Importance of the SARS-CoV-2 genome and spike protein in the immunopathogenesis of COVID-19 and in the efficacy of vaccines.

Coronavirus (CoV) infections cause respiratory and enteric diseases with clinical manifestations ranging from faint to severe, even lead to death of patients. High connectivity between nations and infectivity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), represent a global health problem as the coronavirus disease 19 (COVID-19). This CoV-2 that cause SARS, which appeared in Wuhan, China, in December 2019 originated COVID-19 and declared as pandemic a few months posterior its appearance. In this review, the genomic and spike protein characteristics of SARS-CoV-2, the role of SARS-CoV-2 in the COVID-19 pathogenesis, cytokine storm, the role of cytotoxic T and B cells against SARS-CoV-2, as well as the vaccines efficacy (taking into account mutations in the spike protein) are described.

Los coronavirus (CoV) causan enfermedades respiratorias y entéricas leves, graves o críticas, pudiendo ocasionar la muerte del paciente. Debido a la alta conectividad entre naciones y a la transmisión, actualmente la COVID-19 representa un verdadero problema de salud pública en todo el mundo. El CoV-2 causante del síndrome respiratorio agudo grave (SARS-CoV-2) apareció a finales de diciembre de 2019 en Wuhan, China, y en marzo de 2020 la COVID-19 fue declarada pandemia. En esta revisión se describen las características del genoma y de la proteína espiga del SARS-CoV-2, su papel en la inmunopatogénesis de la COVID-19, la tormenta de citocinas, la actividad citotóxica inducida por células T y la producción de anticuerpos contra el SARS-CoV-2 mediada por células B, así como la eficacia de algunas vacunas, tomando en cuenta las mutaciones presentes en la proteína espiga.

Genomic epidemiology of SARS-CoV-2 in Russia reveals recurring cross-border transmission throughout 2020.

In 2020, SARS-CoV-2 has spread rapidly across the globe, with most nations failing to prevent or substantially delay its introduction. While many countries have imposed some limitations on trans-border passenger traffic, the effect of these measures on the global spread of COVID-19 strains remains unclear. Here, we report an analysis of 3206 whole-genome sequences of SARS-CoV-2 samples from 78 regions of Russia covering the period before the spread of variants of concern (between March and November 2020). We describe recurring imports of multiple COVID-19 strains into Russia throughout this period, giving rise to 457 uniquely Russian transmission lineages, as well as repeated cross-border transmissions of local circulating variants out of Russia. While the phylogenetically inferred rate of cross-border transmissions was somewhat reduced during the period of the most stringent border closure, it still remained high, with multiple inferred imports that each led to detectable spread within the country. These results indicate that partial border closure has had little effect on trans-border transmission of variants, which helps explain the rapid global spread of newly arising SARS-CoV-2 variants throughout the pandemic.

Recombinant Human Interleukin-2 Corrects NK Cell Phenotype and Functional Activity in Patients with Post-COVID Syndrome.

Post-COVID syndrome develops in 10-20% of people who have recovered from COVID-19 and it is characterized by impaired function of the nervous, cardiovascular, and immune systems. Previously, it was found that patients who recovered from infection with the SARS-CoV-2 virus had a decrease in the number and functional activity of NK cells. The aim of the study was to assess the effectiveness of recombinant human IL-2 (rhIL-2) administered to correct NK cell phenotype and functional activity in patients with post-COVID syndrome. Patients were examined after 3 months for acute COVID-19 of varying severity. The phenotype of the peripheral blood NK cells was studied by flow cytometry. It was found that disturbances in the cell subset composition in patients with post-COVID syndrome were characterized by low levels of mature (p = 0.001) and cytotoxic NK cells (p = 0.013), with increased release of immature NK cells (p = 0.023). Functional deficiency of NK cells in post-COVID syndrome was characterized by lowered cytotoxic activity due to the decreased count of CD57+ (p = 0.001) and CD8+ (p < 0.001) NK cells. In the treatment of patients with post-COVID syndrome with recombinant IL-2, peripheral blood NK cell count and functional potential were restored. In general, the effectiveness of using rhIL-2 in treatment of post-COVID syndrome has been proven in patients with low levels of NK cells.

