The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

AnnCovDB: a manually curated annotation database for mutations in SARS-CoV-2 spike protein

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been circulating and adapting within the human population for >4 years. A large number of mutations have occurred in the viral genome, resulting in significant variants known as variants of concern (VOCs) and variants of interest (VOIs). The spike (S) protein harbors many of the characteristic mutations of VOCs and VOIs, and significant efforts have been made to explore functional effects of the mutations in the S protein, which can cause or contribute to viral infection, transmission, immune evasion, pathogenicity, and illness severity. However, the knowledge and understanding are dispersed throughout various publications, and there is a lack of a well-structured database for functional annotation that is based on manual curation. AnnCovDB is a database that provides manually curated functional annotations for mutations in the S protein of SARS-CoV-2. Mutations in the S protein carried by at least 8000 variants in the GISAID were chosen, and the mutations were then utilized as query keywords to search in the PubMed database. The searched publications revealed that 2093 annotation entities for 205 single mutations and 93 multiple mutations were manually curated. These entities were organized into multilevel hierarchical categories for user convenience. For example, one annotation entity of N501Y mutation was 'Infectious cycle➔Attachment➔ACE2 binding affinity➔Increase'. AnnCovDB can be used to query specific mutations and browse through function annotation entities. Database URL: https://AnnCovDB.app.bio-it.tech/.

Inhaled Dry Powder of Antiviral Agents: A Promising Approach to Treating Respiratory Viral Pathogens

Inhaled dry powder formulations of antiviral agents represent a novel and potentially transformative approach to managing respiratory viral infections. Traditional antiviral therapies in the form of tablets or capsules often face limitations in terms of therapeutic activity, systemic side effects, and delayed onset of action. Dry powder inhalers (DPIs) provide a targeted delivery system, ensuring the direct administration of antivirals to the infection site, the respiratory tract, which potentially enhance therapeutic efficacy and minimize systemic exposure. This review explores the current state of inhaled dry powder antiviral agents, their advantages over traditional routes, and specific formulations under development. We discuss the benefits of targeted delivery, such as improved drug deposition in the lungs and reduced side effects, alongside considerations related to the formulation preparation. In addition, we summarize the developed (published and marketed) inhaled dry powders of antiviral agents.

Enhancing protective immunity against SARS-CoV-2 with a self-amplifying RNA lipid nanoparticle vaccine

RNA-based vaccines against SARS-CoV-2 have demonstrated promising protective immunity against the global COVID-19 epidemic. Enhancing the intensity and duration of mRNA antigen expression is anticipated to markedly boost antiviral immune responses. Self-amplifying RNA (saRNA) represents a next-generation platform for RNA-based vaccines, amplifying transcripts in situ to augment the expression of encoded immunogens. Here, we develop a saRNA nanovaccine, formulated with a mutated saRNA encoding the receptor-binding domain (RBD) of the SARS-CoV-2 spike glycoprotein, encapsulated within a lipid nanoparticle (LNP-saRNA-RBD). This LNP-saRNA vaccine platform enables efficient delivery of saRNA-RBD, inducing enhanced and prolonged expression of the RBD antigen. LNP-saRNA-RBD vaccination stimulated the generation of antigen-specific T cells, promoting their differentiation into a long-lived effector memory phenotype. Immunization with LNP-saRNA-RBD induced a germinal center response in draining lymph nodes, leading to the production of anti-RBD IgG antibodies with the ability to neutralize SARS-CoV-2 pseudovirus. Furthermore, prime-boost immunizations with LNP-saRNA-RBD conferred protection to mice against SARS-CoV-2 challenge by suppressing viral infection and replication, as well as pulmonary inflammatory responses and associated damage. Taken together, these findings provide strong support for advancing the development of LNP-saRNA-RBD as a safe and efficacious vaccine candidate against SARS-CoV-2 infection.

H, Figueira FAMDS, Andrade RLM, de Abreu LC. Evolution of COVID-19 in the State of São Paulo: Analysis of Incidence, Mortality and Lethality from 2020 to 2023

INTRODUCTION

COVID-19 is a respiratory disease caused by the SARS-CoV-2 virus, which belongs to the coronavirus family. SARS-CoV-2 is related to other viruses that cause severe acute respiratory syndrome. The emergence of cases of pneumonia of unknown origin triggered the largest viral pandemic in modern times, presenting major challenges to global public health.

OBJECTIVE

To analyze the evolution of the COVID-19 pandemic in the state of São Paulo from 2020 to 2023, focusing on trends in incidence, mortality, and lethality.

METHODS

Ecological study of time series of incidence, mortality and lethality by COVID-19 in the state of São Paulo using Prais-Winsten regression considering the Weekly Percentage Change (WPC) and probability values (p), considering a significance level of 95% (95% CI). To ensure the reliability of the entered data, double-blind typing was performed by different researchers in the same database extracted from the 2024 Ministry of Health Coronavirus dashboard.

RESULTS

From February 2020 and the end of December 2023, 6,763,310 accumulated cases and 182,254 deaths were recorded. Stationary trends were observed for the year 2022, with a reduction in incidence and mortality in the year 2023. However, the epidemiological variable lethality showed a stationary trend.

CONCLUSION

The analysis of the trends in incidence, mortality, and lethality revealed variable dynamics over time, with emphasis on the significant reduction of these indicators in 2023.

Association between blood-urea-nitrogen-to-albumin ratio and in-hospital mortality in patients diagnosed with coronavirus disease 2019: a retrospective cohort study

BACKGROUND

The blood-urea-nitrogen-to-albumin ratio (BAR) is recognized as a novel prognostic indicator; however, there is a limited number of studies investigating the relationship between BAR and in-hospital mortality associated with coronavirus disease 2019 (COVID-19). Therefore, the present investigation aims to explore the correlation between BAR and in-hospital mortality in patients with COVID-19 in China.

METHODS

This retrospective observational study enrolled a cohort of 1027 patients diagnosed with COVID-19 between December 2022 and March 2023. Multivariate Cox regression analyses were used to ascertain the independent association between BAR and in-hospital mortality among patients with COVID-19. Furthermore, stratified analyses were used to investigate potential interaction effects with variables, such as age, sex, COVID-19 Severity, hypertension, coronary artery disease, and diabetes mellitus.

RESULTS

A total of 117 patients (11.4%) died from various causes during hospitalization. Subsequent to adjustment for confounding variables, patients in the highest BAR tertile exhibited an elevated risk for in-hospital mortality relative to those in the lowest tertile (hazard ratio [HR] 2.44 [95% confidence interval CI 1.24-4.79]) when BAR was treated as a categorical variable. When considering BAR as a continuous variable, a 6% increase in the prevalence of in-hospital mortality was observed for each 1-unit increase in BAR (adjusted HR 1.06 [95% CI 1.03-1.08]; P < 0.001). Stratified analyses revealed a consistent association between BAR and in-hospital mortality due to COVID-19.

CONCLUSIONS

BAR exhibited a significant relationship with in-hospital mortality in patients with COVID-19, suggesting that a higher BAR is associated with a poorer prognosis. However, further research is required to confirm these findings.

Infectious agents in the pathogenesis of autoimmune rheumatic diseases

Autoimmune rheumatic diseases (AIRDs) are diseases with complex outset and courses, in which both genetic and environmental factors participate. Many environmental factors can be committed to AIRDs outset and development. The most popular of them, with confirmed impact, are smoking, age, gender, and microorganisms. In light of recent research an assumption about the importance of various microorganisms in the pathogenesis of AIRDs is growing in popularity. The human immune system has various protective mechanisms against infectious antigens which in normal cases let organism manage potential infection faster and more effectively. Unfortunately in some situations, specific errors in those mechanisms can cause an autoreactive response despite mitigation of infection. Viruses including EBV, CMV, and even SARS-CoV2 can cause these errors. This in combination with genetic factors can lead to rheumatic disease development. This research aims to provide a brief review of the role of viruses in the outset and development of AIRDs.

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.

Review of Immunologic Manifestations of COVID-19 Infection and Vaccination

We herein summarize currently available and clinically relevant information regarding the human immune responses to SARS-CoV-2 infection and vaccination, in relation to COVID-19 outcomes with a focus on acute respiratory distress syndrome (ARDS) and myocarditis.

