How SARS-CoV-2 (COVID-19) spreads within infected hosts - what we know so far

Comprehensive proteomic analysis of HCoV-OC43 virions and virus-modulated extracellular vesicles

Viruses are obligate parasites that depend on the cellular machinery for their propagation. Several viruses also incorporate cellular proteins that facilitate viral spread. Defining these cellular proteins is critical to decipher viral life cycles and delineate novel therapeutic strategies. While numerous studies have explored the importance of host proteins in coronavirus spread, information about their presence in mature virions is limited. In this study, we developed a protocol to highly enrich mature HCoV-OC43 virions and characterize them by proteomics. Recognizing that cells release extracellular vesicles whose content is modulated by viruses, and given our ability to separate virions from these vesicles, we also analyzed their protein content in both uninfected and infected cells. We uncovered 69 unique cellular proteins associated with virions including 31 high-confidence hits. These proteins primarily regulate RNA metabolism, enzymatic activities, vesicular transport, cell adhesion, metabolite interconversion, and translation. We further discovered that the virus had a profound impact on exosome composition, incorporating 47 novel cellular proteins (11 high confidence) and excluding 92 others (61 high confidence) in virus-associated extracellular vesicles compared to uninfected cells. Moreover, a dsiRNA screen revealed that 11 of 18 select targets significantly impacted viral yields, including proteins found in virions or extracellular vesicles. Overall, this study provides new and important insights into the incorporation of numerous host proteins into HCoV-OC43 virions, their biological significance, and the ability of the virus to modulate extracellular vesicles.

IMPORTANCE

In recent years, coronaviruses have dominated global attention, making it crucial to develop methods to control them and prevent future pandemics. Besides viral proteins, host proteins play a significant role in viral propagation and offer potential therapeutic targets. Targeting host proteins is advantageous because they are less likely to mutate and develop resistance compared to viral proteins, a common issue with many antiviral treatments. In this study, we examined the protein content of the less virulent biosafety level 2 HCoV-OC43 virus as a stand-in for the more virulent SARS-CoV-2. Our findings reveal that several cellular proteins incorporated into the virion regulate viral spread. In addition, we report that the virus extensively modulates the content of extracellular vesicles, enhancing viral dissemination. This underscores the critical interplay between the virus, host proteins, and extracellular vesicles.

Were metabolic and other chronic diseases the driven onset epidemic forces of COVID-19 in Mexico?

The underline hypothesis of this study was that SARS-CoV-2 can infect individuals regardless of health condition, sex, and age in opposition to the classical epidemiological assumption of an identifiable susceptible subpopulation for epidemic development. To address this issue, a population cohort with 24.4 million metadata associated with 226,089 official RT-qPCR positive and 283,450 negative cases, including 27,769 deceased, linked putatively to B.1. and B.1.1. SARS-CoV-2 lineages were analyzed. The analysis baseline was to determine the infection and mortality structure of the diseased cohort at the onset-exponential phase of the first epidemic wave in Mexico under the assumption of limited herd immunity. Individuals with nonchronic diseases (NOCDs) were compared with those exhibiting at least one of 10 chronic diseases (CDs) adjusted by age and sex. Risk factors for infection and mortality were estimated with classification and regression tree (CART) and cluster analysis based on Spearman's matrix of rho-values in RStudio®, complemented with two proposed mortality indices. SARS-CoV-2 infection was independent of health condition (52.8% NOCD vs. 47.2% CDs; p = 0.001-0.009) but influenced by age >46 in one risk analysis scenario (p < 0.001). Sex contributed 9.7% to the overall risk. The independent effect was supported by the health structure of negative cases with a similar tendency but a higher proportion of NOCDs (61.4%, p = 0.007). The infection probability in individuals with one CD was determined by the disease type and age, which was higher in those older individuals (≥56 years) exhibiting diabetes (12.3%, cp = 0.0006), hypertension (10.1%, cp < 0.0001), and obesity (7.8%, cp = 0.001). In contrast, the mortality risk was heavily influenced by CD conditioned by sex and age, accounting for 72.3% of total deaths (p = 0.001-0.008). Significant mortality risk (48%) was comprised of women and men (w, m) aged ≥56 years with diabetes (19% w and 27.9% m, cp < 0.0004), hypertension (11.5% w, cp = 0.0001), and CKD (3.5% w and 5.3% m, cp = 0.0009). Older people with diabetes and hypertension comorbidity increased the risk to 60.5% (p = 0.001). Based on a mortality-weighted index, women were more vulnerable to preexisting metabolic or cardiovascular diseases. These findings support our hypothesis and justify the need for surveillance systems at a communitarian level. This is the first study addressing this fundamental epidemiological question.

