SARS-CoV-2 Infection: Host Response, Immunity, and Therapeutic Targets

Research progress on critical viral protease inhibitors for coronaviruses and enteroviruses

Viral infectious diseases have been seriously affecting human life and health. SARS-CoV-2 was the pathogen that caused Coronavirus Disease 2019 (COVID-19), and the impact of COVID-19 is still existing. Enterovirus 71 (EV71) is the primary pathogen of hand, foot, and mouth disease (HFMD), and no effective direct-acting antiviral drugs targeting EV71 has been approved yet. Innate antiviral strategies play an important role in preventing virus infections depending on the powerful immune regulatory system of body, while viruses have evolved to exploit diverse methods to overcome immune response. Viral proteases, which are known in cleaving viral polyproteins, have also been found to modulate the innate immunity of host cells, thereby promoting viral proliferation. Herein, we reviewed the current development of SARS-CoV-2 3CLpro, PLpro, and EV71 3Cpro and 2Apro, mainly including structure, function, modulation of immune response, and inhibitors of these four proteases, to further deepen the understanding of viral pathogenesis and provide a new perspective for subsequent corresponding drug development.

Oral hygiene influence on the incidence and severity of oral manifestations in Coronavirus Disease 2019

INTRO

The aim of this study was to evaluate the incidence, severity, duration of oral manifestations in individuals with Coronavirus Disease 2019 (COVID-19) and the association of these manifestations with the severity of COVID-19 and the patient's oral hygiene.

METHODS

This study included 820 patients with confirmed COVID-19. A questionnaire form including oral hygiene habits, the severity of Covid-19, the presence, severity and durations of oral manifestations was prepared, and a web-based survey was performed using Google-forms. Obtained data was analysed with Pearson chi-square and Fisher's exact tests with statistical significance set at P < 0.05.

RESULTS

The most commonly reported manifestations were taste dysfunction (63.4%), xerostomia (59.9%), halitosis (31.1%), dysphagia (27.8%), hypersensitive teeth (27.2%) and gingival bleeding (14.3%). The incidence of the oral manifestations was found significantly associated with severity of COVID-19 (P = 0.000 V = 0.151), presence of systemic diseases (P = 0.034, V = 0.074) and age (P = 0.023, V = 0.099). Tooth brushing decreased the incidence of aphthous like lesions of tongue during Covid-19 (p < 0.05).

CONCLUSION

Maintenance of oral hygiene was associated with a reduced incidence of aphthous-like lesions, underscoring the protective role of routine oral care. These findings highlight the need to integrate oral health assessment and hygiene education into COVID-19 management protocols, which may also be important for potential future pandemics.

NK cells modulate in vivo control of SARS-CoV-2 replication and suppression of lung damage

Natural killer (NK) cells play a critical role in virus control. However, it has remained largely unclear whether NK cell mobilization in SARS-CoV-2 infections is beneficial or pathologic. To address this deficit, we employed a validated experimental NK cell depletion non-human primate (NHP) model with SARS-CoV-2 Delta variant B.1.617.2 challenge. Viral loads (VL), NK cell numbers, activation, proliferation, and functional measures were evaluated in blood and tissues. In non-depleted (control) animals, infection rapidly induced NK cell expansion, activation, and increased tissue trafficking associated with VL. Strikingly, we report that experimental NK cell depletion leads to higher VL, longer duration of viral shedding, significantly increased levels of pro-inflammatory cytokines in the lungs, and overt lung damage. Overall, we find the first significant and conclusive evidence for NK cell-mediated control of SARS-CoV-2 virus replication and disease pathology. These data indicate that adjunct therapies for infection could largely benefit from NK cell-targeted approaches.

High Levels of NfL, GFAP, TAU, and UCH-L1 as Potential Predictor Biomarkers of Severity and Lethality in Acute COVID-19