Factors Associated with Self-reported COVID-19 Infection and Hospitalization among Patients Seeking Care at a Comprehensive Cancer Center

BACKGROUND

COVID-19 infection severity differs by race and ethnicity, but its long-term effect on cancer-related outcomes is unknown. Therefore, information on COVID-19 history is critical to ascertain among new cancer patients in order to advance research on its impact on cancer outcomes and potentially related health disparities.

METHODS

A cross-sectional study was conducted among 16,025 new patients seeking care at Moffitt Cancer Center (MCC) between 2021 and 2022. Patient self-reported histories of COVID-19 infection and other pre-existing health conditions were obtained from electronic questionnaires administered to all new MCC patients. Associations between demographics and COVID-19 infection and hospitalization were examined.

RESULTS

A total of 1,971 patients (12.3%) reported ever having COVID-19. Self-reported COVID-19 history was significantly more prevalent in Hispanic vs. non-Hispanic patients (OR = 1.24, 1.05-1.45) and less prevalent in Asian versus White patients (OR = 0.49, 95% 0.33-0.70). Among patients who ever had COVID-19, 10.6% reported a COVID-19-related hospitalization. Males had higher odds of a COVID-19 related hospitalization than females (OR = 1.50, 95% CI = 1.09-2.05), as did Black/African American patients (OR = 2.11, 95% CI = 1.18-3.60) and patients of races other than Black/African American and Asian (OR = 2.61, 95% CI = 1.43-4.54) compared to White patients. Hispanic patients also experienced higher odds of hospitalization (OR = 2.06, 95% CI-1.29- 3.23) compared with non-Hispanic patients of all races in a sensitivity analysis that combined race/ethnicity. Pre-existing lung and breathing problems were associated with higher odds of being hospitalized with COVID-19 (OR = 2.38, 95% CI = 1.61-3.48), but these and other health conditions did not explain the observed associations between race and COVID-19 hospitalization.

CONCLUSIONS

Higher rates of COVID-19 hospitalization were observed among patients identifying as Black/African American or Hispanic independent of pre-existing health conditions. Future studies evaluating long-term effects of COVID-19 should carefully examine potential racial/ethnic disparities in cancer outcomes.

(R)evolution of Viruses: Introduction to biothermodynamics of viruses

As of 26 April 2024, the International Committee on Taxonomy of Viruses has registered 14690 virus species. Of these, only several dozen have been chemically and thermodynamically characterized. Every virus species is characterized by a specific empirical formula and thermodynamic properties - enthalpy, entropy and Gibbs energy. These physical properties are used in a mechanistic model of virus-host interactions at the cell membrane and in the cytoplasm. This review article presents empirical formulas and Gibbs energies for all major variants of SARS-CoV-2. This article also reports and suggests a mechanistic model of evolutionary changes, with the example of time evolution of SARS-CoV-2 from 2019 to 2024.

The impact of ivermectin on COVID-19 outcomes: a systematic review and meta-analysis

Background

The COVID-19 pandemic, resulting in approximately seven million deaths globally, underscores the urgency for effective treatments. Ivermectin, among several repurposed drugs, garnered interest due to its antiviral properties. However, conflicting evidence from observational studies and randomized controlled trials raised questions about its efficacy and safety.

Method

This systematic review and meta-analysis followed MOOSE and PRISMA guidelines. Comprehensive searches were conducted in databases including Scopus, Embase, PubMed, and Web of Science up to April 2024. Data were extracted independently by two reviewers and analyzed using Comprehensive Meta-Analysis V3 software.

Results

Across 33 studies encompassing 15,376 participants, ivermectin showed no significant impact on critical outcomes such as mortality [risk ratio (RR) 0.911, 95% confidence intervals (CI) 0.732-1.135], mechanical ventilation (RR 0.727, 95% CI 0.521-1.016), polymerase chain reaction conversion (RR 1.024, 95% CI 0.936-1.120), ICU admissions (RR 0.712, 95% CI 0.274-1.850), or hospitalization rates (RR 0.735, 95% CI 0.464-1.165) compared to controls. However, it significantly reduced time to symptom alleviation (standardized mean difference -0.302, 95% CI -0.587 to -0.018) and sustained symptom relief (RR 0.897, 95% CI 0.873-0.921). Adverse event (AE) rates were similar between the ivermectin and control groups (RR 0.896, 95% CI 0.797-1.007). Meta-regression indicated older age and diabetes as predictors of AEs.

Conclusion

Despite its observed benefits in symptom management, ivermectin did not significantly influence critical clinical outcomes in COVID-19 patients. These findings highlight the importance of continued research to identify effective treatments for COVID-19, emphasizing the need for high-quality studies with robust methodology to inform clinical practice and public health policy effectively.

Neuroinvasion via Peripheral Nerves in Epidemic Viral Encephalitis Caused by Enterovirus, Orthoflavivirus and SARS-Coronavirus

Pathogens invade the central nervous system (CNS) and cause infections either through the haematogenous route or via peripheral nerves. Neuroinvasion via peripheral nerves, involving spinal or cranial somatic nerves, is well-established for certain viral encephalitides such as rabies, herpes simplex encephalitis, and poliomyelitis. Advances in understanding emerging and re-emerging viruses that cause epidemic CNS infections have highlighted the growing importance of peripheral nerve pathways in viral neuroinvasion. This review focuses on epidemic viral encephalitides caused by three groups of RNA viruses, viz., enteroviruses (enterovirus A71 and enterovirus D68), orthoflaviviruses (West Nile virus and Japanese encephalitis virus), and severe acute respiratory syndrome coronaviruses (mainly severe acute respiratory coronavirus-2). We examine evidence supporting the hypothesis that peripheral nerve viral transmission may play an increasingly significant if not more critical role than the haematogenous route in neuroinvasion.

Making Accessible and Attractive Porosities in Block Copolymer Nanofibers for Highly Permeable and Durable Air Filtration

Submicron particulate matter (PM) can penetrate deeply into human tissue, posing a serious threat to human health. However, the electrostatic charge of commercial respirators is easily dissipated, making it difficult to maintain long-term filtration. Herein, a hierarchically porous filter based on nanofibers with accessible porosity and particulate-attractive surfaces, achieving significant filtration performance is developed through polarity-driven interactions. This is achieved by selective swelling of electrospun nanofibers of the block copolymer of polysulfone and poly(ethylene glycol) (PSF-b-PEG), in which the originally solid nanofibers are 3D perforated with the PEG chains lined along the pore walls. Thus-produces nanofiber filters exhibit a long-term continuous filtration with an efficiency of over 95% for PM0.3 and a low pressure drop of only 40 Pa. In particular, it maintains superior filtration performance even under high particle concentrations and high humidity conditions. Additionally, the filter exhibits high air permeability (10814 m3 m-2 h-1 kPa-1) and water vapor transmission rate (3707 g m-2 d-1). This work provides new strategies and understandings on the development of porous structures simultaneously exhibiting high gas permeability and efficient particulate rejection.

Leveraging deep transfer learning and explainable AI for accurate COVID-19 diagnosis: Insights from a multi-national chest CT scan study

The COVID-19 pandemic has emerged as a global health crisis, impacting millions worldwide. Although chest computed tomography (CT) scan images are pivotal in diagnosing COVID-19, their manual interpretation by radiologists is time-consuming and potentially subjective. Automated computer-aided diagnostic (CAD) frameworks offer efficient and objective solutions. However, machine or deep learning methods often face challenges in their reproducibility due to underlying biases and methodological flaws. To address these issues, we propose XCT-COVID, an explainable, transferable, and reproducible CAD framework based on deep transfer learning to predict COVID-19 infection from CT scan images accurately. This is the first study to develop three distinct models within a unified framework by leveraging a previously unexplored large dataset and two widely used smaller datasets. We employed five known convolutional neural network architectures, both with and without pretrained weights, on the larger dataset. We optimized hyperparameters through extensive grid search and 5-fold cross-validation (CV), significantly enhancing the model performance. Experimental results from the larger dataset showed that the VGG16 architecture (XCT-COVID-L) with pretrained weights consistently outperformed other architectures, achieving the best performance, on both 5-fold CV and independent test. When evaluated with the external datasets, XCT-COVID-L performed well with data with similar distributions, demonstrating its transferability. However, its performance significantly decreased on smaller datasets with lower-quality images. To address this, we developed other models, XCT-COVID-S1 and XCT-COVID-S2, specifically for the smaller datasets, outperforming existing methods. Moreover, eXplainable Artificial Intelligence (XAI) analyses were employed to interpret the models' functionalities. For prediction and reproducibility purposes, the implementation of XCT-COVID is publicly accessible at https://github.com/cbbl-skku-org/XCT-COVID/.

