The SARS-CoV-2 mutations versus vaccine effectiveness: New opportunities to new challenges

CovidTGI: A tool to investigate the temporal genetic instability of SARS-CoV-2 variants

The COVID-19 pandemic has underscored the need for fast and accurate epidemiology, particularly due to the high observed mutation frequency in SARS-CoV-2. This study aims to explore the evolution of SARS-CoV-2 through a global analysis. To facilitate a comparative analysis of temporal mutation data, we developed CovidTGI, a Shiny web application. CovidTGI provides insights into observed mutation frequencies and the temporal relationships among mutations across various clades in different geographical regions. Our tool relies on a database that includes 2 million samples obtained from the National Center for Biotechnology Information (NCBI), along with 500 in-house Sicilian samples collected between May 2021 and June 2022. From this smaller group of samples, we identified key variants that are prevalent within a specific clade. Our tool is designed to study the evolution of SARS-CoV-2, which clearly follows a complex trajectory. This complexity highlights the necessity for sophisticated tools like CovidTGI to understand and track the evolution of this virus.

In Silico and In Vitro development of novel small interfering RNAs (siRNAs) to inhibit SARS-CoV-2

SARS-CoV-2 is causing severe to moderate respiratory tract infections, posing global health, social life, and economic threats. Our design strategy for siRNAs differs from existing studies through a step-by-step filtration process utilizing integrative bioinformatics protocols and web tools. Stage one: Multiple Sequence Alignment was employed to identify the most conserved areas. Stage two involves using various online tools, among the most reputable tools for building siRNA. The first filtration step of siRNA uses the Huesken dataset, estimating a 90 % experimental inhibition. The second filtration stage involves choosing the most suitable and targeted siRNA by utilizing thermodynamics and Target Accessibility of siRNAs. The final filtration step is off-target filtration using BLAST with specific parameters. Four of the 258 siRNAs were chosen for their potency and specificity, targeting conserved regions (NSP8, NSP12, and NSP14) with minimal human transcripts off-targets. We conducted in-vitro experiments, including cytotoxicity, TCID50, and RT-PCR assays. When tested on the SARS-CoV-2 strain hCoV-19/Egypt/NRC-03/2020 at 100 nM, none showed cellular toxicity. The TCID50 assay confirmed viral replication reduction at 12 h.p.i; the efficacy of the four siRNAs and their P value were highly significant. siRNA2 maintaining efficacy at 24, 36, and 48 h.p.i, while siRNA4 had a significant P value (≤0.0001) at 48 h.p.i. At 24 h.p.i, siRNA2 and siRNA4 showed statistical significance in viral knockdown of the virus's S gene and ORF1b gene by 95 %, 89 %, and 96 %, 97 %, respectively. Our computational method and experimental assessment of specific siRNAs have led us to conclude that siRNA2 and siRNA4 could be promising new therapies for SARS-CoV-2 that need further development.

Revolutionizing immunization: a comprehensive review of mRNA vaccine technology and applications

Messenger RNA (mRNA) vaccines have emerged as a transformative platform in modern vaccinology. mRNA vaccine is a powerful alternative to traditional vaccines due to their high potency, safety, and efficacy, coupled with the ability for rapid clinical development, scalability and cost-effectiveness in manufacturing. Initially conceptualized in the 1970s, the first study about the effectiveness of a mRNA vaccine against influenza was conducted in 1993. Since then, the development of mRNA vaccines has rapidly gained significance, especially in combating the COVID-19 pandemic. Their unprecedented success during the COVID-19 pandemic, as demonstrated by the Pfizer-BioNTech and Moderna vaccines, highlighted their transformative potential. This review provides a comprehensive analysis of the mRNA vaccine technology, detailing the structure of the mRNA vaccine and its mechanism of action in inducing immunity. Advancements in nanotechnology, particularly lipid nanoparticles (LNPs) as delivery vehicles, have revolutionized the field. The manufacturing processes, including upstream production, downstream purification, and formulation are also reviewed. The clinical progress of mRNA vaccines targeting viruses causing infectious diseases is discussed, emphasizing their versatility and therapeutic potential. Despite their success, the mRNA vaccine platform faces several challenges, including improved stability to reduce dependence on cold chain logistics in transport, enhanced delivery mechanisms to target specific tissues or cells, and addressing the risk of rare adverse events. High costs associated with encapsulation in LNPs and the potential for unequal global access further complicate their widespread adoption. As the world continues to confront emerging viral threats, overcoming these challenges will be essential to fully harness the potential of mRNA vaccines. It is anticipated that mRNA vaccines will play a major role in defining and shaping the future of global health.

SARS-CoV-2 Variants: Genetic Insights, Epidemiological Tracking, and Implications for Vaccine Strategies

The emergence of SARS-CoV-2 variants has significantly impacted the global response to the COVID-19 pandemic. This review examines the genetic diversity of SARS-CoV-2 variants, their roles in epidemiological tracking, and their influence on viral fitness. Variants of concern (VOCs) such as Alpha, Beta, Gamma, Delta, and Omicron have demonstrated increased transmissibility, altered pathogenicity, and potential resistance to neutralizing antibodies. Epidemiological tracking of these variants is crucial for understanding their spread, informing public health interventions, and guiding vaccine development. The review also explores how specific mutations in the spike protein and other genomic regions contribute to viral fitness, affecting replication efficiency, immune escape, and transmission dynamics. By integrating genomic surveillance data with epidemiological and clinical findings, this review provides a comprehensive overview of the ongoing evolution of SARS-CoV-2 and its implications for public health strategies and new vaccine development.

