Coronavirus Infections-More Than Just the Common Cold

Enhanced Production of Lipid Mediators in Plasma and Activation of DNA Damage Pathways in PBMCs Are Correlated With the Severity of Ancestral SARS-CoV-2 Infection

Many questions remain unanswered regarding the implication of genetics and lipid metabolites with severe SARS-CoV-2 infections. We performed bulk RNA-seq and a total fatty acid panel analysis on PBMCs and plasma collected from 10 infected and 10 uninfected patients. Univariate comparison of lipid metabolites using the Mann-Whitney U-test revealed that six lipid metabolites were significantly increased in COVID-19 patients, including the lipid mediators arachidonic acid (AA) and eicosapentaenoic acid (EPA), which both give rise to eicosanoids. Key lipids implicated in inflammation, including AA and EPA, along with the fatty acids DHA and DPA, were significantly and positively correlated to the WHO disease severity score. Analysis of our bulk RNA-seq dataset demonstrated distinct transcriptional profiles leading to a segregation of COVID-19 patients based on the WHO score. Ontology, KEGG, and Reactome analysis identified several key pathways and nodes that were enriched for genes related to innate immunity, interactions between lymphoid and nonlymphoid cells, interleukin signaling, and subsequent DNA damage pathways. EPA levels correlated with heightened cell cycling and DNA damage pathways observed in patients with a high WHO score. We studied gene expression in nasopharyngeal swabs from 58 healthy and COVID-19 participants and identified that genes implicated in eicosanoid synthesis, such as alox5, alox12, and alox15B, were specifically up-regulated in high WHO score patients in several cell types of the nasopharynx, especially goblet cells across different viral variants (Deta and Omicron). Using published nasal scRNA-seq datasets from COVID-19 patients, we evaluated the expression of genes implicated in eicosanoid synthesis, such as ALOX5, ALOX15, and ALOX15B, across nasal cell types and COVID-19 severity groups. Altogether, our study highlights the fact that the increase in specific lipids implicated in inflammation and the genes required for their synthesis correlated with the severity of the SARS-CoV-2 infection.

Broad-spectrum coronavirus inhibitors discovered by modeling viral fusion dynamics

Development of oral, broad-spectrum therapeutics targeting SARS-CoV-2, its variants, and related coronaviruses could curb the spread of COVID-19 and avert future pandemics. We created a novel computational discovery pipeline that employed molecular dynamics simulation (MDS), artificial intelligence (AI)-based docking predictions, and medicinal chemistry to design viral entry inhibitors that target a conserved region in the SARS-CoV-2 spike (S) protein that mediates membrane fusion. DrugBank library screening identified the orally available, FDA-approved AXL kinase inhibitor bemcentinib as binding this site and we demonstrated that it inhibits viral entry in a kinase-independent manner. Novel analogs predicted to bind to the same region and disrupt S protein conformational changes were designed using MDS and medicinal chemistry. These compounds significantly suppressed SARS-CoV-2 infection and blocked the entry of S protein-bearing pseudotyped α,β,γ,δ,ο variants as well as SARS CoV and MERS-CoV in human ACE2-expressing or DPP4-expressing cells more effectively than bemcentinib. When administered orally, the optimized lead compound also significantly inhibited SARS-CoV2 infection in mice. This computational design strategy may accelerate drug discovery for a broad range of applications.

Bitter taste receptors establish a stable binding affinity with the SARS-CoV-2-spike 1 protein akin to ACE2

COVID-19 is caused by the highly contagious SARS-CoV-2 virus, which originated in Wuhan, China, resulting in the highest worldwide mortality rate. Gustatory dysfunction is common among individuals infected with the Wild-type Wuhan strain. However, there are no reported cases of gustatory dysfunction among patients infected with the mutant delta variant. The reason behind this remains elusive to date. This in-silico-based study aims to unravel this clinical factor by evaluating the overall binding affinity of predominant bitter taste receptors associated with gustatory function (T2R-4, 10, 14, 19, 31, 38, 43, and 46) with the Receptor Binding Domain (RBD) of spike 1 (S1) protein of Wuhan (Wild)/delta-SARS-CoV-2 (mut1-T478K; mut2-E484K) variants. Based on docking and MM/PBSA free binding energy scores, the Wild RBD showed a stronger interaction with T2R-46 compared to the ACE2 protein. However, both delta variant mutants (mut1 and mut2) could not establish a stronger binding affinity with bitter taste receptor proteins, except for T2R-43 against mut1. In conclusion, the delta variants could not establish a better binding affinity with bitter taste receptors, contradicting the Wild variant that determines the severity of gustatory dysfunction among patients exposed to the delta and Wild SARS-CoV-2 variants. The study's inference also proposes T2R-46 as an alternate binding receptor target for RBD-S1 of Wild SARS-CoV-2, augmenting its virulence in all functional organs with compromised α-gustducin interaction and bitter sensitization. This in-silico-based study needs further wet-lab-based validation for a better understanding of the role of T2R-46-based viral entry in the human host.

Design, Synthesis, Evaluation, and Molecular Dynamics Simulation of SARS-CoV-2 Mpro Inhibitors

COVID-19, caused by SARS-CoV-2, is a highly contagious disease with significant transmissibility and pathogenicity. The main protease of SARS-CoV-2 (Mpro or 3CLpro) is crucial for viral replication, making it a key therapeutic target. Nirmatrelvir, a promising Mpro inhibitor, contains a trifluoroacetyl group in its P4 fragment, which presents opportunities for further optimization. This study aims to enhance the inhibitory activity of nirmatrelvir through structural modification of the P4 fragment. Using a computer-aided drug design (CADD) approach, 11 novel compounds were identified based on molecular docking scores, binding free energy, predicted ADMET properties, structural diversity, synthetic feasibility, and inhibitory activity. IC50 measurements and molecular dynamics (MD) simulations demonstrated significant inhibitory potential for most compounds, with IC50 values ranging from 0.0435-0.9989 μM. Notably, compounds 2-5a and 2-5f exhibited inhibitory activity against SARS-CoV-2 Mpro comparable to that of nirmatrelvir. These findings offer valuable insights for the development of anti-SARS-CoV-2 therapeutics.

Human coronaviruses: activation and antagonism of innate immune responses

SUMMARYHuman coronaviruses cause a range of respiratory diseases, from the common cold (HCoV-229E, HCoV-NL63, HCoV-OC43, and SARS-CoV-2) to lethal pneumonia (SARS-CoV, SARS-CoV-2, and MERS-CoV). Coronavirus interactions with host innate immune antiviral responses are an important determinant of disease outcome. This review compares the host's innate response to different human coronaviruses. Host antiviral defenses discussed in this review include frontline defenses against respiratory viruses in the nasal epithelium, early sensing of viral infection by innate immune effectors, double-stranded RNA and stress-induced antiviral pathways, and viral antagonism of innate immune responses conferred by conserved coronavirus nonstructural proteins and genus-specific accessory proteins. The common cold coronaviruses HCoV-229E and -NL63 induce robust interferon signaling and related innate immune pathways, SARS-CoV and SARS-CoV-2 induce intermediate levels of activation, and MERS-CoV shuts down these pathways almost completely.

Remedying SARS-CoV-2 through nature: a review highlighting the potentiality of herbs, trees, mushrooms, and endophytic microorganisms in controlling Coronavirus

MAIN CONCLUSION

Medicinal plants, mushrooms, and endophytes offer a rich source of secondary metabolites (SMs), including flavonoids, alkaloids, tannins, and terpenoids, with proven antiviral properties against SARS-CoV-2. Plant-associated microorganisms that colonize in living tissues of different parts of a plant possess the ability to produce SMs of immense therapeutic value and this biological interaction between plants and microbes can be exploited to develop antiviral drugs against SARS-CoV-2. The unprecedented lethality of the SARS-CoV-2 virus during the recent global pandemic has prompted extensive research into new treatment options and preventive strategies for COVID-19. Phytochemicals, particularly those derived from medicinal plants, microbes, and mushrooms, show promising results in combating the virus when combined with synthetic components. These natural compounds include terpenes, phenolics, flavonoids, and alkaloids that possess antiviral properties. Medicinal plants and their endophytic microbes, and mushrooms, offer a rich source of secondary metabolites (SMs) with potential antiviral effects against SARS-CoV-2. Given the urgency of addressing the swift spread of the new coronavirus strain, exploring and understanding these SMs could lead to the development of innovative and potent antiviral drugs. This review provides a comprehensive overview of plant-, microbial- and mushroom-derived SMs, their classification, and their applications in treating diseases caused by the coronavirus family, offering insights into the potential future production of natural medicines.