Multicentre analysis of severe perioperative adverse events in children undergoing surgery who were infected with SARS-CoV-2: a propensity score-adjusted analysis

BACKGROUND

The incidence of severe adverse events in children with SARS-CoV-2 undergoing anaesthesia has not been well established. We examined the relationship between SARS-CoV-2 infection and severe perioperative adverse events in children.

METHODS

This multicentre (21 North American institutions), retrospective cohort study included children <18 years old, with American Society of Anesthesiologists physical status (ASA PS) of 1-4 and non-severe SARS-CoV-2, who underwent general anaesthesia between April 1, 2020, and March 31, 2021. The primary outcome was the incidence of severe perioperative adverse events (admission to the intensive care unit for escalation of respiratory support, acute respiratory distress syndrome, postoperative pneumonia, cardiovascular arrest, extracorporeal life support, and death) within 7 days of the anaesthetic, assessed using multivariable analysis with inverse probability of treatment weighting by the propensity score. A propensity score mixed-effects model included variables selected a priori. Inverse probability of treatment weighting was used to retain all data while balancing exposure groups on measured confounders.

RESULTS

We matched 1138 patients with SARS-CoV-2 positive testing within 10 days of the anaesthetic to 3396 non-infected controls. The cohort included 56.6% (2568/4534) male patients, 69.9% (2839/4060) White patients, and 63.5% (2879/4533) ASA PS 1-2 patients. General surgery cases comprised 38.4% (1739/4534) of the cohort, followed by orthopaedic surgery at 12.6% (573/4534) and ear, nose, and throat surgery at 8.2% (371/4534). In the overall sample of 4534 patients, 52 had a severe adverse event (0.01%). Children with SARS-CoV-2 had a higher risk of at least one severe adverse event (25/1138 [2.20%] vs 27/3396 [0.80%] in those non-infected; adjusted odds ratio 2.34; 95% confidence interval 1.25-4.39). None of the children with SARS-CoV-2 had a cardiac arrest, required extracorporeal life support, or died.

CONCLUSIONS

In the largest cohort to date of paediatric patients undergoing general anaesthesia, SARS-CoV-2 infection was associated with severe perioperative adverse events, but no children in the infected cohort died.

Uncovering the Binding Mechanism of Mutated Omicron Variants via Computational Strategies

The COVID-19 pandemic, triggered by the SARS-CoV-2 virus, has resulted in nearly 630 million cases and 6.60 million fatalities globally, as of November 2022. SARS-CoV-2, a species of the Coronaviridae family, has a single-stranded positive-sense RNA genome as well as four main structural proteins (S, E, M, and N) required for viral entrance into target cells. The spike protein (S) influences this entry through interactions with human angiotensin-converting enzyme 2 (hACE2) receptor. The World Health Organization (WHO) recognized numerous variants of concern (VOCs) that involve Alpha, Beta, Gamma, Delta, and Omicron, having multiple mutations within the spike protein, altering infection rates and immunity evasion. The Omicron variant, featuring 50 mutations, mainly within the spike protein's receptor-binding domain (RBD), has a higher transmission rate as compared to other variants. This study focused on two recent Omicron subvariants, XBB.1.5 and CH.1.1, which are known for their high affinity for the human ACE2 receptor. Utilizing an in silico strategy, a total of 1.65 μs molecular dynamics (MD) simulations were performed to assess the stability as well as binding details of these subvariants along with the wild-type Omicron variants. The comprehensive structural stability of the spike protein-hACE2 complexes was evaluated by using numerous parameters including root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), radius of gyration (R g), and principal component analysis (PCA). Moreover, the binding free energies have been determined using the MM-GBSA approach to provide insights into the binding affinities of these variants. Evaluation revealed that the unbound mutant frameworks (SM and TM) displayed higher degrees of instability in comparison to the wild-type (WT) Omicron variant. In contrast, the WT-hACE2 of the Omicron variant complex was less stable than the subvariants, SM-hACE2 and TM-hACE2 complexes. Binding free energy calculations employing MM-PBSA disclosed higher binding energy values for the SM-hACE2 and TM-hACE2 complexes, suggesting a more stable and ordered binding interaction. The observed increase in transmissibility of the new XBB.1.5 and CH.1.1 subvariants, in comparison to the wild-type Omicron, appears to be due to this greater stability and ordered binding.

Analyzing COVID-19 progression with Markov multistage models: insights from a Korean cohort

BACKGROUND

Understanding the progression and recovery process of COVID-19 is crucial for guiding public health strategies and developing targeted interventions. This longitudinal cohort study aims to elucidate the dynamics of COVID-19 severity progression and evaluate the impact of underlying health conditions on these transitions, providing critical insights for more effective disease management.

METHODS

Data from 4549 COVID-19 patients admitted to Seoul National University Boramae Medical Center between February 5th, 2020, and October 30th, 2021, were analyzed using a 5-state continuous-time Markov multistate model. The model estimated instantaneous transition rates between different levels of COVID-19 severity, predicted probabilities of state transitions, and determined hazard ratios associated with underlying comorbidities.

RESULTS

The analysis revealed that most patients stabilized in their initial state, with 72.2% of patients with moderate symptoms remaining moderate. Patients with hypertension had a 67.6% higher risk of progressing from moderate to severe, while those with diabetes had an 89.9% higher risk of deteriorating from severe to critical. Although transition rates to death were low early in hospitalization, these comorbidities significantly increased the likelihood of worsening conditions.

CONCLUSION

This study highlights the utility of continuous-time Markov multistate models in assessing COVID-19 severity progression among hospitalized patients. The findings indicate that patients are more likely to recover than to experience worsening conditions. However, hypertension and diabetes significantly increase the risk of severe outcomes, underscoring the importance of managing these conditions in COVID-19 patients.

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.

Optimized Aluminum Hydroxide Adsorption-Precipitation for Improved Viral Detection in Wastewater

Wastewater-based epidemiology (WBE) is a valuable tool for monitoring pathogen spread in communities; however, current protocols mainly target non-enveloped viruses. This study addresses the need for standardized methods to detect both enveloped and non-enveloped viruses by testing four aluminum hydroxide adsorption-precipitation techniques. Wastewater samples were spiked with an enveloped virus surrogate (Φ6 bacteriophage) and a non-enveloped virus surrogate (MS2 coliphage), and viral recovery was assessed using reverse-transcription quantitative PCR (RT-qPCR). The highest recovery for the enveloped virus was achieved with AlCl3 at pH 3.5, a 15 min flocculation time, and a 3% elution solution concentration. For the non-enveloped virus, optimal recovery was found with AlCl3 at pH 6.0, no flocculation time, and a 10% elution solution. The best method for recovering both virus types used AlCl3 at pH 6.0, 15 min flocculation, and a 3% elution solution concentration. This study shows that while optimal conditions vary between virus types, a standardized AlCl3 flocculation protocol can efficiently recover both, providing a cost-effective approach for outbreak monitoring in Grenada.

3D Printing of Virucidal Polymer Nanocomposites (PLA/Copper Nanoparticles)

Metallic nanoparticles with virucidal properties dispersed in a polymeric matrix have gained prominence in the scientific community as a rapid and effective alternative that employs the additive manufacturing (AM) or 3D printing method. This study aims to produce filaments for 3D printing using polymer nanocomposites based on polylactic acid (PLA) and copper nanoparticles (CuNPs) in different proportions. The virucidal activity of various proportions of nanoparticles in PLA was investigated. The composites were produced following a mixture design (DOE) with concentrations ranging from 1% to 2% copper nanoparticles, which were blended with PLA using a single-screw extruder. The samples were characterized by thermogravimetry (TG), differential scanning calorimetry (DSC), tensile strength testing, and fracture analysis using scanning electron microscopy (SEM). A thermal analysis of the composites indicated that the CuNPs contributed to an increase in the degradation temperature and crystallization of the PLA. Sample S7 (1.25% of CuNPs) exhibited a 4% increase in the degradation temperature compared to pure PLA. The best tensile strength results were observed in sample S7 (1.25% of CuNPs), 30% more than sample S3 (1.33% of CuNPs) due to good material cohesion, as evidenced by microscopy analyses. Regarding virucidal analyses, most composites demonstrated virus inhibition activity.