How well do different COVID-19 vaccines protect against different viral variants? A systematic review and meta-analysis

While the efficacy of coronavirus disease 2019 (COVID-19) vaccines has been evaluated in numerous trials, comprehensive evidence on how protection by different vaccines has varied over time remains limited. We aimed to compare protective effects of different vaccines against different viral variants. To achieve this, we searched Medline, Cochrane Library and Embase for randomized controlled trials assessing the efficacy of COVID-19 vaccines. Forest plots using Mantel-Haenszel and random-effects models were generated showing risk ratios (RRs) and 95% CIs by vaccines and variants. We included 36 studies with 90 variant-specific primary outcomes. We found a RR of 0.26 (95% CI 0.21 to 0.31) against all variants overall, with the highest protective effects against the wild-type (RR 0.13; 95% CI 0.10 to 0.18), followed by Alpha (RR 0.26; 95% CI 0.18 to 0.36), Gamma (RR 0.34; 95% CI 0.21 to 0.55), Delta (RR 0.39; 95% CI 0.28 to 0.56) and Beta (RR 0.49; 95% CI 0.40 to 0.62) variants. Nucleic acid vaccines showed the highest protection levels against all variants (RR 0.11; 95% CI 0.08 to 0.15), followed by protein subunit, inactivated virus and viral vector. In conclusion, we found high but heterogenous levels of protection for most COVID-19 vaccines, with decreasing protective effects for vaccines based on traditional technologies as SARS-CoV-2 variants emerged over time. Novel nucleic acid-based vaccines offered substantially higher and more consistent protection.

Oral Immunisation With Non-GMO Surface Displayed SARS-CoV-2 Spike Epitopes on Bacteria-Like Particles Provokes Robust Humoral and Cellular Immune Responses, and Modulated the Gut Microbiome in Mice

The coronavirus disease 2019 (COVID-19) is a fatal disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). To date, several vaccines have been developed to combat the spread of this virus. Mucosal vaccines using food-grade bacteria, such as Lactobacillus spp., are promising strategies for developing safe and effective vaccines against SARS-CoV-2. In this study, we designed a non-GMO surface-displayed SARS-CoV-2 spike S1 epitope on Limosilactobacillus fermentum-derived bacteria-like particles (BLPs). After that, we evaluated its efficacy to induce immune responses in immunocompetent mice. Moreover, we examined the influence of oral immunisation on the gut microbiome and microbiota metabolites. Twenty-eight 6-week-old male C57BL/6 mice were orally immunised with the following: PBS (control), Lm. fermentum-derived BLPs only, BLPs displaying SARS-CoV-2 spike S1-2, or BLPs displaying SARS-CoV-2 spike S1-3 epitopes. Our results showed that mucosal immunisation of mice with surface-displayed SARS-CoV-2 spike epitopes provoked high-level secretory IgA and systemic IgG production. Moreover, the immunisation exhibited a Th1-like immune response, characterised by an elevated IgG2a-to-IgG1 ratio and high antiviral IFN-γ production. In addition, we observed gut microbiome modulation and increased butyrate production in immunised mice. Overall, the use of Lm. fermentum-derived BLPs and the anchor CshA to display SARS-CoV-2 spike S1epitopes is a promising novel strategy in developing a cost-effective, non-GMO mucosal vaccine alternative against SARS-CoV-2.

Parental intention on getting children COVID-19 vaccinations: Invariance evaluation across parenting roles and COVID-19-like symptoms experiences among Iranians during the pandemic period

Countries worldwide are facing challenges with increasing the COVID-19 vaccination rates for children. This study examined associations between perceived knowledge, coping appraisal, threat appraisal, adaptive response, maladaptive response, and intention, and possible variance across parents (mother or father) and COVID-19-like symptoms experiences regarding parental intentions to vaccinate their children. A total of 836 Iranian parents with children between the ages of 6 and 12 y completed measures assessing perceived knowledge, coping appraisals, threat appraisals, intentions, adaptive responses, and maladaptive responses. Multigroup structural equation modeling revealed that perceived knowledge was positively associated with both coping and threat appraisals, coping appraisals positively associated with adaptive responses, maladaptive responses, and intentions to vaccinate, threat appraisals positively associated with adaptive and maladaptive responses, and adaptive responses positively associated with intentions to vaccinate. The invariance evaluation revealed no differences across parents or COVID-19-like symptoms experiences in parental intentions to get their children vaccinated. The findings suggest that cogent information regarding childhood COVID-19 vaccination may boost parents' knowledge influencing their appraisals, adaptive responses and intentions to vaccinate their children. Specifically, coping appraisals and adaptive responses appeared to be important mediators between knowledge and intentions to vaccinate. Furthermore, intentions to vaccinate children may not be strongly influenced by parental roles or COVID-19-like symptoms experiences. These findings may help multiple stakeholders promote COVID-19 vaccination rates among children, and countries should further examine ways of increasing rates based on their specific needs.