Hydrological and physicochemical parameters associated with SARS-CoV-2 and pepper mild mottle virus wastewater concentrations for a large-combined sewer system

During COVID-19, surveillance of SARS-CoV-2 in wastewater has been a promising tool for tracking viral infection at the community level. However, in addition to the shedding rates within the community, SARS-CoV-2 concentrations in raw wastewater are influenced by several environmental factors. This study investigated the effects of wastewater characteristics on the viral quantification of SARS-CoV-2 and pepper mild mottle virus (PMMoV) for a large wastewater system with combined sewers. Principal component analysis illustrated that water temperature negatively correlates with SARS-CoV-2 and PMMoV in wastewater, but flow rate and EC are highly correlated with SARS-CoV-2 in spring and winter. The normalization using EC enhanced the correlation with clinical data compared to normalization using pH, flow rate, and raw SARS-CoV-2. The normalization using PMMoV reduced the correlation with clinical data. Multiple linear and random forest (RF) applied to predict the concentrations of SARS-CoV-2 in wastewater, given the confirmed cases and physicochemical parameters. RF regression was the best model to predict SARS-CoV-2 in wastewater (R2=0.8), with the most important variables being the confirmed cases followed by water temperature. RF model is a potent predictor of the presence of SARS-CoV-2 in wastewater. This enhances the degree of reliability between community outbreaks and SARS-CoV-2 monitoring.

Neurobiology of COVID-19-Associated Psychosis/Schizophrenia: Implication of Epidermal Growth Factor Receptor Signaling

COVID-19 exhibits not only respiratory symptoms but also neurological/psychiatric symptoms rarely including delirium/psychosis. Pathological studies on COVID-19 provide evidence that the cytokine storm, in particular (epidermal growth factor) EGF receptor (EGFR, ErbB1, Her1) activation, plays a central role in the progression of viral replication and lung fibrosis. Of note, SARS-CoV-2 virus (specifically, S1 spike domain) mimics EGF and directly transactivates EGFR, preceding the inflammatory process. In agreement, the anticancer drugs targeting EGFR such as Nimotuzumab and tyrosine kinase inhibitors are markedly effective on COVID-19. However, these data might raise a provisional caution regarding implication of psychiatric disorder such as schizophrenia. The author's group has been investigating the etiologic and neuropathologic associations of EGFR signaling with schizophrenia. There are significant molecular associations between schizophrenia and EGFR ligand levels in blood as well as in the brain. In addition, perinatal challenges of EGFR ligands and intraventricular administration of EGF to rodents and monkeys both resulted in severe behavioral and/or electroencephalographic endophenotypes relevant to this disorder. These animal models also display postpubertal abnormality in soliloquy-like self-vocalization as well as in intercortical functional connectivity. Here, we discuss neuropsychiatric implication of coronavirus infection and its interaction with the EGFR system, by searching related literatures in PubMed database as of the end of 2023.

Matairesinol Treatment Interferes with the Replication of Coronavirus

The spread of a coronavirus infection can result in a pandemic, similar to the coronavirus disease 2019 pandemic. Such an infection also accounts for a considerable portion of common cold cases. Although coronavirus medicines are already available, alternative treatments are still required as the coronavirus can produce many variants. Matairesinol, a lignan family compound, is the constituent of cereals, such as rye. We used the human coronavirus OC43 to evaluate the antiviral activity of matairesinol. Matairesinol treatment interferes with coronavirus replication. This treatment decreases the expression of coronavirus protein and RNA as well as the number of coronavirus-induced plaque formations. Our experimental results collectively indicate that matairesinol treatment can potentially reduce coronavirus replication.

Effect of Exportin 1/XPO1 Nuclear Export Pathway Inhibition on Coronavirus Replication

The nucleocytoplasmic transport of proteins using XPO1 (exportin 1) plays a vital role in cell proliferation and survival. Many viruses also exploit this pathway to promote infection and replication. Thus, inhibiting the XPO1-mediated nuclear export pathway with selective inhibitors has a diverse effect on virus replication by regulating antiviral, proviral, and anti-inflammatory pathways. The XPO1 inhibitor Selinexor is an FDA-approved anticancer drug predicted to have antiviral or proviral functions against viruses. Here, we observed that the pretreatment of cultured cell lines from human or mouse origin with the nuclear export inhibitor Selinexor significantly enhanced the protein expression and replication of mouse hepatitis virus (MHV), a mouse coronavirus. The knockdown of cellular XPO1 protein expression also significantly enhanced the replication of MHV in human cells. However, for SARS-CoV-2, Selinexor treatment had diverse effects on virus replication in different cell lines. These results indicate that XPO1-mediated nuclear export pathway inhibition might affect coronavirus replication depending on cell types and virus origin.

Selective Control by Pistacia vera L. and Its Carotenoid Zeaxanthin on SARS-CoV-2 Virus

Since the onset of the COVID-19 (COronaVIrus Disease 19) pandemic, SARS-CoV-2 has exhibited a high transmission rate, further enhanced by new variants able to better adapt to humans. Addressing this issue has been challenging due to viral resistance and side effects associated with antiviral drugs and vaccines. As a result, there has been a growing interest in plant-derived compounds with antiviral properties. Our study revealed that pistachio extracts significantly inhibited SARS-CoV-2 viral entry. Employing pseudotyped particles bearing the S protein of SARS-CoV-2, we demonstrated that treatment with pistachio extracts inhibited binding of alpha (α) and omicron (ο) SARS-CoV-2 variants. Furthermore, our study revealed that the pistachio carotenoid zeaxanthin exhibited a different inhibitory activity against two SARS-CoV-2 variants. In silico analyses demonstrated a strong interaction between zeaxanthin and the receptor-binding domain (RBD) domain of the omicron spike (S) protein, thus reducing pseudovirus entry. However, zeaxanthin's weaker interaction with the alpha variant's RBD was insufficient to inhibit entry. Additionally, zeaxanthin suppressed the expression of the host protease TMPRSS2 at the protein level, thereby limiting the internalization of the alpha variant, which relies on TMPRSS2 for cellular entry.

Structural insights into ACE2 interactions and immune activation of SARS-CoV-2 and its variants: an in-silico study

The initial interaction between COVID-19 and the human body involves the receptor-binding domain (RBD) of the viral spike protein with the angiotensin-converting enzyme 2 (ACE2) receptor. Likewise, the spike protein can engage with immune-related proteins, such as toll-like receptors (TLRs) and pulmonary surfactant proteins A (SP-A) and D (SP-D), thereby triggering immune responses. In this study, we utilize computational methods to investigate the interactions between the spike protein and TLRs (specifically TLR2 and TLR4), as well as (SP-A) and (SP-D). The study is conducted on four variants of concern (VOC) to differentiate and identify common virus behaviours. An assessment of the structural stability of various variants indicates slight changes attributed to mutations, yet overall structural integrity remains preserved. Our findings reveal the spike protein's ability to bind with TLR4 and TLR2, prompting immune activation. In addition, our in-silico results reveal almost similar docking scores and therefore affinity for both ACE2-spike and TLR4-spike complexes. We demonstrate that even minor changes due to mutations in all variants, surfactant A and D proteins can function as inhibitors against the spike in all variants, hindering the ACE2-RBD interaction.Communicated by Ramaswamy H. Sarma.

Identification of promising SARS-CoV-2 main protease inhibitor through molecular docking, dynamics simulation, and ADMET analysis

The COVID-19 pandemic caused by SARS-CoV-2 continues to pose a major challenge to global health. Targeting the main protease of the virus (Mpro), which is essential for viral replication and transcription, offers a promising approach for therapeutic intervention. In this study, advanced computational techniques such as molecular docking and molecular dynamics simulations were used to screen a series of antiviral compounds for their potential inhibitory effect on the SARS-CoV-2 Mpro. A comprehensive analysis of compounds from the ChemDiv and PubChem databases was performed. The physicochemical properties, pharmacokinetics, and ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) profiles were evaluated to determine drug similarity and safety. Compound 4896 - 4038 proved to be the most promising candidate. It exhibited a favorable balance between molecular weight (491.06) and lipophilicity (logP 3.957), high intestinal absorption (92.119%), and broad tissue distribution (VDss of 0.529), indicating good oral bioavailability and therapeutic potential. Molecular docking studies showed that 4896 - 4038 has a strong binding affinity to the active site of Mpro and forms key interactions, such as hydrogen bonds, carbon-hydrogen bonds, pi-sulfur, and multiple van der Waals and pi-pi stacked bonds. The binding energy was comparable to that of the reference drug X77, indicating potential efficacy. Molecular dynamics simulations over 300 ns confirmed the stability of the Mpro/4896 - 4038 complex of protein-ligand. Free energy landscape mapping and MM/PBSA calculations further substantiated the favorable binding and stability of the complex. Importantly, 4896 - 4038 exhibited a comparatively favorable safety profile. In summary, compound 4896 - 4038 shows significant potential as a potent SARS-CoV-2 Mpro inhibitor, combining potent inhibitory activity with favorable pharmacokinetic and safety profiles. These results support the further development of 4896 - 4038 as a promising therapeutic agent in the fight against COVID-19 that warrants experimental validation and clinical investigation.