Factors of progression to severity and death in COVID-19 patients at two health care sites in Bamako, Mali

OBJECTIVES

To analyze the clinical and biological characteristics and to evaluate the risk factors associated with the mortality of patients with COVID-19 in Commune IV of the District of Bamako.

METHODS

The cohort consisted of COVID-19 patients managed from March 2020 to June 2022 at the Bamako Dermatology Hospital and the Pasteur Polyclinic in Commune IV in Bamako. The studied variables were sociodemographic, clinical, and biological. For the analysis of deaths, explanatory variables were grouped into sociodemographic factors, comorbidities and symptoms. Binomial logistic regression models were used to identify mortality associated risk factors.

RESULTS

Among the 1319 included patients, 38.4% were asymptomatic, 46% and 15.5% developed moderate or severe COVID-19 respectively. The predominant signs were cough (48.5%), respiratory difficulty (24.6%) and headache (19.7%). Male were more common (58.2%). High blood pressure (19.9%) and diabetes (10%) were the main comorbidities. D-dimers < 0.5 μg/l was found in 53.3% of cases and the mean hemoglobin level was 12.9 ± 1.7 g/l. The case fatality rate was 3.71% in our series. In bivariate analysis, age > 60 years, high blood pressure, diabetes, clinical severity, D-dimers < 0.5 μg/l were associated with death. Using binomial logistic regression method, age > 60 years, increased heart rate, disease severity level and mainly acute respiratory distress syndrome (polypnea, difficulty breathing) were the factors found associated with death. After adjusting for all the assessed factors, age < 60 years [aHR = 0.15 (0.06-0.35)] and administration of azithromycin [aHR = 0.31 (0.1-0.97)] were protective factors while higher respiratory rate [aHR = 1.14 (1.07-1.22)] and difficulty breathing [aHR = 3.06 (1.03-9.13)] were risk factors associated with death.

CONCLUSION

These main findings elucidate the factors associated with severity and lethality external of health care system constraints. Advanced age, higher heart rate and the development of respiratory distress were the factors significantly associated with increased fatalities.

The Effects of Disinfection Byproduct 2,6-Dichloro-1,4-benzoquinone on the Cyanobacterium Microcystis aeruginosa: From the Perspectives of Biochemistry and Non-Targeted Metabolomics

2,6-Dichloro-1,4-benzoquinone (2,6-DCBQ) is an emerging chlorinated disinfection byproduct (DBP) in bodies of water. However, this compound poses an unknown toxic effect on cyanobacteria. In this study, the toxicological mechanisms of 2,6-DCBQ in Microcystis aeruginosa (M. aeruginosa) were investigated through physiological and nontargeted metabolomic assessments. The results show that 2,6-DCBQ inhibited the growth of M. aeruginosa, reduced its photosynthetic pigment and protein contents, increased the levels of reactive oxygen species, damaged the antioxidant defense system, and aggravated the cytomembrane. Meanwhile, 2,6-DCBQ stimulated the production and release of microcystin-LR (MC-LR) and altered the transcripts of genes associated with its synthesis (mcyA, mcyD) and transport (mcyH). In addition, nontargeted metabolomics of M. aeruginosa cells exposed to 0.1 mg/L 2,6-DCBQ identified 208 differential metabolites belonging to 10 metabolic pathways and revealed the considerable interference caused by 2,6-DCBQ among ABC transporters, the two-component system, and folate biosynthesis. This study deepens the understanding of the physiological and nontargeted metabolomic responses of M. aeruginosa exposed to 2,6-DCBQ, offers insights into the toxic effect of 2,6-DCBQ on M. aeruginosa, and provides a theoretical basis for the ecological risk assessment of emerging DBPs in accordance with water quality criteria.

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

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

Dual Inhibitors of SARS-CoV-2 3CL Protease and Human Cathepsin L Containing Glutamine Isosteres Are Anti-CoV-2 Agents

SARS-CoV-2 3CL protease (Main protease) and human cathepsin L are proteases that play unique roles in the infection of human cells by SARS-CoV-2, the causative agent of COVID-19. Both proteases recognize leucine and other hydrophobic amino acids at the P2 position of a peptidomimetic inhibitor. At the P1 position, cathepsin L accepts many amino acid side chains, with a partial preference for phenylalanine, while 3CL-PR protease has a stringent specificity for glutamine or glutamine analogues. We have designed, synthesized, and evaluated peptidomimetic aldehyde dual-target (dual-acting) inhibitors using two peptide scaffolds based on those of two Pfizer 3CL-PR inhibitors, Nirmatrelvir, and PF-835321. Our inhibitors contain glutamine isosteres at the P1 position, including 2-pyridon-3-yl-alanine, 3-pyridinyl-alanine, and 1,3-oxazo-4-yl-alanine groups. Inhibition constants for these new inhibitors ranged from Ki = 0.6-18 nM (cathepsin L) and Ki = 2.6-124 nM (3CL-PR), for which inhibitors with the 2-pyridon-3-yl-alanal substituent were the most potent for 3CL-PR. The anti-CoV-2 activity of these inhibitors ranged from EC50 = 0.47-15 μM. X-ray structures of the peptidomimetic aldehyde inhibitors of 3CL-PR with similar scaffolds all demonstrated the formation of thiohemiacetals with Cys145, and hydrogen-bonding interactions with the heteroatoms of the pyridon-3-yl-alanyl group, as well as the nitrogen of the N-terminal indole and its appended carbonyl group at the P3 position. The absence of these hydrogen bonds for the inhibitors containing the 3-pyridinyl-alanyl and 1,3-oxazo-4-yl-alanyl groups was reflected in the less potent inhibition of the inhibitors with 3CL-PR. In summary, our studies demonstrate the value of a second generation of cysteine protease inhibitors that comprise a single agent that acts on both human cathepsin L and SARS-CoV-2 3CL protease. Such dual-target inhibitors will provide anti-COVID-19 drugs that remain active despite the development of resistance due to mutation of the viral protease. Such dual-target inhibitors are more likely to remain useful therapeutics despite the emergence of inactivating mutations in the viral protease because the human cathepsin L will not develop resistance. This particular dual-target approach is innovative since one of the targets is viral (3CL-PR) required for viral protein maturation and the other is human (hCatL) which enables viral infection.

Polymorphisms Influence the Expression of the Fas and FasL Genes in COVID-19

The apoptotic molecule Fas and its ligand FasL are involved in the process of T-lymphocyte death, which may lead to lymphopenia, a characteristic of severe coronavirus disease 2019 (COVID-19). In this study, we investigated the influence of polymorphisms in the FAS and FASL genes, FAS and FASL gene expression, and plasma cytokine levels on COVID-19 severity and long COVID occurrence. A total of 116 individuals with severe COVID-19 and 254 with the non-severe form of the disease were evaluated. In the post-COVID-19 period, samples from 196 individuals with long COVID and 67 from people who did not have long COVID were included. Genotyping and quantification of gene expression were performed via real-time PCR, and cytokine measurement was performed via flow cytometry. The AA genotype for FAS rs1800682 (A/G) and the TT genotype for FASL rs763110 (C/T) were associated with increased FAS and FASL gene expression, respectively (p < 0.005). Higher plasma IFN-γ levels were associated with higher FAS and FASL gene expression (p < 0.05). Among individuals with non-severe COVID-19, carriers of the AA genotype for FAS rs1800682 (A/G) had higher levels of FAS expression, more symptoms, and higher IFN-γ levels (p < 0.05). No association of the evaluated markers with long COVID were observed. The AA genotype of FAS rs1800682 (A/G) and the TT genotype of FASL rs763110 (C/T) influence the levels of FAS and FASL gene expression. Higher gene expression of FAS and FASL may lead to greater inflammation in COVID-19 patients, with higher levels of IFN-γ and T lymphocyte death.

Exploring lifestyle and dietary pattern shifts among Saudi adults during COVID-19 pandemic: insights from a cross-sectional examination

Background

Since the emergence of COVID-19 and the subsequent imposition of lockdown and movement restrictions, the world has witnessed fundamental lifestyle changes including alterations in dietary patterns and food consumption habits. Here, we investigated how the COVID-19 lockdown impacted dietary patterns and eating behaviors in the Saudi population.

Methodology

This cross-sectional study enrolled 427 participants aged 18 years or more, with 258 of them completing the survey. The survey included questions about demographic and dietary patterns during the COVID-19 lockdown. Data were collected and dietary behaviors before and during the lockdown in Jeddah, Saudi Arabia, were analyzed.