Essential oil constituents of regional ethnomedicinal plants as potential inhibitors of SARS-CoV-2 Mpro: an integrated molecular docking, molecular dynamics and QM/MM study

The scientific community has achieved a remarkable milestone by creating efficacious vaccines against the SARS-CoV-2 virus. The treatment alternatives are still restricted, though. The bioactive ingredients present in natural plants are known to exhibit diverse pharmacological effects against many diseases. Using computational techniques such as molecular docking, drug-likeness, ADMET study, MD simulation, and our own N-layered Integrated molecular Orbital and Molecular mechanics (ONIOM) calculations, this study aimed to investigate essential oil constituents of Lindera neesiana, Litsea cubeba and Zanthoxylum armatum DC plants as a potential natural inhibitor of SARS-CoV-2 main protease (Mpro). To determine their binding affinity, 107 phytochemical substances in total were docked inside the binding pocket of Mpro. Copaene showed the highest binding affinity among the 107 compounds, with an energy of -7.90 kcal/mol. Furthermore, physiochemical and ADMET properties were evaluated for the top five phytocompounds. The studied phytocompounds showed good physiochemical and pharmacokinetic behaviour with no associated toxicity. MD simulation further provided evidence for stable interaction of phytocompounds within the binding pocket of Mpro. Subsequently, ONIOM calculation was done on the best-hit complex, wherein the hydrogen bonding interactions were retained with appreciable negative energy. These in silico results indicate that the specific phytocompounds present in essential oils of L. neesiana, L. cubeba, and Z. armatum DC have significant inhibitor ability against SARS-CoV-2 main protease and could be explored for future therapeutic investigations.

Sulfated Cellulose Nanofiber Hydrogel with Mucus-Like Activities for Virus Inhibition

Mucus is the first defense barrier against viruses in the human immune system. Inspired by the mucus structure, we designed a highly sulfated hydrogel to bind viruses and prevent infection of the underlying cells. The hydrogel was formed by gelation of sulfated cellulose nanofiber (SCNF) with Ca2+. SCNF exhibited a mucin-like nanofiber structure with high numbers of sulfated groups. Based on the electrostatic interactions with a virus, SCNF could efficiently inhibit herpes simplex virus-1 (HSV-1) infection with a half-maximal inhibitory concentration (IC50) of 0.43 μg/mL, which is comparable to that of heparin (IC50 = 0.30 μg/mL). Benefiting from the multiporous structure and sulfate groups, the Ca2+-SCNF hydrogel could efficiently trap HSV-1 and inhibit the virus from attacking the underlying cells in a transwell model. Furthermore, SCNF also inhibited SARS-CoV-2 infection in a similar experimental setting. By integrating the advantages of high and broad-spectrum virus inhibitory activity as well as low toxicity, it is believed that the Ca2+-SCNF hydrogel can promote the development of highly biocompatible and efficient antiviral material with "binding and inhibition" capability and other diverse strategies.

Confounding amplifies the effect of environmental factors on COVID-19

The global COVID-19 pandemic has severely impacted human health and socioeconomic development, posing an enormous public health challenge. Extensive research has been conducted into the relationship between environmental factors and the transmission of COVID-19. However, numerous factors influence the development of pandemic outbreaks, and the presence of confounding effects on the mechanism of action complicates the assessment of the role of environmental factors in the spread of COVID-19. Direct estimation of the role of environmental factors without removing the confounding effects will be biased. To overcome this critical problem, we developed a Double Machine Learning (DML) causal model to estimate the debiased causal effects of the influencing factors in the COVID-19 outbreaks in Chinese cities. Comparative experiments revealed that the traditional multiple linear regression model overestimated the impact of environmental factors. Environmental factors are not the dominant cause of widespread outbreaks in China in 2022. In addition, by further analyzing the causal effects of environmental factors, it was verified that there is significant heterogeneity in the role of environmental factors. The causal effect of environmental factors on COVID-19 changes with the regional environment. It is therefore recommended that when exploring the mechanisms by which environmental factors influence the spread of epidemics, confounding factors must be handled carefully in order to obtain clean quantitative results. This study offers a more precise representation of the impact of environmental factors on the spread of the COVID-19 pandemic, as well as a framework for more accurately quantifying the factors influencing the outbreak.

[Evaluation of the effectiveness of chemical inactivation and immunogenicity of the Omicron variant of the SARS-CoV-2 virus]

INTRODUCTION

The rapid spread of coronavirus infection COVID-19 among the population of many countries around the world has contributed to the emergence of many genetic variants of SARS-CoV-2. Compared to previous coronavirus variants, the new Omicron variants have shown a noticeable degree of mutation. Virus inactivation is one of the most important steps in the development of inactivated vaccines. The chemical inactivation agents currently used are β-propiolactone and formaldehyde, but there is no uniform standard for designing and specifying the inactivation process.

OBJECTIVE

Evaluation and comparison of the effectiveness of chemical inactivation of two agents, formaldehyde and β-propiolactone against immunogenicity of the Omicron variant of the SARS-CoV-2 virus.