Obesity and the Obesity Paradox in Patients with Severe COVID-19 Obesidad y Paradoja de la Obesidad en Pacientes con COVID-19 Severo: Resultados de Dos Cohortes Prospectivas

Objective To test the presence of the obesity paradox in two cohorts of patients hospitalized for COVID-19. Design Two multicenter prospective cohorts. Setting Three fourth level institutions. Patients Adults hospitalized in the general ward for confirmed COVID-19 in the three institutions and those admitted to one of the 9 critical care units of one of the institutions Interventions None Main variables of interest: categorized weight and its relationship with admission to the ICU in hospitalized patients and death in the ICU. Result Of 402 hospitalized patients, 30.1% were obese. Of these, 36.1% were admitted to the ICU vs. 27.1% of non-obese patients. Of the 302 ICU patients, 46.4% were obese. Of these, mortality was 45.0% vs. 52.5% for non-obese. The requirement to transfer hospitalized patients to the ICU admission get a HR of 1.47 (95%CI 0.87-2.51, p = 0.154) in the multivariate analysis. In intensive care patients, an HR of 0.99 (95%CI: 0.92 - 1.07, p = 0.806) was obtained to the association of obesity with mortality. Conclusions The present study does not demonstrate an association between obesity and risk of inpatient transfer to intensive care or death of intensive care patients due to COVID-19 therefore, the presence of an obesity paradox is not confirmed.

ATR-FTIR spectrum analysis of plasma samples for rapid identification of recovered COVID-19 individuals.

The development of fast, cheap and reliable methods to determine seroconversion against infectious agents is of great practical importance. In the context of the COVID-19 pandemic, an important issue is to study the rate of formation of the immune layer in the population of different regions, as well as the study of the formation of post-vaccination immunity in individuals after vaccination. Currently, the main method for this kind of research is enzyme immunoassay (ELISA, enzyme-linked immunosorbent assay). This technique is sufficiently sensitive and specific, but it requires significant time and material costs. We investigated the applicability of attenuated total reflection (ATR) Fourier transform infrared (FTIR) spectroscopy associated with machine learning in blood plasma to detect seroconversion against SARS-CoV-2. The study included samples of 60 patients. Clear spectral differences in plasma samples from recovered COVID-19 patients and conditionally healthy donors were identified using multivariate and statistical analysis. The results showed that ATR-FTIR spectroscopy, combined with principal components analysis (PCA) and linear discriminant analysis (LDA) or artificial neural network (ANN), made it possible to efficiently identify specimens from recovered COVID-19 patients. We built classification models based on PCA associated with LDA and ANN. Our analysis led to 87% accuracy for PCA-LDA model and 91% accuracy for ANN, respectively. Based on this proof-of-concept study, we believe this method could offer a simple, label-free, cost-effective tool for detecting seroconversion against SARS-CoV-2. This approach could be used as an alternative to ELISA.

Cardiac MRI with late gadolinium enhancement shows cardiac involvement 3-6 months after severe acute COVID-19 similar to or worse than PIMS.

Background: Coronavirus disease 2019 (COVID-19) in children is rarely severe. However, severe courses occur, especially in the presence of risk factors. A minority of children develop pediatric inflammatory multisystem syndrome (PIMS) with substantial morbidity. While the importance of cardiac involvement after PIMS is well established, its role after severe acute COVID-19 remains unclear. We aim to compare cardiac sequelae of children after severe acute COVID-19 using cardiac MRI and compare them with patients after PIMS. Methods: For this prospective cohort study, we recruited patients with acute COVID or PIMS in a single center. Clinical follow-up, lab work, ECG, and echocardiography were done within 2 days after disease onset and 3-6 months after discharge. At the last visit 3-6 months later, cardiac MRI (CMR) with late gadolinium enhancement (LGE) was performed to evaluate cardiac sequelae and compare both groups. Results: Data were obtained from n = 14 patients with PIMS and n = 7 patients with severe acute COVID-19. At the start of the respective disease, left ventricular (LV) ejection fraction was reduced in seven patients with PIMS but none in the acute COVID-19 group. Transient mitral valve insufficiency was present in 38% of patients, of whom PIMS accounted for 7/8 cases. Eight patients (38%) with PIMS presented coronary artery abnormalities, with normalization in 7/8 patients. A significant decrease in LV mass index 3-6 months after disease onset was observed in both groups. MRI follow-up revealed non-ischemic myocardial pattern of LGE in 12/21 patients- in all (6/6) after severe acute COVID-19 and in less than half (6/14) after PIMS. Normal body weight-adjusted stroke volumes and end-diastolic volumes were found in 20/21 patients. Conclusions: We show that children suffering from severe acute COVID-19 have a similar, or worse, cardiac risk profile as patients with PIMS. Both patient groups should therefore receive close pediatric cardiac follow-up examinations. Cardiac MRI is the technique of choice, as most patients presented with delayed LGE as a sign of persistent cardiac injury despite normalization of laboratory and echocardiographic findings.