Results

The number of participants who considered lunch as their primary meal significantly decreased (p < 0.001) during the COVID-19 lockdown (74%), compared to before it (86%). By contrast, the number of participants who considered dinner as their primary meal remained almost unchanged (p = 0.079) during (79.1%) and before (84.1%) the lockdown. However, snack consumption significantly increased (p < 0.001) while fast-food consumption significantly decreased (p < 0.01) during the lockdown period. Our results also revealed a significant increase (p < 0.01) in water and coffee intake during the lockdown, with a significant rise in dessert consumption (p < 0.01).

Conclusion

Our results demonstrate that the COVID-19 lockdown caused a marked shift in dietary patterns and eating behaviors among the Saudi population. Notable changes were observed in overall food preferences after the lockdowns were imposed, with reduced consumption of fast foods and increased fluid intake.

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

Background

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

Methods

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

Main Findings

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

Conclusion

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

EACVP: An ESM-2 LM Framework Combined CNN and CBAM Attention to Predict Anti-coronavirus Peptides

BACKGROUND

The novel coronavirus pneumonia (COVID-19) outbreak in late 2019 killed millions worldwide. Coronaviruses cause diseases such as severe acute respiratory syndrome (SARS-CoV) and SARS-CoV-2. Many peptides in the host defense system have antiviral activity. How to establish a set of efficient models to identify anti-coronavirus peptides is a meaningful study.

METHODS

Given this, a new prediction model EACVP is proposed. This model uses the evolutionary scale language model (ESM-2 LM) to characterize peptide sequence information. The ESM model is a natural language processing model trained by machine learning technology. It is trained on a highly diverse and dense dataset (UR50/D 2021_04) and uses the pre-trained language model to obtain peptide sequence features with 320 dimensions. Compared with traditional feature extraction methods, the information represented by ESM-2 LM is more comprehensive and stable. Then, the features are input into the convolutional neural network (CNN), and the convolutional block attention module (CBAM) lightweight attention module is used to perform attention operations on CNN in space dimension and channel dimension. To verify the rationality of the model structure, we performed ablation experiments on the benchmark and independent test datasets. We compared the EACVP with existing methods on the independent test dataset.

RESULTS

Experimental results show that ACC, F1-score, and MCC are 3.95%, 35.65% and 0.0725 higher than the most advanced methods, respectively. At the same time, we tested EACVP on ENNAVIA-C and ENNAVIA-D data sets, and the results showed that EACVP has good migration and is a powerful tool for predicting anti-coronavirus peptides.

CONCLUSION

The results prove that this model EACVP could fully characterize the peptide information and achieve high prediction accuracy. It can be generalized to different data sets. The data and code of the article have been uploaded to https://github.- com/JYY625/EACVP.git.

Angiotensin-Converting Enzyme 2 (G8790A) Gene Polymorphism as a Risk Factor for COVID-19 in Egyptian Children and Adolescents

OBJECTIVE

Recently, angiotensin-converting enzyme 2 (ACE2) gene has emerged as a potential candidate gene for susceptibility to SARS-CoV-2 infection. We investigated whether ACE2 G8790A (rs2285666) polymorphism could be a genetic marker for susceptibility to COVID-19 and disease severity in Egyptian children and adolescents.

METHODS

This was a prospective case-control study included 580 cases diagnosed with COVID-19, and 580 matched control children and adolescents. The ACE2 G8790A (rs2285666) polymorphism was genotyped using polymerase chain reaction (PCR) and ACE2 serum level was measured by ELISA.

RESULTS

The ACE2 A/A genotype and A-allele were significantly more represented in cases with COVID-19 as compared to control group (44% vs. 30%; OR = 2.83; [95% CI: 1.27-2.63]; p = 0.006; for the A/A genotype) and (65% vs. 51%; OR = 1.9; [95% CI: 1.06-1.72]; p = 0.01; for the A-allele). The presence of ACE2 G/G genotype was an independent risk factor for severe disease (adjusted OR: 2.08; [95% CI: 1.57-6.78]; p = 0.003).

CONCLUSION

The ACE2 G8790A (rs2285666) polymorphism may confer susceptibility to COVID-19 in Egyptian children and adolescents. The ACE2 G/G genotype and G-allele was associated with lower ACE2 serum levels and may constitute independent risk factors for disease severity.

Safety and immunogenicity of a SARS-CoV-2 recombinant protein subunit vaccine adjuvanted with Alum + CpG 1018 in healthy Indonesian adults: A multicenter, randomized, comparative, observer-blind, placebo-controlled phase 2 study

Globally, dozens of COVID-19 vaccines are licensed under emergency or conditional authorization, but especially in low and middle-income countries, their availability varies. Indonesia decided to become independent and produce its own vaccines locally. This study investigated the safety and immunogenicity of a SARS-CoV-2 recombinant protein subunit vaccine adjuvanted with Alum + CpG 1018. This study involved 360 adults aged 18 years and above. It compared two vaccine dosages, a-12.5 µg and a 25-µg dose of receptor binding domain protein, to a placebo (1:1:1). A total of 40.6% of participants in this study experienced at least one adverse event (AE), with most being mild. There was no statistically significant difference in AEs between the groups. The microneutralization test showed the highest neutralizing antibody titer (IU/mL) in the 25 µg dose vaccine group at day 28 after the second dose (3,300 95%CI 2,215-4,914), although it was not statistically different from the 12.5 µg dose group (3,157 95%CI 2,135-4,669). Similarly, IgG antibody concentrations in the 25 µg dose vaccine group at day 28 were the highest compared to the 12.5 µg dose and placebo. According to protocol, only the formulation with the better antibody profile and comparable reactogenicity was further evaluated at months three and six. Thus, follow-up was only performed for the 25 µg dose vaccine, demonstrating antibody persistence at month six and had a favorable safety profile. These results position this SARS-CoV-2 recombinant protein subunit vaccine adjuvanted with Alum + CpG 1018 as a promising candidate to fight against COVID-19.

New-onset refractory status epilepticus after SARS-CoV-2 infection: a review of literature

Although severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) primarily affects the respiratory system, neurological symptoms were reported both during acute and post-acute COVID-19. Notably, patients with no history of epilepsy or other neurological conditions developed new-onset refractory status epilepticus (NORSE) weeks, months, or even up to a year following the viral infection. While NORSE is uncommon, it carries a high mortality rate and can result in permanent epilepsy. Therefore, clinicians should consider the possibility of death or epilepsy development when treating individuals with NORSE who have recently contracted SARS-CoV-2. This article compiles comprehensive information on the mechanisms of epileptogenesis linked to SARS-CoV-2, the diagnosis of NORSE syndrome, its treatment options, and associated outcomes. Our aim was to enhance physicians' understanding of the virus's pathogenesis and increase the awareness of NORSE.

Updating the Antimicrobial Resistance Pattern among Critical Priority Pathogens in the Intensive Care Unit in Northern Iran Post COVID-19 Pandemic

Background

During the COVID-19 pandemic, the widespread and indiscriminate prescription of antibiotics led to a significant increase in antibiotic resistance and the emergence of multi-drug-resistant (MDR) strains. This study aims to evaluate the prevalence of antibiotic resistance in MDR Gram-negative isolates in the intensive care unit (ICU) of northern hospitals in Iran following the COVID-19 pandemic.

Materials and Methods

This is a cross-sectional study. The samples were collected from patients with healthcare-associated infections at ICU of hospitals in northern Iran. Antimicrobial resistance was assessed using standard broth macrodilution, and resistance genes were accurately identified using the multiplex polymerase chain reaction method.

Results

The present study revealed that the ICU had the highest frequency of MDR Acinetobacter baumannii infections (32.1%) and the lowest frequency of E. coli infections (12.6%). The frequency of resistance genes of A. baumannii is as follows: bla OXA-51 (100%), ampC (99.12%), apA6 (90.35%), and bla NDM (69.30%). Co-amoxiclav showed a 100% resistance rate, while Piperacillin-tazobactam had the lowest resistance rate at 38.2%.

Conclusions

This study identified a high prevalence of MDR A. baumannii in ICU patients with healthcare-associated infections at northern hospitals in Iran, following COVID-19. Recommended treatments include Piperacillin-tazobactam or Meropenem.

