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

Identifying Inhibitor-SARS-CoV2-3CLpro Binding Mechanism Through Molecular Docking, GaMD Simulations, Correlation Network Analysis and MM-GBSA Calculations

The main protease of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), known as 3CLpro, is crucial in the virus's life cycle and plays a pivotal role in COVID-19. Understanding how small molecules inhibit 3CLpro's activity is vital for developing anti-COVID-19 therapeutics. To this end, we employed Gaussian accelerated molecular dynamics (GaMD) simulations to enhance the sampling of 3CLpro conformations and conducted correlation network analysis (CNA) to explore the interactions between different structural domains. Our findings indicate that a CNA-identified node in domain II of 3CLpro acts as a conduit, transferring conformational changes from the catalytic regions in domains I and II, triggered by the binding of inhibitors (7YY, 7XB, and Y6G), to domain III, thereby modulating 3CLpro's activity. Normal mode analysis (NMA) and principal component analysis (PCA) revealed that inhibitor binding affects the structural flexibility and collective movements of the catalytic sites and domain III, influencing 3CLpro's function. The binding free energies, predicted by both MM-GBSA and QM/MM-GBSA methods, showed a high correlation with experimental data, validating the reliability of our analyses. Furthermore, residues L27, H41, C44, S46, M49, N142, G143, S144, C145, H163, H164, M165, and E166, identified through residue-based free energy decomposition, present promising targets for the design of anti-COVID-19 drugs and could facilitate the development of clinically effective 3CLpro inhibitors.

Genetically edited human placental organoids cast new light on the role of ACE2

ACE2 expression is altered in pregnancy disorders and ACE2 gene variants are associated with several major pregnancy complications including small-for-gestational-age, fetal growth restriction and preeclampsia. This study utilised gene-editing to generate both ACE2 knockout and ACE2 rs2074192 placental organoids, facilitating mechanistic studies into the role of ACE2 in placental development, and the effect of fetal carriage of ACE2 rs2074192 CC, CT and TT genotypes. Parameters of cell and organoid growth were measured, together with qPCR, Western Blotting, and ELISA assessments, in all groups from both organoid models. Here, we report that ACE2 knockout results in delayed placental cell growth and increased cell death. ACE2 knockout organoids had lower ACE protein expression, reduced organoid diameters and asymmetrical growth. Placental organoids with the ACE2 rs2074192 TT genotype had significantly higher expression of ACE2 mRNA and ACE2 protein with elevated ACE2:ACE expression ratio and no change in ACE protein. Despite increased expression of ACE2 protein, ACE2 enzyme activity was significantly decreased in ACE2 rs2074192 TT placental organoids. TT organoids also had reduced diameters and asymmetrical growth. Our research provides a new molecular understanding of the role of ACE2 in placental development, with potential implications for pregnancy in the carriage of the ACE2 rs2074192 gene variant.

Frustration In Physiology And Molecular Medicine

Molecules provide the ultimate language in terms of which physiology and pathology must be understood. Myriads of proteins participate in elaborate networks of interactions and perform chemical activities coordinating the life of cells. To perform these often amazing tasks, proteins must move and we must think of them as dynamic ensembles of three dimensional structures formed first by folding the polypeptide chains so as to minimize the conflicts between the interactions of their constituent amino acids. It is apparent however that, even when completely folded, not all conflicting interactions have been resolved so the structure remains 'locally frustrated'. Over the last decades it has become clearer that this local frustration is not just a random accident but plays an essential part of the inner workings of protein molecules. We will review here the physical origins of the frustration concept and review evidence that local frustration is important for protein physiology, protein-protein recognition, catalysis and allostery. Also, we highlight examples showing how alterations in the local frustration patterns can be linked to distinct pathologies. Finally we explore the extensions of the impact of frustration in higher order levels of organization of systems including gene regulatory networks and the neural networks of the brain.

SARS-CoV-2 Variants and Their Impact on Pediatric COVID-19: Clinical Manifestations and Hematological Profiles

BACKGROUND

The aim of this study was to analyze data on pediatric cases of COVID-19 admitted to a tertiary referral hospital in northwest Greece.

METHODS

A retrospective analysis was conducted on the most common clinical manifestations and laboratory findings, stratified by age group and SARS-CoV-2 strain.

RESULTS

A total of 254 children were hospitalized, with a mean age of 4.5 years. Underlying conditions were present in 10.2% of cases; two children required pediatric intensive care unit (PICU) admission, and one child died. The most common hematological manifestations, in general, were neutropenia (30%) and lymphopenia (23%), whereas the findings varied when the children were stratified by age group. Eight children developed multisystem inflammatory syndrome (MIS-C), with the most common findings being anemia (75%), lymphopenia (50%), and thrombocytopenia (25%). Analysis of the SARS-CoV-2 strains revealed the proportions of the dominant strain over time. Fever was the predominant symptom across all strains, particularly in the Omicron group, which also had a high incidence of gastrointestinal symptoms. The longest hospital admission occurred in children with the Omicron strain, followed by the Wuhan, Alpha, and Delta strains.

CONCLUSIONS

Fever was the most consistent symptom across all age groups and virus strains. The most common hematological manifestations were neutropenia (30%) and lymphopenia (23%). The Omicron strain was associated with the longest hospital stay.

Impact of African-Specific ACE2 Polymorphisms on Omicron BA.4/5 RBD Binding and Allosteric Communication Within the ACE2-RBD Protein Complex

Severe acute respiratory symptom coronavirus 2 (SARS-CoV-2) infection occurs via the attachment of the spike (S) protein's receptor binding domain (RBD) to human ACE2 (hACE2). Natural polymorphisms in hACE2, particularly at the interface, may alter RBD-hACE2 interactions, potentially affecting viral infectivity across populations. This study identified the effects of six naturally occurring hACE2 polymorphisms with high allele frequency in the African population (S19P, K26R, M82I, K341R, N546D and D597Q) on the interaction with the S protein RBD of the BA.4/5 Omicron sub-lineage through post-molecular dynamics (MD), inter-protein interaction and dynamic residue network (DRN) analyses. Inter-protein interaction analysis suggested that the K26R variation, with the highest interactions, aligns with reports of enhanced RBD binding and increased SARS-CoV-2 susceptibility. Conversely, S19P, showing the fewest interactions and largest inter-protein distances, agrees with studies indicating it hinders RBD binding. The hACE2 M82I substitution destabilized RBD-hACE2 interactions, reducing contact frequency from 92 (WT) to 27. The K341R hACE2 variant, located distally, had allosteric effects that increased RBD-hACE2 contacts compared to WThACE2. This polymorphism has been linked to enhanced affinity for Alpha, Beta and Delta lineages. DRN analyses revealed that hACE2 polymorphisms may alter the interaction networks, especially in key residues involved in enzyme activity and RBD binding. Notably, S19P may weaken hACE2-RBD interactions, while M82I showed reduced centrality of zinc and chloride-coordinating residues, hinting at impaired communication pathways. Overall, our findings show that hACE2 polymorphisms affect S BA.4/5 RBD stability and modulate spike RBD-hACE2 interactions, potentially influencing SARS-CoV-2 infectivity-key insights for vaccine and therapeutic development.

Severity and risk to inhalation of pathogen-laden aerosol in large public spaces: Insights from fangcang shelter hospitals under multi-location release

The key to strengthening the inherent safety of large public spaces and implementing precise preventive measures lies in clarifying the transmission risks of respiratory infectious diseases based on multiple factors. This work innovatively improves a pathogen inhalation infection risk prediction model and attempts to apply it to a Fangcang Shelter Hospital to investigate the effect of pathogen release location on risk distribution and the role of airflow distribution in risk control mechanisms. The model used in the study improved in resolution and accuracy, shedding light on the airflow distribution mechanisms involved in pathogen transport and risk control, thus providing a quantitatively realistic landscape of the spread of respiratory infectious diseases in large indoor environments. Predictions reveal a significant unevenness in the spatial distribution of infection probabilities within the multi-patient shelter unit, which is further exacerbated by different release locations, and that extreme infection risks can reach 4 to 14 times the average. Additionally, the study noted that the infection probability in the medical staff area due to the long-distance transmission of contaminants can reach as high as 1.72 % and that patients from ward 6# could potentially infect a healthcare worker every four days.