MATERIALS AND METHODS

Nasopharyngeal swabs were used to obtain the SARS-CoV-2 Omicron variant virus. Vero cell culture was used to isolate, reproduce, titrate the virus, and perform a neutralization reaction. The kinetics of studying the inactivation of the virus by chemical agents such as formaldehyde and β-propiolactone was carried out.

RESULTS

Studies have been conducted to comparatively evaluate the effectiveness of chemical agents used to inactivate the SARS-CoV-2 virus of the Omicron variant, planned for use in the production of an inactivated whole-virion vaccine. Formaldehyde and β-propiolactone were used as inactivation agents in concentrations of 0.05, 0.1, 0.5% of the total volume of the virus suspension. It has been established that complete inactivation of the virus by formaldehyde in the concentrations used at a temperature of 37 °C occurs within up to 2 hours, and when using beta-propiolactone, within up to 12 hours.

CONCLUSION

Inactivated virus samples have different antigenic activity depending on the concentration of the inactivation agents used. The most pronounced antigenic activity is manifested in samples of the pathogen that were treated with an inactivation agent at a mild concentration of 0.05%. Increasing the concentration of inactivation agent by 5 or more times leads to a significant decrease in the antigenicity of the SARS-CoV-2 virus. With the inactivation modes used, the loss of biological activity of the virus occurs faster and antigenicity is retained largely when treated with formaldehyde.

An Immunoinformatic Approach for Identifying and Designing Conserved Multi-Epitope Vaccines for Coronaviruses

BACKGROUND/OBJECTIVES

The COVID-19 pandemic caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has exposed the vulnerabilities and unpreparedness of the global healthcare system in dealing with emerging zoonoses. In the past two decades, coronaviruses (CoV) have been responsible for three major viral outbreaks, and the likelihood of future outbreaks caused by these viruses is high and nearly inevitable. Therefore, effective prophylactic universal vaccines targeting multiple circulating and emerging coronavirus strains are warranted.

METHODS

This study utilized an immunoinformatic approach to identify evolutionarily conserved CD4+ (HTL) and CD8+ (CTL) T cells, and B-cell epitopes in the coronaviral spike (S) glycoprotein.

RESULTS

A total of 132 epitopes were identified, with the majority of them found to be conserved across the bat CoVs, pangolin CoVs, endemic coronaviruses, SARS-CoV-2, and Middle East respiratory syndrome coronavirus (MERS-CoV). Their peptide sequences were then aligned and assembled to identify the overlapping regions. Eventually, two major peptide assemblies were derived based on their promising immune-stimulating properties.

CONCLUSIONS

In this light, they can serve as lead candidates for universal coronavirus vaccine development, particularly in the search for pan-coronavirus multi-epitope universal vaccines that can confer protection against current and novel coronaviruses.

Engineered protein destabilization reverses intrinsic immune evasion for candidate vaccine pan-strain KSHV and SARS-CoV-2 antigens

Both Kaposi sarcoma herpesvirus LANA and SARS coronavirus 2 RdRp/nsp12 are highly conserved replication proteins that evade immune processing. By deleting the LANA central repeat 1 domain (LANA ΔCR1 ) or by dividing RdRp into two separated fragments (RdRp Frag ) to maximize nascent protein mis-folding, cis peptide presentation was increased. Native LANA or RdRp SIINFEKL fusion proteins expressed in MC38 cancer cells were not recognized by activated OT-1 CD8 + cells against SIINFEKL but cytotoxic recognition was restored by expression of the corresponding modified proteins. Immunocompetent syngeneic mice injected with LANA- or RdRp-SIINFEKL MC38 cells developed rapidly-growing tumors with short median survival times. Mice injected with LANA ΔCR1 - or RdRp Frag -SIINFEKL had partial tumor regression, slower tumor growth, longer median survival, as well as increased effector-specific tumor-infiltrating lymphocytes. These mice developed robust T cell responses lasting at least 90 days post-injection that recognized native viral protein epitopes. Engineered vaccine candidate antigens can unmask virus-specific CTL responses that are typically suppressed during native viral infection.

A novel multitargeted self-assembling peptide-siRNA complex for simultaneous inhibition of SARS-CoV-2-host cell interaction and replication

Effective therapeutics are necessary for managing severe COVID-19 disease despite the availability of vaccines. Small interfering RNA (siRNA) can silence viral genes and restrict SARS-CoV-2 replication. Cell-penetrating peptides is a robust method for siRNA delivery, enhancing siRNA stability and targeting specific receptors. We developed a peptide HE25 that blocks SARS-CoV-2 replication by various mechanisms, including the binding of multiple receptors involved in the virus's internalization, such as ACE2, integrins and NRP1. HE25 not only acts as a vehicle to deliver the SARS-CoV-2 RNA-dependent RNA polymerase siRNA into cells but also facilitates their internalization through endocytosis. Once inside endosomes, the siRNA is released into the cytoplasm through the Histidine-proton sponge effect and the selective cleavage of HE25 by cathepsin B. These mechanisms effectively inhibited the replication of the ancestral SARS-CoV-2 and the Omicron variant BA.5 in vitro. When HE25 was administered in vivo, either by intravenous injection or inhalation, it accumulated in lungs, veins and arteries, endothelium, or bronchial structure depending on the route. Furthermore, the siRNA/HE25 complex caused gene silencing in lung cells in vitro. The SARS-CoV-2 siRNA/HE25 complex is a promising therapeutic for COVID-19, and a similar strategy can be employed to combat future emerging viral diseases.

