A pneumonia outbreak associated with a new coronavirus of probable bat origin

Dynamic Combinatorial Chemistry Unveils Nsp10 Inhibitors with Antiviral Potential Against SARS-CoV-2

The development of antiviral drugs against the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) responsible for the recent Covid-19 pandemic is crucial, as treatment options remain limited and vaccination does not prevent (re)infection. Two relatively underexplored targets of this virus are the 3'-5' exoribonuclease (ExoN) and the 2'-O-methyltransferase (2'-O-MTase), both essential for viral viability. The non-structural proteins Nsp14 and Nsp16 exhibit enzymatic activities for ExoN and 2'-O-MTase, respectively, especially when in complex with their co-factor protein Nsp10. The study focuses on the use of target-directed dynamic combinatorial chemistry (tdDCC) to identify binders of Nsp10, aiming to disturb the protein-protein interactions (PPI) involving Nsp10-Nsp14, as well as Nsp10-Nsp16. We synthesised the hits and evaluated them to assess Nsp10 affinity, ExoN and 2'-O-MTase activities inhibition, and antiviral activity in hCoV-229E and SARS-CoV-2-infected whole-cell settings. This study reports a novel class of ExoN and/or 2'-O-MTase inhibitors exhibiting antiviral activity against coronaviruses.

Ultra-Sensitive Aptamer-Based Diagnostic Systems for Rapid Detection of All SARS-CoV-2 Variants

The emergence of numerous SARS-CoV-2 variants, characterized by mutations in the viral RNA genome and target proteins, has presented challenges for accurate COVID-19 diagnosis. To address this, we developed universal aptamer probes capable of binding to the spike proteins of SARS-CoV-2 variants, including highly mutated strains like Omicron. These aptamers were identified through protein-based SELEX using spike proteins from three key variants (D614G-substituted Wuhan-Hu-1, Delta, and Omicron) and virus-based SELEX, known as viro-SELEX. Leveraging these universal aptamers, we created a highly sensitive lateral flow assay (LFA) and an ultra-sensitive molecular diagnostic platform that integrates a novel rapid PCR technique, enabling fast and reliable detection across all SARS-CoV-2 variants.

Identification of potential inhibitors for MAP4K4 in glaucoma using meta-dynamics-based dissociation free energy calculation

Glaucoma, a prevalent eye ailment causing irreversible vision loss, affects over 295 million individuals globally, necessitating the exploration of novel therapeutic avenues. Despite extensive research on targets like the phosphodiesterase enzyme and rho kinase, the potential of MAP4K4 in glaucoma remains untapped. This study aims to identify potent MAP4K4 inhibitors to counteract retinal cell apoptosis and oxidative stress associated with glaucoma. Using HTVS and XP docking, 911,059 compounds were screened. The MMGBSA calculation and pharmacokinetics analysis were used to shortlist the compounds. After performing 75 molecular dynamics simulations, further meta-dynamics were employed to calculate dissociation-free energy and find potential MAP4K4 inhibitors. Findings indicated that ZINC06717217 and ZINC38836256 exhibited remarkable promise, with docking scores of -9.57 and -11.12 and MMGBSA binding energies of -91.07 kcal/mol and -87.52 kcal/mol, respectively. Comparative analysis with the reference compound Q27453723 underscored their superior stability, requiring dissociation-free energies of -15.11 kcal/mol and -12.46 kcal/mol to disengage from the docked complex. This underscored their robust binding affinity. ZINC06717217 and ZINC38836256 show promising stability and strong binding to the MAP4K4 protein. Hence, these findings are promising in inhibiting MAP4K4 for glaucoma treatment, potentially leading to more effective treatment and curing blindness. KEY MESSAGES: First to incorporate the dissociation-free energy for identifying compounds for glaucoma treatment. In-silico analysis showed that ZINC06717217 and ZINC38836256 are promising compounds for targeting MAP4K4.

SARS-CoV-2 nsp1 mediates broad inhibition of translation in mammals

SARS-CoV-2 nonstructural protein 1 (nsp1) promotes innate immune evasion by inhibiting host translation in human cells. However, the role of nsp1 in other host species remains elusive, especially in bats which are natural reservoirs of sarbecoviruses and possess a markedly different innate immune system than humans. Here, we reveal that SARS-CoV-2 nsp1 potently inhibits translation in bat cells from Rhinolophus lepidus, belonging to the same genus as known sarbecovirus reservoirs hosts. We determined a cryo-electron microscopy structure of SARS-CoV-2 nsp1 bound to the Rhinolophus lepidus 40S ribosome and show that it blocks the mRNA entry channel via targeting a highly conserved site among mammals. Accordingly, we found that nsp1 blocked protein translation in mammalian cell lines from several species, underscoring its broadly inhibitory activity and conserved role in numerous SARS-CoV-2 hosts. Our findings illuminate the arms race between coronaviruses and mammalian host immunity (including bats), providing a foundation for understanding the determinants of viral maintenance in bat hosts and spillovers.

Genetic proxies for clinical traits are associated with increased risk of severe COVID-19

Routine use of genetic data in healthcare is much-discussed, yet little is known about its performance in epidemiological models including traditional risk factors. Using severe COVID-19 as an exemplar, we explore the integration of polygenic risk scores (PRS) into disease models alongside sociodemographic and clinical variables. PRS were optimized for 23 clinical variables and related traits previously-associated with severe COVID-19 in up to 450,449 UK Biobank participants, and tested in 9,560 individuals diagnosed in the pre-vaccination era. Associations were further adjusted for (i) sociodemographic and (ii) clinical variables. Pathway analyses of PRS were performed to improve biological understanding of disease. In univariate analyses, 17 PRS were associated with increased risk of severe COVID-19 and, of these, four remained associated with COVID-19 outcomes following adjustment for sociodemographic/clinical variables: hypertension PRS (OR = 1.1, 95%CI 1.03-1.18), atrial fibrillation PRS (OR = 1.12, 95%CI 1.03-1.22), peripheral vascular disease PRS (OR = 0.9, 95%CI 0.82-0.99), and Alzheimer's disease PRS (OR = 1.14, 95%CI 1.05-1.25). Pathway analyses revealed enrichment of genetic variants in pathways for cardiac muscle contraction (genes N = 5; beta[SE] = 3.48[0.60]; adjusted-P = 1.86 × 10-5). These findings underscore the potential for integrating genetic data into epidemiological models and highlight the advantages of utilizing multiple trait PRS rather than a single PRS for a specific outcome of interest.

Impact of SARS-CoV-2 vaccination and of seasonal variations on the innate immune inflammatory response

Introduction

The innate immune response is an important first checkpoint in the evolution of an infection. Although adaptive immunity is generally considered the immune component that retains antigenic memory, innate immune responses can also be affected by previous stimulations. This study evaluated the impact of vaccination on innate cell activation by TLR7/8 agonist R848, as well as seasonal variations.

Methods

To this end, blood samples from a cohort of 304 food and retail workers from the Quebec City region were collected during three visits at 12-week intervals. Peripheral blood mononuclear cells and polymorphonuclear neutrophils were isolated during the first and third visits and were stimulated with R848 to assess the innate immune response.

Results

Our results show that IL-8 production after stimulation decreased after vaccination. In addition, the IL-8 response was significantly different depending on the season when the visit occurred, for both COVID-19 vaccinated and unvaccinated individuals.

Discussion

This study highlights that innate immune responses can be affected by SARS-CoV-2 vaccination and fluctuate seasonally.

Green Synthesis of Tetrahydropyrazino[2,1-a:5,4-a']diisoquinolines as SARS-CoV-2 Entry Inhibitors

A class of tetrahydropyrazino[2,1-a:5,4-a']diisoquinoline derivatives were synthesized under environmentally friendly conditions using water as the solvent. The 3-D structures of some synthesized compounds were determined by X-ray diffraction. Since naturally occurring isoquinoline alkaloids have significant antiviral activities against a wide range of viruses, including coronaviruses, the synthesized compounds were assayed for their inhibitory activities against SARS-CoV-2. Our results showed that the active compounds 50 and 96 blocked the delta SARS-CoV-2 entry into VeroE6 cells to display EC50 of 26.5 ± 6.9 and 17.0 ± 3.7 μM, respectively, by inhibiting the interaction between SARS-CoV-2 Spike's receptor binding domain (RBD) and human receptor angiotensin-converting enzyme 2 (ACE2), and CC50 greater than 100 μM. This study provides a green synthesis method of tetrahydropyrazinodiisoquinoline for antiviral or other applications.