Insilico targeting of virus entry facilitator NRP1 to block SARS-CoV2 entry

The entry and infectivity of a virus are determined by its interaction with the host. SARS-CoV-2, the virus responsible for COVID-19, utilizes the spike (S) protein to attach to and enter host cells. Recent studies have identified neuropilin-1 (NRP1) as a crucial facilitator for the entry of SARS-CoV-2. The binding of the spike protein to the b1 domain of NRP1 has been shown to enhance viral infection twofold. Consequently, targeting NRP1 to disrupt this interaction represents a promising strategy to mitigate viral infection. In this study, a small molecule library of approximately 10,000 compounds was screened to identify those that could inhibit the interaction between NRP1 and the spike protein by targeting the b1 domain of NRP1. The crystallographic structure of the b1 domain of human NRP1 (PDB entry: 7JJC) was used for this purpose. Following virtual screening, docking studies, and evaluation of binding affinity and ADMET properties, 10 compounds were shortlisted. The top two candidates, AZD3839 and LY2090314, were selected for molecular dynamics simulation studies over 100 ns to assess binding stability. MM/GBSA calculations indicated that both AZD3839 and LY2090314 exhibited strong and stable binding to the b1 domain of NRP1. Computational modeling of the interaction between the b1 domain of NRP1 and the receptor-binding domain of the spike protein suggested that AZD3839 and LY2090314 could effectively hinder the NRP1-spike interaction. Therefore, these compounds may serve as potential drug candidates to reduce SARS-CoV-2 infectivity.

Ocular neuroinflammatory response secondary to SARS-CoV-2 infection-a review

With the consistent occurrence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the prevalence of various ocular complications has increased over time. SARS-CoV-2 infection has been shown to have neurotropism and therefore to lead to not only peripheral inflammatory responses but also neuroinflammation. Because the receptor for SARS-CoV-2, angiotensin-converting enzyme 2 (ACE2), can be found in many intraocular tissues, coronavirus disease 2019 (COVID-19) may also contribute to persistent intraocular neuroinflammation, microcirculation dysfunction and ocular symptoms. Increased awareness of neuroinflammation and future research on interventional strategies for SARS-CoV-2 infection are important for improving long-term outcomes, reducing disease burden, and improving quality of life. Therefore, the aim of this review is to focus on SARS-CoV-2 infection and intraocular neuroinflammation and to discuss current evidence and future perspectives, especially possible connections between conditions and potential treatment strategies.

Establishment of a bat lung organoid culture model for studying bat-derived infectious diseases

Bat is considered a natural reservoir of various important pathogens, including severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2, Ebola virus, and Nipah virus. To study these viruses' pathogenicity and proliferation efficacy and viral tolerance mechanisms in bats, bat-derived cell lines, and primary cultured cells are used. However, these do not adequately reflect the exact biology of bats, and establishing new bat-related research models is necessary. Organoid culture can recapitulate organ structure, functions, and diseases. The respiratory tract is one of the primary routes of viral infection, and the establishment of bat lung organoids (BLO) is necessary to study the viral susceptibility in bats. Therefore, we aimed to establish a culture method of BLO from Rousettus leschenaultia that died of natural causes. The generated BLO successfully recapitulated the characteristics of pulmonary epithelial structure and morphology. BLO expressed the entry receptors for coronavirus, Angiotensin-converting enzyme 2 (ACE2), and Transmembrane Protease Serine 2 (TMPRSS2), and alveolar type 2 cells were successfully sorted from BLO, which has an important role for the development of viral infection in the respiratory system. Furthermore, we showed that BLO had no susceptibility to Pteropine orthoreovirus (PRV) compared to bat intestinal organoids. Collectively, our established bat organoid culture models including this BLO might become promising in vitro biomaterials to study the biology of bat-derived infectious diseases.

Single-cell and Spatial Transcriptomics Illuminate Bat Immunity and Barrier Tissue Evolution

Bats have adapted to pathogens through diverse mechanisms, including increased resistance-rapid pathogen elimination, and tolerance-limiting tissue damage following infection. In the Egyptian fruit bat (an important model in comparative immunology), several mechanisms conferring disease tolerance were discovered, but mechanisms underpinning resistance remain poorly understood. Previous studies on other species suggested that the elevated basal expression of innate immune genes may lead to increased resistance to infection. Here, we test whether such transcriptional patterns occur in Egyptian fruit bat tissues through single-cell and spatial transcriptomics of gut, lung, and blood cells, comparing gene expression between bat, mouse, and human. Despite numerous recent loss and expansion events of interferons in the bat genome, interferon expression and induction are remarkably similar to that of mouse. In contrast, central complement system genes are highly and uniquely expressed in key regions in bat lung and gut epithelium, unlike in human and mouse. Interestingly, the unique expression of these genes in the bat gut is strongest in the crypt, where developmental expression programs are highly conserved. The complement system genes also evolve rapidly in their coding sequences across the bat lineage. Finally, the bat complement system displays strong hemolytic activity. Together, these results indicate a distinctive transcriptional divergence of the complement system, which may be linked to bat resistance, and highlight the intricate evolutionary landscape of bat immunity.

Intra-host variability of SARS-CoV-2: Patterns, causes and impact on COVID-19

Intra-host viral variability is related to pathogenicity, persistence, drug resistance, and the emergence of new clades. This work reviews the large amount of data on SARS-CoV-2 intra-host variability accumulated to date, addressing known and potential implications in COVID-19 and the emergence of VOCs and lineage-defining mutations. Topics covered include the distribution of intra-host polymorphisms across the genome, the corresponding mutational signatures, their patterns of emergence and extinction throughout infection, and the processes governing their abundance, frequency, and type (synonymous, nonsynonymous, indels, nonsense). Besides, evidence is reviewed that the virus can replicate and mutate in isolation at different anatomical compartments, which may imply that what we have learned from respiratory samples could be part of a broader picture.

Comparative study of alpha, beta, and omicron spike protein by computing the IR/Raman frequencies and UV-vis adsorption - A computational analysis through DFT

The outbreak of COVID-19 coronavirus disease around the end of 2019 was a pandemic. The virus has been mutated and so many strains like Alpha, Beta, and Omicron are present in different parts of the world. Hence, timely detection technique is important to overcome the diagnostic challenges. Considering the need for this pandemic situation, we used a spectroscopy test methodology to distinguish different strains of Covid-19 by computing the infrared & Raman frequencies and the optical absorption data. Optimization of spike protein of Alpha, and Omicron mutations showed the high value of dipole moment (4.44, and 4.36) Debye, and polarizability [Alpha (233.62), Omicron (228.65)] indicating more bioactivity of Alpha and Omicron instead of Beta. Molecular electrostatic potential map exhibits the presence of electrophilic and nucleophilic region suggesting charge transfer of spikes to accept/donate electrons and hence the system increased reactiveness. UV-Vis absorption analysis also shows electronic transitions (σ to π∗ and π to π∗) due to that protein probe mechanism of Alpha and Omicron becomes increasingly become unsaturated thus confirming its easy binding ability to the target human protein as compared to binding affinity of Beta spike protein.

A multiplex method for rapidly identifying viral protease inhibitors

With current treatments addressing only a fraction of pathogens and new viral threats constantly evolving, there is a critical need to expand our existing therapeutic arsenal. To speed the rate of discovery and better prepare against future threats, we establish a high-throughput platform capable of screening compounds against 40 diverse viral proteases simultaneously. This multiplex approach is enabled by using cellular biosensors of viral protease activity combined with DNA-barcoding technology, as well as several design innovations that increase assay sensitivity and correct for plate-to-plate variation. Among >100,000 compound-target interactions explored within our initial screen, a series of broad-acting inhibitors against coronavirus proteases were uncovered and validated through orthogonal assays. A medicinal chemistry campaign was performed to improve one of the inhibitor's potency while maintaining its broad activity. This work highlights the power of multiplex screening to efficiently explore chemical space at a fraction of the time and costs of previous approaches.

ACE2, From the Kidney to SARS-CoV-2: Donald Seldin Award Lecture 2023

ACE2 (angiotensin-converting enzyme 2) is a monocarboxypeptidase that cleaves Ang II (angiotensin II) among other substrates. ACE2 is present in the cell membrane of many organs, most abundantly in epithelial cells of kidney proximal tubules and the small intestine, and also exists in soluble forms in plasma and body fluids. Membrane-bound ACE2 exerts a renoprotective action by metabolizing Ang II and therefore attenuating the undesirable actions of excess Ang II. Therefore, soluble ACE2, by downregulating this peptide, may exert a therapeutic action. Our laboratory has designed ACE2 truncates that pass the glomerular filtration barrier to target the kidney renin-angiotensin system directly and, therefore, compensate for loss of kidney membrane-bound ACE2. Membrane-bound ACE2 is also the essential receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Soluble ACE2 proteins have been studied as a way to intercept SARS-CoV-2 from binding to membrane-bound ACE2 and prevent cell entry of SARS-CoV-2 altogether. We bioengineered a soluble ACE2 protein, termed ACE2 618-DDC-ABD, with increased binding affinity for SARS-CoV-2 and prolonged duration of action, which, when administered intranasally, provides near-complete protection from lethality in k18hACE2 mice infected with different SARS-CoV-2 variants. The main advantage of soluble ACE2 proteins for the neutralization of SARS-CoV-2 is their immediate onset of action and universality for current and future emerging SARS-CoV-2 variants. It is notable that ACE2 is critically involved in 2 dissimilar functions: as a receptor for cell entry of many coronaviruses and as an enzyme in the metabolism of Ang II, and yet in both cases, it is a therapeutic target.