Exploring the Immunomodulatory Properties of Stem Cells in Combating COVID-19: Can We Expect More?

Since the first appearance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in December 2019, the disease has displayed a remarkable interindividual variability in the global population, resulting in different mortality and morbidity rates. Still, an effective cure against SARS-CoV-2 has not been developed, and therefore, alternative therapeutic protocols must also be evaluated. Considering that stem cells, especially Mesenchymal Stromal Cells (MSCs), are characterized by both regenerative and immunomodulatory properties and that their safety and tolerability have been investigated previously, these cells could potentially be applied against coronavirus disease 19 (COVID-19). In addition, an individual's genetic background is further related to disease pathogenesis, especially rare Inborn Errors of Immunity (IEIs), autoantibodies against Interferon type I, and the presence of different Human Leukocyte Antigens (HLA) alleles, which are actively associated with protection or susceptibility in relation to SARS-CoV-2. Herein, the use of MSCs as a potential stem cell therapy will require a deep understanding of their immunomodulatory properties associated with their HLA alleles. In such a way, HLA-restricted MSC lines can be developed and applied precisely, offering more solutions to clinicians in attenuating the mortality of SARS-CoV-2.

Viral subversion of selective autophagy is critical for biogenesis of virus replication organelles

Infection by many (+)RNA viruses is accompanied by ER-expansion and membrane remodelling to form viral replication organelles, followed by assembly and secretion of viral progenies. We previously identified that virus-triggered lipophagy was critical for flaviviral assembly, and is driven by the lipid droplet associated protein Ancient ubiquitin protein 1 (Aup1). A ubiquitin conjugating protein Ube2g2 that functions as a co-factor for Aup1 was identified as a host dependency factor in our study. Here we characterized its function: Ube2g2-deficient cells displayed a dramatic reduction in virus production, which could be rescued by reconstituting the wild-type but not the catalytically deficient (C89K) mutant of Ube2g2, suggesting that its enzymatic activity is necessary. Ube2g2 deficiency did not affect entry of virus particles but resulted in a profound loss in formation of replication organelles, and production of infectious progenies. This phenomenon resulted from its dual activity in (i) triggering lipophagy in conjunction with Aup1, and (ii) degradation of ER chaperones such as Herpud1, SEL1L, Hrd1, along with Sec62 to restrict ER-phagy upon Xbp1-IRE1 triggered ER expansion. Our results therefore underscore an exquisite fine-tuning of selective autophagy by flaviviruses that drive host membrane reorganization during infection to enable biogenesis of viral replication organelles.

PubExN: An Automated PubMed Bulk Article Extractor with Affiliation Normalization Package

Biomedical article extraction is the preliminary step for every biomedical application. These applications are helpful in finding the gene, disease, chemical, drugs, protein entities. Finding entities relation such as gene-gene entities, drug-disease interaction, and chemical protein relation the PubExN can be helpful for these types of biomedical applications. In most cases, domain experts do this extraction process on their own. Human interference makes this process time-consuming and there is a high probability, that documents can be missed during the extraction process. To get rid of these complicated processes a python package is introduced to automate the process of bulk extraction from the PubMed database. The extraction process covers all the citation information with the associated abstract. The batch approach is used to extract the bulk extraction. The motivation for the development of PubExN was to provide flexibility for the extraction process of biomedical article's text data from NCBI's PubMed database. Basically, NCBI's PubMed database article contains the article id or can say PubMed-id (PMID), the title of the article, abstract, authors information, etc. This package will benefit many biomedical texts mining research including biomedical named entity recognition, biomedical relation extraction, literature discovery, knowledgebase creation, and various biomedical Natural Language Processing (NLP) tasks. In addition, it could be used in the author name disambiguation problems and new drug discoveries. This package will help save time and extra effort for the extraction and normalization process of PubMed articles.