Leveraging artificial intelligence in vaccine development: A narrative review

Vaccine development stands as a cornerstone of public health efforts, pivotal in curbing infectious diseases and reducing global morbidity and mortality. However, traditional vaccine development methods are often time-consuming, costly, and inefficient. The advent of artificial intelligence (AI) has ushered in a new era in vaccine design, offering unprecedented opportunities to expedite the process. This narrative review explores the role of AI in vaccine development, focusing on antigen selection, epitope prediction, adjuvant identification, and optimization strategies. AI algorithms, including machine learning and deep learning, leverage genomic data, protein structures, and immune system interactions to predict antigenic epitopes, assess immunogenicity, and prioritize antigens for experimentation. Furthermore, AI-driven approaches facilitate the rational design of immunogens and the identification of novel adjuvant candidates with optimal safety and efficacy profiles. Challenges such as data heterogeneity, model interpretability, and regulatory considerations must be addressed to realize the full potential of AI in vaccine development. Integrating emerging technologies, such as single-cell omics and synthetic biology, promises to enhance vaccine design precision and scalability. This review underscores the transformative impact of AI on vaccine development and highlights the need for interdisciplinary collaborations and regulatory harmonization to accelerate the delivery of safe and effective vaccines against infectious diseases.

Prospects of Innovative Therapeutics in Combating the COVID-19 Pandemic

The sudden global crisis of COVID-19, driven by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), demands swift containment measures due to its rapid spread and numerous problematic mutations, which complicate the establishment of herd immunity. With escalating fatalities across various nations no foreseeable end in sight, there is a pressing need to create swiftly deployable, rapid, cost-effective detection, and treatment methods. While various steps are taken to mitigate the transmission and severity of the disease, vaccination is proven throughout mankind history as the best method to acquire immunity and circumvent the spread of infectious diseases. Nonetheless, relying solely on vaccination might not be adequate to match the relentless viral mutations observed in emerging variants of SARS-CoV-2, including alterations to their RBD domain, acquisition of escape mutations, and potential resistance to antibody binding. Beyond the immune system activation achieved through vaccination, it is crucial to develop new medications or treatment methods to either impede the infection or enhance existing treatment modalities. This review emphasizes innovative treatment strategies that aim to directly disrupt the virus's ability to replicate and spread, which could play a role in ending the SARS-CoV-2 pandemic.

Olive Leaf Extract Downregulates the Protein Expression of Key SARS-CoV-2 Entry Enzyme ACE-2, TMPRSS2, and Furin

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses ongoing global health challenges due to its propensity for mutations, which can undermine vaccine efficacy. With no definitive treatment available, urgent research into affordable and biocompatible therapeutic agents is extremely urgent. Angiotensin converting enzyme-2 (ACE-2), transmembrane protease serine subtype 2 (TMPRSS2), and Furin enzymes, which allow the virus to enter cells, are particularly important as potential drug targets among scientists. Olive leaf extract (OLE) has garnered attention for its potential against Coronavirus Disease-9 (COVID-19), yet its mechanism remains understudied. In this study, we aimed to investigate the effects of OLE on ACE-2, TMPRSS2, and Furin protein expressions by cell culture study. Total phenol, flavonoid content, and antioxidant capacity were measured by photometric methods, and oleuropein levels were measured by liquid LC-HR-MS. Cell viability was analyzed by ATP levels using a luminometric method. ACE-2, TMPRSS2, and Furin expressions were analyzed by the Western Blotting method. ACE-2, TMPRSS2, and Furin protein expression levels were significantly lower in a dose dependent manner and the highest inhibition was seen at 100 μg/ml OLE. The results showed that OLE may be a promising treatment candidate for COVID-19 disease. However, further studies need to be conducted in cells co-infected with the virus.

A benchmark for evaluation of structure-based online tools for antibody-antigen binding affinity

The prediction of binding affinity changes caused by missense mutations can elucidate antigen-antibody interactions. A few accessible structure-based online computational tools have been proposed. However, selecting suitable software for particular research is challenging, especially research on the SARS-CoV-2 spike protein with antibodies. Therefore, benchmarking of the mutation-diverse SARS-CoV-2 datasets is critical. Here, we collected the datasets including 1216 variants about the changes in binding affinity of antigens from 22 complexes for SARS-CoV-2 S proteins and 22 monoclonal antibodies as well as applied them to evaluate the performance of seven binding affinity prediction tools. The tested tools' Pearson correlations between predicted and measured changes in binding affinity were between -0.158 and 0.657, while accuracy in classification tasks on predicting increasing or decreasing affinity ranged from 0.444 to 0.834. These tools performed relatively better on predicting single mutations, especially at epitope sites, whereas poor performance on extremely decreasing affinity. The tested tools were relatively insensitive to the experimental techniques used to obtain structures of complexes. In summary, we constructed a list of datasets and evaluated a range of structure-based online prediction tools that will explicate relevant processes of antigen-antibody interactions and enhance the computational design of therapeutic monoclonal antibodies.