Revolutionizing Synthetic Antibody Design: Harnessing Artificial Intelligence and Deep Sequencing Big Data for Unprecedented Advances

Synthetic antibodies (Abs) represent a category of engineered proteins meticulously crafted to replicate the functions of their natural counterparts. Such Abs are generated in vitro, enabling advanced molecular alterations associated with antigen recognition, paratope site engineering, and biochemical refinements. In a parallel realm, deep sequencing has brought about a paradigm shift in molecular biology. It facilitates the prompt and cost-effective high-throughput sequencing of DNA and RNA molecules, enabling the comprehensive big data analysis of Ab transcriptomes, including specific regions of interest. Significantly, the integration of artificial intelligence (AI), based on machine- and deep- learning approaches, has fundamentally transformed our capacity to discern patterns hidden within deep sequencing big data, including distinctive Ab features and protein folding free energy landscapes. Ultimately, current AI advances can generate approximations of the most stable Ab structural configurations, enabling the prediction of de novo synthetic Abs. As a result, this manuscript comprehensively examines the latest and relevant literature concerning the intersection of deep sequencing big data and AI methodologies for the design and development of synthetic Abs. Together, these advancements have accelerated the exploration of antibody repertoires, contributing to the refinement of synthetic Ab engineering and optimizations, and facilitating advancements in the lead identification process.

Examining the feasibility of replacing ORF3a with fluorescent genes to construct SARS-CoV-2 reporter viruses

The SARS-CoV-2 genome encodes at least nine accessory proteins, including innate immune antagonist and putative viroporin ORF3a. ORF3a plays a role in many stages of the viral replication cycle, including immune modulation. We constructed two recombinant (r)SARS-CoV-2 viruses in which the ORF3a gene was replaced with mScarlet (mS) or mNeonGreen (mNG), denoted as rSARS-CoV-2-Δ3a-mS and rSARS-CoV-2-Δ3a-mNG, respectively. rSARS-CoV-2-Δ3a-mNG generated a fluorescent signal after infection in both A549-ACE-2-TMPRSS2 (AAT) and Vero-E6-TMPRSS2 (VTN) cells, unlike rSARS-CoV-2-Δ3a-mS. rSARS-CoV-2-Δ3a-mS mS protein could be detected immunologically in VTN but not AAT cells, indicating the expression of a non-fluorescent mS protein. The analysis of the viral transcriptomes in infected AAT cells by nanopore direct RNA sequencing (dRNAseq) revealed that the level of mS transcript was below the limit of detection in AAT cells. rSARS-CoV-2-Δ3a-mNG virus was found to be genetically stable in AAT and VTN cells, but rSARS-CoV-2-Δ3a-mS acquired partial deletions of the mS gene during sequential passaging in VTN cells, creating the virus rSARS-CoV-2-Δ3a-ΔmS. The mS deletion in VTN cells removes the chromophore coding sequence, and this may explain the presence of a non-fluorescent mS protein detected in VTN cells. The rSARS-CoV-2-Δ3a-mNG, rSARS-CoV-2-Δ3a-mS and rSARS-CoV-2-Δ3a-ΔmS viruses all replicated to a lower titre and produced smaller plaques than the parental rSARS-CoV-2-S-D614G. Interestingly, the rSARS-CoV-2-Δ3a-ΔmS virus produced higher virus titres and larger plaque sizes than rSARS-CoV-2-Δ3a-mS. This suggested that both the insertion of mS coding sequence and the deletion of ORF3a coding sequence contributed to attenuation. In comparison with rSARS-CoV-2, the rSARS-CoV-2-Δ3a-mS and rSARS-CoV-2-Δ3a-mNG viruses showed increased sensitivity to pre-treatment of cells with IFN-α but did not exhibit a dose-dependent increase in replication in the presence of the Janus kinase-signal transducer and activator of transcription signalling pathway inhibitor, ruxolitinib. In conclusion, the replacement of the ORF3a coding sequence with those of fluorescent reporter proteins attenuated the replication of SARS-CoV-2 and its ability to effectively evade the innate immune response in vitro.

An assessment of the Chilean COVID-19 surveillance program through the comparison between reported and true SARS-CoV-2 infection prevalence: A case study of three urban centers in southern Chile

OBJECTIVES

Estimate the detection limits of the COVID-19 surveillance system (SS) in Chile, by estimating the SARS-CoV-2 true prevalence (TP) and the reported official positivity prevalence (OPP) gap.

STUDY DESIGN

Randomized cross-sectional.

METHODS

Two sampling campaigns (SC) were conducted (October-November 2020 and December 2020-January 2021) in the cities of Temuco, Valdivia, and Osorno. Blood was collected from adults from randomly selected households. Sera were analyzed using a commercial later flow test (LFT). A meta-analysis was performed to estimate LFT-performance in asymptomatic-cases. Data were analyzed using a Bayesian latent class model (BLCM) to estimate TP. Finally, BLCM outputs were compared with the OPP, by calculating the TP/OPP rate.

RESULTS

1124 and 1017 households were visited during the 1st and 2nd SC, respectively. The BLCM rendered TP estimates of 6.5 %, 3.2 %, and 6.6 % for the cities of Temuco, Valdivia, and Osorno, respectively (1stSC), increasing to 9.4 %, 5.0 %, and 7.5 %, 60 days later (2ndSC). Depending on the city and SC, TP/OPP rates varied between 2.3 and 5.7.

CONCLUSION

The national SS was unable to detect 70-79 % of all infected cases, suggesting that mild and asymptomatic cases were scarcely detected.

Individual patient and donor seroprofiles in convalescent plasma treatment of COVID-19 in REMAP-CAP clinical trial

OBJECTIVES

Convalescent plasma (CP) treatment of COVID-19 has shown significant therapeutic effect only when administered early. We investigated the importance of patient and CP seroprofiles on treatment outcome in REMAP-CAP CP trial.

METHODS

We evaluated neutralising antibodies (nAb), anti-spike (S) IgM, IgG, IgG avidity, IgG fucosylation and respiratory viral loads in a sub-set of patients (n=80) and controls (n=51) before and after transfusion, comparing them to those in the CP units (n=157) they received.

RESULTS

Most patients were SARS-CoV-2 seropositive pre-transfusion (72% nAb; 89% S-IgG seropositivity). The majority (80%) had higher pre-transfusion S-IgG levels (median 1.7×106 arbitrary units (AU); 56%) or S-IgG production rates (median 1.1×106 AU/day; 64%) than they received from CP (median 2.2×105 AU). Only 22% of the patients demonstrated significant (median 24-fold) increase in their S-IgG levels acquired from transfusion. Better outcomes, measured by organ support-free days, were associated with increase in S-IgM levels (p=0.007), decreased S-IgG fucosylation (p<0.001), lower patient age (p<0.001) but not with receiving CP (p=0.337).

CONCLUSIONS

Based on our data, increased S-antibody levels linked to transfused CP were only observed in pre-seroconversion or immunodeficient patients lacking their own SARS-CoV-2 antibodies, representing the groups where CP treatment has previously shown most benefit.

Targeting SARS-CoV2 spike glycoprotein: molecular insights into phytocompounds binding interactions - in-silico molecular docking

This study utilized small molecular characterization and docking study to evaluate the binding affinity of seven antiviral phytocompounds with the SARS CoV-2 variants (SARS-CoV-2 Spike Glycoprotein, SARS-CoV-2 Spike Protein Variant in 1-RBD, Alpha Variant SARS-CoV2- Spike Protein). The results revealed that five of seven compounds, possesses excellent drug lead property reveled through in-silico ADMET analysis. In addition, six of seven except D-Glucosamine, exhibited excellent binding affinity. Six ligands possess significant binding affinity towards SARS-CoV-2 variants 6VXX, 7LWV and 7R13, which is certainly greater than Remdesivir. Fagaronine found to be the best drug candidate against SARS-CoV-2 variants, It was found that -7.4, -5.6 and -6.3 is the docking score respectively. Aranotin, Beta aescin, Gliotoxin, and Fagaronine formed hydrogen bonds with specific amino acids and exhibited significant binding interactions. These findings suggest that these phytocompounds could be promising candidates for developing antiviral therapies against SARS-CoV-2. Moreover, the study underscores the importance of molecular docking in understanding protein-ligand interactions and its role in drug discovery. The documented pharmacological properties of these compounds in the literature further support their potential therapeutic relevance in various diseases.

