise a warning on the underestimated role of the E protein in the pathogenic mechanism and open the route to detailed experimental investigations.     

Development of a T cell-based immunodiagnostic system to effectively distinguish SARS-CoV-2 infection and COVID-19 vaccination status

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Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4+ T cell immunity

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Enhancing estimation methods for integrating probability and nonprobability survey samples with machine-learning techniques. An application to a Survey on the impact of the COVID-19 pandemic in Spain

Web surveys have replaced Face-to-Face and computer assisted telephone interviewing (CATI) as the main mode of data collection in most countries. This trend was reinforced as a consequence of COVID-19 pandemic-related restrictions. However, this mode still faces significant limitations in obtaining probability-based samples of the general population. For this reason, most web surveys rely on nonprobability survey designs. Whereas probability-based designs continue to be the gold standard in survey sampling, nonprobability web surveys may still prove useful in some situations. For instance, when small subpopulations are the group under study and probability sampling is unlikely to meet sample size requirements, complementing a small probability sample with a larger nonprobability one may improve the efficiency of the estimates. Nonprobability samples may also be designed as a mean for compensating for known biases in probability-based web survey samples by purposely targeting respondent profiles that tend to be underrepresented in these surveys. This is the case in the Survey on the impact of the COVID-19 pandemic in Spain (ESPACOV) that motivates this paper. In this paper, we propose a methodology for combining probability and nonprobability web-based survey samples with the help of machine-learning techniques. We then assess the efficiency of the resulting estimates by comparing them with other strategies that have been used before. Our simulation study and the application of the proposed estimation method to the second wave of the ESPACOV Survey allow us to conclude that this is the best option for reducing the biases observed in our data.