Assessment of upper respiratory and gut bacterial microbiomes during COVID-19 infection in adults: potential aerodigestive transmission

SARS-CoV-2 is the viral pathogen responsible for COVID-19. Although morbidity and mortality frequently occur as a result of lung disease, the gastrointestinal (GI) tract is recognized as a primary location for SARS-CoV-2. Connections and interactions between the microbiome of the gut and respiratory system have been linked with viral infections via what has been referred to as the 'gut-lung axis' with potential aerodigestive communication in health and disease. This research explored the relationship between the microbiomes of the upper respiratory and GI tracts in patients with COVID-19 and examined Extraesophageal reflux (EOR), a mechanism which could contribute to dysregulated communication between the GI and respiratory tract (as identified in COVID-19). 97 patients with a laboratory diagnosis of COVID-19 infection, and 50 age-matched controls were recruited and stool, saliva and sputum were obtained from each participant. ELISA Pepsin tests and Reflux Symptom Index scores (RSI) were conducted for EOR assessment. DNA sequencing of the V4 region of the 16 S rRNA gene was performed for microbiome analysis. No differences were observed between the fecal microbiome's alpha and Shannon diversity indices; however, a distinct microbial composition was observed in COVID-19 patients (when compared to the controls). The respiratory microbiota from individuals with COVID-19 demonstrated a statistically significant reduction in Shannon diversity and bacterial richness alongside an overall reduction in the prevalence of organisms from a typical healthy respiratory microbiome. Furthermore, the bacterial richness of the stool and sputum samples was significantly lower among COVID-19 patients admitted to ICU. A significantly higher RSI score and salivary pepsin level were detected among those with COVID-19. The data indicates that COVID-19 is associated with a dysregulation of both the gut and lung microbiome with a more marked perturbation in the lung, particularly among COVID-19 patients who had been admitted to the ICU. The presence of increased RSI scores, combined with elevated levels of Pepsin, suggests that increased micro-aspiration may occur, which is consistent with of under-recognized interactions between the GI and lung microbiomes in COVID-19 patients and requires additional study. Such studies would benefit from the insights provided by biological samples which reflect the continuum of the aerodigestive tract.

Hormonal Implications of SARS-CoV-2: A Review of Endocrine Disruptions

To improve medical care and rehabilitation algorithms for patients affected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), it is important to evaluate and summarize the available data on the effect of coronavirus infection (COVID-19) on the endocrine system. The purpose of this review was to study the effect of COVID-19 on the endocrine system. The scientific novelty of this study is the evaluation of the effect of coronavirus infection on the endocrine system and the potential effect of hormones on susceptibility to COVID-19. The results of this review show that the endocrine system is vulnerable to disorders caused by COVID-19, mainly thyroid dysfunction and hyperglycemia. The information in the published literature mentioned here contains some unclear aspects and contradictory data, but much remains to be studied and clarified regarding the impact of COVID-19 on the endocrine system. In particular, this concerns the study of the hyperglycemic status of patients who have had coronavirus infection, which is extremely important for the future metabolic health of COVID-19 survivors. This review contributes to the scientific discourse by systematically synthesizing disparate studies to identify patterns, gaps, and emerging trends in the literature concerning the effects of COVID-19 on the endocrine system. By integrating these findings, this study offers a novel perspective on potential hormonal interactions influencing COVID-19 susceptibility and outcomes, proposing new hypotheses and frameworks for future research.

Challenges faced by the Iranian health system in containing COVID-19: insights from a conventional content analysis

BACKGROUND

The COVID-19 pandemic is a global crisis, and health systems worldwide have faced numerous challenges in containing it. This study aimed to identify the challenges faced by the Iranian health system in controlling the COVID-19 pandemic.

METHODS

A conventional content analysis approach was employed in this qualitative study. The research sample included experts responsible for managing, making decisions about preventing COVID-19, and caring for and treating patients. The purposive sampling technique was used to select the participants. Data saturation was achieved after 29 interviews. Additionally, conventional content analysis was applied for data analysis.

RESULTS

The participants in this study identified the most significant challenges faced by Iran's health system in controlling the COVID-19 pandemic, including issues related to human resources, physical and organizational structures, financial resources, inter-sectoral collaboration, personal protective equipment (PPE), social responsibility, and information services.

CONCLUSIONS

Identifying these challenges can help health system managers prioritize the most critical issues. Addressing these challenges requires more than just the efforts of health systems; cooperation at the macro governance level is essential. Governments should start planning to formulate appropriate strategies.

In silico Evaluation of H1-Antihistamine as Potential Inhibitors of SARS-CoV-2 RNA-dependent RNA Polymerase: Repurposing Study of COVID-19 Therapy

Introduction

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), from the family Coronaviridae, is the seventh known coronavirus to infect humans and cause acute respiratory syndrome. Although vaccination efforts have been conducted against this virus, which emerged in Wuhan, China, in December 2019 and has spread rapidly around the world, the lack of an Food and Drug Administration-approved antiviral agent has made drug repurposing an important approach for emergency response during the COVID-19 pandemic. The aim of this study was to investigate the potential of H1-antihistamines as antiviral agents against SARS-CoV-2 RNA-dependent RNA polymerase enzyme.

Materials and Methods

Using molecular docking techniques, we explored the interactions between H1-antihistamines and RNA-dependent RNA polymerase (RdRp), a key enzyme involved in viral replication. The three-dimensional structure of 37 H1-antihistamine molecules was drawn and their energies were minimized using Spartan 0.4. Subsequently, we conducted a docking study with Autodock Vina to assess the binding affinity of these molecules to the target site. The docking scores and conformations were then visualized using Discovery Studio.

Results

The results examined showed that the docking scores of the H1-antihistamines were between 5.0 and 8.3 kcal/mol. These findings suggested that among all the analyzed drugs, bilastine, fexofenadine, montelukast, zafirlukast, mizolastine, and rupatadine might bind with the best binding energy (< -7.0 kcal/mol) and inhibit RdRp, potentially halting the replication of the virus.

Conclusion

This study highlights the potential of H1-antihistamines in combating COVID-19 and underscores the value of computational approaches in rapid drug discovery and repurposing efforts. Finally, experimental studies are required to measure the potency of H1-antihistamines before their clinical use against COVID-19 as RdRp inhibitors.

Herbal and Dietary Supplements as Adjunctive Treatment for Mild SARS-CoV-2 Infection in Italy

During the COVID-19 pandemic, several observational studies proved a certain efficacy of nutraceuticals, herbal products, and other dietary supplements as adjuvant therapies used alongside antiviral drugs. Although their use has not been widespread in Italy, according to preliminary evidence, many supplements with demonstrated immunomodulatory effects, such as vitamins C and D, herbal medicines and essential oils, might relieve the respiratory symptoms of COVID-19, since SARS-CoV-2 can activate inflammasome-mediated inflammatory signaling pathways. Other observational studies have shown that herbal treatments, such as Echinacea purpurea and ginseng, help alleviate respiratory symptoms and reduce serum levels of inflammatory cytokines, which are typically overexpressed in both adult and pediatric SARS-CoV-2 patients. Further, vitamins C and D can attenuate the immune response thanks to their cytokine suppression ability and to their known antimicrobial activity and potential to modulate T helper cell response. The strong immune response triggered by SARS-CoV-2 infection is responsible for the severity of the disease. Preliminary data have also shown that L-arginine, an endothelial-derived relaxing factor, is able to modulate endothelial damage, which appears to be one of the main targets of this systemic disease. Finally, some essential oils and their isolated compounds, such as eucalyptol, may be helpful in reducing many of the respiratory symptoms of COVID-19, although others, such as menthol, are not recommended, since it can lead to an undervaluation of the clinical status of a patient. In this narrative review, despite the lack of strong evidence in this field, we aimed to give an overview of the current available literature (mainly observational and cross-sectional studies) regarding herbal products and dietary supplements and their use in the treatment of mild disease from SARS-CoV-2 infection. Obviously, dietary supplements and herbal products do not constitute a standardized treatment for COVID-19 disease, but they could represent an adjunctive and useful treatment when used together with antivirals.