Cardiac MRI with late gadolinium enhancement shows cardiac involvement 3–6 months after severe acute COVID-19 similar to or worse than PIMS

Background Coronavirus disease 2019 (COVID-19) in children is rarely severe. However, severe courses occur, especially in the presence of risk factors. A minority of children develop pediatric inflammatory multisystem syndrome (PIMS) with substantial morbidity. While the importance of cardiac involvement after PIMS is well established, its role after severe acute COVID-19 remains unclear. We aim to compare cardiac sequelae of children after severe acute COVID-19 using cardiac MRI and compare them with patients after PIMS. Methods For this prospective cohort study, we recruited patients with acute COVID or PIMS in a single center. Clinical follow-up, lab work, ECG, and echocardiography were done within 2 days after disease onset and 3–6 months after discharge. At the last visit 3–6 months later, cardiac MRI (CMR) with late gadolinium enhancement (LGE) was performed to evaluate cardiac sequelae and compare both groups. Results Data were obtained from n = 14 patients with PIMS and n = 7 patients with severe acute COVID-19. At the start of the respective disease, left ventricular (LV) ejection fraction was reduced in seven patients with PIMS but none in the acute COVID-19 group. Transient mitral valve insufficiency was present in 38% of patients, of whom PIMS accounted for 7/8 cases. Eight patients (38%) with PIMS presented coronary artery abnormalities, with normalization in 7/8 patients. A significant decrease in LV mass index 3–6 months after disease onset was observed in both groups. MRI follow-up revealed non-ischemic myocardial pattern of LGE in 12/21 patients- in all (6/6) after severe acute COVID-19 and in less than half (6/14) after PIMS. Normal body weight-adjusted stroke volumes and end-diastolic volumes were found in 20/21 patients. Conclusions We show that children suffering from severe acute COVID-19 have a similar, or worse, cardiac risk profile as patients with PIMS. Both patient groups should therefore receive close pediatric cardiac follow-up examinations. Cardiac MRI is the technique of choice, as most patients presented with delayed LGE as a sign of persistent cardiac injury despite normalization of laboratory and echocardiographic findings.

The DataHarmonizer: a tool for faster data harmonization, validation, aggregation and analysis of pathogen genomics contextual information.

Pathogen genomics is a critical tool for public health surveillance, infection control, outbreak investigations as well as research. In order to make use of pathogen genomics data, they must be interpreted using contextual data (metadata). Contextual data include sample metadata, laboratory methods, patient demographics, clinical outcomes and epidemiological information. However, the variability in how contextual information is captured by different authorities and how it is encoded in different databases poses challenges for data interpretation, integration and their use/re-use. The DataHarmonizer is a template-driven spreadsheet application for harmonizing, validating and transforming genomics contextual data into submission-ready formats for public or private repositories. The tool's web browser-based JavaScript environment enables validation and its offline functionality and local installation increases data security. The DataHarmonizer was developed to address the data sharing needs that arose during the COVID-19 pandemic, and was used by members of the Canadian COVID Genomics Network (CanCOGeN) to harmonize SARS-CoV-2 contextual data for national surveillance and for public repository submission. In order to support coordination of international surveillance efforts, we have partnered with the Public Health Alliance for Genomic Epidemiology to also provide a template conforming to its SARS-CoV-2 contextual data specification for use worldwide. Templates are also being developed for One Health and foodborne pathogens. Overall, the DataHarmonizer tool improves the effectiveness and fidelity of contextual data capture as well as its subsequent usability. Harmonization of contextual information across authorities, platforms and systems globally improves interoperability and reusability of data for concerted public health and research initiatives to fight the current pandemic and future public health emergencies. While initially developed for the COVID-19 pandemic, its expansion to other data management applications and pathogens is already underway.