Few studies showed that neurofilament light chain (NfL), glial fibrillary acidic protein (GFAP), total tubulin-associated unit (TAU), and ubiquitin carboxy-terminal hydrolase-L1 (UCH-L1) may be related to neurological manifestations and severity during and after SARS-CoV-2 infection. The objective of this work was to investigate the relationship among nervous system biomarkers (NfL, TAU, GFAP, and UCH-L1), biochemical parameters, and viral loads with heterogeneous outcomes in a cohort of severe COVID-19 patients admitted in Intensive Care Unit (ICU) of a university hospital. For that, 108 subjects were recruited within the first 5 days at ICU. In parallel, 16 mild COVID-19 patients were enrolled. Severe COVID-19 group was divided between "deceased" and "survivor." All subjects were positive for SARS-CoV-2 detection. NfL, total TAU, GFAP, and UCH-L1 quantification in plasma was performed using SIMOA SR-X platform. Of 108 severe patients, 36 (33.33%) presented neurological manifestation and 41 (37.96%) died. All four biomarkers - GFAP, NfL, TAU, and UCH-L1 - were significantly higher among deceased patients in comparison to survivors (p < 0.05). Analyzing biochemical biomarkers, higher Peak Serum Ferritin, D-Dimer Peak, Gamma-glutamyltransferase, and C-Reactive Protein levels were related to death (p < 0.0001). In multivariate analysis, GFAP, NfL, TAU, UCH-L1, and Peak Serum Ferritin levels were correlated to death. Regarding SARS-CoV-2 viral load, no statistical difference was observed for any group. Thus, Ferritin, NFL, GFAP, TAU, and UCH-L1 are early biomarkers of severity and lethality of SARS-COV-2 infection and may be important tools for therapeutic decision-making in the acute phase of disease.

Identification of Hammerhead-variant ribozyme sequences in SARS-CoV-2

The SARS-CoV-2 RNA virus and variants, responsible for the COVID-19 pandemic has become endemic, raised a need for further understanding of the viral genome and biology. Despite vast research on SARS-CoV-2, no ribozymes have been found in the virus genome. Here we report the identification of 39 Hammerhead-variant ribozyme sequences (CoV-HHRz) in SARS-CoV-2. These sequences are highly conserved within SARS-CoV-2 variants but show large diversity among other coronaviruses. In vitro CoV-HHRz sequences possess the characteristics of typical ribozymes; cleavage is pH and ion dependent, although their activity is relatively low and Mn2+ is required for cleavage. The cleavage sites of four CoV-HHRz coincide with the breakpoint of expressed subgenomic RNA (sgRNAs) in SARS-CoV-2 transcriptome data suggesting in vivo activity. The CoV-HHRz are involved in processing sgRNAs for ORF7b, ORF 10 and ORF1ab nsp13 which are essential for viral packaging and life cycle.

Emerging role of N6-methyladenosine RNA modification in regulation of SARS-CoV-2 infection and virus-host interactions

Since December 2019, the infection caused by Severe Acute Respiratory Syndrome Coronavirus Type 2 (SARS-CoV-2) has posed an enormous threat to human health security worldwide. Constant mutation of viral genome and varying therapeutic responses of patients infected with this virus prompted efforts to uncover more novel regulators in the pathogenesis. The involvement of N6-methyladenosine, a modified form of RNA, plays a crucial role in viral replication, viral pathogenicity, and intricate signaling pathways connected with immune responses. This review discusses research advances revealing the regulation of the life cycle of SARS-CoV-2 and antiviral responses of host cells by RNA m6A modification, highlights the biological functions of N6-methyladenosine components in SARS-CoV-2 infection and virus-host interactions, and outlines current challenges and future directions for exploring the potential clinical value of m6A modification in COVID-19.

Purinergic signaling: decoding its role in COVID-19 pathogenesis and promising treatment strategies

The pathogenesis of coronavirus disease (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2), is complex and involves dysregulated immune responses, inflammation, and coagulopathy. Purinergic signaling, mediated by extracellular nucleotides and nucleosides, has emerged as a significant player in the pathogenesis of COVID-19. Extracellular adenosine triphosphate (ATP), released from damaged or infected cells, is a danger signal triggering immune responses. It activates immune cells, releasing pro-inflammatory cytokines, contributing to the cytokine storm observed in severe COVID-19 cases. ATP also promotes platelet activation and thrombus formation, contributing to the hypercoagulability seen in COVID-19 patients. On the other hand, adenosine, an immunosuppressive nucleoside, can impair anti-viral immune responses and promote tissue damage through its anti-inflammatory effects. Modulating purinergic receptors represents a promising therapeutic strategy for COVID-19. Understanding the role of purinergic signaling in COVID-19 pathogenesis and developing targeted therapeutic approaches can potentially improve patient outcomes. This review focuses on the part of purinergic signaling in COVID-19 pathogenesis and highlights potential therapeutic approaches targeting purinergic receptors.