ISG15 driven cellular responses to virus infection

One of the hallmarks of antiviral responses to infection is the production of interferons and subsequently of interferon stimulated genes. Interferon stimulated gene 15 (ISG15) is among the earliest and most abundant proteins induced upon interferon signalling, encompassing versatile functions in host immunity. ISG15 is a ubiquitin like modifier that can be conjugated to substrates in a process analogous to ubiquitylation and referred to as ISGylation. The free unconjugated form can either exist intracellularly or be secreted to function as a cytokine. Interestingly, ISG15 has been reported to be both advantageous and detrimental to the development of immunopathology during infection. This review describes recent findings on the role of ISG15 in antiviral responses in human infection models, with a particular emphasis on autophagy, inflammatory responses and cellular metabolism combined with viral strategies of counteracting them. The field of ISGylation has steadily gained momentum; however much of the previous studies of virus infections conducted in mouse models are in sharp contrast with recent findings in human cells, underscoring the need to summarise our current understanding of its potential antiviral function in humans and identify knowledge gaps which need to be addressed in future studies.

A Review Pertaining to SARS-CoV-2 and Autoimmune Diseases: What Is the Connection?

Coronavirus disease 2019 (COVID-19) is an infectious viral disease caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). It is known that infection with SARS-CoV-2 can lead to various autoimmune and autoinflammatory diseases. There are few reports in the literature on the association between SARS-CoV-2 and autoimmune diseases, and the number of reports has been increasing since 2020. Autoimmune diseases and SARS-CoV-2 infections are intertwined in several ways. Both conditions lead to immune-mediated tissue damage, the immune response is accompanied by the increased secretion of inflammatory cytokines and both conditions can be treated using immunomodulatory drugs. Patients with certain autoimmune diseases, such as systemic lupus erythematosus, rheumatoid arthritis, type 1 diabetes, cardiac sarcoidosis, idiopathic pulmonary fibrosis, autoimmune hepatitis, multiple sclerosis and others, are more susceptible to SARS-CoV-2 infection, either because of the active autoimmune disease or because of the medications used to treat it. Conversely, SARS-CoV-2 infection can also cause certain autoimmune diseases. In this paper, we describe the development of autoimmune diseases after COVID-19 and the recovery from COVID-19 in people with autoimmune diseases.

Identification of COVID-19 severity biomarkers based on feature selection on single-cell RNA-Seq data of CD8+ T cells

The global outbreak of the COVID-19 epidemic has become a major public health problem. COVID-19 virus infection triggers a complex immune response. CD8+ T cells, in particular, play an essential role in controlling the severity of the disease. However, the mechanism of the regulatory role of CD8+ T cells on COVID-19 remains poorly investigated. In this study, single-cell gene expression profiles from three CD8+ T cell subtypes (effector, memory, and naive T cells) were downloaded. Each cell subtype included three disease states, namely, acute COVID-19, convalescent COVID-19, and unexposed individuals. The profiles on each cell subtype were individually analyzed in the same way. Irrelevant features in the profiles were first excluded by the Boruta method. The remaining features for each CD8+ T cells subtype were further analyzed by Max-Relevance and Min-Redundancy, Monte Carlo feature selection, and light gradient boosting machine methods to obtain three feature lists. These lists were then brought into the incremental feature selection method to determine the optimal features for each cell subtype. Their corresponding genes may be latent biomarkers to determine COVID-19 severity. Genes, such as ZFP36, DUSP1, TCR, and IL7R, can be confirmed to play an immune regulatory role in COVID-19 infection and recovery. The results of functional enrichment analysis revealed that these important genes may be associated with immune functions, such as response to cAMP, response to virus, T cell receptor complex, T cell activation, and T cell differentiation. This study further set up different gene expression pattens, represented by classification rules, on three states of COVID-19 and constructed several efficient classifiers to distinguish COVID-19 severity. The findings of this study provided new insights into the biological processes of CD8+ T cells in regulating the immune response.