Targeted and untargeted cross-sectional study for sex-specific identification of plasma biomarkers of COVID-19 severity

Coronavirus disease 2019 is a highly contagious respiratory illness caused by the coronavirus SARS-CoV-2. Symptoms can range from mild to severe and typically appear 2-14 days after virus exposure. While vaccination has significantly reduced the incidence of severe complications, strategies for the identification of new biomarkers to assess disease severity remains a critical area of research. Severity biomarkers are essential for personalizing treatment strategies and improving patient outcomes. This study aimed to identify sex-specific biomarkers for COVID-19 severity in a Chilean population (n = 123 female, n = 115 male), categorized as control, mild, moderate, or severe. Data were collected using clinical biochemistry parameters and mass spectrometry-based metabolomics and lipidomics to detect alterations in plasma cytokines, metabolites, and lipid profiles related to disease severity. Principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) were performed to select significant characteristic features for each group. The results revealed distinct biomarkers for males and females. In males, COVID-19 severity of was associated with inflammation parameters, triglycerides content, and phospholipids profiles. For females, liver damage parameters, triglycerides content, cholesterol derivatives, and phosphatidylcholine were identified as severity biomarkers. For both sexes, most of the biomarker combinations evaluated got areas under the ROC curve greater than 0.8 and low prediction errors. These findings suggest that sex-specific biomarkers can help differentiate the levels of COVID-19 severity, potentially aiding in the development of tailored treatment approaches.

Calceolarioside B inhibits SARS-CoV-2 Omicron BA.2 variant cell entry and modulates immune response

This study evaluated the inhibitory effects of calceolarioside B, extracted from the traditional Chinese herb Mutong (Akebia quinata Thumb), on the SARS-CoV-2 Omicron BA.2 variant. Molecular docking and molecular dynamics simulations predicted the binding sites and interactions between calceolarioside B and the Omicron BA.2 spike (S) protein. Biolayer interferometry (BLI) and immunofluorescence assays validated its high-affinity binding. Pseudovirus entry assays assessed the inhibitory effects of calceolarioside B on viral entry into host cells, while enzyme-linked immunosorbent assay (ELISA) measured inflammatory cytokine levels. Flow cytometry was used to analyze its effects on macrophage phenotype switching. Results demonstrated that calceolarioside B could bind to the Omicron BA.2 S protein with high affinity, and significantly inhibited viral entry into host cells by interfering with the binding of angiotensin-converting enzyme 2 (ACE2) receptor and S protein. Additionally, calceolarioside B reduced IL(interleukin)-6 expression levels and promoted the switch of macrophages from the pro-inflammatory M1 phenotype to the anti-inflammatory M2 phenotype. These findings suggest that calceolarioside B possesses antiviral and immunomodulatory effects, making it a potential dual-function inhibitor for the treatment of COVID-19.

Berbamine prevents SARS-CoV-2 entry and transmission

Effective antiviral drugs are essential to combat COVID-19 and future pandemics. Although many compounds show antiviral in vitro activity, only a few retain effectiveness in vivo against SARS-CoV-2. Here, we show that berbamine (Berb) is effective against SARS-CoV, MER-CoV, SARS-CoV-2 and its variants, including the XBB.1.16 variant. In hACE2.Tg mice, Berb suppresses SARS-CoV-2 replication through two distinct mechanisms: inhibiting spike-mediated viral entry and enhancing antiviral gene expression during infection. The administration of Berb, in combination with remdesivir (RDV), clofazimine (Clof) and fangchinoline (Fcn), nearly eliminated viral load and promoted recovery from acute SARS-CoV-2 infection and its variants. Co-housed mice in direct contact with either pre-treated or untreated infected mice exhibited negligible viral loads, reduced lung pathology, and decreased viral shedding, suggesting that Berb may effectively hinder virus transmission. This broad-spectrum activity positions Berb as a promising preventive or therapeutic option against betacoronaviruses.

Catalytic Mechanism of SARS-CoV-2 3-Chymotrypsin-Like Protease as Determined by Steady-State and Pre-Steady-State Kinetics

The 3-chymotrypsin-like protease (3CL-PR; also known as Main protease) of SARS-CoV-2 is a cysteine protease that is the target of the COVID-19 drug, Paxlovid. Here, we report for 3CL-PR, the pH-rate profiles of a substrate, an inhibitor, affinity agents, and solvent kinetic isotope effects (sKIEs) obtained under both steady-state and pre-steady-state conditions. "Bell-shaped" plots of log(k cat/K a) vs pH for the substrate (Abz)SAVLQ*SGFRK(Dnp)-NH2 and pK i vs pH for a peptide aldehyde inhibitor demonstrated that essential acidic and basic groups of pK 2 = 8.2 ± 0.4 and pK 1 = 6.2 ± 0.3, respectively, are required for catalysis, and the pH-dependence of inactivation of 3CL-PR by iodoacetamide and diethylpyrocarbonate identified enzymatic groups of pK 2 = 7.8 ± 0.1 and pK 1 = 6.05 ± 0.07, which must be unprotonated for maximal inactivation. These data are most consistent with the presence of a neutral catalytic dyad (Cys-SH-His) in the 3CL-PR free enzyme, with respective pK values for the cysteine and histidine groups of pK 2 = 8.0 and pK 1 = 6.5. The steady-state sKIEs were D2O(k cat/K a) = 0.56 ± 0.05 and D2O k cat = 1.0 ± 0.1, and sKIEs indicated that the Cys-S--HisH+ tautomer was enriched in D2O. Presteady-state kinetic analysis of (Abz)SAVLQ*SGFRK(Dnp)-NH2 exhibited transient lags preceding steady-state rates, which were considerably faster in D2O than in H2O. The transient rates encompass steps that include substrate binding and acylation, and are faster in D2O wherein the more active Cys-S--HisH+ tautomer predominates. A full catalytic mechanism for 3CL-PR is proposed.

Recombination across distant coronavirid species and genera is a rare event with distinct genomic features

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; family Coronaviridae, genus Betacoronavirus, subgenus Sarbecovirus) has caused millions of deaths, prompting a need for better understanding of coronavirid emergence and spillover to humans. As an evaluation of how some features of SARS-CoV-2, unique among sarbecoviruses, may have been acquired from related viruses, we conducted phylogenetic and recombination analyses to compare the frequency of recombination among coronavirids across vs within genera, subgenera, and species. Among known betacoronaviruses, we identified 199 (183 intraspecies, 16 interspecies, but no intersubgenera) recombination events. Phylogenetic analyses revealed that the ancestry of interspecies events was limited and less prone to affect 5' regions of coronavirid genome open reading frame 1 (ORF1) than intraspecies events. On the contrary, interspecies events were significantly more prone to impact the 3' end (ORF6-ORF8 and the nucleocapsid protein [N] ORF), suggesting the existence of region-specific constraints on recombination. This work substantiated that recombination among betacoronaviruses is limited by the genome similarity between their parental viruses. We conclude that SARS-CoV-2 likely acquired unique features through recombination with closely related circulating sarbecoviruses (most likely from the same species) that co-existed geographically.

IMPORTANCE

Understanding the evolutionary events that led to SARS-CoV-2 emergence, spillover, and spread is crucial to prevent, or at least be prepared for, the same type of occurrence in the future. Given that SARS-CoV-2 has some characteristics not found in other closely related viruses, we aimed to systematically assess how likely these unique features may have been acquired through recombination. We found that, although recombination is a frequent phenomenon among betacoronaviruses, it is mostly limited to closely related members of the same species. Therefore, we conclude that the most likely scenario involved feature acquisition from recombination with a closely related virus that was circulating in a geographically overlapping area or through a different biological process, but not recombination from a virus of a different species, genus, or subgenus.

Structural Basis for Inhibition of the SARS-CoV-2 nsp16 by Substrate-Based Dual Site Inhibitors

Coronaviruses, including SARS-CoV-2, possess an mRNA 5' capping apparatus capable of mimicking the natural eukaryotic capping signature. Two SAM-dependent methylating enzymes play important roles in this process: nsp14 methylates the N7 of the guanosine cap, and nsp16-nsp10 methylates the 2'-O- of subsequent nucleotides of viral mRNA. The 2'-O-methylation performed by nsp16-nsp10 is crucial for the escape of the viral RNA from innate immunity. Inhibition of this enzymatic activity has been proposed as a way to combat coronaviruses. In this study, we employed X-ray crystallography to analyze the binding of the SAM analogues to the active site of nsp16-nsp10. We obtained eleven 3D crystal structures of the nsp16-nsp10 complexes with SAM-derived inhibitors, demonstrated different conformations of the methionine substituting part of the molecules, and confirmed that simultaneous dual-site targeting of both SAM and RNA sites correlates with higher inhibitory potential.