Single-cell RNA-Seq reveals intracellular microbial diversity within immune cells during SARS-CoV-2 infection and recovery

Intracellular microorganisms, like viruses, bacteria, and fungi, pose challenges in detection due to their non-culturable forms. Transcriptomic analysis at cellular level enables exploration of distributions and the impact of these microorganisms on host cells, a domain that remains underexplored because of methodological limitations. Single-cell technology shows promise in addressing this by capturing polyadenine-tailed transcripts, because recent studies confirmed polyadenylation in microbial transcriptomes. We utilized single-cell RNA-seq from PBMCs to probe intracellular microbes in healthy, SARS-CoV-2-positive, and recovered individuals. Among 76 bacterial species detected, 16 showed significant abundance differences. Buchnera aphidicola, Streptomyces clavuligerus, and Ehrlichia canis emerged significantly in memory-B, Naïve-T, and Treg cells. Staphylococcus aureus, Mycoplasma mycoides, Leptospira interrogans, and others displayed elevated levels in SARS-CoV-2-positive patients, suggesting possible disease association. This highlights the strength of single-cell technology in revealing potential microorganism's cell-specific functions. Further research is essential for functional understanding of their cell-specific abundance across physiological states.

An integrative approach for compressive quality control of RespireAid™, a traditional Chinese medicine formula against SARS-CoV-2

RespireAid™ (NRICM101) is an effective anti-SARS-CoV-2 traditional Chinese medicine formula and has been licensed as a drug or dietary supplement in Taiwan, Luxembourg, Australia, Singapore, Cambodia, Philippines, and Canada. In this study, we provided integrated quality control strategy to analyze the ingredient of RespireAid™. In addition, the lot-to-lot efficacy stabilities were also evaluated. We found that RespireAid™ comprised of monosaccharides and disaccharides (34.0%), maltodextrin (23.5%), inorganic elements and ash (12.2%), oligosaccharides and polysaccharides (11.4%), principal components (4.4%), moisture (4.0%), amino acids (3.5%), β-Cyclodextrin (0.25%), menthol (0.25%), and nucleotides (0.14%), while the remainder was unidentified (6.36%). This is the first time that the chemical composition of a complex traditional Chinese medicine was clarified using various analytical instruments. The lot-to-lot anti-oxidation and anti-inflammation efficacies of RespireAid™ were consistent, with average 50% scavenging concentrations of 0.22 ± 0.02 mg/mL and 5.76 ± 0.59 mg/mL, respectively. From a comprehensive quality control strategy point of view, RespireAid™, designed from a traditional Chinese medicine formula, displayed high quality, transparency, and efficacy. This integrated strategy provides a clear and reliable way to evaluate the quality of complex traditional Chinese medicines.

Lipid Mediators and Cytokines/Chemokines Display Differential Profiles in Severe versus Mild/Moderate COVID-19 Patients

Host immune responses play a key role in COVID-19 pathogenesis. The underlying phenomena are orchestrated by signaling molecules such as cytokines/chemokines and lipid mediators. These immune molecules, including anti-SARS-CoV-2 antibodies, interact with immune cells and regulate host responses, contributing to inflammation that drives the disease. We investigated 48 plasma cytokines/chemokines, 21 lipid mediators, and anti-S protein (RBD) antibodies in COVID-19 patients (n = 56) and non-COVID-19 respiratory disease controls (n = 49), to identify immune-biomarker profiles. Cytokines/chemokines (IL-6, CXCL-10 (IP-10), HGF, MIG, MCP-1, and G-CSF) and lipid mediators (TxB2, 11-HETE, 9-HODE, 13-HODE, 5-HETE, 12-HETE, 15-HETE, 14S-HDHA, 17S-HDHA, and 5-oxo ETE) were significantly elevated in COVID-19 patients compared to controls. In patients exhibiting severe disease, pro-inflammatory cytokines/chemokines (IL-6, CXCL-10, and HGF) and anti-SARS-CoV-2 antibodies were significantly elevated. In contrast, lipid mediators involved in the reduction/resolution of inflammation, in particular, 5-HETE, 11-HETE, and 5-oxoETE, were significantly elevated in mild/moderate disease. Taken together, these immune-biomarker profiles provide insight into immune responses related to COVID-19 pathogenesis. Importantly, our findings suggest that elevation in plasma concentrations of IL-6, CXCL-10, HGF, and anti-SARS-CoV-2 antibodies can predict severe disease, whereas elevation in lipid mediators peaks early (compared to cytokines) and includes induction of mechanisms leading to reduction of inflammation, associated complications, and maintenance of homeostasis.