Evaluating the Synergistic Effects of Multi-Epitope Nanobodies on BA.2.86 Variant Immune Escape

Addressing the frequent emergence of SARS-CoV-2 mutant strains requires therapeutic approaches with innovative neutralization mechanisms. The targeting of multivalent nanobodies can enhance potency and reduce the risk of viral escape, positioning them as promising drug candidates. Here, the synergistic mechanisms of the two types of nanobodies are investigated deeply. Our research revealed that the Fu2-1-Fu2-2 system exhibited significant synergy, whereas the Sb#15-Sb#68 system demonstrated antagonism, in which entropy was the dominant contributor to antagonism. Conformational analysis further demonstrated that the presence of a monomeric nanobody influenced the flexibility of residues near other epitopes, thereby affecting the overall synergy of the systems. Moreover, we identified that changes in the hydrogen bond network and the charge of residues played a critical role in the binding between nanobodies and spike. We hope this study will provide novel insights into the development of multivalent nanobody combinations.

Molecular characterization of swine acute diarrhea syndrome coronavirus detected in Vietnamese pigs

Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a novel porcine coronavirus that was recently identified in southern China in 2017. At present, there is a lack of nationwide epidemiological investigations of the newly emerged SADS-CoV. Because Vietnam is geographically adjacent to southern China, many diseases have spread from China to Vietnam. To assess SADS-CoV transmission to Vietnam, we conducted a retrospective study to detect SADS-CoV in samples collected from pig farms in northern Vietnam. Among the 69 fecal samples tested, 5 were positive for SADS-CoV. The spike gene sequence showed high genetic homology with strains circulating in China. Our study is the first to show that SADS-CoV has spread from China to Vietnam and highlights the need for global epidemiological investigations of SADS-CoV.

Research Status and Direction of Chronic Obstructive Pulmonary Disease Complicated with Coronary Heart Disease: A Bibliometric Analysis from 2005 to 2024

Objective

There is increasing evidence that chronic obstructive pulmonary disease (COPD) is associated with coronary heart disease (CHD). In this study, we provide valuable insights in the field by examining the evolution of the relationship between COPD and CHD over the past 20 years.

Methods

A comprehensive computer search was conducted in the Web of Science (WOS) core dataset, covering literature on COPD combined with CHD from January 1, 2005, to August 20, 2024. Visual analyses were performed using VOSviewer, CiteSpace, and Bibliometrix to assess countries, institutions, the centrality of institutional intermediaries, authorship patterns, including co-cited authors and references, and keywords; Excel (version 2021) software was utilized for generating relevant descriptive analysis tables.

Results

A total of 2420 publications sourced from WOS were included in this study. Since 2005, there has been a continuous increase in the literature about COPD combined with CHD; polynomial fitting yielded an R² value of 0.7758. The volume of literature in this domain is projected to continue growing steadily. The United States emerged as the leading country by publication count; Lin Cheng-li ranked first among authors, while China Medical University topped institutional contributions. Notably, Sin dd, Mannino dm, and Helvaci Mr were identified as the top three authors based on citation frequency. The Journal of Vascular Surgery recorded the highest number of publications, whereas The Lancet was recognized as the most influential among the top ten co-cited journals. The most frequently cited reference pertains to systemic inflammation's role in increasing cardiovascular risk among patients with COPD. Through keyword clustering analysis, we categorized all keywords into three distinct groups: management strategies for COPD and CHD; diseases associated with both conditions; and epidemiological characteristics concerning their burden-current hotspots include multimorbidity factors such as hypertension and obesity alongside outcomes like diagnosis during COVID-19 pandemic implications within societal contexts are highlighted here too.

Conclusion

Presently focused research on COPD coupled with CHD primarily revolves around five key areas: pathogenesis exploration, early diagnostic techniques, COVID-19 infection, dynamics intervention, methodologies, and treatment protocol development efforts. To improve the early detection rate of COPD complicated with CHD, the main development direction in the future is to extract computed tomography (CT) features using imaging omics and establish an early prediction model. The results of this study will provide new ideas and directions for subsequent related research.

The Conformational Space of the SARS-CoV-2 Main Protease Active Site Loops Is Determined by Ligand Binding and Interprotomer Allostery

The main protease (Mpro) of SARS-CoV-2 is essential for viral replication and is, therefore, an important drug target. Here, we investigate two flexible loops in Mpro that play a role in catalysis. Using all-atom molecular dynamics simulations, we analyze the structural ensemble of Mpro in an apo state and substrate-bound state. We find that the flexible loops can adopt open, intermediate (partly open), and closed conformations in solution, which differs from the partially closed state observed in crystal structures of Mpro. When the loops are in closed or intermediate states, the catalytic residues are more likely to be in close proximity, which is crucial for catalysis. Additionally, we find that substrate binding to one protomer of the homodimer increases the frequency of intermediate states in the bound protomer while also affecting the structural propensity of the apo protomer's flexible loops. Using dynamic network analysis, we identify multiple allosteric pathways connecting the two active sites of the homodimer. Common to these pathways is an allosteric hotspot involving the N-terminus, a critical region that comprises part of the binding pocket. Taken together, the results of our simulation study provide detailed insight into the relationships between the flexible loops and substrate binding in a prime drug target for COVID-19.

The impact of inflammatory response on psychological status of medical staff during COVID-19 pandemic

BACKGROUND

Limited research has been conducted on the relationship between inflammatory markers and psychological status in medical staff fighting COVID-19.

OBJECTIVE

This article examines the psychological and inflammatory conditions of medical personnel working on the front lines of the battle against COVID-19.

METHODS

A total of 102 clinical staff members were included in this study. All subjects received the Symptom Checklist-90 questionnaire (SCL-90) and Posttraumatic Stress Disorder Checklist-Civilian questionnaires for assessing different mental symptoms. The levels of various inflammatory markers, including IL-1β, IL-2, IL-6, IL-8, TNF-a, and IFN-γ, along with GDNF, were evaluated.

RESULTS

Spearman correlation analysis showed that the levels of IL-6 were positively associated with the anxiety score (Spearman's rho = .230, p = .021), obsessive-compulsive symptoms (Spearman's rho = .201, p = .042). The levels of IL-8 were negatively associated with the anxiety score (Spearman's rho = -.223, p = .028), obsessive-compulsive symptoms (Spearman's rho = -.252, p = .012), hyperarousal (Spearman's rho = -.221, p = .028). The levels of TNF-α were positively associated with the anxiety score (Spearman's rho = .201, p = .045), obsessive-compulsive symptoms (Spearman's rho = .222, p = .035).

CONCLUSION

Generally, our results suggested that IL-6, IL-8 and TNF-α might play a role in the development of psychological symptoms among medical staff.

Dampened TLR2-mediated Inflammatory Signaling in Bats

Bats are considered natural hosts for numerous viruses. Their ability to carry viruses that cause severe diseases or even death in other mammals without falling ill themselves has attracted widespread research attention. Toll-like receptor 2 forms heterodimers with Toll-like receptor 1 or Toll-like receptor 6 on cell membranes, recognizing specific pathogen-associated molecular patterns and playing a key role in innate immune responses. Previous studies have shown that moderate Toll-like receptor 2-mediated immune signals aid in pathogen clearance, while excessive or inappropriate Toll-like receptor 2-mediated immune signals can cause self-damage. In this study, we observed that TLR2, unlike TLR1 or TLR6, has undergone relaxed selection in bats compared with other mammals, indicating a reduced functional constraint on TLR2 specifically in bats. Indeed, our cell-based functional assays demonstrated that the ability of Toll-like receptor 2 to bind with Toll-like receptor 1 or Toll-like receptor 6 was significantly reduced in bats, leading to dampened inflammatory signaling. We identified mutations unique to bats that were responsible for this observation. Additionally, we found that mutations at residues 375 and 376 of Toll-like receptor 2 in the common ancestor of bats also resulted in reduced inflammatory response, suggesting that this reduction occurred early in bat evolution. Together, our study reveals that the Toll-like receptor 2-mediated inflammatory response has been specifically dampened in bats, which may be one of the reasons why they could harbor many viruses without falling ill.

Architects of infection: A structural overview of SARS-related coronavirus spike glycoproteins

The frequency of zoonotic viral emergence within the Coronaviridae family highlights the critical need to understand the structural features of spike proteins that govern viral entry and host adaptation. Investigating the structural conservation and variation in key regions of the spike protein-those involved in host range, binding affinity, viral entry, and immune evasion-is essential for predicting the evolutionary pathways of coronaviruses, assessing the risk of future host-jumping events, and discovering pan-neutralising antibodies. Here we summarise our current structural understanding of the spike proteins similar to SARS-CoV-2 from the Coronaviridae family and compare key functional similarities and differences. Our aim is to demonstrate the significant structural and sequence conservation between spike proteins from a range of host species and to outline the importance of animal coronavirus surveillance and structural investigation in our endeavour for pandemic preparedness against emerging viruses.