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.

Temporal, spatial and demographic distributions characteristics of COVID-19 symptom clusters from chinese medicine perspective: a systematic cross-sectional study in China from 2019 to 2023

BACKGROUND

The subtypes diagnosis of disease symptom clusters, grounded in the theory of "Treatment in Accordance with Three Categories of Etiologic Factors" and International Classification of Diseases 11th Revision (ICD-11), is a vital strategy for Chinese Medicine (CM) in treating unknown respiratory infectious diseases. However, the classification of disease symptom clusters continues to depend on empirical observations and lacks robust scientific evidence. Consequently, this study seeks to explore the temporal, spatial and demographic distributions characteristics of Corona Virus Disease 2019 (COVID-19) symptom clusters in China.

METHODS

PubMed, Web of Science, Science direct, WHO, Litcovid, CNKI databases were searched from inception until December 31, 2023. Optical character recognition technology and image recognition technology were employed to identify tables within the papers. Four researchers independently screened and extracted data, resolving conflicts through discussion. Heat mapping and hierarchical clustering techniques were utilized to analyze COVID-19 symptom clusters. Data analysis and visualization were conducted using R software (4.2.0), while the association analysis of symptom clusters was performed using Cytoscape (3.10.2).

RESULTS

A total of 366 COVID-19 clinical trials with 86,972 cases including 66 clinical symptoms of 7 disease systems and other clinical manifestations in China were included. In temporal distribution, 63 symptoms centered around fatigue and 44 symptoms focused on chest tightness are characteristic of symptom clusters in spring and winter, respectively. With the addition of spatial distribution, the symptom clusters in middle and low latitudes during spring are characterized by 53 symptoms centered around fatigue and cough, and 51 symptoms focused on fatigue, respectively. During winter, the symptom clusters in middle and low latitudes are characterized by 38 symptoms centered around chest tightness and 37 symptoms focused on fever, respectively. When considering demographic distribution, the symptom clusters for < 50 years are characterized by fatigue as the core symptom in middle (44 symptoms)/low (28 symptoms) latitudes during spring and middle latitude (25 symptoms) during winter. For ≥ 50 years, the symptom clusters in middle latitude (49 symptoms) during spring and low latitudes (35 symptoms) during winter are centered around cough, while in low latitude (27 symptoms) focuses on diarrhea during spring, and middle latitude (35 symptoms) emphasizes both diarrhea and chest tightness during winter.

CONCLUSION

In summary, variations in symptom clusters and core symptoms of COVID-19 in temporal, spatial and demographic distributions in China offer a scientific rationale for the "Treatment in Accordance with Three Categories of Etiologic Factors" theory. These interesting findings prompt further investigation into CM patterns in the ICD-11, and suggest potential strategies for personalized precision treatment of COVID-19. High-quality clinical studies focusing on individual symptoms are warranted to enhance understanding of respiratory infectious diseases.

Effect of exportin 1/XPO1 nuclear export pathway inhibition on coronavirus replication

Nucleocytoplasmic transport of proteins using XPO1 (exportin 1) plays a vital role in cell proliferation and survival. Many viruses also exploit this pathway to promote infection and replication. Thus, inhibiting the XPO1-mediated nuclear export pathway with selective inhibitors has a diverse effect on virus replication by regulating antiviral, proviral, and anti-inflammatory pathways. The XPO1 inhibitor, Selinexor, is an FDA-approved anticancer drug predicted to have antiviral or proviral functions against viruses. Here, we observed that pretreatment of cultured cell lines from human or mouse origin with nuclear export inhibitor Selinexor significantly enhanced protein expression and replication of Mouse Hepatitis Virus (MHV), a mouse coronavirus. Knockdown of cellular XPO1 protein expression also significantly enhanced the replication of MHV in human cells. However, for SARS-CoV-2, selinexor treatment had diverse effects on virus replication in different cell lines. These results indicate that XPO1-mediated nuclear export pathway inhibition might affect coronavirus replication depending on cell types and virus origin.

Impact of Prolonged SARS-CoV-2 Viral Shedding on COVID-19 Disease Outcome and Viral Dynamics

This article aimed to review the current literature on the impact of continuous shedding of the COVID-19 virus in infected patients in relation to disease outcome variables and viral dynamics. Electronic databases PubMed, Google Scholar, and MedlinePlus were searched using relevant keywords, restricting the selection to thirty-two peer-reviewed articles and four gray literatures from the WHO websites. Findings from this study showed that several variables such as sex, age, immune status, treatments, and vaccines were found to affect the outcomes associated with the COVID-19 virus shedding. These findings highlight the need for further research using longitudinal whole-genome sequencing of the virus and its variants to increase the understanding.

Impact of pharmaceutical and non-pharmaceutical interventions on COVID-19 in Tunisia

BACKGROUND

In COVID-19 management, a variety of pharmaceutical interventions (PI) and non- pharmaceutical interventions (NPI) were adopted to limit the spread of the disease and its associated deaths. We aimed to evaluate the impact of PI and NPI on risks of COVID-19 transmission and deaths.

METHOD

We collected aggregate data from March 2nd, 2020, to December 1, 2022 from the Tunisian Ministry of Health's website and OurWorldInData.org site. NPI Periods (NPIP: March 2020 to March 2021) and PI Periods (PIP) were distributed to NPIP1, 2, 3 and 4 and to PIP1, 2, 3 and 4, respectively. We calculated the Relative Risks (RR) and 95% Confidence Intervals (CI) by comparing the subsequent period with previous one.

RESULTS

The risk of SARS-CoV-2 transmission increased progressively from the zero cases period (NPIP2) to the mitigate strategy period (NPIP3) (RR = 14.0; 95% CI: 12.4-15.8) and to the stop-and-go epidemic control period (NPIP4) (RR = 23.1 (95% CI: 22.4-23.9). It was stabilized in the targeted vaccination period (PIP1) (RR = 1.08, 95% CI: 1.07-1.08) and reduced during the mass vaccination period (PIP2) (RR: 0.50, 95% CI: 0.50-0.51). SARS-CoV-2 transmission, increased during PIP3 concomitant with the Omicron wave (RR = 2.65, 95% CI: 2.64-2.67). It remained at a low level in PIP4 (RR = 0.18; 95% CI: 0.18-0.18). Compared to NPIP2, NPIP3 and NPIP4 were associated with a higher risk of COVID-19 mortality (RR = 3.337; 95% CI: 1.797-6.195) and (RR = 72.63 (95% CI: 54.01-97.68), respectively. Since the start of the immunization program, the risk of COVID-19 death has consistently decreased. In comparison to each previous period, the risk transitioned in PIP1 to RR = 0.91; 95% CI: 0.88-0.93, then to RR = 0.85; 95% CI: 0.83-0.88 in PIP2, to RR = 0.47; 95% CI: 0.45-0.50 in PIP3, and to RR = 0.19; 95% CI: 0.18-0.24 during PIP4.

CONCLUSION

In terms of lowering the risk of transmission and mortality, the NP strategy at the beginning of the epidemic outperformed the IP strategy during the outbreak.

COVID-19 vaccinations and their side effects: a scoping systematic review

Introduction: The COVID-19 virus has impacted people worldwide, causing significant changes in their lifestyles. Since the emergence of the epidemic, attempts have begun to prepare a vaccine that can eliminate the virus and restore balance to life in the entire world. Over the past two years, countries and specialized companies have competed to obtain a license from the World Health Organization for the vaccines that were discovered. After the appearance of vaccines in the health community, comparisons and fears of their side effects began, but people don't get an answer to the question of which is the best vaccine. Methods: IEEE Xplore, ScienceDirect, the New England Journal of Medicine, Google Scholar, and PubMed databases were searched for literature on the COVID-19 vaccine and its side effects. we surveyed the literature on the COVID-19 vaccine's side effects and the sorts of side effects observed after vaccination. Depending on data from the literature, we compared these vaccines in terms of side effects, then we analyzed the gaps and obstacles of previous studies and made proposals to process these gaps in future studies. Results: Overall, 17 studies were included in this scoping systematic review as they fulfilled the criteria specified, the majority of which were cross-sectional and retrospective cross-sectional studies. Most of the side effects were mild, self-limiting, and common. Thus, they usually resolve within 1-3 days after vaccination. Factors associated with higher side effects included advanced age, allergic conditions, those taking other medications (particularly immunosuppressive ones), those with a history of type II diabetes, heart disease, hypertension, COVID-19 infection, and female sex. Our meta-analyses also found that mRNA vaccines looked to be more effective, while inactivated vaccinations had fewer side effects. Conclusion: This review shows that the COVID-19 vaccine is safe to administer and induces protection.