Immune response against the SARS-CoV-2 spike protein in cancer patients after COVID-19 vaccination during the Omicron wave: a prospective study

BACKGROUND

Cancer patients often have weakened immune systems, resulting in a lower response to vaccines, especially those receiving immunosuppressive oncological treatment (OT). We aimed to assess the impact of OT on the humoral and T-cell response to the B.1 lineage and Omicron variant following COVID-19 vaccination in patients with solid and hematological neoplasms.

METHODS

We conducted a prospective study on cancer patients, stratified into OT and non-OT groups, who received a two-dose series of the COVID-19 mRNA vaccine and a booster six months later. The outcomes measured were the humoral (anti-SARS-CoV-2 S IgG titers and ACE2-S interaction inhibition capacity) and cellular (SARS-CoV-2 S-specific T-cell spots per million PBMCs) responses against the B.1 lineage and Omicron variant. These responses were evaluated four weeks after the second dose (n = 98) and eight weeks after the booster dose (n = 71).

RESULTS

The humoral response after the second vaccine dose against the B.1 lineage and Omicron variant was significantly weaker in the OT group compared to the non-OT group (q-value<0.05). A booster dose of the mRNA-1273 vaccine significantly improved the humoral response in the OT group, making it comparable to the non-OT group. The mRNA-1273 vaccine, designed for the original Wuhan strain, elicited a weaker humoral response against the Omicron variant compared to the B.1 lineage, regardless of oncological treatment or vaccine dose. In contrast, T-cell responses against SARS-CoV-2, including the Omicron variant, were already present after the second vaccine dose and were not significantly affected by oncological treatments.

CONCLUSIONS

Cancer patients, particularly those receiving immunosuppressive oncological treatments, should require booster doses and adapted COVID-19 vaccines for new SARS-CoV-2 variants like Omicron. Future studies should evaluate the durability of the immune response and the efficacy of individualized regimens.

Phenotype clustering of hospitalized high-risk patients with COVID-19 - a machine learning approach within the multicentre, multinational PCHF-COVICAV registry

IMTRODUCTION

The high-risk population of patients with cardiovascular (CV) disease or risk factors (RF) suffering from COVID-19 is heterogeneous. Several predictors for impaired prognosis have been identified. However, with machine learning (ML) approaches, certain phenotypes may be confined to classify the affected population and to predict outcome. This study aimed to phenotype patients using unsupervised ML technique within the International Postgraduate Course Heart Failure Registry for patients hospitalized with COVID-19 and Cardiovascular disease and/or RF (PCHF-COVICAV).

MATERIAL AND METHODS

Patients from the eight centres with follow-up data available from the PCHF-COVICAV registry were included in this ML analysis (K-medoids algorithm).

RESULTS

Out of 617 patients included into the prospective part of the registry, 458 [median age: 76 (IQR:65-84) years, 55% male] were analyzed and 46 baseline variables, including demographics, clinical status, comorbidities and biochemical characteristics were incorporated into the ML. Three clusters were extracted by this ML method. Cluster 1 (n = 181) represents mainly women with the least number of overall comorbidities and cardiovascular RF. Cluster 2 (n = 227) is characterized mainly by men with non-CV conditions and less severe symptoms of infection. Cluster 3 (n=50) mainly represents men with the highest prevalence of cardiac comorbidities and RF, more extensive inflammation and organ dysfunction with the highest 6-month all-cause mortality risk.

CONCLUSIONS

The ML process has identified three important clinical clusters from hospitalized COVID-19 CV and/or RF patients. The cluster of males with severe CV disease, particularly HF, and multiple RF presenting with increased inflammation had a particularly poor outcome.

Safety and efficacy of Paxlovid in the treatment of adults with mild to moderate COVID-19 during the omicron epidemic: a multicentre study from China

BACKGROUND

Since December 2022, the Omicron variant has led to a widespread pandemic in China. The study was to explore the safety and effectiveness of Paxlovid for the treatment of coronavirus disease 2019 (COVID-19).

RESEARCH DESIGN AND METHODS

We included patients at risk of developing severe COVID-19, all of whom exhibited mild to moderate symptoms and were admitted to three hospital centers. Patients were divided into two groups: one received Paxlovid alongside standard care, while the other was given only standard care. We compared clinical characteristics, hospital stay duration, and clinical outcomes between two groups. Multi-factor analysis determined the independent risk factors influencing the duration of hospitalization and disease progression.

RESULTS

In the study, those treated with Paxlovid shorter hospital stays than those in the control group (p < 0.001). Multivariate analysis indicated that the absence of Paxlovid treatment was a distinct risk factor for hospitalizations lasting over 7 days (OR: 4.983, 95% CI: 3.828-6.486, p < 0.001) and 14 days (OR: 2.940, 95% CI: 2.402-3.597, p < 0.001).

CONCLUSION

Amid the Omicron outbreak, Paxlovid has proven to be a safe and effective treatment for reducing hospitalization durations for patients with mild to moderate COVID-19.

The outcome and related risk factors of unvaccinated patients with end-stage kidney disease during the Omicron pandemic: a multicentre retrospective study

OBJECTIVES

The study aims to identify the outcome and the related factors of unvaccinated patients with end-stage kidney disease during the Omicron pandemic.