Binding ability of Delta and Omicron towards the angiotensin-converting enzyme 2 receptor and antibodies: a computational study

The COVID-19 pandemic posed a threat to global society. Delta and Omicron are concerning variants due to the risk of increasing human-to-human transmissibility and immune evasion. This study aims to evaluate the binding ability of these variants toward the angiotensin-converting enzyme 2 receptor and antibodies using a computational approach. The receptor-binding domain (RBD) of the two variants was created by CHARMM-GUI and then docked to the hACE2 receptor and two antibodies (REGN10933 and REGN10987). These complexes were also subjected to molecular dynamics simulation within 100 ns. As a result, the two variants, Omicron and Delta, exhibited stronger interaction with the hACE2 receptor than the wild type. The mutations in the RBD region also facilitated the virus's escape from antibody neutralization.

Conformational dynamics of the membrane protein of MERS-CoV in comparison with SARS-CoV-2 in ERGIC complex

The present study explores the conformational dynamics of the membrane protein of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) within the Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC) complex using an all-atomistic molecular dynamics simulation approach. Significant structural changes were observed in the N-terminal, C-terminal, transmembrane, and beta-sheet sandwich domains of the MERS-CoV membrane protein. This study also highlights the structural similarities between the MERS-CoV and the SARS-CoV-2 membrane proteins, particularly in how both exhibit a distinct kink in the transmembrane helix caused by aromatic residue-lipid interactions. A structural expansion below the transmembrane and above the beta-sheet sandwich domain within the dimer was observed in all the M-proteins. This site on the beta-sheet sandwich domains near the C-terminal end could serve as a potential drug-binding site. Notably, a stable helical structure was identified in the C-terminal domain of the MERS-CoV membrane protein, whereas a proper secondary structural conformation was not observed in the SARS-CoV-2 membrane protein. Further, the SARS-CoV-2 membrane protein exhibited stronger binding to the lipid bilayer than the MERS-CoV, indicating its greater structural stability within the ERGIC complex. The structural similarity between the membrane protein of MERS-CoV and SARS-CoV-2 suggests the feasibility of employing a common inhibitor against these beta-coronaviruses. Furthermore, this analysis enhances our understanding of the membrane protein's interactions with proteins and lipids, paving the way for therapeutic developments against these viruses.

Two Years of SARS-CoV-2 Omicron Genomic Evolution in Brazil (2022-2024): Subvariant Tracking and Assessment of Regional Sequencing Efforts

SARS-CoV-2, the virus responsible for COVID-19, has undergone significant genetic evolution since its emergence in 2019. This study examines the genomic diversity of SARS-CoV-2 in Brazil after the worst phase of the pandemic, the wider adoption of routine vaccination, and the abolishment of other non-pharmacological preventive measures from July 2022 to July 2024 using 55,951 sequences retrieved from the GISAID database. The analysis focuses on the correlation between confirmed COVID-19 cases, sequencing efforts across Brazilian states, and the distribution and evolution of viral lineages. Our findings reveal significant regional disparities in genomic surveillance, with São Paulo and Rio de Janeiro recovering the largest number of genomes, while Tocantins and Amazonas showed higher sequencing rates relative to their reported case numbers, indicating proactive surveillance efforts. We identified 626 distinct SARS-CoV-2 lineages circulating in Brazil, with dominant subvariants shifting over time from BA.5 in 2022 to XBB and JN.1 in 2023-2024. The emergence of new subvariants in this new epidemiological scenario underscores the importance of ongoing genomic surveillance to track viral evolution and inform public health strategies, providing valuable information to update vaccines and implement other measures, such as lockdowns, mask usage, social distancing, health education, and self-testing.

The role of artificial intelligence in pandemic responses: from epidemiological modeling to vaccine development

Integrating Artificial Intelligence (AI) across numerous disciplines has transformed the worldwide landscape of pandemic response. This review investigates the multidimensional role of AI in the pandemic, which arises as a global health crisis, and its role in preparedness and responses, ranging from enhanced epidemiological modelling to the acceleration of vaccine development. The confluence of AI technologies has guided us in a new era of data-driven decision-making, revolutionizing our ability to anticipate, mitigate, and treat infectious illnesses. The review begins by discussing the impact of a pandemic on emerging countries worldwide, elaborating on the critical significance of AI in epidemiological modelling, bringing data-driven decision-making, and enabling forecasting, mitigation and response to the pandemic. In epidemiology, AI-driven epidemiological models like SIR (Susceptible-Infectious-Recovered) and SIS (Susceptible-Infectious-Susceptible) are applied to predict the spread of disease, preventing outbreaks and optimising vaccine distribution. The review also demonstrates how Machine Learning (ML) algorithms and predictive analytics improve our knowledge of disease propagation patterns. The collaborative aspect of AI in vaccine discovery and clinical trials of various vaccines is emphasised, focusing on constructing AI-powered surveillance networks. Conclusively, the review presents a comprehensive assessment of how AI impacts epidemiological modelling, builds AI-enabled dynamic models by collaborating ML and Deep Learning (DL) techniques, and develops and implements vaccines and clinical trials. The review also focuses on screening, forecasting, contact tracing and monitoring the virus-causing pandemic. It advocates for sustained research, real-world implications, ethical application and strategic integration of AI technologies to strengthen our collective ability to face and alleviate the effects of global health issues.

Genetic and Epigenetic Determinants of COVID-19 Susceptibility: A Systematic Review

BACKGROUND

The molecular mechanisms regulating coronavirus pathogenesis are complex, including virus-host interactions associated with replication and innate immune control. However, some genetic and epigenetic conditions associated with comorbidities increase the risk of hospitalization and can prove fatal in infected patients. This systematic review will provide insight into host genetic and epigenetic factors that interfere with COVID-19 expression in light of available evidence.

METHODS

This study conducted a systematic review to examine the genetic and epigenetic susceptibility to COVID-19 using a comprehensive approach. Through systematic searches and applying relevant keywords across prominent online databases, including Scopus, PubMed, Web of Science, and Science Direct, we compiled all pertinent papers and reports published in English between December 2019 and June 2023.

RESULTS

The findings reveal that the host's HLA genotype plays a substantial role in determining how viral protein antigens are showcased and the subsequent immune system reaction to these antigens. Within females, genes responsible for immune system regulation are found on the X chromosome, resulting in reduced viral load and inflammation levels when contrasted with males. Possessing blood group A may contribute to an increased susceptibility to contracting COVID-19 as well as a heightened risk of mortality associated with the disease. The capacity of SARS-CoV-2 involves inhibiting the antiviral interferon (IFN) reactions, resulting in uncontrolled viral multiplication.

CONCLUSION

There is a notable absence of research into the gender-related predisposition to infection, necessitating a thorough examination. According to the available literature, a significant portion of individuals affected by the ailment or displaying severe ramifications already had suppressed immune systems, categorizing them as a group with elevated risk.

SARS-CoV-2 main protease (M-pro) mutational profiling: An insight into mutation coldspots

SARS-CoV-2 and the COVID-19 pandemic have marked a milestone in the history of scientific research worldwide. To ensure that treatments are successful in the mid-long term, it is crucial to characterize SARS-CoV-2 mutations, as they might lead to viral resistance. Data from >5,700,000 SARS-CoV-2 genomes available at GISAID was used to report SARS-CoV-2 mutations. Given the pivotal role of its main protease (M-pro) in virus replication, a detailed analysis of SARS-CoV-2 M-pro mutations was conducted, with particular attention to mutation-resistant residues or mutation coldspots, defined as those residues that have mutated in five or fewer genomes. 32 mutation coldspots were identified, most of which mediate interprotomer interactions or funneling interaction networks from the substrate-binding site towards the dimerization surface and vice versa. Besides, mutation coldspots were virtually conserved in all main proteases from other CoVs. Our results provide valuable information about key residues to M-pro structure that could be useful in rational target-directed drug design and establish a solid groundwork based on mutation analyses for the inhibition of M-pro dimerization, with a potential applicability to future coronavirus outbreaks.