[Symptoms and options in rehabilitation of post-COVID-19 syndrome (long-COVID)]

Manapság a járványok korát éljük. Egyre több és egyre súlyosabb járvány jelenik meg. A 2019. évi koronavírus-betegség (COVID–19) rendkívül fertőző betegség, amelyet a súlyos akut légúti szindrómát okozó új koronavírus (SARS-CoV-2) idéz elő. A vírus feltételezhetően denevérről terjedt át az emberre. A Rhinolophus sinicus egyik vírusa 80%-os, míg a Rhinolophus affinis vírustörzse 96%-os hasonlóságot mutatott a SARS-CoV-2-vel. A COVID–19-fertőzés emberről emberre történő átvitele a betegek elkülönítéséhez vezetett. A betegség a globalizált utazások következtében világszerte elterjedt, az Egészségügyi Világszervezet (WHO) világjárványnak nyilvánította, ma pedig jelentős közegészségügyi problémaként tartják számon. A fertőzés okozta akut tünetek mellett a pácienseknek és a társadalomnak szembesülnie kell a vírusfertőzés hosszú távú egészségkárosító szövődményeivel is, mely állapotot poszt-COVID–19-szindrómának (angolul: long-COVID) neveznek. A posztakut-COVID–19-szindrómán belül két szakaszt különítenek el: az akut fertőzést követő 4–12 hét közötti szubakut-COVID–19-szindrómát és a 12 héten túl is fennmaradó tünetekkel jellemzett poszt-COVID–19-szindrómát. A betegséget a tünetek sokféle skálája jellemzi, amelyek több szervrendszerre is kiterjednek. A panaszok kezelése elsősorban a tünetek kezeléséből, valamint multidiszciplináris rehabilitációból áll. A COVID–19 elleni védőoltás a világjárvány mérséklésének egyik legfontosabb eszköze. Az elmúlt évek kiterjedt kutatásai igazolják a COVID–19-vakcinák hatékonyságát. Nemzetközi tanulmányok kimutatták, hogy a vakcina protektív tényezőnek bizonyult a hosszan tartó COVID-tünetekkel szemben. Az összefoglaló tanulmányban irodalmi adatok alapján áttekintettem a COVID–19 tüneteit, epidemiológiáját, átvitelét, patogenezisét, továbbá a poszt-COVID–19-szindróma egyes szervrendszerekre gyakorolt hatásait, a rehabilitáció lehetőségeit és a vakcinák hatását a tünetek kialakulására. Orv Hetil. 2024; 165(33): 1266–1274.

The small molecule inhibitor of SARS-CoV-2 3CLpro EDP-235 prevents viral replication and transmission in vivo

The COVID-19 pandemic has led to the deaths of millions of people and severe global economic impacts. Small molecule therapeutics have played an important role in the fight against SARS-CoV-2, the virus responsible for COVID-19, but their efficacy has been limited in scope and availability, with many people unable to access their benefits, and better options are needed. EDP-235 is specifically designed to inhibit the SARS-CoV-2 3CLpro, with potent nanomolar activity against all SARS-CoV-2 variants to date, as well as clinically relevant human and zoonotic coronaviruses. EDP-235 maintains potency against variants bearing mutations associated with nirmatrelvir resistance. Additionally, EDP-235 demonstrates a ≥ 500-fold selectivity index against multiple host proteases. In a male Syrian hamster model of COVID-19, EDP-235 suppresses SARS-CoV-2 replication and viral-induced hamster lung pathology. In a female ferret model, EDP-235 inhibits production of SARS-CoV-2 infectious virus and RNA at multiple anatomical sites. Furthermore, SARS-CoV-2 contact transmission does not occur when naïve ferrets are co-housed with infected, EDP-235-treated ferrets. Collectively, these results demonstrate that EDP-235 is a broad-spectrum coronavirus inhibitor with efficacy in animal models of primary infection and transmission.

Post COVID-19 vaccination medium vessel vasculitis: a systematic review of case reports

PURPOSE

Vaccinations are essential in minimizing the effects of global health crises including COVID-19 pandemic. This study investigates the potential association between COVID-19 vaccination and the occurrence of medium vessel vasculitis.

METHODS

Several databases were utilized to conduct a comprehensive literature review. The studies were carefully evaluated to ensure their quality and eliminate any potential bias.

RESULTS

After reviewing 935 search results and removing duplicates, we selected 10 case reports. We discovered that medium vessel vasculitis may occur after COVID-19 vaccination, typically appearing around 16.2 days after vaccination. The patients in the study had a median age of 43.5 years and were predominantly males (80%). Additionally, half of the cases were reported after the second dose of vaccination.

CONCLUSIONS

Vaccination-associated vasculitis is a rare yet possible complication of COVID-19 vaccination and lacks a clear treatment protocol.

Assessment and design of filters and masks against COVID-19 via modeling and simulations

This study aimed to evaluate and design masks against viruses, especially SARS-CoV-2 associated with COVID-19. A continuum filtration model was developed where the rate of particle deposition and "sticking" on the filter fibers is a critical term in the mass transfer, together with permeation velocity, filter porosity, tortuosity, and Brownian diffusion. CFD simulations of the airflow during respiration lead to the recommendation that the filter permeability should be above 4 × 10-11 m2 to direct the airflow for effectiveness against virus particles; otherwise, low filter permeabilities cause the unfiltered air to flow preferentially through the leak gaps between the mask and the headform. Different mask filters with microstructural and geometry data from the literature are assessed via filtration simulations for breathability and filtration efficiency. The results demonstrate that a surgical mask of 25% porosity, pore size of 150 µm and permeability of 4.4 × 10-11 m2 can achieve 100% minimum efficiency while demonstrating high breathability, complying with the criteria of FFP3, N95, and surgical Class II and IIR masks. Selected cotton and synthetic cloths as well as electrospun fiber layers are predicted to comply with FFP2, N95, and surgical mask Class II and IIR standards.

Binding of SARS-CoV-2 Nonstructural Protein 1 to 40S Ribosome Inhibits mRNA Translation

Experimental evidence has established that SARS-CoV-2 NSP1 acts as a factor that restricts cellular gene expression and impedes mRNA translation within the ribosome's 40S subunit. However, the precise molecular mechanisms underlying this phenomenon have remained elusive. To elucidate this issue, we employed a combination of all-atom steered molecular dynamics and coarse-grained alchemical simulations to explore the binding affinity of mRNA to the 40S ribosome, both in the presence and absence of SARS-CoV-2 NSP1. Our investigations revealed that the binding of SARS-CoV-2 NSP1 to the 40S ribosome leads to a significant enhancement in the binding affinity of mRNA. This observation, which aligns with experimental findings, strongly suggests that SARS-CoV-2 NSP1 has the capability to inhibit mRNA translation. Furthermore, we identified electrostatic interactions between mRNA and the 40S ribosome as the primary driving force behind mRNA translation. Notably, water molecules were found to play a pivotal role in stabilizing the mRNA-40S ribosome complex, underscoring their significance in this process. We successfully pinpointed the specific SARS-CoV-2 NSP1 residues that play a critical role in triggering the translation arrest.

Safety and Efficacy of Antiviral Drugs and Vaccines in Pregnant Women: Insights from Physiologically Based Pharmacokinetic Modeling and Integration of Viral Infection Dynamics

Addressing the complexities of managing viral infections during pregnancy is essential for informed medical decision-making. This comprehensive review delves into the management of key viral infections impacting pregnant women, namely Human Immunodeficiency Virus (HIV), Hepatitis B Virus/Hepatitis C Virus (HBV/HCV), Influenza, Cytomegalovirus (CMV), and SARS-CoV-2 (COVID-19). We evaluate the safety and efficacy profiles of antiviral treatments for each infection, while also exploring innovative avenues such as gene vaccines and their potential in mitigating viral threats during pregnancy. Additionally, the review examines strategies to overcome challenges, encompassing prophylactic and therapeutic vaccine research, regulatory considerations, and safety protocols. Utilizing advanced methodologies, including PBPK modeling, machine learning, artificial intelligence, and causal inference, we can amplify our comprehension and decision-making capabilities in this intricate domain. This narrative review aims to shed light on diverse approaches and ongoing advancements, this review aims to foster progress in antiviral therapy for pregnant women, improving maternal and fetal health outcomes.