Hypertonic saline nasal irrigation and gargling for suspected or confirmed COVID-19: Pragmatic randomised controlled trial (ELVIS COVID-19)

Background

In a previous pilot randomised controlled trial conducted on UK adults, we found that hypertonic saline nasal irrigation and gargling (HSNIG) reduced common cold symptoms, the need for over-the-counter medications, viral shedding, and the duration and transmission of the illness. It is unclear whether HSNIG improves outcomes of the coronavirus disease 2019 (COVID-19). Hypertonic saline can be prepared and HSNIG performed at home, making it a safe and scalable intervention, particularly well-suited for low- and middle-income countries.

Methods

We conducted a pragmatic randomised controlled trial in Pakistan on adults with suspected or confirmed COVID-19, initially within 48 hours of symptom onset, later extended to within five days due to recruitment challenges. Participants were randomised to one of two groups: the intervention group received instructions on preparing a 2.6% hypertonic saline solution for HSNIG, while the control group was instructed on performing ablution for Muslim prayers (wudu), which involves nasal washing and gargling with tap water. Our primary outcome was the time to symptom resolution, measured by two consecutive days of scoring zero on relevant questions from the validated, self-reported, adapted short form of the Wisconsin Upper Respiratory Symptom Survey (WURSS-24). Secondary outcomes included the severity of all symptoms, the severity and time to resolution of individual symptoms, health care contacts (GP/physician, emergency contacts), hospital attendance (and length of stay if admitted), over-the-counter (OTC) medication (frequency and cost), and transmission to household contacts. The analysis was conducted on an intention-to-treat basis. Logistic regression was used to calculate adjusted odds ratios (aORs) of improvement and Cox regression to calculate adjusted hazard ratios (aHRs) for the time to improvement with accompanying 95% confidence intervals (CIs).

Results

We randomised 576 people: 279 to the HSNIG group and 297 to the control group. Among those, 10 out of 279 (3.6%) in the HSNIG had symptom resolution, compared with 11 out of 297 (3.7%) in the control group (aOR = 1.20, 95% CI = 0.46- 3.22). The time-to-event analysis also showed no significant benefit (aHR = 1.23, 95% CI = 0.51-2.97). Excluding the 127 participants with no data on the primary outcome (who did not complete the study), 10 out of 222 (4.5%) in the HSNIG group had symptom resolution, compared to 11 out of 227 (4.8%) in the control group.

Conclusions

HSNIG was not effective for individuals with suspected or confirmed COVID-19 who began the intervention within five days of symptoms onset and therefore cannot be recommended for use. Further investigation is needed for interventions started within 48 hours of illness onset.

Registration

ClinicalTrials.gov (NCT05104372).

Docking heparan sulfate-based ligands as a promising inhibitor for SARS-CoV-2

CONTEXT

Heparan sulfate (HS) linear polysaccharide glycosaminoglycan compound is linked to components from the cell surface and the extracellular matrix. HS mediates SARS-CoV-2 infection through spike protein binding to cell surface receptors and is required to bind ACE2, prompting the need for electronic structure and molecular docking evaluation of this core system to exploit this attachment in developing new derivatives. Therefore, we have studied five molecules based on HS using molecular docking and electronic structure analysis. Non-covalent interaction analysis shows hydrogen bonding and van der Waals interactions in the binding to RBD-ACE2 interface and 3CLpro. SDM3 and SDM1 molecules present the lowest gap, including solvent effect under 154.6 kcal/mol, and exhibit the most reactivity behavior in this group, potentially leading to enhanced interaction in docking studies.

METHODS

Heparan sulfate and four derivatives were optimized using B3LYP functional with two basis sets 6-31 + G(d,p) and def2SVP. Electronic structure was used to explore the main interactions and the reactivity of these molecules, and these optimized structures were used in the molecular docking study against 3CLpro, RBD, and ACE2.

An integrative analysis of SARS-CoV 2 during the first and second waves of COVID-19 in Salta, Argentina

Wastewater surveillance has been extensively applied to provide information about SARS-CoV-2 circulation in the community. However, its applicability is limited in regions lacking adequate sewerage infrastructure, without wastewater treatment plants (WWTP) or with insufficient coverage. During the COVID-19 pandemic, from July 2020 to September 2021, comprehensive epidemiological data encompassing positive, recovered, and deceased cases were collected alongside precipitation records. Additionally, wastewater samples from 13 main sewersheds and river water from two points (up- and downstream the main WWTP), in the city of Salta, were gathered. A total of 452 water samples were analyzed for quantitative detection of SARS-CoV-2 using reverse transcription real-time PCR. Across the 62-week study period, two distinct waves of COVID-19 were identified. The dynamics of deceased cases showed peaks 10 and 28 days after the peaks of positive cases in the first and second waves, respectively. Downstream river water exhibited higher fecal contamination than the upstream samples, evincing the impact of the WWTP discharges. Viral concentration in river waters mirrored those from wastewater, reflecting the progression of cases. Despite the lower reported number of cases during the first wave in comparison to the second (5420 vs. 8516 cases at the respective peaks), higher viral concentrations were detected in water samples (1.97 × 107 vs. 2.36 × 106 gc/L, respectively), suggesting underreporting during the first wave, and highlighting the positive effect of vaccination during the second. To the best of our knowledge, this is the first study that simultaneously and systematically analyzed surface water and wastewater over a prolonged period, the effect of precipitations were considered for the variations in the concentrations, and the findings compared with epidemiological information. Environmental surveillance was demonstrated to be a great tool to obtain valuable information about the circulation patterns of SARS-CoV-2, especially under resource constraints to massively test the population, thus, underreporting cases. Furthermore, the methodology employed herein can be easily expanded to the community-level surveillance of other pathogens excreted in urine and feces, encompassing viruses, bacteria, and protozoa.

Rural residents' Knowledge, Attitude, and Practice in relation to infection risk during the late stage of an epidemic: a cross-sectional study of COVID-19

Background

In the field of public health, the prevention and management of infectious diseases in rural regions have always been crucial. This study aims to analyze the factors influencing rural residents' Knowledge, Attitude, and Practices and their correlation with infection risk during the late stage of an epidemic, with a focus on the COVID-19 case.

Methods

A cross-sectional study was conducted in rural regions of China's Guangdong province, using a multi-stage sampling technique to select rural residents for a validated questionnaire survey in February 2023. Descriptive statistical method was used to describe the infection status of rural residents and Chi-Square Test was used to explore the influencing factors of Knowledge, Attitude and Practice in this population. Multivariable binary logistic regression analysis was conducted to determine the presence of a statistically significant association between explanatory variables and outcome variables at corresponding 95% CI.

Results

A total of 3,125 rural residents were investigated, of whom 805 had never been infected with COVID-19. The survey participants had an average score of 5.84 ± 1.419 for COVID-19 knowledge. (The total score range is from 0 to 8. A score greater than 6.4 indicates good knowledge acquisition.) Regarding the attitude and practice sections, the average scores were 23.68 ± 3.169 and 23.45 ± 5.030, respectively. (The total score range of both these sections is from 0 to 32. A score greater than 25.6 represents positive attitudes and good practices.) The reduction of COVID-19 risk is significantly associated with an increase in Knowledge scores (p trend < 0.01). In stratified analyses, the Knowledge, Attitudes, and Practices scores of residents in each region have varying degrees of correlation with the risk of SARS-CoV-2 infection.

Conclusion

Rural residents' Knowledge, Attitudes, and Practices on COVID-19 prevention and control requires improvement. Efforts to promote their' perceptions and habits regarding COVID-19 prevention and control are crucial in reducing the risk of infection.