Harnessing Epigenetics: Innovative Approaches in Diagnosing and Combating Viral Acute Respiratory Infections

Acute respiratory infections (ARIs) caused by viruses such as SARS-CoV-2, influenza viruses, and respiratory syncytial virus (RSV), pose significant global health challenges, particularly for the elderly and immunocompromised individuals. Substantial evidence indicates that acute viral infections can manipulate the host's epigenome through mechanisms like DNA methylation and histone modifications as part of the immune response. These epigenetic alterations can persist beyond the acute phase, influencing long-term immunity and susceptibility to subsequent infections. Post-infection modulation of the host epigenome may help distinguish infected from uninfected individuals and predict disease severity. Understanding these interactions is crucial for developing effective treatments and preventive strategies for viral ARIs. This review highlights the critical role of epigenetic modifications following viral ARIs in regulating the host's innate immune defense mechanisms. We discuss the implications of these modifications for diagnosing, preventing, and treating viral infections, contributing to the advancement of precision medicine. Recent studies have identified specific epigenetic changes, such as hypermethylation of interferon-stimulated genes in severe COVID-19 cases, which could serve as biomarkers for early detection and disease progression. Additionally, epigenetic therapies, including inhibitors of DNA methyltransferases and histone deacetylases, show promise in modulating the immune response and improving patient outcomes. Overall, this review provides valuable insights into the epigenetic landscape of viral ARIs, extending beyond traditional genetic perspectives. These insights are essential for advancing diagnostic techniques and developing innovative treatments to address the growing threat of emerging viruses causing ARIs globally.

Analysis of bioactive compounds of Olea europaea as potential inhibitors of SARS-CoV-2 main protease: a pharmacokinetics, molecular docking and molecular dynamics simulation studies

COVID-19 is a highly infectious disease caused by a new type of extremely contagious coronavirus called SARS-CoV-2. The virus's main protease enzyme, SARS-CoV-2 Mpro, is essential for its replication and transcription processes. Targeting this enzyme presents a promising avenue for antiviral drug development. Researchers have explored the intricate three-dimensional configurations of the enzyme, analyzing its interactions with various inhibitors. These findings provide a foundation for designing specific and powerful inhibitors targeting SARS-CoV-2 Mpro. Certain plants possess medicinal attributes due to the presence of bioactive compounds that inhibit pathogens. The olive tree (Olea europaea) has served as a source of food and medicine, containing bioactive compounds in its leaves that hinder the proliferation of various pathogens including viruses. This study explores the potential of bioactive compounds from olive leaf extract (OLE) to inhibit SARS-CoV-2 Mpro. In-silico study was conducted to predict the pharmacokinetic and toxicity profiles of these compounds. Molecular docking was utilized to assess their binding affinity to SARS-CoV-2 Mpro and their potential interference with its function. The top three compounds, apigenin (Api), luteolin-7-O-glucoside (Lut) and rutin (Rut), were chosen based on their favorable drug-like properties and strong binding affinities to Mpro. Detailed molecular dynamics simulations demonstrated the stability of SARS-CoV-2 Mpro in conjunction with these compounds, showing minimal structural alterations over the simulation period. Particularly, Lut and Rut formed bonds with critical amino acid residues His41 and Cys145 of Mpro, suggesting their potential inhibitory effect. These findings suggest that these compounds hold promise as natural drug candidates for combating COVID-19.Communicated by Ramaswamy H. Sarma.

CRTC3 restricts SARS-CoV-2 replication and is antagonized by CREB

Virus-encoding RNA-dependent RNA polymerase (RdRp) is essential for genome replication and gene transcription of human coronaviruses (HCoVs), including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We previously identified the interaction between the catalytic subunit NSP12 of SARS-CoV-2 RdRp and the host protein CREB-regulated transcription coactivator 3 (CRTC3), a member of the CRTC family that regulates cyclic AMP response element-binding protein (CREB)-mediated transcriptional activation. Currently, the implication of CRTC3 in the pathogenesis of HCoVs is poorly understood. Herein, we demonstrated that CRTC3 attenuates RdRp activity and SARS-CoV-2 genome replication, therefore reducing the production of progeny viruses. The interaction of CRTC3 with NSP12 contributes to its inhibitory effect on RdRp activity. Furthermore, we expanded the suppressive effects of two other CRTC family members (CRTC1 and CRTC2) on the RdRp activities of lethal HCoVs, including SARS-CoV-2 and Middle East respiratory syndrome coronavirus (MERS-CoV), along with the CREB antagonization. Overall, our research suggests that CRTCs restrict the replication of HCoVs and are antagonized by CREB, which not only provides new insights into the replication regulation of HCoVs, but also offers important information for the development of anti-HCoV interventions.

19F qNMR based pharmacokinetics, metabolism and mass balance studies of SARS-CoV-2-3CL protease inhibitor simnotrelvir (SIM0417) in humans

Simnotrelvir (SIM0417), an inhibitor of the 3CL protease of SARS-CoV-2, has been identified as a CYP3A sensitive substrate. This study investigated the pharmacokinetics, metabolism, and mass balance of simnotrelvir following a single oral dose of 750 mg in six healthy Chinese male subjects, co-administered with four doses of 100 mg ritonavir. Analysis using 19F qNMR combined with LC-MS/MS showed that the parent drug M0 constituted over 90% of the drug-related components in plasma. Of the administered dose, 55.4% (54.3% of M0) was recovered in urine, while 36.7% (4.57% of M0) was excreted in feces. UPLC/Q-TOF MS was used to identify metabolites in human plasma, urine and feces. Notably, oxidative metabolites catalyzed by CYP3A were scarcely detected in these matrixes. The amide hydrolyzed metabolite M9 and the cyano hydrolyzed metabolite M10 were recognized as the predominant metabolites, with the main excretion being through feces (19.0% and 12.7% of the administered dose, respectively). In vitro experiments indicated that M10 is primarily formed in the duodenum and jejunum, with further metabolism to M9 by microbiota in the large intestine. Overall, the co-administration of simnotrelvir with ritonavir led to predominant metabolism by intestinal enzymes or microbiota, resulting in hydrolyzed metabolites. These findings highlight the critical role of intestinal metabolism in the pharmacokinetics of simnotrelvir and emphasize the need to consider interactions with antibiotics and individual differences of intestinal microbiota.

A compendium of 8,176 bat RNA viral metagenomes reveals ecological drivers and circulation dynamics

Bats are natural hosts for many emerging viruses for which spillover to humans is a major risk, but the diversity and ecology of bat viruses is poorly understood. Here we generated 8,176 RNA viral metagenomes by metatranscriptomic sequencing of organ and swab samples from 4,143 bats representing 40 species across 52 locations in China. The resulting database, the BtCN-Virome, expands bat RNA virus diversity by over 3.4-fold. Some viruses in the BtCN-Virome are traced to mammals, birds, arthropods, mollusks and plants. Diet, infection dynamics and environmental parameters such as humidity and forest coverage shape virus distribution. Compared with those in the wild, bats dwelling in human settlements harboured more diverse viruses that also circulated in humans and domestic animals, including Nipah and Lloviu viruses not previously reported in China. The BtCN-Virome provides important insights into the genetic diversity, ecological drivers and circulation dynamics of bat viruses, highlighting the need for surveillance of bats near human settlements.

The relationship between microRNAs and COVID-19 complications

Over the past three years, since the onset of COVID-19, several scientific studies have concentrated on understanding susceptibility to the virus, the progression of the illness, and possible long-term complexity. COVID-19 is broadly recognized with effects on multiple systems in the body, and various factors related to society, medicine, and genetics/epigenetics may contribute to the intensity and results of the disease. Additionally, a SARS-CoV-2 infection can activate pathological activities and expedite the emergence of existing health issues into clinical problems. Forming easily accessible, distinctive, and permeable biomarkers is essential for categorizing patients, preventing the disease, predicting its course, and tailoring treatments for COVID-19 individually. One promising candidate for such biomarkers is microRNAs, which could serve various purposes in understanding diverse forms of COVID-19, including susceptibility, intensity, disease progression, outcomes, and potential therapeutic options. This review provides an overview of the most significant findings related to the involvement of microRNAs in COVID-19 pathogenesis. Furthermore, it explores the function of microRNAs in a broad span of effects that may arise from accompanying or underlying health status. It underscores the value of comprehending how diverse conditions, such as neurological disorders, diabetes, cardiovascular diseases, and obesity, interact with COVID-19.