SARS-CoV-2 Mutation Mechanism, Features, and Future Perspective

Over two years, the SARS-CoV-2 virus has evolved by producing several variants by RNA polymerase mutation. This mutation created many virus variants that five of them are designated by WHO. These are Alpha, Beta, Gamma, Delta, and Omicron, among them Alpha, Delta, and Omicron spread faster. Coronaviruses (CoVs) are enveloped in positive-sense RNA viruses and contain huge RNA virus genomes. RNA polymerase controls the replication in which the genomic material is copied, and it often makes errors that lead to create a new mutation. Most mutations create a virus that cannot replicate and spread among people. However, some mutations lead to a virus that can replicate and create a variant. This chapter will discuss the mechanism of the mutations during the last two years and the future of these mutations in SARS-CoV-2.

Safety, Tolerability, and Pharmacokinetics of the Novel Antiviral Agent Ensitrelvir Fumaric Acid, a SARS-CoV-2 3CL Protease Inhibitor, in Healthy Adults

Ensitrelvir is a novel selective inhibitor of the 3C-like protease of SARS-CoV-2, which is essential for viral replication. This phase 1 study of ensitrelvir assessed its safety, tolerability, and pharmacokinetics of single (part 1, n = 50) and multiple (part 2, n = 33) ascending oral doses. Effect of food on the pharmacokinetics of ensitrelvir, differences in pharmacokinetics of ensitrelvir between Japanese and white participants, and effect of ensitrelvir on the pharmacokinetics of midazolam (a cytochrome P450 3A [CYP3A] substrate) were also assessed. In part 1, Japanese participants were randomized to placebo or ensitrelvir at doses of 20, 70, 250, 500, 1,000, or 2,000 mg. In part 2, Japanese and white participants were randomized to placebo or once-daily ensitrelvir at loading/maintenance dose 375/125 mg or 750/250 mg for 5 days. Most treatment-related adverse events observed were mild in severity and were resolved without treatment. Plasma exposures showed almost dose proportionality, and geometric mean half-life of ensitrelvir following the single dose was 42.2 to 48.1 h. Food intake reduced C_max and delayed T_max of ensitrelvir but did not impact the area under the curve (AUC), suggesting suitability for administration without food restriction. Compared with Japanese participants, plasma exposures were slightly lower for white participants. Ensitrelvir affected the pharmacokinetics of CYP3A substrates because of increase in AUC of midazolam coadministered with ensitrelvir 750/250 mg on day 6. In conclusion, ensitrelvir was well-tolerated and demonstrated favorable pharmacokinetics, including a long half-life, supporting once-daily oral dosing. These results validate further assessments of ensitrelvir in participants with SARS-CoV-2 infection.

Roles and functions of SARS-CoV-2 proteins in host immune evasion

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evades the host immune system through a variety of regulatory mechanisms. The genome of SARS-CoV-2 encodes 16 non-structural proteins (NSPs), four structural proteins, and nine accessory proteins that play indispensable roles to suppress the production and signaling of type I and III interferons (IFNs). In this review, we discussed the functions and the underlying mechanisms of different proteins of SARS-CoV-2 that evade the host immune system by suppressing the IFN-β production and TANK-binding kinase 1 (TBK1)/interferon regulatory factor 3 (IRF3)/signal transducer and activator of transcription (STAT)1 and STAT2 phosphorylation. We also described different viral proteins inhibiting the nuclear translocation of IRF3, nuclear factor-κB (NF-κB), and STATs. To date, the following proteins of SARS-CoV-2 including NSP1, NSP6, NSP8, NSP12, NSP13, NSP14, NSP15, open reading frame (ORF)3a, ORF6, ORF8, ORF9b, ORF10, and Membrane (M) protein have been well studied. However, the detailed mechanisms of immune evasion by NSP5, ORF3b, ORF9c, and Nucleocapsid (N) proteins are not well elucidated. Additionally, we also elaborated the perspectives of SARS-CoV-2 proteins.