TBC and COVID: an interplay between two infections

INTRODUCTION

In a historical era dominated by the SARS-CoV-2 pandemic, a fact of growing interest emerges regarding co-infection with Mycobacterium tuberculosis (M. tuberculosis). This represents today an important clinical and diagnostic challenge, as the two pathogens are capable, through specific immunopathological mechanisms, of interacting with each other, determining a severe respiratory condition with a severe prognosis.

AREAS COVERED

With this review, we wanted to collect and analyze the latest scientific evidence concerning the main immunopathogenetic mechanisms shared by these two respiratory pathogens, with particular interest in the possible iatrogenic factors favoring coinfection and the need to define multidisciplinary and standardized screening tools aimed to identify coinfection early, ensuring the best clinical and therapeutic management.

EXPERT OPINION

The existence of a direct immunopathogenetic link between COVID-19 and TB indirectly contributes to mutual morbidity and mortality. The identification and application of early and standardized screening tools aimed at the identification of this condition is essential, in addition to vaccine prevention.

Computed tomography and nuclear medicine for the assessment of coronary inflammation: clinical applications and perspectives

There is increasing evidence that in patients with atherosclerotic cardiovascular disease (ASCVD) under optimal medical therapy, a persisting dysregulation of the lipid and glucose metabolism, associated with adipose tissue dysfunction and inflammation, predicts a substantial residual risk of disease progression and cardiovascular events. Despite the inflammatory nature of ASCVD, circulating biomarkers such as high-sensitivity C-reactive protein and interleukins may lack specificity for vascular inflammation. As known, dysfunctional epicardial adipose tissue (EAT) and pericoronary adipose tissue (PCAT) produce pro-inflammatory mediators and promote cellular tissue infiltration triggering further pro-inflammatory mechanisms. The consequent tissue modifications determine the attenuation of PCAT as assessed and measured by coronary computed tomography angiography (CCTA). Recently, relevant studies have demonstrated a correlation between EAT and PCAT and obstructive coronary artery disease, inflammatory plaque status and coronary flow reserve (CFR). In parallel, CFR is well recognized as a marker of coronary vasomotor function that incorporates the haemodynamic effects of epicardial, diffuse and small-vessel disease on myocardial tissue perfusion. An inverse relationship between EAT volume and coronary vascular function and the association of PCAT attenuation and impaired CFR have already been reported. Moreover, many studies demonstrated that 18F-FDG PET is able to detect PCAT inflammation in patients with coronary atherosclerosis. Importantly, the perivascular FAI (fat attenuation index) showed incremental value for the prediction of adverse clinical events beyond traditional risk factors and CCTA indices by providing a quantitative measure of coronary inflammation. As an indicator of increased cardiac mortality, it could guide early targeted primary prevention in a wide spectrum of patients. In this review, we summarize the current evidence regarding the clinical applications and perspectives of EAT and PCAT assessment performed by CCTA and the prognostic information derived by nuclear medicine.

Molecular Pathogenesis of Fibrosis, Thrombosis and Surfactant Dysfunction in the Lungs of Severe COVID-19 Patients

The global scope and scale of the SARS-CoV-2 pandemic led to huge amounts of important data from clinical observations and experimental analyses being collected, in particular, regarding the long-term impact of COVID-19 on lung tissue. Visible changes in lung tissue mainly relate to the destruction of the alveolar architecture, dense cellularity, and pulmonary fibrosis with myofibroblast proliferation and collagen deposition. These changes are the result of infection, mainly with virus variants from the first pandemic waves (Alpha to Delta). In addition, proper regulation of immune responses to pathogenic viral stimuli is critical for the control of and recovery from tissue/organ damage, including in the lungs. We can distinguish three main processes in the lungs during SARS-CoV-2 infection: damage or deficiency of the pulmonary surfactant, coagulation processes, and fibrosis. Understanding the molecular basis of these processes is extremely important in the context of elucidating all pathologies occurring after virus entry. In the present review, data on the abovementioned three biochemical processes that lead to pathological changes are gathered together and discussed. Systematization of the knowledge is necessary to explore the three key pathways in lung tissue after SARS-CoV-2 virus infection as a result of a prolonged and intense inflammatory process in the context of pulmonary fibrosis, hemostatic disorders, and disturbances in the structure and/or metabolism of the surfactant. Despite the fact that the new Omicron variant does not affect the lungs as much as the previous variants, we cannot ignore the fact that other new mutations and emerging variants will not cause serious damage to the lung tissue. In the future, this review will be helpful to stratify the risk of serious complications in patients, to improve COVID-19 treatment outcomes, and to select those who may develop complications before clinical manifestation.