Host Specificity and Geographic Dispersion Shape Virome Diversity in Rhinolophus Bats

Rhinolophus bats have been identified as natural reservoirs for viruses with global health implications, including severe acute respiratory syndrome-related coronaviruses (SARSr-CoV) and swine acute diarrhoea syndrome-related coronavirus (SADSr-CoV). In this study, we characterised the individual viromes of 603 bats to systematically investigate the diversity, abundance and geographic distribution of viral communities within R. affinis, R. sinicus and 11 other bat species. The massive metatranscriptomic data revealed substantial viral genome resources of 133 vertebrate-infecting viral clusters, which contain occasional cross-species transmission across mammalian orders and especially across bat families. Notably, those viruses included nine clusters closely related to human and/or livestock pathogens, such as SARS-CoVs and SADS-CoVs. The investigation also highlighted distinct features of viral diversity between and within bat colonies, which appear to be influenced by the distinct host population genetics of R. affinis and R. sinicus species. The comparison of SARSr-CoVs further showed varied impact of host specificity along genome-wide diversification and modular viral evolution among Rhinolophus species. Overall, the findings point to a complex interaction between host genetic diversity, and the way viruses spread and structure within natural populations, calling for continued surveillance efforts to understand factors driving viral transmission and emergence in human populations. These results present the underestimated spillover risk of bat viruses, highlighting the importance of enhancing preparedness and surveillance for emerging zoonotic viruses.

COVID-19 clinical presentation, management, and epidemiology: a concise compendium

Coronavirus Disease 2019, caused by severe acute respiratory coronavirus 2, has been an ever-evolving disease and pandemic, profoundly impacting clinical care, drug treatments, and understanding. In response to this global health crisis, there has been an unprecedented increase in research exploring new and repurposed drugs and advancing available clinical interventions and treatments. Given the widespread interest in this topic, this review aims to provide a current summary-for interested professionals not specializing in COVID-19-of the clinical characteristics, recommended treatments, vaccines, prevention strategies, and epidemiology of COVID-19. The review also offers a historical perspective on the pandemic to enhance understanding.

Upregulation of the MAP2K4 gene triggers endothelial-mesenchymal transition in COVID-19

BACKGROUND

SARS-CoV-2 infection is marked by an excessive inflammatory response, leading to elevated production of pro-inflammatory cytokines through activation of intracellular pathways like mitogen-activated protein kinase (MAPK). Viruses can use the MAPK signaling pathway to their advantage, but the relationship of this pathway to the severe SARS-CoV-2 period has not been fully elucidated. MAP2K4 is involved in the MAPK signaling pathway and affects cellular processes such as cell-cell junction, cell proliferation, differentiation and apoptosis.

METHODS AND RESULTS

In this study, we sought to determine the associated biomarkers that are involved in the MAP2K4 pathway and elucidate its possible roles in terms of some clinical features associated with COVID-19. We evaluated the expressions of MAP2K4, SNAI1, SLUG, ZEB1 and E-Cadherin. For this purpose, we prospectively recruited 66 individuals, 39 of whom were women and had a mean age of 65 years. The results revealed that MAP2K4 upregulation increased SNAI1 gene expression level whereas E- Cadherin level was decreased in SARS-CoV-2 positive participants. In addition, negative correlations were determined with PLT, Lymphocyte and CKMB and E- Cadherin levels in positive participants. We also observed a negative correlation between the MAP2K4 and AST, and a positive correlation between SLUG and BUN, ZEB1 and CK.

CONCLUSIONS

We conclude that SARS-CoV-2 infection triggers fibrosis by increasing MAP2K4 regulation. Additionally, this is the first study to demonstrate the possible contribution of MAP2K4 in influencing COVID-19 clinical features, which may be relevant for identifying COVID-19 positive participants with severe complications.

The respective roles of TMPRSS2 and cathepsins for SARS-CoV-2 infection in human respiratory organoids

A critical aspect of the mechanism of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is the protease-mediated activation of the viral spike (S) protein. The type II transmembrane serine protease TMPRSS2 is crucial for SARS-CoV-2 infection in lung epithelial Calu-3 cells and murine airways. However, the importance of TMPRSS2 needs to be re-examined because the ability to utilize TMPRSS2 is significantly reduced in the Omicron variants that spread globally. For this purpose, replication profiles of SARS-CoV-2 were analyzed in human respiratory organoids. All tested viruses, including Omicron variants, replicated efficiently in these organoids. Notably, all SARS-CoV-2 strains retained replication ability in TMPRSS2-gene knockout (KO) respiratory organoids, suggesting that TMPRSS2 is not essential for SARS-CoV-2 infection in human respiratory tissues. However, TMPRSS2-gene knockout significantly reduces the inhibitory effect of nafamostat, indicating the advantage of TMPRSS2-utilizing ability for the SARS-CoV-2 infection in these organoids. Interestingly, Omicron variants regained the TMPRSS2-utilizing ability in recent subvariants. The basal infectivity would be supported mainly by cathepsins because the cathepsin inhibitor, EST, showed a significant inhibitory effect on infection with any SARS-CoV-2 strains, mainly when used with nafamostat. A supplementary contribution of other serine proteases was also suggested because the infection of the Delta variant was still inhibited partially by nafamostat in TMPRSS2 KO organoids. Thus, various proteases, including TMPRSS2, other serine proteases, and cathepsins, co-operatively contribute to SARS-CoV-2 infection significantly in the respiratory organoids. Thus, SARS-CoV-2 infection in the human respiratory tissues would be more complex than observed in cell lines or mice.

IMPORTANCE

We explored how the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus infects human respiratory organoids, which are a cultured cell model made to mimic the physiological conditions of the human airways. We focused on understanding the role of different proteases of host cells in activating the virus spike proteins. Specifically, we looked at TMPRSS2, a transmembrane serine protease, and cathepsin L, a lysosomal enzyme, which helps the virus enter cells by cutting the viral spike protein. We discovered that while TMPRSS2 is crucial for the virus in certain cells and animal models, other proteases, including cathepsins and various serine proteases, also play significant roles in the SARS-CoV-2 infection of human respiratory organoids. We suggest that SARS-CoV-2 uses a more complex mechanism involving multiple proteases to infect human airways, differing from what we see in conventional cell lines or animal models. This complexity might help explain how different variants can spread and infect people effectively.

SARS-CoV-2 drug resistance and therapeutic approaches

In light of the transition of COVID-19 from a pandemic to an endemic phase, there is still a dire need to address challenges associated with drug resistance, particularly among immunocompromised and high-risk populations. This review explores the current state of research on SARS-CoV-2 drug resistance and underscores the ongoing need for effective therapeutic strategies. It critically evaluates existing knowledge on resistance mechanisms and therapeutic options, aiming to consolidate information and highlight areas for future research. By examining the complex interactions between the virus and its host, the review advocates for a multifaceted approach, including combination therapies, targeted drug development, and continuous surveillance of viral mutations. It also emphasizes the impact of evolving viral variants on antiviral efficacy and suggests adaptive treatment protocols. This review aims to enhance our understanding of SARS-CoV-2 drug resistance and contribute to more effective management of COVID-19 through a discussion of promising strategies such as drug repurposing and combination therapies.

Simultaneous determination of nirmatrelvir, ritonavir, and beta-D-N4-hydroxycytidine in human plasma and epithelial lining fluid using LC-MS/MS and its clinical application to compare rates of achieving effective concentrations

Currently, the trials found that the clinical efficacy of molnupiravir is lower than ritonavir-boosted nirmatrelvir. An explanation for these different efficacies in clinical treatments is still limited. The analysis method was developed and validated to simultaneously quantify nirmatrelvir, ritonavir, and beta-D-N4-hydroxycytidine (NHC) in human plasma and bronchoalveolar lavage fluid (BALF) by electrospray ionization mass spectrometry. Our method was validated over a linear range of 30-10000 ng/mL for both matrices, with precision and accuracy within 15 % across four concentrations. Recovery rates for both analytes from plasma and BALF were between 90.7-102.2 % and 90.5-107.7 %, respectively. The analytical method was then applied to monitor therapeutic drug concentrations in 59 plasma samples from 23 patients receiving ritonavir-boosted nirmatrelvir or molnupiravir. By setting target plasma concentrations of 292 ng/mL for nirmatrelvir and 1205 ng/mL for NHC, based on in vitro antiviral 90 % virus inhibitory concentrations (EC90), the drug's molecular weight and its binding to human plasma proteins, we observed that ritonavir-boosted nirmatrelvir had substantially greater rates of achieving target plasma concentrations. Additionally, we monitored epithelial lining fluid in 4 BALF samples from 4 patients and observed that NHC exhibited higher permeability in lung tissue (approximately 20 % higher than nirmatrelvir). However, subtherapeutic antiviral concentrations of NHC were also present in epithelial lining fluid. These findings highlight the importance of considering these factors in determining the efficacy of these drugs in treating coronavirus disease 2019 (COVID-19).