A20 as a Potential Therapeutic Target for COVID-19

BACKGROUND

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a major concern due to its astonishing prevalence and high fatality rate, especially among elderly people. Patients suffering from COVID-19 may exhibit immunosuppression in the initial stage of infection, while a cytokine storm can occur when the disease progresses to a severe stage. This inopportune immune rhythm not only makes patients more susceptible to the virus but also leads to numerous complications resulting from the excessive production of inflammatory factors. A20, which is widely accepted as a pivotal regulator of inflammation, has been shown to be implicated in the processes of antiviral responses and immunosuppression. Thus, A20 may participate in regulating the pathological processes of COVID-19.

METHODS

This narrative literature review summarizes recent evidence on the mechanisms of A20 in regulating the pathological processes of COVID-19. We also downloaded single-cell RNA-seq data sets from healthy individuals and patients with varying severities of COVID-19 from the NCBI GEO database to further dissect A20's regulatory mechanisms of these intricate cytokine pathways that are closely associated with SARS-CoV-2 infection.

RESULTS

A20 might be one of the most critical anti-infectious and anti-inflammatory factors involved in the pathogenesis of COVID-19. It effectively suppresses the immune damage and inflammatory storm caused by viral infection.

CONCLUSIONS

Understanding the relationship between A20-regulated signaling pathways and pathological processes of COVID-19 can provide insight into potential targets for intervention. Precise regulation of A20 to induce antiviral activity and an anti-inflammatory response could mediate the pathogenesis of COVID-19 and could become an effective treatment.

A 10 Year Long-Lived Cellular and Humoral MERS-CoV Immunity Cross-Recognizing the Wild-Type and Variants of SARS-CoV-2: A Potential One-Way MERS-CoV Cross-Protection Toward a Pan-Coronavirus Vaccine

MERS is a respiratory disease caused by MERS-CoV. Multiple outbreaks have been reported, and the virus co-circulates with SARS-CoV-2. The long-term (> 6 years) cellular and humoral immune responses to MERS-CoV and their potential cross-reactivity to SARS-CoV-2 and its variants are unknown. We comprehensively investigated long-lasting MERS-CoV-specific cellular and humoral immunity, and its cross-reactivity against SARS-CoV-2 and its variants, in individuals recovered from MERS-CoV infection 1-10 years prior. Two cohorts of MERS-CoV survivors (31 unvaccinated, 38 COVID-19 vaccinated) were assessed for MERS-CoV IgG, memory CD4+/CD8+ T cells, and neutralizing antibodies against MERS-CoV and SARS-CoV-2 variants. MERS-CoV IgG levels and T cell responses were higher in the 1-5 vs 6-10 year postinfection groups. Vaccinated MERS-CoV survivors had significantly elevated MERS-CoV IgG and neutralization compared to unvaccinated. Both groups demonstrated cross-reactive neutralization of SARS-CoV-2 variants. MERS-CoV survivors vaccinated against SARS-CoV-2 had higher anti-MERS IgG, cellular immunity, and neutralization than unvaccinated survivors. MERS-CoV immune responses can persist for a decade. COVID-19 vaccination boosted humoral and cellular immunity in MERS-CoV survivors, suggesting the benefits of vaccination for this population. These findings have implications for pan-coronavirus vaccine development.

Possible mechanisms of spermatogenic dysfunction induced by viral infections: Insights from COVID-19

Background

As the COVID-19 pandemic nears resolution in 2024, the mechanisms by which SARS-CoV-2 and other viral infections induce spermatogenic dysfunction remain poorly understood. This review examines the mechanisms by which viral infections, particularly COVID-19, disrupt spermatogenesis and highlights the implications for male reproductive health. While reports suggest that spermatogenic dysfunction caused by COVID-19 is mild and transient, these findings may have broader applications in understanding and treating spermatogenic dysfunction caused by future viral infections.

Methods

The PubMed database was searched to identify original and review articles investigating the mechanisms by which viral infections, particularly SARS-CoV-2, contribute to spermatogenic dysfunction.

Main Findings

SARS-CoV-2 affects the testis through multiple mechanisms, including ACE2 receptor-mediated entry, direct viral damage, inflammatory response, blood-testis barrier disruption, hormonal imbalance, oxidative stress, and impaired spermatogenesis. The combination of these factors can disrupt testicular function and highlights the complexity of the effects of COVID-19 on male reproductive health.

Conclusion

COVID-19 may disrupt spermatogenesis through direct testicular infection, systemic inflammation, hormonal disruption, and oxidative stress. Ongoing research, vaccination efforts, and clinical vigilance are essential to address these challenges and develop effective treatment and prevention strategies.

Investigation of the circulatory microRNAs and their involvement in regulation of inflammation in patients with COVID-19

BACKGROUND

Dysregulated levels of cytokines may lead to cytokine storm, which has been implicated in the immunopathogenesis of coronavirus disease 2019 (COVID-19). Here in the current study, the role of microRNA (miR)-155-5p, miR-146a, and miR-221-3p in the regulation of the immune responses and inflammatory state in patients with COVID-19 was investigated.

METHODS

In this case-control study, peripheral blood samples were obtained from 75 COVID-19 subjects and 100 healthy controls. From the plasma samples, RNA was extracted and cDNA was synthesized, and subsequently the transcript level of miRNAs was measured by Real-time PCR. The plasma levels of interleukin (IL)-4 and interferon (IFN)-γ were determined using ELISA.

RESULTS

miR-155-5p (fold change = 1.87, P = 0.020) and miR-221-3p (fold change = 2.26, P = 0.008), but not miR-146a, was upregulated in the plasma sample of COVID-19 cases compared to controls. The level of IFN-γ (but not IL-4) was significantly higher in the plasma samples of COVID-19 patients compared to control group. The expression level of miR-155-5p (r = 0.35, corrected P = 0.066) and miR-221-3p (r = 0.25, corrected P = 0.066) had positive correlation with the plasma levels of IFN-γ.

CONCLUSIONS

IFN-γ pathway in involved in the pathogenesis of COVID-19 that is regulated through miR-155-5p and miR-221-3p. These miRNAs showed potential utility as biomarkers for predicting the severity of COVID-19.

Humoral Immunity Profiling to Pandemic and Bat-Derived Coronavirus Variants: A Geographical Comparison

Dynamic pathogen exposure may impact the immunological response to SARS-CoV-2 (SCV2). One potential explanation for the lack of severe SCV2-related morbidity and mortality in Southeast Asia is prior exposure to related betacoronaviruses. Recent discoveries of SCV2-related betacoronaviruses from horseshoe bats (Rhinolophus sinicus) in Thailand, Laos, and Cambodia suggest the potential for bat-to-human spillover exposures in the region. In this work, serum antibodies to protein constructs from SCV2 and a representative bat coronavirus isolated in Cambodia (RshSTT182) are measured in pre-pandemic Cambodian human sera using ELISA assays. Of 293 Cambodian samples tested (N = 131 with acute malaria, n = 162 with acute undifferentiated febrile illness), 32 (10.9%) are seropositive for SCV2 based on established Spike and receptor-binding domain (RBD) cutoffs. Within SCV2 seropositive samples, 16 (50%) have higher antibody levels to antigens from the representative virus RshSTT182 versus SCV2 antigens; competitive binding ELISA assays demonstrate inhibition of reactivity to SCV2 Spike after pre-incubation with RshSTT182 Spike. Surrogate virus neutralization tests demonstrate that 8/30 (26.7%) SCV2 ELISA positive pre-pandemic Cambodian samples have neutralizing activity against SCV2, while 14/30 (46.7%) have activity against other SCV2-related betacoronaviruses. These data suggest that exposure to related betacoronaviruses may elicit cross-reactive immunity to SCV2 prior to the global pandemic.

Rapid Generation of Reverse Genetics Systems for Coronavirus Research and High-Throughput Antiviral Screening Using Gibson DNA Assembly

Coronaviruses (CoVs) pose a significant threat to human health, as demonstrated by the COVID-19 pandemic. The large size of the CoV genome (around 30 kb) represents a major obstacle to the development of reverse genetics systems, which are invaluable for basic research and antiviral drug screening. In this study, we established a rapid and convenient method for generating reverse genetic systems for various CoVs using a bacterial artificial chromosome (BAC) vector and Gibson DNA assembly. Using this system, we constructed infectious cDNA clones of coronaviruses from three genera: human coronavirus 229E (HCoV-229E) of the genus Alphacoronavirus, mouse hepatitis virus A59 (MHV-59) of Betacoronavirus, and porcine deltacoronavirus (PDCoV-Haiti) of Deltacoronavirus. Since beta coronaviruses including severe acute respiratory syndrome coronavirus (SARS-CoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and Middle East respiratory syndrome coronavirus (MERS-CoV) represent major human pathogens, we modified the infectious clone of the beta coronavirus MHV-A59 by replacing its NS5a gene with a fluorescent reporter gene to create a system suitable for high-throughput drug screening. Thus, this study provides a practical and cost-effective approach to developing reverse genetics platforms for CoV research and antiviral drug screening.