Photodynamic Therapy: A Prospective Therapeutic Approach for Viral Infections and Induced Neoplasia.

The recent COVID-19 pandemic outbreak and arising complications during treatments have highlighted and demonstrated again the evolving ability of microorganisms, especially viral resistance to treatment as they develop into new and strong strains. The search for novel and effective treatments to counter the effects of ever-changing viruses is undergoing. Although it is an approved procedure for treating cancer, photodynamic therapy (PDT) was first used against bacteria and has now shown potential against viruses and certain induced diseases. PDT is a multi-stage process and uses photosensitizing molecules (PSs) that accumulate in diseased tissues and eradicates them after being light-activated in the presence of oxygen. In this review, studies describing viruses and their roles in disrupting cell regulation mechanisms and signaling pathways and facilitating tumorigenesis were described. With the development of innovative "or smart" PSs through the use of nanoparticles and two-photon excitation, among other strategies, PDT can boost immune responses, inactivate viral infections, and eradicate neoplastic cells. Visualization and monitoring of biological processes can be achieved in real-time with nanomedicines and better tissue penetration strategies. After photodynamic inactivation of viruses, signaling pathways seem to be restored but the underlying mechanisms are still to be elucidated. Light-mediated treatments are suitable to manage both oncogenic viral infections and induced neoplasia.

Lineage BA.2 dominated the Omicron SARS-CoV-2 epidemic wave in the Philippines.

The Omicron severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant led to a dramatic global epidemic wave following detection in South Africa in November 2021. The BA.1 Omicron lineage was dominant and responsible for most SARS-CoV-2 outbreaks in countries around the world during December 2021-January 2022, while other Omicron lineages, including BA.2, accounted for the minority of global isolates. Here, we describe the Omicron wave in the Philippines by analysing genomic data. Our results identify the presence of both BA.1 and BA.2 lineages in the Philippines in December 2021, before cases surged in January 2022. We infer that only the BA.2 lineage underwent sustained transmission in the country, with an estimated emergence around 18 November 2021 (95 per cent highest posterior density: 6-28 November), while despite multiple introductions, BA.1 transmission remained limited. These results suggest that the Philippines was one of the earliest areas affected by BA.2 and reiterate the importance of whole genome sequencing for monitoring outbreaks.

Short-Term Effect of SARS-CoV-2 Spike Protein Receptor-Binding Domain-Specific Antibody Induction on Neutrophil-Mediated Immune Response in Mice.

Vaccination protects against COVID-19 via the spike protein receptor-binding domain (RBD)-specific antibody formation, but it also affects the innate immunity. The effects of specific antibody induction on neutrophils that can cause severe respiratory inflammation are important, though not completely investigated. In the present study, using a mouse model mimicking SARS-CoV-2 virus particle inhalation, we investigated neutrophil phenotype and activity alterations in the presence of RBD-specific antibodies. Mice were immunized with RBD and a week after a strong antibody response establishment received 100 nm particles in the RBD solution. Control mice received injections of a phosphate buffer instead of RBD. We show that the application of 100 nm particles in the RBD solution elevates neutrophil recruitment to the blood and the airways of RBD-immunized mice rather than in control mice. Analysis of bone marrow cells of mice with induced RBD-specific antibodies revealed the increased population of CXCR2+CD101+ neutrophils. These neutrophils did not demonstrate an enhanced ability of neutrophil extracellular traps (NETs) formation compared to the neutrophils from control mice. Thus, the induction of RBD-specific antibodies stimulates the activation of mature neutrophils that react to RBD-coated particles without triggering excessive inflammation.