Accelerated Adaptation of SARS-CoV-2 Variants in Mice Lacking IFITM3 Preserves Distinct Tropism and Pathogenesis

Here we investigated whether interferon induced transmembrane protein 3 (IFITM3), a key antiviral protein deficient in certain human populations, affects interspecies adaptation of SARS-CoV-2. We found that SARS-CoV-2 Beta and Omicron variants passaged through IFITM3-deficient versus wild type mice exhibit enhanced replication and pathogenesis in this new host species. Enhancements associated with amino acid substitutions in the viral genome, suggesting that IFITM3 limits accumulation of adaptive mutations. Mouse-adapted viruses enabled comparative studies of variants in mice. Beta caused lung dysfunction and altered cilia-associated gene programs, consistent with broad viral antigen distribution in lungs. Omicron, which shows low pathogenicity and upper respiratory tract preference in humans, replicated to high nasal titers while showing restrained spatial distribution in lungs and diminished lung inflammatory responses compared to Beta. Our findings demonstrate that IFITM3 deficiency accelerates coronavirus adaptation and reveal that intrinsic SARS-CoV-2 variant traits shape tropism, immunity, and pathogenesis across hosts.

HIGHLIGHTS

IFITM3 is a critical barrier to SARS-CoV-2 adaptation in new host speciesMouse-adapted SARS-CoV-2 strains enable comparative pathologyOmicron favors nose and large airways, leading to mild lung pathologyBeta exhibits broad lung replication, driving severe inflammation and dysfunction.

The Interplay of Furin Cleavage and D614G in Modulating SARS-CoV-2 Spike Protein Dynamics

We report a detailed analysis of the full-length SARS-CoV-2 spike dynamics within a native-like membrane environment and variants inaccessible to studies on soluble constructs by conducting hydrogen-deuterium exchange mass spectrometry (HDX-MS) on enveloped virus-like particles (eVLPs) displaying various spike constructs. We find that the previously identified open-interface trimer conformation is sampled in all eVLP-displayed spike variants studied including sequences from engineered vaccine constructs and native viral sequences. The D614G mutation, which arose early in the pandemic, favors the canonical 'closed-interface' prefusion conformation, potentially mitigating premature S1 shedding in the presence of a cleaved furin site and providing an evolutionary advantage to the virus. Remarkably, furin cleavage at the S1/S2 boundary allosterically increases the flexibility of the S2' site, which may facilitate increased TMPRSS2 processing, enhancing viral infectivity. The use of eVLPs in HDX-MS studies provides a powerful platform for studying viral and membrane proteins in near-native environments.

Differences in clinical characteristics between coronavirus disease 2019 (COVID-19) and influenza: a systematic review and meta-analysis

The coronavirus disease 2019 (COVID-19) epidemic has brought major challenges to the global health system, and influenza is also a problem that cannot be ignored. We aimed to explore and compare the clinical characteristics of COVID-19 and influenza to deepen the understanding of these two diseases and provide some guidance for clinicians to make differential diagnoses. We searched PubMed, Embase and Web of Science for articles and performed a meta-analysis using Stata 14.0 with a random-effects model. This meta-analysis was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. One hundred articles involving 226,913 COVID-19 patients and 201,617 influenza patients were included, and all the articles included patients with these two diseases as experimental and control groups. Compared to influenza, COVID-19 was more common among men (OR = 1.46, 95% CI: 1.23-1.74) and people with a higher body mass index (MD = 1.43, 95% CI: 1.09-1.77). The proportion of current smokers among COVID-19 patients was lower than that among influenza patients (OR = 0.25, 95% CI: 0.18-0.33). Patients with COVID-19 had longer stays in the hospital (MD = 3.20, 95% CI: 2.58-3.82) and ICU (MD = 3.10, 95% CI: 1.44-4.76), required mechanical ventilation more frequently (OR = 2.30, 95% CI: 1.77-3.00), and had higher mortality (OR = 2.22, 95% CI: 1.93-2.55). We also found significant differences in some blood parameters between the two groups of patients. Upper respiratory symptoms were more obvious in influenza patients, and the proportion of comorbidities was higher than that among COVID-19 patients. There are some differences in the major characteristics, symptoms, laboratory findings and comorbidities between COVID-19 patients and influenza patients. COVID-19 patients often require more medical resources and have worse clinical outcomes.

Environmental biocontamination by SARS-CoV-2 Virus in the hospital setting

Background

Demonstrating the capability to isolate biological material from the environment was fundamental to supporting any transmission route. Various and inconsistent methodologies have been used to address this issue; however, the debate in scientific societies about the possibility of airborne transmission as a source of SARS-CoV-2 spread remained open.

Objective

To analyze SARS-CoV-2 contamination in the air and on surfaces in a hospital setting during the COVID-19 pandemic.

Methods

This study involved air and surface sampling in the emergency, hospitalization, and intensive care unit areas of the Ramón y Cajal University Hospital. A consistent methodology was used for all samples, and clinical and environmental parameters and characterization of each location were recorded.

Results

A total of 234 samples were collected, comprising 160 surface samples and 74 air samples, of which 6.84 % tested positive (13/160 surface samples and 3/74 air samples). High-contact surfaces had the highest proportion of positive samples (12/13). All positive air samples were identified within 2 m of patients who had recently developed symptoms (<5 days). High dependency and elevated temperatures seemed to indicate a higher risk of environmental biocontamination. Additionally, there was a higher risk of contamination in the intensive care units than in the hospitalization or emergency units.

Vaccination with Plasmids Encoding the Fusion Proteins D-S1, D-S1N and O-SN from SARS-CoV-2 Induces an Effective Humoral and Cellular Immune Response in Mice

BACKGROUND

Next-generation vaccines against coronavirus disease 2019 (COVID-19) focus on inducing a long-lasting immune response against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and its emerging variants. To achieve this, antigens other than spike proteins have been proposed, and different platforms have been evaluated. Nucleic acid-based vaccines are fundamental for this process. Preclinical data have shown that the SARS-CoV-2 nucleocapsid protein induces a protective cellular immune response, and when combined with the spike protein, the resulting humoral and cellular immune responses are effective against some SARS-CoV-2 variants.

METHODS

We designed a DNA vaccine against the spike and nucleocapsid proteins of SARS-CoV-2 to generate fusion proteins based on the Delta and Omicron B.5 strains. The most immunogenic regions of the spike and nucleocapsid proteins of the Delta and Omicron B strains were selected using bioinformatics. The nucleotide sequences were cloned into pcDNA3.1, and named pcDNA3.1/D-S1, pcDNA3.1/D-S1N, and pcDNA3.1/O-SN. The immunogenicity of the generated fusion proteins was evaluated by analyzing the humoral and cellular responses elicited after the immunization of BALB/c mice.

RESULTS

DNA immunization induced antibody production, neutralization activity, and IFN-γ production. The inclusion of the nucleocapsid regions in the plasmid greatly enhanced the immune response. Moreover, cross-reactions with the variants of interest were confirmed.

CONCLUSIONS

Plasmids-encoding fusion proteins combining the most immunogenic regions of the spike and nucleocapsid proteins present a promising strategy for designing new and effective vaccines against SARS-CoV-2.

Bats as a mixing vessel for generation of novel coronaviruses: Co-circulation and co-infection of coronaviruses and other viruses

Bats are the hosts of a wide variety of coronaviruses (CoVs) of the genera Alphacoronavirus and Betacoronavirus. The presence of more than one CoV species or strain in a single bat species greatly enhances the chance of genetic exchange among the CoVs, mainly through homologous recombination, and hence enhance the generation of novel CoV species or strains that may adapt to human or other animals and result in future epidemics. In this article, we review the evidence for co-circulation and/or co-infection of two or more CoVs in the same bat species, including co-infection with different strains of a CoV, co-circulation/co-infection of different alphaCoVs or betaCoVs, and co-circulation/co-infection of alphaCoVs and betaCoVs together. With next-generation sequencing, there has been a recent explosion of such discoveries. It is anticipated that countless more similar findings will be made in the near future.

Alpha and Betacoronavirus Detection in Neotropical Bats from Northeast Brazil Suggests Wide Geographical Distribution and Persistence in Natural Populations

The emergence of zoonotic viral diseases, notably exemplified by the recent coronavirus disease pandemic in 2019 (COVID-19), underscores the critical need to understand the dynamics of viruses circulating in wildlife populations. This study aimed to investigate the diversity of coronaviruses in bat populations from northeastern Brazil, particularly in the state of Ceará, where little research on bat pathogens has been conducted previously. Bat sampling was performed between March 2021 and March 2022 across three municipalities, resulting in the collection of oral and rectal swabs from 298 captured individuals. Molecular analyses revealed alphacoronaviruses in multiple bat species. Additionally, a novel Betacoronavirus was identified in Artibeus planirostris, which did not fall within an established subgenus. Phylogenetic placement of these new coronavirus sequences suggests that closely related coronavirus lineages can infect a wide range of bat species sampled in distantly related Brazilian states and biomes. No SARS-CoV-2 and influenza A viruses were found in the sampled bats. These findings expand our understanding of coronavirus diversity in Brazilian bats. The detection of coronaviruses in various bat species underscores the importance of bats as reservoirs for these viruses. The absence of SARS-CoV-2 in the sampled bats indicates a lack of spillback events from human or environmental sources. However, the potential for future transmission events underscores the importance of ongoing surveillance and transmission mitigation protocols in wildlife management practices.