Arctigenin from Forsythia viridissima Fruit Inhibits the Replication of Human Coronavirus

Coronavirus can cause various diseases, from mild symptoms to the recent severe COVID-19. The coronavirus RNA genome is frequently mutated due to its RNA nature, resulting in many pathogenic and drug-resistant variants. Therefore, many medicines should be prepared to respond to the various coronavirus variants. In this report, we demonstrated that Forsythia viridissima fruit ethanol extract (FVFE) effectively reduces coronavirus replication. We attempted to identify the active compounds and found that actigenin from FVFE effectively reduces human coronavirus replication. Arctigenin treatment can reduce coronavirus protein expression and coronavirus-induced cytotoxicity. These results collectively suggest that arctigenin is a potent natural compound that prevents coronavirus replication.

Dynamic Patterns and Predominance of Respiratory Pathogens Post-COVID-19: Insights from a Two-Year Analysis

INTRODUCTION

Respiratory tract infections (RTIs) stand out as the most frequent causes leading to visits to the emergency department and hospitalizations. This study aims to assess the types and prevalence of respiratory infections across two years following the end of the COVID-19 pandemic.

METHODS

Patients presenting with an influenza-like illness (ILI) were tested using multiplex RT-PCR (QIAstat-Dx, Qiagen). The multiplexed RT- PCR test detects 21 respiratory viruses and bacteria.

RESULTS

During the study period, PCR test was done on a total of 1,790 samples were tested, and 712 (40%) were positive for a total of 796 pathogens. The mean age (± SD) of the participants was 20.1 ± 28.4 years in 2022 and 21.9 ± 27.6 years in 2023. Among the detected pathogens, the most prevalent were Rhinovirus/Enterovirus 222 (12.4%), followed by RSV A&B (103 cases, 5.7%), and H1N1 Influenza (77 cases, 4.3%). Additionally,  Influenza A/B constituted 172 (9.6%) while parainfluenza constituted (58, 3.2%). SARS-CoV-2 was identified in 3.97% of the samples. Over the two-year period, the monthly pattern of the identified pathogens exhibited fluctuations in the prevalence. Furthermore, variations were observed in the detected pathogens across different age groups.

CONCLUSION

In addition to adding significant knowledge to the field of respiratory viral infections, this study emphasizes the necessity of ongoing research and surveillance for the detection and characterization of respiratory viruses, particularly those with the potential for emergence. Such studies would also require setting up a strategy for genotyping and/or sequencing of viruses.

DNA vaccine prime and replicating vaccinia vaccine boost induce robust humoral and cellular immune responses against MERS-CoV in mice

As of December 2022, 2603 laboratory-identified Middle East respiratory syndrome coronavirus (MERS-CoV) infections and 935 associated deaths, with a mortality rate of 36%, had been reported to the World Health Organization (WHO). However, there are still no vaccines for MERS-CoV, which makes the prevention and control of MERS-CoV difficult. In this study, we generated two DNA vaccine candidates by integrating MERS-CoV Spike (S) gene into a replicating Vaccinia Tian Tan (VTT) vector. Compared to homologous immunization with either vaccine, mice immunized with DNA vaccine prime and VTT vaccine boost exhibited much stronger and durable humoral and cellular immune responses. The immunized mice produced robust binding antibodies and broad neutralizing antibodies against the EMC2012, England1 and KNIH strains of MERS-CoV. Prime-Boost immunization also induced strong MERS-S specific T cells responses, with high memory and poly-functional (CD107a-IFN-γ-TNF-α) effector CD8+ T cells. In conclusion, the research demonstrated that DNA-Prime/VTT-Boost strategy could elicit robust and balanced humoral and cellular immune responses against MERS-CoV-S. This study not only provides a promising set of MERS-CoV vaccine candidates, but also proposes a heterologous sequential immunization strategy worthy of further development.

Post-partum hemorrhage: a multidisciplinary approach to 'the golden hour' quantum leadership and communication

Background: Quantum leadership in postpartum hemorrhage (PPH) simulation training remains underexplored. Quantum leaders excel in PPH's chaotic settings, differing from traditional leaders. Aiming: To assess the impact of simulation training on quantum leadership skills in maternity teams. Research design: A quasi-experimental approach. Sample: 60 maternity professionals from Rafik Hariri University Hospital, Lebanon. Tools: Structured interviews, observational checklists and a leadership skills scale. Results: Most participants had limited PPH simulation experience and showed an initial low proficiency. Significant improvements were evident, post training. Conclusion: Simulation training enhances quantum leadership in PPH management among maternity professionals.

Enhancing SARS-CoV-2 surveillance in Malawi using telephone syndromic surveillance from July 2020 to April 2022

INTRODUCTION

Monitoring the SARS-CoV-2 pandemic in low-resource countries such as Malawi requires cost-effective surveillance strategies. This study explored the potential utility of phone-based syndromic surveillance in terms of its reach, monitoring trends in reported SARS-CoV-2-like/influenza-like symptoms (CLS/ILS), SARS-CoV-2 testing and mortality.

METHODS

Mobile phone-based interviews were conducted between 1 July 2020 and 30 April 2022, using a structured questionnaire. Randomly digital dialled numbers were used to reach individuals aged ≥18 years who spoke Chichewa or English. Verbal consent was obtained, and trained research assistants with clinical and nursing backgrounds collected information on age, sex, region of residence, reported CLS/ILS in the preceding 2 weeks, SARS-CoV-2 testing and history of household illness and death. Data were captured on tablets using the Open Data Kit database. We performed a descriptive analysis and presented the frequencies and proportions with graphical representations over time.

FINDINGS

Among 356 525 active phone numbers, 138 751 (38.9%) answered calls, of which 104 360 (75.2%) were eligible, 101 617 (97.4%) consented to participate, and 100 160 (98.6%) completed the interview. Most survey respondents were aged 25-54 years (72.7%) and male (65.1%). The regional distribution of the respondents mirrored the regional population distribution, with 45% (44%) in the southern region, 41% (43%) in the central region and 14% (13%) in the northern region. The reported SARS-CoV2 positivity rate was 11.5% (107/934). Of the 7298 patients who reported CLS/ILS, 934 (12.8%) reported having undergone COVID-19 testing. Of the reported household deaths, 47.2% (982 individuals) experienced CLS/ILS 2 weeks before their death.

CONCLUSION

Telephonic surveillance indicated that the number of SARS-CoV-2 cases was at least twice as high as the number of confirmed cases in Malawi. Our findings also suggest a substantial under-reporting of SARS-CoV-2-related deaths. Telephonic surveillance has proven feasible in Malawi, achieving the ability to characterise SARS-CoV-2 morbidity and mortality trends in low-resource settings.

Association depressive symptoms with memory function and social capital before and during COVID-19 in community-dwelling older adults in rural Japan: A retrospective study with a longitudinal data

OBJECTIVES

This study aimed to investigate the impact of memory function and social capital on depressive symptoms during the COVID-19 pandemic among older adults in rural Japan.

METHODS

A retrospective study with longitudinal data was conducted during COVID-19 from May 2021 to November 2021 (T2) in Kurogawa, Japan. The candidate population for this study was 145 with the following requirements: (1) older individuals aged 65 years or above who were registered in the Kurogawa study, and (2) those with previous data (from November 2016 to February 2020; T1 as pre-pandemic). Memory function was assessed using the Wechsler Memory Scale-Revised Logical Memory II delayed recall part A (LM II-DR). Depressive symptoms were assessed using the Japanese version of the 15-item Geriatric Depression Scale (GDS-15). Social capital was evaluated through civic participation, social cohesion, and reciprocity. Fear of the COVID-19 infection (FCV-19S) was evaluated.

RESULTS

The final analysis included 96 participants (mean age = 81.0 years, SD = 4.8) Multivariate analysis for GDS-15 score by Mixed Model Repeated Measures (MMRM) revealed significant associations between LM II-DR (β = -0.13, 95% CI: -0.21-0.05, p = 0.002) and FCV-19S during COVID-19 (β = 0.08, 95% CI: 0.01-0.15, p = 0.02) with GDS-15 score. However, civic participation, social cohesion and reciprocity were not associated with GDS-15 score.

CONCLUSIONS

Among older adults in rural Japan, memory function and fear of the COVID-19 infection were significantly associated with depressive symptoms in MMRM analysis. However, social capital was not associated with depressive symptoms. This highlights the need to address memory function and fear of the COVID-19 infection in interventions for older adults during crises like the COVID-19 pandemic.