The Impact of Maternal SARS-CoV-2 Infection Next to Pre-Immunization with Gam-COVID-Vac (Sputnik V) Vaccine on the 1-Day-Neonate's Blood Plasma Small Non-Coding RNA Profile: A Pilot Study

The antenatal and postnatal effects of maternal SARS-CoV-2 on the fetus outcomes, especially in the case of maternal pre-vaccination against this infection, are still under investigation. Such effects may be due to placental insufficiency caused by maternal hypoxia and inflammatory response associated with SARS-CoV-2, and/or be a direct cytopathic effect of the virus. In this work, we studied the profile of small non-coding RNAs (sncRNAs) in the blood plasma of a newborn from a mother who had SARS-CoV-2 at the 22nd week of gestation after immunization with Gam-COVID-Vac (Sputnik V). The fetus had ultrasound signs of hypertrophy of the right heart and hydropericardium 4 weeks after infection of the mother with SARS-CoV-2, as well as cysts of the cerebral vascular plexuses by the time of birth. Taking this into account, we compared the sncRNA profile of this newborn on the first postpartum day with that of neonates born to COVID-19-negative women with different perinatal outcomes: severe cardiovascular and/or neurological disorders, or absence of any perinatal complications. According to next-generation sequencing data, we found that the fetus born to a COVID-19-affected mother pre-immunized with Gam-COVID-Vac (Sputnik V) vaccine differs from newborns with severe cardiovascular and/or nervous system abnormalities either in multidirectional changes in circulating sncRNAs or in less pronounced unidirectional changes in the level of sncRNAs relative to control samples. Considering this, it can be concluded that maternal vaccination against SARS-CoV-2 before pregnancy has a protective effect in preventing antenatal development of pathological processes in the cardiovascular and nervous systems of the neonate associated with COVID-19.

COVID-MVP: an interactive visualization for tracking SARS-CoV-2 mutations, variants, and prevalence, enabled by curated functional annotations and portable genomics workflow (preprint)

The SARS-CoV-2 pandemic has reemphasized the importance of genomic epidemiology to track the evolution of the virus, dynamics of epidemics, geographic origins, and the emerging variants. It is vital in understanding the epidemiological spread of the virus on global, national, and local scales. Several analytical (bioinformatics) resources have been developed for molecular surveillance. However, a resource that combines genetic mutations and functional annotations on the impact of these mutations has been lacking in SARS-CoV-2 genomics surveillance. COVID-MVP provides an interactive visualization application that summarizes the mutations and their prevalence in SARS-CoV-2 viral lineages and provides functional annotations from the literature curated in an ongoing effort, Pokay. COVID-MVP is a tool that can be used for routine surveillance including spatio-temporal analyses. We have powered the visualization through a scalable and reproducible genomic analysis workflow nf-ncov-voc wrapped in Nextflow. COVID-MVP allows users to interactively explore data and download summarized surveillance reports. COVID-MVP, Pokay, and nf-ncov-voc are open-source tools available under the Massachusetts Institute of Technology (MIT) and GPL-3.0 licenses. COVID-MVP source code is available at https://github.com/cidgoh/COVID-MVP and an instance is hosted at https://covidmvp.cidgoh.ca.

Lineage BA.2 dominated the Omicron SARS-CoV-2 epidemic wave in the Philippines (preprint)

The Omicron SARS-CoV-2 variant led to a dramatic global epidemic wave following detection in South Africa in November, 2021. The Omicron lineage BA.1 was dominant and responsible for most domestic outbreaks during December 2021-January 2022, whilst other Omicron lineages including BA.2 accounted for the minority of global isolates. Here, we describe the Omicron wave in the Philippines by analysing genomic data. Our results identify the presence of both BA.1 and BA.2 lineages in the Philippines in December 2021, before cases surged in January 2022. We infer that only lineage BA.2 underwent sustained transmission in the country, with an estimated emergence around November 18th, 2021 [95% highest posterior density: November 6-28th], whilst despite multiple introductions BA.1 transmission remained limited. These results suggest the Philippines was one of the earliest areas affected by BA.2, and reiterate the importance of whole-genome sequencing for monitoring outbreaks.