Consequences of COVID-19 for geriatric patients during a pandemic

To investigate the outcomes of geriatric COVID-19 patients in a German academic setting during the pandemic. This study included 468 consecutive geriatric patients (≥ 70 years) who tested positive for SARS-CoV-2 and were treated at the University of Duisburg-Essen from 2/2020 to 3/2021. 74 patients were transferred to a geriatric hospital and a 12-month follow-up (prospective study) was performed in 51 patients. Clinical assessments evaluated depression (GDS), apathy (AES), cognitive status (MMST), mobility (TUG), health status (EQ-5D-5 L), and daily living activities (Barthel Index). Demographic and clinical data were also analyzed. Results showed that the mortality in this vulnerable group was 52% (n = 209). Long-term survival was higher in patients who received comprehensive geriatric treatment (74.3% vs. 51.8%). The duration of inpatient stay at the primary hospital was 13.3 ± 3.6 days, with 28.8% (n = 135) requiring intensive care. At the 12-month mark more patients with geriatric treatment lived in nursing homes. Barthel-Index/Timed-Up-and-Go-Test/MMST/AES/GDS, and EQ-5D-5 L indicated worse outcomes in the group who received geriatric treatment. Specialized geriatric care may improve survival in geriatric COVID-19 patients despite decreased long-term outcomes. Further research, including international studies like NAPKON, are encouraged to confirm these findings and explore potential interventions for improved outcomes in this vulnerable population.

SARS-CoV-2 XEC: A Genome-Based Survey

Recombination, a process of genetic exchange between distinct organisms, has played a critical role in the emergence of SARS-CoV-2 variants such as the XEC recombinant. This study provides a detailed genomic and structural characterization of XEC, derived from the recombination of lineages KP.3.3 (donor) and KS.1.1 (acceptor). Phylogenomic analyses reveal that XEC and its descendant XEC.1 form a monophyletic clade with close evolutionary ties to KP.3.3. The genomic breakpoint, spanning nucleotide positions 22,363-22,463, marks the shift from KS.1.1 to KP.3.3 within the spike protein gene. Mutational analysis highlights shared traits with its parental lineages, including mutations associated with immune evasion, receptor affinity, and fusogenicity. Notable changes, such as Q493E and L455S, may confer unique immunogenic properties, though XEC's overall immune escape potential is limited by the absence of new mutations in conserved epitopes. Despite these mutations, XEC demonstrates restricted geographical spread, low genetic variability, and an evolutionary trajectory indicative of an evolutionary dead-end. Bayesian Skyline Plot analysis corroborates this, showing stable but declining population size. These findings underscore the need for ongoing genomic surveillance to monitor recombinant variants' characteristics and public health impact. This study contributes to understanding viral evolution and highlights the importance of distinguishing variants of concern from those with minimal epidemiological significance.

Secondary metabolites of Alternaria alternate appraisal of their SARS-CoV-2 inhibitory and anti-inflammatory potentials

This study identifies the secondary metabolites from Alternaria alternate and evaluates their ACE-2: Spike RBD (SARS-CoV-2) inhibitory activity confirmed via immunoblotting in human lung microvascular endothelial cells. In addition, their in vitro anti-inflammatory potential was assessed using a cell-based assay in LPS-treated RAW 264.7 macrophage cells. Two novel compounds, altenuline (1), phthalic acid bis (7'/7'' pentyloxy) isohexyl ester (2), along with 1-deoxyrubralactone (3) alternariol-5-O-methyl ether (4) and alternariol (5) were identified. Molecular docking and in vitro studies showed that compounds 2 and 4 were promising to counteract SARS-CoV-2 attachment to human ACE-2. Thus, they are considered promising natural anti-viral agents. SwissADME in silico analysis was conducted to predict the drug-like potential. Immunoblotting analysis confirmed that the tested compounds (1-4) demonstrated downregulation of ACE-2 expression in the endothelial cells from the lungs with variable degrees. Furthermore, the tested compounds (1-4) showed promising anti-inflammatory activities through TNF-α: TNFR2 inhibitory activity and their inhibitory effect on the proinflammatory cytokines (TNF-α and IL-6) in LPS-stimulated monocytes. In conclusion, our study, for the first time, provides beneficial experimental confirmation for the efficiency of the A. alternate secondary metabolites for the treatment of COVID-19 as they hinder SARS-CoV-2 infection and lower inflammatory responses initiated by SARS-CoV-2. A. alternate and its metabolites are considered in developing preventative and therapeutic tactics for COVID-19.

Advancements in the development of antivirals against SARS-Coronavirus

Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) caused an outbreak in 2002-2003, spreading to 29 countries with a mortality rate of about 10%. Strict quarantine and infection control methods quickly stopped the spread of the disease. Later research showed that SARS-CoV came from animals (zoonosis) and stressed the possibility of a similar spread from host to human, which was clearly shown by the COVID-19 outbreak. The COVID-19 pandemic, instigated by SARS-CoV-2, has affected 776 million confirmed cases and more than seven million deaths globally as of Sept 15, 2024. The existence of animal reservoirs of coronaviruses continues to pose a risk of re-emergence with improved fitness and virulence. Given the high death rate (up to 70 percent) and the high rate of severe sickness (up to 68.7 percent in long-COVID patients), it is even more critical to identify new therapies as soon as possible. This study combines research on antivirals that target SARS coronaviruses that have been conducted over the course of more than twenty years. It is a beneficial resource that might be useful in directing future studies.

Analysis of Structures of SARS-CoV-2 Papain-like Protease Bound with Ligands Unveils Structural Features for Inhibiting the Enzyme

The COVID-19 pandemic, driven by the novel coronavirus SARS-CoV-2, has drastically reshaped global health and socioeconomic landscapes. The papain-like protease (PLpro) plays a critical role in viral polyprotein cleavage and immune evasion, making it a prime target for therapeutic intervention. Numerous compounds have been identified as inhibitors of SARS-CoV-2 PLpro, with many characterized through crystallographic studies. To date, over 70 three-dimensional (3D) structures of PLpro complexed ligands have been deposited in the Protein Data Bank, offering valuable insight into ligand-binding features that could aid the discovery and development of effective COVID-19 treatments targeting PLpro. In this study, we reviewed and analyzed these 3D structures, focusing on the key residues involved in ligand interactions. Our analysis revealed that most inhibitors bind to PLpro's substrate recognition sites S3/S4 and SUb2. While these sites are highly attractive and have been extensively explored, other potential binding regions, such as SUb1 and the Zn(II) domain, are less explored and may hold untapped potential for future COVID-19 drug discovery and development. Our structural analysis provides insights into the molecular features of PLpro that could accelerate the development of novel therapeutics targeting this essential viral enzyme.

Endemic coronavirus in children and adults with acute respiratory infection before the COVID-19 pandemic

Acute respiratory infection (ARI) is one of the principal causes of morbidity worldwide, with respiratory viruses being common etiological agents. Among them, endemic human coronaviruses (hCoVs) including CoV-229E, CoV-OC43, CoV-NL63, and CoV-HKU1 can cause mild ARI but are usually not evaluated in the clinical setting. The aim of this work was to determine the prevalence of all respiratory pathogens, with the focus placed on endemic hCoVs in the pre-pandemic period. Circulating species, clinical associations and coinfections with other respiratory pathogens were evaluated in 510 immunocompetent patients (children and adults) with ARI using the FilmArray® Respiratory Panel (BioFire/bioMérieux). A total of 399 children (252 outpatients and 147 hospitalized) and 111 adult outpatients were enrolled in the pre-pandemic period (2008-2010 and 2016). Endemic hCoVs were the third and fifth more frequently detected viruses among adults and outpatient children, respectively, with an overall frequency close to 10%. The most prevalent species were CoV-OC43 (42.8%) and CoV-HKU1 (40.5%), followed by CoV-NL63 (19.0%) and CoV-229E (4.8%). Tachypnea, wheezing and chest indrawing were more frequent in hospitalized children compared to outpatients. All adult patients presented with symptoms of a common cold. Endemic hCoVs were detected year-round, primarily between June and November. Our results highlight their clinical relevance, and the need to include endemic hCoVs in routine screening. In the post-pandemic period, further long-term surveillance is needed for understanding the epidemiology of endemic hCoVs and their evolution, as a tool to anticipate the possible emergence of new species.

Fu Tu Sheng Jin Rehabilitation Formula Mitigate Airway Inflammation, Mucus Secretion and Immune Dysfunction Induced by SARS-CoV-2 Spike Protein

Objective

To evaluate the effects of Fu Tu Sheng Jin Rehabilitation Formula (FTSJRF) on airway inflammation, mucus secretion, and immunoreaction in a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein-induced mouse model.