Aerosol Transport Modeling: The Key Link Between Lung Infections of Individuals and Populations

The recent COVID-19 pandemic has propelled the field of aerosol science to the forefront, particularly the central role of virus-laden respiratory droplets and aerosols. The pandemic has also highlighted the critical need, and value for, an information bridge between epidemiological models (that inform policymakers to develop public health responses) and within-host models (that inform the public and health care providers how individuals develop respiratory infections). Here, we review existing data and models of generation of respiratory droplets and aerosols, their exhalation and inhalation, and the fate of infectious droplet transport and deposition throughout the respiratory tract. We then articulate how aerosol transport modeling can serve as a bridge between and guide calibration of within-host and epidemiological models, forming a comprehensive tool to formulate and test hypotheses about respiratory tract exposure and infection within and between individuals.

Modeling insights into SARS-CoV-2 respiratory tract infections prior to immune protection

Mechanistic insights into human respiratory tract (RT) infections from SARS-CoV-2 can inform public awareness as well as guide medical prevention and treatment for COVID-19 disease. Yet the complexity of the RT and the inability to access diverse regions pose fundamental roadblocks to evaluation of potential mechanisms for the onset and progression of infection (and transmission). We present a model that incorporates detailed RT anatomy and physiology, including airway geometry, physical dimensions, thicknesses of airway surface liquids (ASLs), and mucus layer transport by cilia. The model further incorporates SARS-CoV-2 diffusivity in ASLs and best-known data for epithelial cell infection probabilities, and, once infected, duration of eclipse and replication phases, and replication rate of infectious virions. We apply this baseline model in the absence of immune protection to explore immediate, short-term outcomes from novel SARS-CoV-2 depositions onto the air-ASL interface. For each RT location, we compute probability to clear versus infect; per infected cell, we compute dynamics of viral load and cell infection. Results reveal that nasal infections are highly likely within 1-2 days from minimal exposure, and alveolar pneumonia occurs only if infectious virions are deposited directly into alveolar ducts and sacs, not via retrograde propagation to the deep lung. Furthermore, to infect just 1% of the 140 m2 of alveolar surface area within 1 week, either 103 boluses each with 106 infectious virions or 106 aerosols with one infectious virion, all physically separated, must be directly deposited. These results strongly suggest that COVID-19 disease occurs in stages: a nasal/upper RT infection, followed by self-transmission of infection to the deep lung. Two mechanisms of self-transmission are persistent aspiration of infected nasal boluses that drain to the deep lung and repeated rupture of nasal aerosols from infected mucosal membranes by speaking, singing, or cheering that are partially inhaled, exhaled, and re-inhaled, to the deep lung.

Activation of NLRP3 Inflammasome by Virus-Like Particles of Human Polyomaviruses in Macrophages

Viral antigens can activate phagocytes, inducing inflammation, but the mechanisms are barely explored. The aim of this study is to investigate how viral oligomeric proteins of different structures induce inflammatory response in macrophages. Human THP-1 cell line was used to prepare macrophages that were treated with filamentous nucleocapsid-like particles (NLPs) of paramyxoviruses and spherical virus-like particles (VLPs) of human polyomaviruses. The effects of viral proteins on cell viability, pro-inflammatory cytokines’ production, and NLRP3 inflammasome activation were investigated. Filamentous NLPs did not induce inflammation while spherical VLPs mediated inflammatory response followed by NLRP3 inflammasome activation. Inhibitors of cathepsins and K⁺ efflux decreased IL-1β release and cell death, indicating a complex inflammasome activation process. A similar activation pattern was observed in primary human macrophages. Single-cell RNAseq analysis of THP-1 cells revealed several cell activation states different in inflammation-related genes. This study provides new insights into the interaction of viral proteins with immune cells and suggests that structural properties of oligomeric proteins may define cell activation pathways.