State-space modelling using wastewater virus and epidemiological data to estimate reported COVID-19 cases and the potential infection numbers

The current situation of COVID-19 measures makes it difficult to accurately assess the prevalence of SARS-CoV-2 due to a decrease in reporting rates, leading to missed initial transmission events and subsequent outbreaks. There is growing recognition that wastewater virus data assist in estimating potential infections, including asymptomatic and unreported infections. Understanding the COVID-19 situation hidden behind the reported cases is critical for decision-making when choosing appropriate social intervention measures. However, current models implicitly assume homogeneity in human behaviour, such as virus shedding patterns within the population, making it challenging to predict the emergence of new variants due to variant-specific transmission or shedding parameters. This can result in predictions with considerable uncertainty. In this study, we established a state-space model based on wastewater viral load to predict both reported cases and potential infection numbers. Our model using wastewater virus data showed high goodness-of-fit to COVID-19 case numbers despite the dataset including waves of two distinct variants. Furthermore, the model successfully provided estimates of potential infection, reflecting the superspreading nature of SARS-CoV-2 transmission. This study supports the notion that wastewater surveillance and state-space modelling have the potential to effectively predict both reported cases and potential infections.

Coronavirus Cryptic Landscape and Draft Genome of a Novel CoV Clade Related to MERS From Bats Circulating in Northeastern Brazil

We identified seven distinct coronaviruses (CoVs) in bats from Brazil, classified into 229E-related (Alpha-CoV), Nobecovirus, Sarbecovirus, and Merbecovirus (Beta-CoV), including one closely related to MERS-like CoV with 82.8% genome coverage. To accomplish this, we screened 423 oral and rectal swabs from 16 different bat species using molecular assays, RNA sequencing, and evolutionary analysis. Notably, gaps in the spike-encoding gene led us to design new primers and perform Sanger sequencing, which revealed high similarities to MERS-related (MERSr) CoV strains found in humans and camels. Additionally, we identified key residues in the receptor-binding domain (RBD) of the spike protein, suggesting potential interactions with DPP4, the receptor for MERSr-CoV. Our analyses also revealed evidence of recombination involving our laboratory-produced sequences. These findings highlight the extensive genetic diversity of CoVs, the presence of novel viral lineages, and the occurrence of recombination events among bat CoVs circulating in Brazil, underscoring the critical role bats play as reservoirs for emerging viruses and emphasizing the necessity of ongoing surveillance to monitor the public health risks associated with CoV spillover events.

SARS-CoV-2 transmission dynamics in Mozambique and Zimbabwe during the first 3 years of the pandemic

The 2019 emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its rapid spread created a public health emergency of international concern. However, the impact of the pandemic in Sub-Saharan Africa, as documented in cases, hospitalizations and deaths, appears far lower than in the Americas, Europe and Asia. Characterization of the transmission dynamics is critical for understanding how SARS-CoV-2 spreads and the true scale of the pandemic. Here, to better understand SARS-CoV-2 transmission dynamics in two southern African countries, Mozambique and Zimbabwe, we developed a dynamic model-Bayesian inference system to estimate key epidemiological parameters, namely the transmission and ascertainment rates. Total infection burdens (reported and unreported) during the first 3 years of the pandemic were reconstructed using a model-inference approach. Transmission rates rose with each successive wave, which aligns with observations in other continents. Ascertainment rates were found to be low and consistent with other African countries. Overall, the estimated disease burden was higher than the documented cases, indicating a need for improved reporting and surveillance. These findings aid understanding of COVID-19 disease and respiratory virus transmission dynamics in two African countries little investigated to date and can help guide future public health planning and control strategies.

A Snapshot of Cytokine Dynamics: A Fine Balance Between Health and Disease

Health and disease are intricately intertwined and often determined by the delicate balance of biological processes. Cytokines, a family of small signalling molecules, are pivotal in maintaining this balance, ensuring the body's immune system functions optimally. In a healthy condition, cytokines act as potent mediators of immune responses. They orchestrate the activities of immune cells, coordinating their proliferation, differentiation, and migration. This intricate role of cytokine signalling enables the body to effectively combat infections, repair damaged tissues, and regulate inflammation. However, the delicate equilibrium of cytokine production is susceptible to disruption. Excessive or abnormal cytokine levels can lead to a cascade of pathological conditions, including autoimmune diseases, chronic inflammation, infections, allergies, and even cancer. Interestingly, from the bunch of cytokines, few cytokines play an essential role in maintaining the balance between normal physiological status and diseases. In this review, we have appraised key cytokines' potential role and feedback loops in augmenting the imbalances in the body's biological functions, presenting a critical link between inflammation and disease pathology. Moreover, we have also highlighted the significance of cytokines and their molecular interplay, particularly in the recent viral pandemic COVID-19 disease. Hence, understandings regarding the interplay between viral infection and cytokine responses are essential and fascinating for developing effective therapeutic strategies.

Exploring the Relationship Between Humoral and Cellular T Cell Responses Against SARS-CoV-2 in Exposed Individuals From Emilia Romagna Region and COVID-19 Severity

COVID-19 remains a significant global health problem with uncertain long-term consequences for convalescents. We investigated the relationships between anti-N protein antibody levels, severe acute respiratory syndrome (SARS)-CoV-2-associated TCR repertoire parameters, HLA type and epidemiological information from three cohorts of 524 SARS-CoV-2-infected subjects subgrouped in acute phase, seronegative and seropositive convalescents from the Emilia Romagna region. Epidemiological information and anti-N antibody index were associated with TCR repertoire data. HLA type was inferred from TCR repertoire using the HLA3 tool and its association with clonal breadth (CB) and clonal depth (CD) was assessed. Age above 58 years, male and COVID-19 hospitalisation were significantly and independently associated with seropositivity (p = 0.004; p = 0.004; p = 0.04), suggesting an association between high antibody titres and symptoms' severity. As for the TCR repertoire analysis, we found no difference in CB among the cohorts, while CD was higher in seronegative than acute (p = 0.04). However, clustering analysis supported that seronegative patients are endowed with broader CB and deeper CD indicating a compensatory mechanism without effective seroconversion. The CD calculated on the TCRs associated with the single SARS-CoV-2 ORFs in convalescents is higher when compared to the acute. Lastly, we identified and reported on novel HLAs significantly associated with increased risk of hospitalisation such as HLA-C*07:02 carriers (OR = 3.9, CI = 1.1-13.4, p = 0.03) and on HLAs that associate significantly with lower or higher TCR repertoire parameters in a population exposed for the first time to SARS-CoV-2.

SARS-CoV-2 Productively Infects Human Hepatocytes and Induces Cell Death

SARS-CoV-2 infection is accompanied by elevated liver enzymes, and patients with pre-existing liver conditions experience more severe disease. While it was known that SARS-CoV-2 infects human hepatocytes, our study determines the mechanism of infection, demonstrates viral replication and spread, and highlights direct hepatocyte damage. Viral replication was readily detectable upon infection of primary human hepatocytes and hepatoma cells with the ancestral SARS-CoV-2, Delta, and Omicron variants. Hepatocytes express the SARS-CoV-2 receptor ACE2 and the host cell protease TMPRSS2, and knocking down ACE2 and TMPRSS2 impaired SARS-CoV-2 infection. Progeny viruses released from infected hepatocytes showed the typical coronavirus morphology by electron microscopy and proved infectious when transferred to fresh cells, indicating that hepatocytes can contribute to virus spread. Importantly, SARS-CoV-2 infection rapidly induced hepatocyte death in a replication-dependent fashion, with the Omicron variant showing faster onset but less extensive cell death. C57BL/6 wild-type mice infected with a mouse-adapted SARS-CoV-2 strain showed high levels of viral RNA in liver and lung tissues. ALT peaked when viral RNA was cleared from the liver. Liver histology revealed profound tissue damage and immune cell infiltration, indicating that direct cytopathic effects of SARS-CoV-2 and immune-mediated killing of infected hepatocytes contribute to liver pathology.