DESIGN

A multicentre retrospective study of patients with end-stage kidney disease undergone maintenance haemodialysis (HD) in China.

SETTING

6 HD centres in China.

PARTICIPANTS

A total of 654 HD patients who tested positive for SARS-CoV-2 were ultimately included in the study.

OUTCOME MEASURES

The primary outcomes of interest were adverse outcomes, including hospitalisation due to COVID-19 and all-cause mortality.

RESULTS

The average age of the patients was 57 years, with 33.6% of them being over 65 years. Among the patients, 57.5% were male. During the follow-up period, 158 patients (24.2%) experienced adverse outcomes, and 93 patients (14.2%) died. The majority of patients (88/158) developed adverse outcomes within 30 days, and most deaths (77/93) occurred within 1 month. An advanced multivariable Cox regression analysis identified that adverse outcomes were associated with various factors while all-cause mortality was related to advanced age, male gender, high levels of C reactive protein (CRP) and low levels of prealbumin. The Kaplan-Meier curves demonstrated significantly higher all-cause mortality rates in the older, male, high CRP and low prealbumin subgroups.

CONCLUSIONS

Among unvaccinated HD patients with confirmed Omicron infections, various factors were found to be linked to adverse outcomes. Notably, age, sex, CRP and prealbumin had a substantial impact on the risk of all-cause mortality.

De novo design of potential peptide analogs against the main protease of Omicron variant using in silico studies

SARS-CoV-2 and its variants are crossing the immunity barrier induced through vaccination. Recent Omicron sub-variants are highly transmissible and have a low mortality rate. Despite the low severity of Omicron variants, these new variants are known to cause acute post-infectious syndromes. Nowadays, novel strategies to develop new potential inhibitors for SARS-CoV-2 and other Omicron variants have gained prominence. For viral replication and survival the main protease of SARS-CoV-2 plays a vital role. Peptide-like inhibitors that mimic the substrate peptide have already proved to be effective in inhibiting the Mpro of SARS-CoV-2 variants. Our systematic canonical amino acid point mutation analysis on the native peptide has revealed various ways to improve the native peptide of the main protease. Multi mutation analysis has led us to identify and design potent peptide-analog inhibitors that act against the Mpro of the Omicron sub-variants. Our in-depth analysis of all-atom molecular dynamics studies has paved the way to characterize the atomistic behavior of Mpro in Omicron variants. Our goal is to develop potent peptide-analogs that could be therapeutically effective against Omicron and its sub-variants.

Hyperglycemia facilitates EV71 replication: Insights into miR-206-mediated regulation of G3BP2 promoting EV71 IRES activity

Background: Neurotropic virus infections actively manipulate host cell metabolism to enhance virus neurovirulence. Although hyperglycemia is common during severe infections, its specific role remains unclear. This study investigates the impact of hyperglycemia on the neurovirulence of enterovirus 71 (EV71), a neurovirulent virus relying on internal ribosome entry site (IRES)-mediated translation for replication. Methods: Utilizing hSCARB2-transgenic mice, we explore the effects of hyperglycemia in EV71 infection and elucidate the underlying mechanisms. Results: Remarkably, administering insulin alone to reduce hyperglycemia in hSCARB2-transgenic mice results in a decrease in brainstem encephalitis and viral load. Conversely, induced hyperglycemia exacerbates neuropathogenesis, highlighting the pivotal role of hyperglycemia in neurovirulence. Notably, miR-206 emerges as a crucial mediator induced by viral infection, with its expression further heightened by hyperglycemia and concurrently repressed by insulin. The use of antagomiR-206 effectively mitigates EV71-induced brainstem encephalitis and reduces viral load. Mechanistically, miR-206 facilitates IRES-driven virus replication by repressing the stress granule protein G3BP2. Conclusions: Novel therapeutic approaches against severe EV71 infections involve managing hyperglycemia and targeting the miR-206-stress granule pathway to modulate virus IRES activity.

Short-term side effects of BNT162b2 vaccine in primary care settings in Qatar: a retrospective study

Background

Despite the established effectiveness of the BNT162b2 Vaccine, the novel technology demands careful safety monitoring. While global studies have explored its safety, local data remains limited and exhibits some variability. This study investigated short-term side effects among BNT162b2 vaccinated individuals in Qatar.

Methods

A retrospective analysis was conducted using data extracted from the electronic health records of individuals aged 18 or older across 8 primary health centers who received either the first or second dose of the BNT162b2 vaccine during the period from December 23, 2020, to April 24, 2021. The proportions of individuals experiencing short-term side effects after each dose were calculated. Logistic regression and log binomial regression analyses were used to explore associations with the side effects.

Results

Among 7,764 participants, 5,489 received the first dose and 2,275 the second, with similar demographics between the groups. After the first dose, 5.5% reported at least one local side effect, compared to 3.9% after the second, with a 1.4 times higher incidence after the first dose (RR 1.4, 95% CI 1.14-1.75) compared to the second. Systemic side effects after the second dose were 2.6 times more common than after the first (RR 2.6, 95% CI 2.15-3.14). Gender, nationality, history of prior COVID-19 infection, and obesity were significantly associated with side effects after the first dose, while age, gender, and nationality, were significant factors after the second dose.