Methods

Forty-two mice were randomly divided into seven groups: normal, D1, D3, D10, D10H, D10M and D10L, according to the days of modeling and different dosages of FTSJRF. D1, D3, D10, D10H, D10M and D10L group mice were intratracheally administered with 15 µg SARS-CoV-2 spike protein; mice in the D10H, D10M, and D10L groups were intragastrically administered FTSJRF (46, 23 and 11.5 g/kg, respectively). Observe the pathological changes in lung tissues, expression of inflammatory factors, and mucins in different groups of mice using HE and PAS staining methods, as well as ELISA and RT-qPCR. Flow cytometry was used to detect T helper 17 (Th17)/regulatory T (Treg) cells and T helper 1(Th1)/T helper 2 (Th2) lymphocyte ratios and the proportions of conventional myeloid dendritic cells (cDCs), plasma cell-like DCs, CD80 and CD86 cells in mouse spleens.

Results

HE and PAS staining showed that, compared to that in the normal group, the lung tissue of the D1 group mice showed a significant inflammatory damage response, whereas the D3 and D10 groups showed a gradual recovery trend. Groups D1 and D3 showed mild mucus secretion, whereas the D10 group had excessive mucus secretion. The D10 group of mice displayed increased levels of IL-4, TNF-α, IL-33 and mucin genes such as MUC1, MUC4, etc, and FTSJRF inhibited the expression of these molecules, mucus secretion and lung damage in SARS-CoV-2 spike protein-induced mouse model. Flow cytometry results showed a decrease in the number of cDCs and an abnormal recovery of DC mature cells in the D10 group. FTSJRF increased the number of cDCs and promoted DC maturation. A higher Th17/Treg ratio was observed in the D3 and D10 groups than in the normal group, whereas this ratio decreases under the effect of FTSJRF. D10 had significantly lower Th1/Th2 ratio than normal, D1 and D3 groups, and high doses of FTSJRF increased it.

Conclusion

FTSJRF mitigates airway inflammation and mucus secretion induced by SARS-CoV-2 spike protein. Additionally, FTSJRF regulates immune functions by promoting DC maturation and Th17/Treg and Th1/Th2 cell homeostasis.

Inhalable siRNA Targeting IL-11 Nanoparticles Significantly Inhibit Bleomycin-Induced Pulmonary Fibrosis

For idiopathic pulmonary fibrosis (IPF), interleukin 11 (IL-11) is a pivotal cytokine that stimulates the transformation of fibroblasts into myofibroblasts, thus accelerating the progression of pulmonary fibrosis. Here, we develop an innovative inhalable small interfering RNA (siRNA) delivery system termed PEI-GBZA, which demonstrates impressive efficiency in loading siIL-11 targeting IL-11 (siIL-11) and substantially suppresses the differentiation of fibroblasts into myofibroblasts and epithelial-mesenchymal transition (EMT), reduces neutrophil and macrophage recruitment, and ultimately relieves the established fibrotic lesions in the IPF model. PEI-GBZA is prepared by modifying low-molecular-weight polyethylenimine (PEI) with 4-guanidinobenzoic acid (GBZA). The resulting PEI-GBZA may effectively encapsulate siIL-11 through a variety of interactions such as hydrophobic, hydrogen bonding, and electrostatic interactions, creating stable carrier/siIL-11 nanoparticles (PEI-GBZA/siIL-11 NPs). Upon inhalation, PEI-GBZA/siIL-11 NPs demonstrate effective retention in fibrotic lesions, leading to a marked mitigation of disease progression in a bleomycin-induced pulmonary fibrosis model. Impressively, this inhalation therapy exhibits negligible systemic toxicity. This work provides a universal and noninvasive RNA therapeutic delivery platform that holds significant promise for respiratory diseases. The potential for clinical application of this platform is substantial, offering a frontier for the treatment of IPF and potentially other pulmonary disorders.

Robotic versus manual disinfection of global priority pathogens at COVID-19-dedicated hospitals

BACKGROUND

Twelve bacterial families identified as global priority pathogens (GPPs) pose the greatest threat to human health due to declining antibiotic efficacy. Robotics, a swift and contactless tool for disinfecting hospital surfaces, was sought to compare with manual disinfection.

METHODS

The disinfection efficacy of a robot was compared with manual disinfection for multiple clinical surfaces and inanimate objects at two hospitals in Nepal using bleach (NaOCl). Surfaces were swabbed pre- and post-disinfection and total heterotrophic plate count evaluated, and bacterial pathogens identified using Gram's staining and biochemical characteristics. Disinfection outcomes were reported as log reduction (log10 CFU/inch2) of heterotrophic count and presence or absence of GPPs: Staphylococcus aureus, Escherichia coli, Acinetobacter spp., and Klebsiella pneumoniae, among others.

RESULTS

Both robotic and manual disinfection significantly reduced the microbial load (log 2.3 to log 5.8) on hospital surfaces. No pathogens were detected post-disinfection using the robot. Robotic disinfection was more effective, significantly reducing the bacterial load (log 5.8) compared to manual disinfection (log 3.95).

CONCLUSIONS

Our results showed better efficacy of robotic disinfection over manual disinfection of hospital surfaces, and thus contactless robotic disinfection is recommended for disinfecting surfaces in the hospital and clinical settings as it favors patient safety against GPPs.

Reverse mutational scanning of SARS-CoV-2 spike BA.2.86 identifies epitopes contributing to immune escape from polyclonal sera

The recently detected Omicron BA.2.86 lineage contains more than 30 amino acid mutations relative to BA.2. BA.2.86 and its JN.1 derivative evade neutralization by serum antibodies of fully vaccinated individuals. In this study, we elucidate epitopes driving the immune escape of BA.2.86 and JN.1 via pseudovirus neutralization. Here we generate 33 BA.2.86 mutants, each reverting a single mutation back to BA.2. We use this library in an approach that we call reverse mutational scanning to define distinct neutralization titers against each epitope. Mutations within the receptor binding domain at K356T, V483Δ, and to a lesser extent N460K, A484K, and F486P enhance immune escape. Interestingly, 16insMPLF within the spike N-terminal domain and P621S within S1/S2 also significantly contribute to antibody escape of BA.2.86. Upon XBB.1.5 booster vaccination, neutralization titers against JN.1 and BA.2.86 improve considerably, and residual immune escape is driven by 16insMPLF, N460K, E554K, and to a lesser extent P621S, and A484K.

Human ACE2 transgenic pigs are susceptible to SARS-CoV-2 and develop COVID-19-like disease

Animal models that accurately reflect COVID-19 are vital for understanding mechanisms of disease and advancing development of improved vaccines and therapeutics. Pigs are increasingly recognized as valuable models for human disease due to their genetic, anatomical, physiological, and immunological similarities to humans, and they present a more ethically viable alternative to non-human primates. However, pigs are not susceptible to SARS-CoV-2 infection which limits their utility as a model. To address this, we have developed transgenic pigs expressing human ACE2 that are susceptible to SARS-CoV-2 infection. Following challenge, clinical signs consistent with COVID-19, including fever, coughing and respiratory distress were observed, with virus replication detected in the nasal turbinates, trachea and lungs up to the study endpoint, seven days post-infection. Notably, examination of tissues revealed immunopathology in the lungs consistent with histological changes observed in fatal human COVID-19 cases. This study establishes human ACE2 transgenic pigs as a large animal model that accurately reflects many aspects of COVID-19 disease.

Deltacoronavirus HKU11, HKU13, PDCoV (HKU15) and HKU17 spike pseudoviruses enter avian DF-1 cells via clathrin-mediated endocytosis in a Rab5-, Rab7- and pH-dependent manner

Porcine deltacoronavirus (PDCoV), also known as HKU15, is a swine enteropathogenic virus that is believed to have originated in birds. PDCoV belongs to the genus Deltacoronavirus (DCoV), the members of which have mostly been identified in diverse avian species. We recently reported that chicken or porcine aminopeptidase N (APN), the major cellular receptor for PDCoV, can mediate cellular entry via three pseudotyped retroviruses displaying spike proteins from three avian DCoVs (HKU11, HKU13, and HKU17). In the present work, to better understand how avian-origin CoVs may be transmitted to pigs, we investigated the unknown DCoV entry pathway in avian cells. We show that clathrin-mediated endocytosis is involved in the entry of these DCoV pseudoviruses into chicken-origin DF-1 cells. Pseudovirus entry was suppressed by means of pharmacological inhibitors, dominant-negative mutants, and siRNAs targeting various cellular proteins and signalling molecules, suggesting that PDCoV and avian DCoV pseudovirus entry into DF-1 cells depends on clathrin, dynamin-2, cathepsins and a low-pH environment but is independent of caveolae and macropinocytosis. Furthermore, we found that DCoV pseudovirus entry was linked to Rab5- and Rab7-dependent pathways. This is the first report demonstrating that these DCoVs utilize clathrin-mediated endocytosis pathways to enter avian-origin cells, providing new insights into interspecies transmission of DCoVs.