Strengths and limitations of SARS-CoV-2 virus-like particle systems

Virus-like particles (VLPs) resemble the parent virus but lack the viral genome, providing a safe and efficient platform for the analysis of virus assembly and budding as well as the development of vaccines and drugs. During the COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the formation of SARS-CoV-2 VLPs was investigated as an alternative to authentic virions because the latter requires biosafety level 3 (BSL-3) facilities. This allowed researchers to model its assembly and budding processes, examine the role of mutations in variants of concern, and determine how the structural proteins interact with each other. Also, the absence of viral genome in VLPs circumvents worries of gains in infectivity via mutagenesis. This review summarizes the strengths and limitations of several SARS-CoV-2 VLP systems and details some of the strides that have been made in using these systems to study virus assembly and budding, viral entry, and antibody and vaccine development.

Targeted Drug Delivery to ACE2+ Cells Using Engineered Extracellular Vesicles: A Potential Therapeutic Approach for COVID-19

BACKGROUND

Extracellular vesicles (EVs) are emerging as potential drug carriers in the fight against COVID-19. This study investigates the ability of EVs as drug carriers to target SARS-CoV-2-infected cells.

METHODS

EVs were modified using Xstamp technology to carry the virus's RBD, enhancing targeting ability to hACE2+ cells and improving drug delivery efficiency. Characterization confirmed EVs' suitability as drug carriers. For in vitro tests, A549, Caco-2, and 4T1 cells were used to assess the targeting specificity of EVRs (EVs with membrane-surface enriched RBD). Moreover, we utilized an ex vivo lung tissue model overexpressing hACE2 as an ex vivo model to confirm the targeting capability of EVRs toward lung tissue. The study also evaluated drug loading efficiency and assessed the potential of the anti-inflammatory activity on A549 lung cancer cells exposed to lipopolysaccharide.

RESULTS

The results demonstrate the successful construction of RBD-fused EVRs on the membrane- surface. In both in vitro and ex vivo models, EVRs significantly enhance their targeting ability towards hACE2+ cells, rendering them a safe and efficient drug carrier. Furthermore, ultrasound loading efficiently incorporates IL-10 into EVRs, establishing an effective drug delivery system that ameliorates the pro-inflammatory response induced by LPS-stimulated A549 cells.

CONCLUSION

These findings indicate promising opportunities for engineered EVs as a novel nanomedicine carrier, offering valuable insights for therapeutic strategies against COVID-19 and other diseases.

Glutamine metabolism is essential for coronavirus replication in host cells and in mice

Understanding the fundamental biochemical and metabolic requirements for the replication of coronaviruses within infected cells is of notable interest for the development of broad-based therapeutic strategies, given the likelihood of the emergence of new pandemic-potential virus species, as well as future variants of SARS-CoV-2. Here we demonstrate members of the glutaminase family of enzymes (GLS and GLS2), which catalyze the hydrolysis of glutamine to glutamate (i.e., the first step in glutamine metabolism), play key roles in coronavirus replication in host cells. Using a range of human seasonal and zoonotic coronaviruses, we show three examples where GLS expression increases during coronavirus infection of host cells, and another where GLS2 is upregulated. The viruses hijack the metabolic machinery responsible for glutamine metabolism to generate the building blocks for biosynthetic processes and satisfy the bioenergetic requirements demanded by the "glutamine addiction" of virus-infected cells. We demonstrate that genetic silencing of glutaminase enzymes reduces coronavirus infection and that newer members of two classes of allosteric inhibitors targeting these enzymes, designated as SU1, a pan-GLS/GLS2 inhibitor, and UP4, a specific GLS inhibitor, block viral replication in epithelial cells. Moreover, treatment of SARS-CoV-2 infected K18-human ACE2 transgenic mice with SU1 resulted in their complete survival compared to untreated control animals, which succumbed within 10 days post-infection. Overall, these findings highlight the importance of glutamine metabolism for coronavirus replication in human cells and mice and show that glutaminase inhibitors can block coronavirus infection and thereby may represent a novel class of broad-based anti-viral drug candidates.

Broadening sarbecovirus neutralization with bispecific antibodies combining distinct conserved targets on the receptor binding domain

Monoclonal neutralizing antibodies (mAbs) are considered an important prophylactic against SARS-CoV-2 infection in at-risk populations and a strategy to counteract future sarbecovirus-induced disease. However, most mAbs isolated so far neutralize only a few sarbecovirus strains. Therefore, there is a growing interest in bispecific antibodies (bsAbs) which can simultaneously target different spike epitopes and thereby increase neutralizing breadth and prevent viral escape. Here, we generate and characterize a panel of 30 novel broadly reactive bsAbs using an efficient controlled Fab-arm exchange protocol. We specifically combine some of the broadest mAbs described so far, which target conserved epitopes on the receptor binding domain (RBD). Several bsAbs show superior cross-binding and neutralization compared to the parental mAbs and cocktails against sarbecoviruses from diverse clades, including recent SARS-CoV-2 variants. BsAbs which include mAb COVA2-02 are among the most potent and broad combinations. As a result, we study the unknown epitope of COVA2-02 and show that this mAb targets a distinct conserved region at the base of the RBD, which could be of interest when designing next-generation bsAb constructs to contribute to a better pandemic preparedness.

SARS-CoV-2 vaccine-elicited immune responses in solid organ transplant recipients

Solid organ transplant recipients (SOTRs) are considered a high-risk group for coronavirus disease 2019 (COVID-19). The adaptive immune responses generated by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination include humoral and cellular immune responses. Most studies on the SARS-CoV-2 vaccine have focused primarily on humoral immunity, but cellular immunity is vital for effectively controlling progression to severe COVID-19. In SOTRs, the vaccine-induced adaptive immune response is significantly attenuated compared to the response in healthy individuals. Nevertheless, vaccinated SOTRs exhibit a reduced rate and severity of SARS-CoV-2 infection. This review aims to provide a concise overview of the current understanding of SARS-CoV-2 vaccine-induced immune responses in SOTRs.

Childhood vaccination trends during 2019 to 2022 in Tanzania and the impact of the COVID-19 pandemic

The COVID-19 pandemic has significantly disrupted healthcare systems at all levels globally, notably affecting routine healthcare services, such as childhood vaccination. This study examined the impact of these disruptions on routine childhood vaccination programmes in Tanzania. We conducted a longitudinal study over four years in five Tanzanian regions: Mwanza, Dar es Salaam, Mtwara, Arusha, and Dodoma. This study analyzed the trends in the use of six essential vaccines: Bacille Calmette-Guérin (BCG), bivalent Oral Polio Vaccine (bOPV), Diphtheria Tetanus Pertussis, Hepatitis-B and Hib (DTP-HepB-Hib), measles-rubella (MR), Pneumococcal Conjugate Vaccine (PCV), and Rota vaccines. We evaluated annual and monthly vaccination trends using time-series and regression analyses. Predictive modeling was performed using an autoregressive integrated moving average (ARIMA) model. A total of 32,602,734 vaccination events were recorded across the regions from 2019 to 2022. Despite declining vaccination rates in 2020, there was a notable rebound in 2021, indicating the resilience of Tanzania's immunization program. The analysis also highlighted regional differences in vaccination rates when standardized per 1000 people. Seasonal fluctuations were observed in monthly vaccination rates, with BCG showing the most stable trend. Predictive modeling of BCG indicated stable and increasing vaccination coverage by 2023. These findings underscore the robustness of Tanzania's childhood immunization infrastructure in overcoming the challenges posed by the COVID-19 pandemic, as indicated by the strong recovery of vaccination rates post-2020. We provide valuable insights into the dynamics of vaccination during a global health crisis and highlight the importance of sustained immunization efforts to maintain public health.

An adenosine analog shows high antiviral potency against coronavirus and arenavirus mainly through an unusual base pairing mode

By targeting the essential viral RNA-dependent RNA polymerase (RdRP), nucleoside analogs (NAs) have exhibited great potential in antiviral therapy for RNA virus-related diseases. However, most ribose-modified NAs do not present broad-spectrum features, likely due to differences in ribose-RdRP interactions across virus families. Here, we show that HNC-1664, an adenosine analog with modifications both in ribose and base, has broad-spectrum antiviral activity against positive-strand coronaviruses and negative-strand arenaviruses. Importantly, treatment with HNC-1664 demonstrate anti-SARS-CoV-2 efficacy in infected K18-human ACE2 mice, with reduced viral titer and mortality, as well as improved lung injury. Enzymology data demonstrate that HNC-1664 inhibits RNA synthesis mainly at the pre-catalysis stage. The cryo-EM structures of HNC-1664-bound RdRP-RNA complexes from both SARS-CoV-2 and LASV reveal an unusual base pairing mode of HNC-1664 in part due to its base modification, thus revealing its great potency in binding but not catalysis. Under certain circumstances, 1664-TP can be slowly incorporated by RdRP through regular Watson-Crick base pairing, as evidenced by enzymology data and an HNC-1664-incorporated crystal structure of the RdRP-RNA complex. Overall, HNC-1664 achieves broad-spectrum characteristics by favoring an alternative base pairing strategy to non-catalytically block RNA synthesis, providing a novel concept for the rational development of NA drugs.