Altered ACE2 and interferon landscape in the COVID-19 microenvironment correlate with the anti-PD-1 response in solid tumors

Angiotensensin-converting enzyme-2 (ACE2) is a receptor for SARS-CoV-2, allowing the virus to enter cells. Although tumor patients infected by SARS-CoV-2 often have a worse outcome, the expression, function and clinical relevance of ACE2 in tumors has not yet been thoroughly analyzed. In this study, RNA sequencing (RNA-seq) data from tumors, adjacent tissues and whole blood samples of COVID-19 patients from genome databases and from tumor cell lines and endothelial cells infected with different SARS-CoV-2 variants or transfected with an ACE2 expression vector (ACE2high) or mock (ACE2low) were analyzed for the expression of ACE2 and immune response relevant molecules in silico or by qPCR, flow cytometry, Western blot and/or RNA-seq. The differential expression profiles in ACE2high vs. ACE2low cells correlated with available SARS-CoV-2 RNA-seq datasets. ACE2high cells demonstrated upregulated mRNA and/or protein levels of HLA class I, programmed death ligand 1 (PD-L1), components of the antigen processing machinery (APM) and the interferon (IFN) signaling pathway compared to ACE2low cells. Co-cultures of ACE2high cells with peripheral blood mononuclear cells increased immune cell migration and infiltration towards ACE2high cells, apoptosis of ACE2high cells, release of innate immunity-related cytokines and altered NK cell-mediated cytotoxicity. Thus, ACE2 expression was associated in different model systems and upon SARS-CoV-2 infection with an altered host immunogenicity, which might influence the efficacy of immune checkpoint inhibitors. These results provide novel insights into the (patho)physiological role of ACE2 on immune response-relevant mechanisms and suggest an alternative strategy to reduce COVID-19 severity in infected tumor patients targeting the ACE2-induced IFN-PD-L1 axis.

Establishment of a human organoid-based evaluation system for assessing interspecies infection risk of animal-borne coronaviruses

The COVID-19 pandemic presents a major threat to global public health. Several lines of evidence have shown that the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), along with two other highly pathogenic coronaviruses, SARS-CoV and Middle East Respiratory Syndrome (MERS-CoV) originated from bats. To prevent and control future coronavirus outbreaks, it is necessary to investigate the interspecies infection and pathogenicity risks of animal-related coronaviruses. Currently used infection models, including in vitro cell lines and in vivo animal models, fail to fully mimic the primary infection in human tissues. Here, we employed organoid technology as a promising new model for studying emerging pathogens and their pathogenic mechanisms. We investigated the key host-virus interaction patterns of five human coronaviruses (SARS-CoV-2 original strain, Omicron BA.1, MERS-CoV, HCoV-229E, and HCoV-OC43) in different human respiratory organoids. Five indicators, including cell tropism, invasion preference, replication activity, host response and virus-induced cell death, were developed to establish a comprehensive evaluation system to predict coronavirus interspecies infection and pathogenicity risks. Using this system, we further examined the pathogenicity and interspecies infection risks of three SARS-related coronaviruses (SARSr-CoV), including WIV1 and rRsSHC014S from bats, and MpCoV-GX from pangolins. Moreover, we found that cannabidiol, a non-psychoactive plant extract, exhibits significant inhibitory effects on various coronaviruses in human lung organoid. Cannabidiol significantly enhanced interferon-stimulated gene expression but reduced levels of inflammatory cytokines. In summary, our study established a reliable comprehensive evaluation system to analyse infection and pathogenicity patterns of zoonotic coronaviruses, which could aid in prevention and control of potentially emerging coronavirus diseases.

The PARP inhibitor rucaparib blocks SARS-CoV-2 virus binding to cells and the immune reaction in models of COVID-19

BACKGROUND AND PURPOSE

To date, there are limited options for severe Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2 virus. As ADP-ribosylation events are involved in regulating the life cycle of coronaviruses and the inflammatory reactions of the host; we have, here, assessed the repurposing of registered PARP inhibitors for the treatment of COVID-19.

EXPERIMENTAL APPROACH

The effects of PARP inhibitors on virus uptake were assessed in cell-based experiments using multiple variants of SARS-CoV-2. The binding of rucaparib to spike protein was tested by molecular modelling and microcalorimetry. The anti-inflammatory properties of rucaparib were demonstrated in cell-based models upon challenging with recombinant spike protein or SARS-CoV-2 RNA vaccine.

KEY RESULTS

We detected high levels of oxidative stress and strong PARylation in all cell types in the lungs of COVID-19 patients, both of which negatively correlated with lymphocytopaenia. Interestingly, rucaparib, unlike other tested PARP inhibitors, reduced the SARS-CoV-2 infection rate through binding to the conserved 493-498 amino acid region located in the spike-ACE2 interface in the spike protein and prevented viruses from binding to ACE2. In addition, the spike protein and viral RNA-induced overexpression of cytokines was down-regulated by the inhibition of PARP1 by rucaparib at pharmacologically relevant concentrations.

CONCLUSION AND IMPLICATIONS

These results point towards repurposing rucaparib for treating inflammatory responses in COVID-19.

Characterization of monoclonal antibodies targeting SARS-CoV-2 spike glycoprotein: Reactivity against Delta and Omicron BA.1 variants

The cross-species transmissibility of SARS-CoV-2 infection has necessitated development of specific reagents for detecting infection in various animal species. The spike glycoprotein of SARS-CoV-2, which is involved in viral entry, is a highly immunogenic protein. To develop assays targeting this protein, we generated eight monoclonal antibodies (mAbs) against the S1 and seven against the S1/S2 protein (ectodomain) of SARS CoV-2. Based on neutralization capability and reactivity profile observed in ELISA, the mAbs generated against the S1/S2 antigen exhibited a broader spectrum of epitope specificity than those produced against the S1 domain alone. The full-length ectodomain induced antibodies that could neutralize the two most important variants of the virus encountered during the pandemic, namely Delta and Omicron. The availability of these reagents could greatly enhance the development of precise diagnostics for detecting COVID-19 infections in various host species and contribute to the advancement of mAb-based therapeutics.

Plant resources for immunonutrients and immunomodulators to combat infectious respiratory viral diseases: a review

Boosting the immune system has become a crucial aspect in the global battle against the COVID-19 pandemic and other similar infections to protect oneself against symptoms, especially in the prevention of viral infections of the lower respiratory tract. The importance of conducting more studies to create successful herbal formulations as infection prevention measures is emphasized in this review, which looks at the function of immune-boosting nutrients, medicinal plants, and herbal treatments. We reviewed and analyzed 207 studies published from 1946 to the present using reputable databases like Google Scholar, PubMed, and NCBI. The review examined 115 plant species in total and identified 12 key nutrients, including vitamins A, D, C, omega-3 fatty acids, iron, and zinc, while noting that four plant families, Rosaceae, Asteraceae, Amaryllidaceae, and Acanthaceae, show potential against respiratory infections like influenza, RSV, and SARS-CoV. To lower the risk of infection, it is recommended to consume nutritious meals that have immune-modulating qualities. Information on the bioactive components of medicinal herbs, spices, and plants that have been effective in treating respiratory viral infections and related conditions is compiled in this review, which highlights phytoactive substances with antibacterial and antiviral activity as effective modulators to lower the risk of infections. Furthermore, it is highlighted that ancient knowledge systems, like Ayurveda and Naturopathy, should be integrated to help develop new herbal formulations. To improve immunity and lessen vulnerability to serious respiratory infections, the results highlight the need for including immune-modulating foods and plant-based medicines into everyday routines.

First detection of Omicron variant BA.4.1 lineage in dogs, Chile

SARS-CoV-2's rapid global spread caused the declaration of COVID-19 as a pandemic in March 2020. Alongside humans, domestic dogs and cats are also susceptible to infection. However, limited reports on pet infections in Chile prompted a comprehensive study to address this knowledge gap. Between March 2021 and March 2023, the study assessed 65 pets (26 dogs and 39 cats) from 33 COVID-19+ households alongside 700 nasal swabs from animals in households with unknown COVID-19 status. Using RT-PCR, nasal, fecal, and environmental samples were analyzed for the virus. In COVID-19+ households, 6.06% tested positive for SARS-CoV-2, belonging to 3 dogs, indicating human-to-pet transmission. Pets from households with unknown COVID-19 status tested negative for the virus. We obtained 2 SARS-CoV-2 genomes from animals, that belonged to Omicron BA.4.1 variant, marking the first report of pets infected with this lineage globally. Phylogenetic analysis showed these sequences clustered with human sequences collected in Chile during the same period when the BA.4.1 variant was prevalent in the country. The prevalence of SARS-CoV-2 in Chilean pets was relatively low, likely due to the country's high human vaccination rate. Our study highlights the importance of upholding and strengthening human vaccination strategies to mitigate the risk of interspecies transmission. It underscores the critical role of the One Health approach in addressing emerging zoonotic diseases, calling for further research on infection dynamics and risk factors for a comprehensive understanding.