Impact of latent toxoplasmosis on pneumonic and non-pneumonic COVID-19 patients with estimation of relevant oxidative stress biomarkers

Susceptibility to COVID-19, the most devastating global pandemic, appears to vary widely across different population groups. Exposure to toxoplasmosis has been proposed as a theory to explain the diversity of these populations. The aim of the present study was to investigate the possible association between latent toxoplasmosis and COVID-19 and its probable correlation with markers of oxidative stress, C-reactive protein (CRP) and ferritin. In a case-control study, blood samples were collected from 91 confirmed (48 non-pneumonic; NP, and 43 pneumonic; P) COVID-19 patients and 45 healthy controls. All participants were tested for IgG anti-Toxoplasma gondii antibodies and oxidative stress markers (nitric oxide [NO], superoxide dismutase [SOD] and reduced glutathione [GSH]), and CRP and serum ferritin levels were determined. In COVID-19 patients, IgG anti-T. gondii antibodies were found in 54% compared to 7% in the control group, with the difference being statistically significant (P ˂ 0.001). However, no significant correlation was found between the severity of COVID-19 and latent T. gondii infection. Latent toxoplasmosis had a strong influence on the risk of COVID-19. NO and SOD levels were significantly increased in COVID-19 patients, while GSH levels decreased significantly in them compared to control subjects (P ˂ 0.001 for both values). CRP and ferritin levels were also significantly elevated in P COVID-19 patients infected with toxoplasmosis. This is the first study to look at the importance of oxidative stress indicators in co-infection between COVID-19 and T. gondii. The high prevalence of latent toxoplasmosis in COVID-19 suggests that T. gondii infection can be considered a strong indicator of the high risk of COVID-19.

Lung as a target for COVID-19: Mechanistic insights and probable candidate molecules for cure

Novel coronavirus (SARS nCoV2), belonging to the family coronaviridae, remains a dreadful pathogen affecting the respiratory tract and lungs. COVID-19 declared a global pandemic by WHO, has become a serious cause of concern for clinicians and researchers, who need to understand the significant biology and pathogenicity of this virus to design better treatment modalities. Existing antiretroviral drugs remain partially ineffective in critical subjects with associated co-morbidities. This review provides an insight into the molecular mechanisms by which SARS-CoV2 targets the lungs leading to ARDS in severe cases. This also addresses the possible drug targets and certain anti-inflammatory natural compounds that can be looked upon as promising adjuvant therapeutics for COVID-19.

Apabetalone (RVX-208): A Potential Epigenetic Therapy for the Treatment of Cardiovascular, Renal, Neurological, Viral, and Cancer Disorders

Bromodomain and extra-terminal domain proteins (BET proteins) are epigenetic reader proteins that have been implicated in regulating gene expression through binding to chromatin and interaction with transcription factors. These proteins are located in the nucleus and are responsible for recognizing acetylated lysine residues on histones, reading epigenetic messages, recruiting key transcription factors, and thereby regulating gene expression. BET proteins control the transcription of genes responsible for maladaptive effects in inflammation, cancer, and renal and cardiovascular diseases. Given the multifaceted role of BET proteins in the pathogenesis of various diseases, several small molecule inhibitors of BET proteins have been developed as potential therapeutic targets for treating different diseases in recent years. However, while many nonselective BET inhibitors are indicated for the treatment of cancer, a selective BET inhibitor, apabetalone, is the only oral BET inhibitor in phase III clinical trials for the treatment of cardiovascular diseases and others. Thus, this review aims to present and discuss the preclinical and clinical evidence for the beneficial effects and mechanism of action of apabetalone for treating various diseases.

Structure-based design of pan-coronavirus inhibitors targeting host cathepsin L and calpain-1

Respiratory disease caused by coronavirus infection remains a global health crisis. Although several SARS-CoV-2-specific vaccines and direct-acting antivirals are available, their efficacy on emerging coronaviruses in the future, including SARS-CoV-2 variants, might be compromised. Host-targeting antivirals provide preventive and therapeutic strategies to overcome resistance and manage future outbreak of emerging coronaviruses. Cathepsin L (CTSL) and calpain-1 (CAPN1) are host cysteine proteases which play crucial roles in coronaviral entrance into cells and infection-related immune response. Here, two peptidomimetic α-ketoamide compounds, 14a and 14b, were identified as potent dual target inhibitors against CTSL and CAPN1. The X-ray crystal structures of human CTSL and CAPN1 in complex with 14a and 14b revealed the covalent binding of α-ketoamide groups of 14a and 14b to C25 of CTSL and C115 of CAPN1. Both showed potent and broad-spectrum anticoronaviral activities in vitro, and it is worth noting that they exhibited low nanomolar potency against SARS-CoV-2 and its variants of concern (VOCs) with EC50 values ranging from 0.80 to 161.7 nM in various cells. Preliminary mechanistic exploration indicated that they exhibited anticoronaviral activity through blocking viral entrance. Moreover, 14a and 14b exhibited good oral pharmacokinetic properties in mice, rats and dogs, and favorable safety in mice. In addition, both 14a and 14b treatments demonstrated potent antiviral potency against SARS-CoV-2 XBB 1.16 variant infection in a K18-hACE2 transgenic mouse model. And 14b also showed effective antiviral activity against HCoV-OC43 infection in a mouse model with a final survival rate of 60%. Further evaluation showed that 14a and 14b exhibited excellent anti-inflammatory effects in Raw 264.7 mouse macrophages and in mice with acute pneumonia. Taken together, these results suggested that 14a and 14b are promising drug candidates, providing novel insight into developing pan-coronavirus inhibitors with antiviral and anti-inflammatory properties.

Automated machine learning for the identification of asymptomatic COVID-19 carriers based on chest CT images

BACKGROUND

Asymptomatic COVID-19 carriers with normal chest computed tomography (CT) scans have perpetuated the ongoing pandemic of this disease. This retrospective study aimed to use automated machine learning (AutoML) to develop a prediction model based on CT characteristics for the identification of asymptomatic carriers.

METHODS

Asymptomatic carriers were from Yangzhou Third People's Hospital from August 1st, 2020, to March 31st, 2021, and the control group included a healthy population from a nonepizootic area with two negative RT‒PCR results within 48 h. All CT images were preprocessed using MATLAB. Model development and validation were conducted in R with the H2O package. The models were built based on six algorithms, e.g., random forest and deep neural network (DNN), and a training set (n = 691). The models were improved by automatically adjusting hyperparameters for an internal validation set (n = 306). The performance of the obtained models was evaluated based on a dataset from Suzhou (n = 178) using the area under the curve (AUC), accuracy, sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and F1 score.

RESULTS

A total of 1,175 images were preprocessed with high stability. Six models were developed, and the performance of the DNN model ranked first, with an AUC value of 0.898 for the test set. The sensitivity, specificity, PPV, NPV, F1 score and accuracy of the DNN model were 0.820, 0.854, 0.849, 0.826, 0.834 and 0.837, respectively. A plot of a local interpretable model-agnostic explanation demonstrated how different variables worked in identifying asymptomatic carriers.

CONCLUSIONS

Our study demonstrates that AutoML models based on CT images can be used to identify asymptomatic carriers. The most promising model for clinical implementation is the DNN-algorithm-based model.

SARS-CoV-2 Specific Nanobodies Neutralize Different Variants of Concern and Reduce Virus Load in the Brain of h-ACE2 Transgenic Mice

Since the beginning of the COVID-19 pandemic, there has been a significant need to develop antivirals and vaccines to combat the disease. In this work, we developed llama-derived nanobodies (Nbs) directed against the receptor binding domain (RBD) and other domains of the Spike (S) protein of SARS-CoV-2. Most of the Nbs with neutralizing properties were directed to RBD and were able to block S-2P/ACE2 interaction. Three neutralizing Nbs recognized the N-terminal domain (NTD) of the S-2P protein. Intranasal administration of Nbs induced protection ranging from 40% to 80% after challenge with the WA1/2020 strain in k18-hACE2 transgenic mice. Interestingly, protection was associated with a significant reduction in virus replication in nasal turbinates and a reduction in virus load in the brain. Employing pseudovirus neutralization assays, we identified Nbs with neutralizing capacity against the Alpha, Beta, Delta, and Omicron variants, including a Nb capable of neutralizing all variants tested. Furthermore, cocktails of different Nbs performed better than individual Nbs at neutralizing two Omicron variants (B.1.529 and BA.2). Altogether, the data suggest the potential of SARS-CoV-2 specific Nbs for intranasal treatment of COVID-19 encephalitis.