Prognostic Markers in Hospitalized COVID-19 Patients: The Role of IP-10 and C-Reactive Protein

Background

SARS-CoV-2 is responsible for COVID-19, a clinically heterogeneous disease, ranging from being completely asymptomatic to life-threating manifestations. An unmet clinical need is the identification at disease onset or during its course of reliable biomarkers allowing patients' stratification according to disease severity. In this observational prospective cohort study, patients' immunologic and laboratory signatures were analyzed to identify independent predictors of unfavorable (either death or intensive care unit admission need) or favorable (discharge and/or clinical resolution within the first 14 days of hospitalization) outcome.

Methods

Between January and May 2021 (third wave of the pandemic), we enrolled 139 consecutive SARS-CoV-2 positive patients hospitalized in Northern Italy to study their immunological and laboratory signatures. Multiplex cytokine, chemokine, and growth factor analysis, along with routine laboratory tests, were performed at baseline and after 7 days of hospital stay.

Results

According to their baseline characteristics, the majority of our patients experienced a moderate to severe illness. At multivariate analysis, the only independent predictors of disease evolution were the serum concentrations of IP-10 (at baseline) and of C-reactive protein (CRP) after 7 days of hospitalization. Receiver-operating characteristic (ROC) curve analysis confirmed that baseline IP − 10 > 4271 pg/mL and CRP > 2.3 mg/dL at 7 days predict a worsening in clinical conditions (87% sensitivity, 66% specificity, area under the curve (AUC) 0.772, p < 0.001 and 83% sensitivity, 73% specificity, AUC 0.826, p < 0.001, respectively).

Conclusions

According to our results, baseline IP-10 and CRP after 7 days of hospitalization could be useful in driving clinical decisions tailored to the expected disease trajectory in hospitalized COVID-19 patients.

Case Report: Myocarditis After COVID-19 Vaccination - Case Series and Literature Review

BACKGROUND

The ongoing COVID-19 pandemic demands a series of measures and, above all, the vaccination of a substantial proportion of the population. Acute myocarditis is a rare complication of the widely used mRNA-based vaccines.

CASE PRESENTATION

We present a case series of four patients (three men and one woman, 16 to 47 years old) with acute pericarditis/myocarditis 3 to 17 days after mRNA vaccination. They presented with chest pain, fever, and flu-like symptoms. Diagnosis was made based on the synopsis of clinical presentation, elevated levels of troponin T and NT-proBNP, impaired systolic function on echocardiography, and findings in non-invasive tissue characterization by cardiovascular magnetic resonance imaging. Two patients also underwent endomyocardial biopsies. As none of the patients showed signs of cardiogenic shock, they were discharged from ward care only a few days after their initial presentations.

CONCLUSIONS

Our data are consistent with other case reports of myocarditis early after mRNA vaccination and demonstrate the need for multimodal diagnostics. In view of its rarity and mild course, the risk-benefit ratio of vaccination remains positive compared to potential SARS-CoV-2 infection.

Thrombotic and Hypercoagulability Complications of COVID-19: An Update

The current COVID-19 pandemic emerged in December 2019, in China, affecting millions of people worldwide. COVID-19 is mainly a disease of the respiratory system, yet systematic complications have also been reported among SARS-CoV-2 infected patients. Thrombotic complications are one of the severe clinical outcomes of COVID-19, especially among critically ill patients, and are associated with poor prognosis. To date, many studies have concluded that COVID-19 increases the incidence of thrombotic events and coagulopathies; however, the exact mechanism behind such a disease outcome is not well known. Various pathophysiological mechanisms for thrombotic events in COVID-19 have been proposed, these include virus-induced endothelial cell damage, inflammation, and excess production of pro-inflammatory cytokines. As a result, most critically diseased COVID-19 patients are managed with prophylactic anticoagulant, yet some still develop thrombotic episodes. Therefore, better understanding of the mechanisms behind the thrombotic complications is needed to develop treatments that specifically target such pathways, which may aid in better disease management and improve the prognosis.