The SARS-CoV-2 receptor-binding domain facilitates neutrophil transepithelial migration and nanoparticle uptake in the mice airways (preprint)

SARS-CoV-2-induced infection is still dangerous. Mouse models are convenient to the investigation of virus-activated immune response mechanisms. However, mice are not proper model organisms to study COVID-19 due to decreased interaction affinity between the SARS-CoV-2 receptor-binding domain (RBD) and mouse angiotensin-converting enzyme 2 (ACE2) compared with human ACE2. In the present study, we propose a mouse model that allows estimating the influence of SARS-CoV-2 on the immune system. To mimic the effects of RBD-ACE2 high-affinity interaction, mice received the ACE2 inhibitor MLN-4760. To simulate virus loading, we applied 100 nm particles suspended in the solution of RBD via the oropharyngeal route to mice. In this model, MLN-4760 application enhanced neutrophil egress from the bone marrow to the bloodstream and RBD attracted neutrophils to the luminal side of the conducting airway epithelium. By contrast, inert 100 nm particles were not potent to stimulate neutrophil recruitment to the conducting airway mucosa. Using this model, and by altering the dosage of the ACE2 inhibitor, nanoparticles, and RBD, one can adapt it to investigate different COVID-19 states characterized with mild or severe airway inflammation.

Am I Being Bullied on Social Media? An Ensemble Approach to Categorize Cyberbullying

People can easily reveal their aggressive remarks on social media platforms using the anonymity it provides. During the COVID-19 pandemic, the usage of social media has been increased several times according to surveys and people are vulnerable to cyber attacks now more than ever. Prevention of cyberbullying needs careful monitoring and identification. Most of the existing works on cyberbullying detection employed traditional machine learning classifiers with handcrafted fea-tures, and deep learning-based models have made their way in this domain very recently. Categorizing cyberbullying based on traits is a complex task and needs contextual consideration. In this work, we have proposed a new approach to detect cyberbullying on social media platforms using a neural ensemble method of transformer-based architectures with attention mechanism. Our proposed architecture is trained on one balanced and one imbalanced dataset and outperforms the given ML and DNN baselines by a significant margin in both cases. We achieved an average F1-score of 95.59% for five classes and 90.65% for six classes on the Fine-Grained Cyberbullying Dataset (FGCD), and 87.28% on Twitter parsed dataset. Our in-depth results provide great insights into the effectiveness of transformer-based models in cyberbullying detection and paves the way for future researches to combat this serious online issue. We have released our models and code.1 © 2021 IEEE.

COVID-19: Generalities and kidney disease. Review article

Introduction: COVID-19 infection is the current pandemic that is lurking in the world, knowing its behavior is essential to face it in the most effective way. The objective of this study is to carry out a literature review Material and methods: an exhaustive search of the COVID-19 topic is made from its pathophysiology, replication, through its clinical picture, treatment and prognosis. Similarly, the renal behavior associated with this infection is addressed. Results: after SARS in 2002 and MERS in 2012, there is previous experience with coronaviruses in all areas, knowing that this can and will surely have its peculiarities. A review is shown regarding the topic and also its behavior in kidney diseases Conclusions: there is still a lot to know about the current pandemic, but the experience generated in previous ones by coronavirus should help us to understand a bit the current one. © 2021 Academia de Ciencias Médicas de Bilbao. All rights reserved.

Development of a Promising Method for Producing Oligomeric Mixture of Branched Alkylene Guanidines to Improve Substance Quality and Evaluate Their Antiviral Activity against SARS-CoV-2.

This paper reports the synthesis of branched alkylene guanidines using microfluidic technologies. We describe the preparation of guanidine derivatives at lower temperatures, and with significantly less time than that required in the previously applicable method. Furthermore, the use of microfluidics allows the attainment of high-purity products with a low residual monomer content, which can expand the range of applications of this class of compounds. For all the samples obtained, the molecular-weight characteristics are calculated, based on which the optimal condensation conditions are established. Additionally, in this work, the antiviral activity of the alkylene guanidine salt against the SARS-CoV-2 virus is confirmed.