Drug Discovery in Low Data Regimes: Leveraging a Computational Pipeline for the Discovery of Novel SARS-CoV-2 Nsp14-MTase Inhibitors

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has led to significant global morbidity and mortality. A crucial viral protein, the non-structural protein 14 (nsp14), catalyzes the methylation of viral RNA and plays a critical role in viral genome replication and transcription. Due to the low mutation rate in the nsp region among various SARS-CoV-2 variants, nsp14 has emerged as a promising therapeutic target. However, discovering potential inhibitors remains a challenge. In this work, we introduce a computational pipeline for the rapid and efficient identification of potential nsp14 inhibitors by leveraging virtual screening and the NCI open compound collection, which contains 250,000 freely available molecules for researchers worldwide. The introduced pipeline provides a cost-effective and efficient approach for early-stage drug discovery by allowing researchers to evaluate promising molecules without incurring synthesis expenses. Our pipeline successfully identified seven promising candidates after experimentally validating only 40 compounds. Notably, we discovered NSC620333, a compound that exhibits a strong binding affinity to nsp14 with a dissociation constant of 427 ± 84 nM. In addition, we gained new insights into the structure and function of this protein through molecular dynamics simulations. We identified new conformational states of the protein and determined that residues Phe367, Tyr368, and Gln354 within the binding pocket serve as stabilizing residues for novel ligand interactions. We also found that metal coordination complexes are crucial for the overall function of the binding pocket. Lastly, we present the solved crystal structure of the nsp14-MTase complexed with SS148 (PDB:8BWU), a potent inhibitor of methyltransferase activity at the nanomolar level (IC50 value of 70 ± 6 nM). Our computational pipeline accurately predicted the binding pose of SS148, demonstrating its effectiveness and potential in accelerating drug discovery efforts against SARS-CoV-2 and other emerging viruses.

The association between autoimmune encephalitis mediated by N-methyl-ᴅ-aspartate receptor autoantibodies and COVID-19: a systematic review

Neurological complications related to coronavirus disease 2019 (COVID-19) infection have been increasingly reported. One of the most serious neurological complications is encephalitis, which could be due either to direct viral invasion or an immune-mediated inflammatory reaction. In this study, we conducted a systematic review of reported cases of autoimmune encephalitis mediated by N-methyl-ᴅ-aspartate receptor antibodies in conjunction with or after diagnosis of COVID-19 infection.

Repurposing of Plant-based Antiviral Molecules for the Treatment of COVID-19

COVID-19, stemming from SARS-CoV-2, poses a formidable threat to global healthcare, with a staggering 77 million confirmed cases and 690,067 deaths recorded till December 24, 2023. Given the absence of specific drugs for this viral infection, the exploration of novel antiviral compounds becomes imperative. High-throughput technologies are actively engaged in drug discovery, and there is a parallel effort to repurpose plant-based molecules with established antiviral properties. In this context, the review meticulously delves into the potential of plant-based folk remedies and existing molecules. These substances have showcased substantial viral inhibition in diverse in vivo, in silico, and in vitro studies, particularly against critical viral protein targets, including SARS-CoV-2. The findings position these plant-based molecules as promising antiviral drug candidates for the swift advancement of treatments for COVID-19. It is noteworthy that the inherent attributes of these plant-based molecules, such as their natural origin, potency, safety, and cost-effectiveness, contribute to their appeal as lead candidates. The review advocates for further exploration through comprehensive in vivo studies conducted on animal models, emphasizing the potential of plant-based compounds to help in the ongoing quest to develop effective antivirals against COVID-19.

Preclinical and Clinical Investigations of Potential Drugs and Vaccines for COVID-19 Therapy: A Comprehensive Review With Recent Update

The COVID-19 pandemic-led worldwide healthcare crisis necessitates prompt societal, ecological, and medical efforts to stop or reduce the rising number of fatalities. Numerous mRNA based vaccines and vaccines for viral vectors have been licensed for use in emergencies which showed 90% to 95% efficacy in preventing SARS-CoV-2 infection. However, safety issues, vaccine reluctance, and skepticism remain major concerns for making mass vaccination a successful approach to treat COVID-19. Hence, alternative therapeutics is needed for eradicating the global burden of COVID-19 from developed and low-resource countries. Repurposing current medications and drug candidates could be a more viable option for treating SARS-CoV-2 as these therapies have previously passed a number of significant checkpoints for drug development and patient care. Besides vaccines, this review focused on the potential usage of alternative therapeutic agents including antiviral, antiparasitic, and antibacterial drugs, protease inhibitors, neuraminidase inhibitors, and monoclonal antibodies that are currently undergoing preclinical and clinical investigations to assess their effectiveness and safety in the treatment of COVID-19. Among the repurposed drugs, remdesivir is considered as the most promising agent, while favipiravir, molnupiravir, paxlovid, and lopinavir/ritonavir exhibited improved therapeutic effects in terms of elimination of viruses. However, the outcomes of treatment with oseltamivir, umifenovir, disulfiram, teicoplanin, and ivermectin were not significant. It is noteworthy that combining multiple drugs as therapy showcases impressive effectiveness in managing individuals with COVID-19. Tocilizumab is presently employed for the treatment of patients who exhibit COVID-19-related pneumonia. Numerous antiviral drugs such as galidesivir, griffithsin, and thapsigargin are under clinical trials which could be promising for treating COVID-19 individuals with severe symptoms. Supportive treatment for patients of COVID-19 may involve the use of corticosteroids, convalescent plasma, stem cells, pooled antibodies, vitamins, and natural substances. This study provides an updated progress in SARS-CoV-2 medications and a crucial guide for inventing novel interventions against COVID-19.

Therapeutic Management with Repurposing Approaches: A Mystery During COVID-19 Outbreak

The ubiquitous pandemic that emerged due to COVID-19 affected the whole planet. People all over the globe became vulnerable to the unpredictable emergence of coronavirus. The sudden emergence of respiratory disease in coronavirus infected several patients. This affected human life drastically, from mild symptoms to severe illness, leading to mortality. COVID-19 is an exceptionally communicable disease caused by SARS-CoV-2. According to a genomic study, the viral spike RBD interactions with the host ACE2 protein from several coronavirus strains and the interaction between RBD and ACE2 highlighted the potential change in affinity from the virus causing the COVID-19 outbreak to a progenitor type of SARS-CoV-2. SARS-CoV-2, which could be the principal reservoir, is phylogenetically related to the SARS-like bat virus. Other research works reported that intermediary hosts for the transmission of viruses to humans could include cats, bats, snakes, pigs, ferrets, orangutans, and monkeys. Even with the arrival of vaccines and individuals getting vaccinated and treated with FDAapproved repurposed drugs like Remdesivir, the first and foremost steps aimed towards the possible control and minimization of community transmission of the virus include social distancing, self-realization, and self-health care. In this review paper, we discussed and summarized various approaches and methodologies adopted and proposed by researchers all over the globe to help with the management of this zoonotic outbreak by following repurposed approaches.

Codon usage bias analysis of the spike protein of human coronavirus 229E and its host adaptability

Human coronavirus 229E (HCoV-229E) represents one of the known coronaviruses capable of infecting humans and causes mild respiratory symptoms. It is also considered to have a zoonotic source, originating from animals and being transmitted the humans. In this study, a comprehensive phylogenetic and codon usage analysis of the spike (S) gene of HCoV-229E was conducted. Utilizing phylogenetic analysis and principal component analysis, HCoV-229E was categorized into four distinct clusters, each demonstrating unique host affiliations. Furthermore, it was observed that the codon usage bias within the S gene of HCoV-229E is relatively low, primarily influenced by natural selection patterns, with contributions from mutation pressure and dinucleotide abundance. Comparative analysis involving Codon Adaptation Index (CAI) and Relative Codon Deoptimization Index (RCDI) revealed that the codon usage pattern of HCoV-229E mirrors more closely that of camels, as opposed to alpacas and humans. The elucidation of the codon usage pattern within HCoV-229E, which we have meticulously examined, offers valuable insights for a more comprehensive comprehension of viral features, history, and evolutionary trajectory.

Stratification of COVID-19 Patients with Moderate-to-Severe Hypoxemic Respiratory Failure for Response to High-Flow Nasal Cannula: A Retrospective Observational Study

Background and Objectives: In patients with COVID-19, high-flow nasal cannula (HFNC) and continuous positive airway pressure (CPAP) are widely applied as initial treatments for moderate-to-severe acute hypoxemic respiratory failure. The aim of the study was to assess which respiratory supports improve 28-day mortality and to identify a predictive index of treatment response. Materials and Methods: This is a single-center retrospective observational study including 159 consecutive adult patients with COVID-19 and moderate-to-severe hypoxemic acute respiratory failure. Results: A total of 159 patients (82 in the CPAP group and 77 in the HFNC group) were included in the study. Mortality within 28 days was significantly lower with HFNC compared to CPAP (16.8% vs. 50%), while ICU admission and tracheal intubation within 28 days were significantly higher with CPAP compared to HFNC treatment (32% vs. 13%). We identified an index for survival in HFNC by including three variables easily available at admission (LDH, age, and respiratory rate) and the PaO2/FiO2 ratio at 48 h. The index showed high discrimination for survival with an AUC of 0.88, a negative predictive value of 86%, and a positive predictive value of 95%. Conclusions: Treatment with HFNC appears to be associated with greater survival and fewer ICU admission than CPAP. LDH, respiratory rate, age, and PaO2/FiO2 at 48 h were independently associated with survival and an index based on these variables allows for the prediction of treatment success and the assessment of patient allocation to the appropriate intensity of care after 48 h. Further research is warranted to determine effects on other outcomes and to assess the performance of the index in larger cohorts.