Systematic surveillance of SARS-CoV-2 reveals dynamics of variant mutagenesis and transmission in a large urban population

Highly mutable pathogens generate viral diversity that impacts virulence, transmissibility, treatment, and thwarts acquired immunity. We previously described C19-SPAR-Seq, a high-throughput, next-generation sequencing platform to detect SARS-CoV-2 that we here deployed to systematically profile variant dynamics of SARS-CoV-2 for over 3 years in a large, North American urban environment (Toronto, Canada). Sequencing of the ACE2 receptor binding motif and polybasic furin cleavage site of the Spike gene in over 70,000 patients revealed that population sweeps of canonical variants of concern (VOCs) occurred in repeating wavelets. Furthermore, we found that VOC mutant derivatives and putative quasispecies that targeted functionally important residues and were found in future VOCs arose frequently, but were always extinguished. Systematic screening of functionally relevant domains in pathogens could thus provide a powerful tool for monitoring spread and mutational trajectories, particularly those with zoonotic potential.

Persistent Health and Cognitive Impairments up to Four Years Post-COVID-19 in Young Students: The Impact of Virus Variants and Vaccination Timing

Background: The long-term consequences of COVID-19 infection are becoming increasingly evident in recent studies. This repeated cross-sectional study aimed to explore the long-term health and cognitive effects of COVID-19, focusing on how virus variants, vaccination, illness severity, and time since infection impact post-COVID-19 outcomes. Methods: We examined three cohorts of university students (N = 584) and used non-parametric methods to assess correlations of various health and cognitive variables with SARS-CoV-2 infection, COVID-19 severity, vaccination status, time since infection, time since vaccination, and virus variants. Results: Our results suggest that some health and cognitive impairments may persist, with some even appearing to progressively worsen-particularly fatigue in women and memory in men-up to four years post-infection. The data further indicate that the ancestral SARS-CoV-2 variant may have the most significant long-term impact, while the Omicron variant appears to have the least. Interestingly, the severity of the acute illness was not correlated with the variant of SARS-CoV-2. The analysis also revealed that individuals who contracted COVID-19 after vaccination had better health and cognitive outcomes compared to those infected before vaccination. Conclusions: Overall, our results indicate that even in young individuals who predominantly experienced only mild forms of the infection, a gradual decline in health and fitness can occur over a span of four years post-infection. Notably, some negative trends-at least in men-only began to stabilize or even reverse during the fourth year, whereas in women, these trends showed no such improvement. These findings suggest that the long-term public health impacts of COVID-19 may be more severe and affect a much broader population than is commonly assumed.

Daphnetin may protect from SARS-CoV-2 infection by reducing ACE2

To combat the SARS-CoV-2 pandemic, innovative prevention strategies are needed, including reducing ACE2 expression on respiratory cells. This study screened approved drugs in China for their ability to downregulate ACE2. Daphnetin (DAP) was found to significantly reduce ACE2 mRNA and protein levels in PC9 cells. DAP exerts its inhibitory effects on ACE2 expression by targeting HIF-1α and JAK2, thereby impeding the transcription of the ACE2 gene. The SARS-CoV-2 pseudovirus infection assay confirmed that DAP-treated PC9 cells exhibited decreased susceptibility to viral infection. At therapeutic doses, DAP effectively lowers ACE2 expression in the respiratory systems of mice and humans. This suggests that DAP, already approved for other conditions, could be a new preventive measure against SARS-CoV-2, offering a cost-effective and accessible way to reduce SARS-CoV-2 spread.

Neutrophil-to-Lymphocyte and Platelet Ratio (N/LP Ratio), a Reliable Criterion for Predicting In-Hospital Mortality in Both Genders Infected With SARS-CoV-2

Background: The neutrophil-to-lymphocyte ratio (NLR), monocyte-to-lymphocyte ratio (MLR), platelet-to-lymphocyte ratio (PLR), derived neutrophil-to-lymphocyte ratio (dNLR), neutrophil-to-lymphocyte and platelet ratio (N/LP ratio), aggregate index of systemic inflammation (AISI), systemic inflammation response index (SIRI), and systemic inflammation index (SII) have emerged as noteworthy determinants in evaluating the severity and mortality prognosis of inflammatory diseases. In order to predict mortality rate, this study aimed to assess the impact of systemic inflammatory markers on both men and women who were admitted to the hospital due to SARS-CoV-2 infection. Methods: The laboratory parameters of the 2007 COVID-19 patients were analyzed in a retrospective study (men = 1145 and women = 862). Receiver operating characteristic (ROC) analysis was used to determine the capability of inflammatory markers to differentiate the severity of COVID-19, while survival probability was determined using Kaplan-Meier curves, with the endpoint being death. To prevent any linear bias, the inflammatory indices were assessed separately using univariate analysis for Charlson comorbidity index (CCI), and adjustments were made for confounding factors if p < 0.2. Results: Adjusted-NLR, adjusted-MLR, N/LP ratio, adjusted-dNLR, adjusted-AISI, adjusted-SII, and adjusted-SIRI exhibited remarkably higher values in patients who did not survive as compared to those who did. The multivariate Cox regression models demonstrated significant association between survival and N/LP ratio (HR = 1.564, 95% CI = 1.161 to 2.107, p < 0.01) in men and N/LP ratio (HR = 1.745, 95% CI = 1.230 to 2.477, p < 0.01) and adjusted-SII (HR = 6.855, 95% CI = 1.454 to 32.321, p < 0.05) in women. Conclusion: A reliable predictor in the current study of men and women with COVID-19 was N/LP ratio.

SARS-CoV-2 Evolution: Implications for Diagnosis, Treatment, Vaccine Effectiveness and Development

The COVID-19 pandemic, driven by the rapid evolution of the SARS-CoV-2 virus, presents ongoing challenges to global public health. SARS-CoV-2 is characterized by rapidly evolving mutations, especially in (but not limited to) the spike protein, complicating predictions about its evolutionary trajectory. These mutations have significantly affected transmissibility, immune evasion, and vaccine efficacy, leading to multiple pandemic waves with over half a billion cases and seven million deaths globally. Despite several strategies, from rapid vaccine development and administration to the design and availability of antivirals, including monoclonal antibodies, already having been employed, the persistent circulation of the virus and the emergence of new variants continue to result in high case numbers and fatalities. In the past four years, immense research efforts have contributed much to our understanding of the viral pathogenesis mechanism, the COVID-19 syndrome, and the host-microbe interactions, leading to the development of effective vaccines, diagnostic tools, and treatments. The focus of this review is to provide a comprehensive analysis of the functional impact of mutations on diagnosis, treatments, and vaccine effectiveness. We further discuss vaccine safety in pregnancy and the implications of hybrid immunity on long-term protection against infection, as well as the latest developments on a pan-coronavirus vaccine and nasal formulations, emphasizing the need for continued surveillance, research, and adaptive public health strategies in response to the ongoing SARS-CoV-2 evolution race.

Is it feasible to use AI-based drug design methods in the process of generating effective COVID-19 inhibitors? A validation study using molecular docking, molecular simulation, and pharmacophore methods

Although the COVID-19 pandemic has been brought under control to some extent globally, there is still debate in the industry about the feasibility of using artificial intelligence (AI) to generate COVID small-molecule inhibitors. In this study, we explored the feasibility of using AI to design effective inhibitors of COVID-19. By combining a generative model with reinforcement learning and molecular docking, we designed small-molecule inhibitors targeting the COVID-19 3CLpro enzyme. After screening based on molecular docking scores and physicochemical properties, we obtained five candidate inhibitors. Furthermore, theoretical calculations confirmed that these candidate inhibitors have significant binding stability with COVID-19 3CLpro, comparable to or better than existing COVID-19 inhibitors. Additionally, through ligand-based pharmacophore model screening, we validated the effectiveness of the generative model, demonstrating the potential value of AI in drug design.