SARS-CoV-2 Monitoring in Wastewater Reveals Novel Variants and Biomarkers of Infection

Wastewater-based epidemiology (WBE) is a popular tool for the early indication of community spread of infectious diseases. WBE emerged as an effective tool during the COVID-19 pandemic and has provided meaningful information to minimize the spread of infection. Here, we present a combination of analyses using the correlation of viral gene copies with clinical cases, sequencing of wastewater-derived RNA for the viral mutants, and correlative analyses of the viral gene copies with the bacterial biomarkers. Our study provides a unique platform for potentially using the WBE-derived results to predict the spread of COVID-19 and the emergence of new variants of concern. Further, we observed a strong correlation between the presence of SARS-CoV-2 and changes in the microbial community of wastewater, particularly the significant changes in bacterial genera belonging to the families of Lachnospiraceae and Actinomycetaceae. Our study shows that microbial biomarkers could be utilized as prediction tools for future infectious disease surveillance and outbreak responses. Overall, our comprehensive analyses of viral spread, variants, and novel bacterial biomarkers will add significantly to the growing body of literature on WBE and COVID-19.

Osteoporosis in Patients With Respiratory Diseases

Climate change, environmental pollution, and virus epidemics have sharply increased the number of patients suffering from respiratory diseases in recent years. Prolonged periods of illness and drug use increase the occurrence of complications in these patients. Osteoporosis is the common bone metabolism disease with respiratory disturbance, which affects prognosis and increases mortality of patients. The problem of osteoporosis in patients with respiratory diseases needs more attention. In this review, we concluded the characteristics of osteoporosis in some respiratory diseases including COPD, asthma, COVID-19, tuberculosis, and lung cancer. We revealed that hypoxia was the common pathogenesis of osteoporosis secondary to respiratory diseases, with malnutrition and corticosteroid abuse driving the progression of osteoporosis. Hypoxia-induced ROS accumulation and activated HIF-1α lead to attenuated osteogenesis and enhanced osteoclastogenesis in patients with respiratory diseases. Tuberculosis and cancer also invaded bone tissue and reduced bone strength by direct infiltration. For the treatment of osteoporosis in respiratory patients, oral-optimized bisphosphonates were the best treatment modality. Vitamin D was a necessary supplement, both for calcium absorption in osteogenesis and for improvement of respiratory lesions. Reasonable adjustment of the dose and course of corticosteroids according to the etiology and condition of patients is beneficial to prevent the occurrence and development of osteoporosis. Additionally, HIF-1α was a potential target for the treatment of osteoporosis in respiratory patients, which could be activated under hypoxia condition and involved in the process of bone remodeling.

Cut-off point of CT-assessed epicardial adipose tissue volume for predicting worse clinical burden of SARS-CoV-2 pneumonia

Objective

To identify a cut-off value of epicardial adipose tissue (EAT) volume quantified by CT associated with a worse clinical outcome in patients with SARS-CoV-2 pneumonia.

Materials and methods

In this retrospective study, sixty patients with a diagnosis of laboratory-confirmed COVID-19 pneumonia and a chest CT exam on admission were enrolled. Based on a total severity score (range 0–20), patients were divided into two groups: ordinary group (total severity score < 7) and severe/critical group (total severity score > 7). Clinical results and EAT volume were compared between the two groups.

Results

The severe/critical patients, compared to the ordinary ones, were older (66.83 ± 11.72 vs 58.57 ± 16.86 years; p = 0.031), had higher body mass index (27.77 ± 2.11 vs 25.07 ± 2.80 kg/m²; p < 0.001) and higher prevalence of comorbidities. EAT volume was higher in severe/critical group, compared with the ordinary group (151.40 ± 66.22 cm³ vs 92.35 ± 44.46 cm³, p < 0.001). In severe/critical group, 19 (73%) patients were admitted in intensive care unit (ICU), compared with 6 (20%) patients in the ordinary group (p < 0.001). The area under the ROC curve (AUC) is equal to 0.781 (p < 0.001) (95% CI: 0.662–0.900). The cut-off found, in correspondence with the highest value of the Youden Index, is 97 cm³: the sensitivity is equal to 83.3%, while the specificity is equal to 70% for predicting a worse outcome. The risk (odds ratio) of belonging to the severe/critical group in this population due to EAT ≥ 97 cm³ is 11.667 (95% CI: 3.384–40.220; p < 0.001).

Conclusion

An EAT volume of 97 cm³ has good sensitivity and specificity to predict a greater extent of pulmonary involvement and therefore a worse clinical outcome in patients with SARS-CoV-2 pneumonia.