Knowledge, attitude, and practice of virtual consultation among outpatients at a teaching hospital in Malaysia

INTRODUCTION

During the coronavirus disease 2019 (COVID-19) pandemic, the use of virtual consultations has accelerated to ensure continued access to healthcare despite lockdowns and physical distancing measures. We aimed to determine the knowledge (awareness) of, attitude (acceptability) to, and practice (exposure) [KAP] of virtual consultations (VC), the demographic factors associated with poor KAP, and the correlation between the three KAP domains.

METHODS

A cross-sectional study, using a convenience sampling technique, was conducted from 13 September, 2021 to 28 November, 2021. We designed a 45-item VC KAP questionnaire. This was distributed to outpatient users attending cardiovascular, dermatology, geriatrics, haematology, endocrine, respiratory, gastroenterology, rheumatology, or neurology clinics at the University Malaya Medical Centre. It was completed during face-to-face, online, or telephone interviews. The data were analysed using SPSS version 24.0. Binary logistic regression was used to determine the demographic factors associated with KAP. Correlation between KAP domains was determined using Spearman's rho (r). A p-value of <0.05 was considered statistically significant.

RESULTS

A total of 366 questionnaires were completed. Knowledge (awareness), attitude (acceptability), and practice (exposure) were considered good in 69.7%, 80.9%, and 24.6% of participants, respectively. There were no significant relationships between age, gender, ethnicity, and duration of hospital attendance (years) with knowledge (awareness), attitude (acceptability), and practice (exposure). A moderate positive correlation was seen between knowledge (awareness) and attitude (acceptability) (Attitude total [Atotal]) (r = 0.48, p<0.001), with no significant correlation between knowledge (awareness) and practice (exposure) (r = 0.04, p = 0.45), and attitude (acceptability) (Atotal) and practice (r = 0.01, p = 0.82).

CONCLUSION

Overall, outpatient clinic users had good knowledge (awareness) of and were receptive towards VC but had poor practice (exposure). More opportunities for VC use in healthcare can increase exposure and subsequent utilisation. Interventions to increase the effectiveness of VC use should be explored in future studies.

The impact of Sars-Cov-2 infection on the wound healing of cervical treatment in patients with squamous intraepithelial lesions: a retrospective cohort study

Objective

SARS-CoV-2 infection has been associated with an increase in inflammatory factors, a weakening of the immune system, and a potentially delay in wound healing following surgery or ablative treatment. In this retrospective cohort study, we aimed to investigate the impact of SARS-CoV-2 infection on wound healing following cervical treatment in patients with squamous intraepithelial lesions (SIL).

Method

From November 2022 to February 2023, patients with SIL who underwent cervical ablative treatment or loop electrosurgical excision procedure at the People's Hospital of Guangxi Zhuang Autonomous Region, China, were enrolled in the study. Of these, 29 patients who developed symptoms of SARS-CoV-2 infection and confirmed by an antigen test within one month after cervical treatment were included as experimental group, while the other 31 patients who received cervical treatment after recovering from SARS-CoV-2 infection were included in the control group. The cervical wound condition of all patients was documented using colposcopy immediately and one month after the procedure. Image J software was utilized to analyze the wound healing rate at one month post-treatment, and the wound healing status between two groups was compared. A vaginal discharge examination was performed before and one month after cervical treatment.

Results

No significant differences in age, severity, treatment, or time between groups. Experimental group had significantly lower healing rate 83.77(62.04, 97.09) % than control 98.64(97.10, 99.46)%，p < 0.001, and a higher scab non-shedding rate (24.14% vs. 3.22%, p = 0.024). Among patients who were infected with SARS-CoV-2 after undergoing cervical treatment, we observed 5 out of 7 patients (71.43%) contracted SARS-CoV-2 within 2 weeks after cervical treatment. No significant correlation was found between white blood cell count or leukocyte esterase in vaginal discharge and delayed wound healing of the cervix (p = 0.947 and 0.970, respectively).

Conclusion

SARS-CoV-2 infection may prolong the healing time of cervical treatment in patients with SIL. To minimize the risk of delayed healing, it's crucial for patients to avoid viral infections such as SARS-CoV-2 within the first month of treatment. Taking necessary precautions to prevent infection is essential for successful cervical treatment outcomes in patients with SIL.

Immune responses of lung transplant recipients against SARS-CoV-2 and common respiratory coronaviruses: Evidence for pre-existing cross-reactive immunity

Humoral and cellular immune responses to SARS-CoV-2 and other coronaviruses in lung transplant recipients are unknown. We measured antibodies and T cell responses against the SARS-CoV-2 spike S2 and nucleocapsid antigens and spike antigens from common respiratory coronaviruses (229E, NL63, OC43, and HKU1) after vaccination or infection of LTxRs. 148 LTxRs from single center were included in this study: 98 after vaccination and 50 following SARS-CoV-2 infection. Antibodies were quantified by enzyme-linked immunosorbent assay. The frequency of T cells secreting IL2, IL4, IL10, IL17, TNFα, and IFNγ were enumerated by enzyme-linked immunospot assay. Our results have shown the development of antibodies to SARS-CoV-2 spike protein in infected LTxRs (39/50) and vaccinated LTxRs (52/98). Vaccinated LTxRs had higher number of T cells producing TNFα but less cells producing IFNγ than infected LTxRs in response to the nucleocapsid antigen and other coronavirus spike antigens. We didn't find correlation between the development of antibodies and cellular immune responses against the SARS-CoV-2 spike protein after vaccination. Instead, LTxRs have pre-existing cellular immunity to common respiratory coronaviruses, leading to cross-reactive immunity against SARS-CoV-2 which likely will provide protection against SARS-Cov-2 infection.

Wastewater-based Epidemiology and SARS-CoV-2: Variant Trends in the Apulia Region (Southern Italy) and Effect of Some Environmental Parameters

During the COVID-19 pandemic, wastewater monitoring has been used to monitor the levels of SARS-CoV-2 RNA entering the sewerage system. In Italy, the Istituto Superiore di Sanità coordinated the SARI project (Sorveglianza Ambientale Reflue in Italia) to detect SARS-CoV-2 and its variants. In this study, the concentration of SARS-CoV-2 and its variants in raw wastewater against COVID-19 cases was evaluated together with the effect of temperature and precipitation on virus spread. We validated a predictive model, proposed by De Giglio et al., 2021, to establish the number of COVID-19 cases/100,000 inhabitants. A receiver operating characteristic curve model was applied to predict the number of COVID-19 cases and Poisson regression was applied to study the effect of temperature and rainfall on viral load. In Apulia, from October 2021 to December 2022, we analyzed 1041 samples, of which 985 (94.6%) tested positive for SARS-CoV-2. Median atmospheric temperature was inversely proportional to viral load in wastewater; no correlation was found with precipitation. The predictive model confirmed that at least 11 cases/100,000 inhabitants would occur in the 15 days following the detection of the virus in wastewater. Environmental surveillance of SARS-CoV-2 can be used to map the virus and its variants.

Evaluation of in vitro antiviral activity of SARS-CoV-2 Mpro inhibitor pomotrelvir and cross-resistance to nirmatrelvir resistance substitutions

The unprecedented scale of the COVID-19 pandemic and the rapid evolution of SARS-CoV-2 variants underscore the need for broadly active inhibitors with a high barrier to resistance. The coronavirus main protease (Mpro) is an essential cysteine protease required for viral polyprotein processing and is highly conserved across human coronaviruses. Pomotrelvir is a novel Mpro inhibitor that has recently completed a phase 2 clinical trial. In this report, we demonstrated that pomotrelvir is a potent competitive inhibitor of SARS-CoV-2 Mpro with high selectivity against human proteases. In the enzyme assay, pomotrelvir is also active against Mpro proteins derived from human coronaviruses CoV-229E, CoV-OC43, CoV-HKU1, CoV-NL63, MERS, and SARS-CoV. In cell-based SARS-CoV-2 replicon and SARS-CoV-2 infection assays, pomotrelvir has shown potent inhibitory activity and is broadly active against SARS-CoV-2 clinical isolates including Omicron variants. Many resistance substitutions of the Mpro inhibitor nirmatrelvir confer cross-resistance to pomotrelvir, consistent with the finding from our enzymatic analysis that pomotrelvir and nirmatrelvir compete for the same binding site. In a SARS-CoV-2 infection assay, pomotrelvir is additive when combined with remdesivir or molnupiravir, two nucleoside analogs targeting viral RNA synthesis. In conclusion, our results from the in vitro characterization of pomotrelvir antiviral activity support its further clinical development as an alternative COVID-19 therapeutic option.