Conclusion

The rates of side effects following the BNT162b2 vaccine in Qatar were relatively low, with age, gender, nationality, previous infection, and obesity identified as significant predictors. These results emphasize the need for tailored vaccination strategies and contributes valuable insights for evidence-based decision-making in ongoing and future vaccination campaigns.

The Outcomes of Patients with Omicron Variant Infection who Undergo Elective Surgery: A Propensity-score-matched Case-control Study

Aim: To investigate whether it is safe for patients with Omicron variant infection to undergo surgery during perioperative period. Methods: A total of 3,661 surgical patients were enrolled: 3,081 who were not infected with the Omicron variant and 580 who were infected with the Omicron variant. We conducted propensity score matching (PSM) with a ratio of 1:4 and a caliper value of 0.1 to match the infected and uninfected groups based on 13 variables. After PSM, we further divided the Infected group (560 cases) by the number of days between the preoperative Omicron variant infection and surgery: 0-7, 8-14, 15-30, and >30 days. Multivariate logistic regression analysis was subsequently conducted on the categorical variables and continuous variables with a P value below 0.05, thereby comparing the infected group (0-7, 8-14, 15-30, >30 days) and the uninfected group for perioperative complications. Results: Multivariate logistic regression analysis revealed that, compared to the uninfected group, among the four subgroups of the infected patients (0-7, 8-14, 15-30, >30 days), only renal insufficiency in the 8-14 days subgroup (OR: 0.09, 95%CI 0.01-0.74, P = 0.025) and anemia in the > 30 days subgroup (OR 0.6, 95%CI 0.4-0.9, P < 0.017) showed significant difference. However, there was no statistically significant difference in the incidence rate of blood transfusion, postoperative intensive care unit transfer, lung infection/pneumonia, pleural effusion, atelectasis, respiratory failure, sepsis, postoperative deep vein thrombosis, hypoalbuminemia, urinary tract infections, and medical expenses. Conclusion: Omicron infection does not significantly increase the risk of perioperative major complications. The Omicron infection may not be a sufficient risk factor to postpone elective surgery.

Ferritin-binding and ubiquitination-modified mRNA vaccines induce potent immune responses and protective efficacy against SARS-CoV-2

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) incessantly engenders mutating strains via immune escape mechanisms, substantially escalating the risk of severe acute respiratory syndrome. In this context, the urgent development of innovative and efficacious mRNA vaccines is imperative. In our study, we synthesized six unique mRNA vaccine formulations: the Receptor Binding Domain (RBD) monomer vaccine, RBD dimer (2RBD) vaccine, RBD-Ferritin (RBD-Fe) vaccine, ubiquitin-modified wild-type Nucleocapsid gene (WT-N) vaccine, rearranged Nucleocapsid gene (Re-N) vaccine, and an epitope-based (COVID-19 epitope) vaccine, all encapsulated within the lipid nanoparticle SM102. Immunization studies conducted on C57BL/6 mice with these vaccines revealed that the RBD monomer, RBD dimer (2RBD), and RBD-Fe vaccines elicited robust titers of specific antibodies, including neutralizing antibodies. In contrast, the wild-type N gene (WT-N), rearrange N gene (Re-N), and COVID-19 epitope vaccines predominantly induced potent cellular immune responses. Protective efficacy assays in golden hamsters demonstrated that vaccinated cohorts showed significant reduction in lung pathology, markedly lower viral loads in the lungs, nasal turbinates, and trachea, and substantially reduced transcriptional and expression levels of pro-inflammatory cytokines. Overall, our vaccine candidates pave the way for novel strategies in vaccine development against various infectious agents and establish a critical foundation for the formulation of advanced vaccines targeting emerging pathogens.

Dynamic Evolution of SARS-CoV-2 in West Sumatra: Analyzing S Gene Mutations Across Variants and Their Impact on Public Health and Vaccine Strategies

<b>Background and Objective:</b> The global SARS-CoV-2 pandemic highlights the importance of tracking virus evolution through genomic surveillance, especially concerning mutations in the SARS-CoV-2 spike protein, crucial for vaccine development. Despite global concern over variants, regions like West Sumatra, Indonesia, lack thorough genomic analysis, prompting this study to analyze S gene mutations across three pandemic waves in West Sumatra. <b>Materials and Methods:</b> Next-generation sequencing was conducted through the Illumina MiSeq instrument to leverage a dataset of 352 anonymized samples collected between March, 2020 and November, 2022 and rigorous analysis of S gene mutation using CLC Genomics Workbench^® 21 version 21.0.3 were employed. Statistical analyses assessed mutation prevalence over time, exploring associations with clinical outcomes. <b>Results:</b> The findings revealed significant variability in mutation profiles across different variants. Notably, the Omicron variant (21K) exhibited a high mutation rate, suggesting enhanced immune evasion capabilities. Comparative analysis highlighted evolutionary trends, from early variants with fewer mutations to highly adapted forms like Delta (21I) and Omicron. The dynamic nature of SARS-CoV-2 evolution underscores the importance of continuous surveillance, rapid public health response and vaccine adaptation. <b>Conclusion:</b> This study contributes valuable insights into the virus's evolving landscape, emphasizing the need for ongoing research, global collaboration and adaptable vaccine strategies to manage the evolving threat of COVID-19 effectively.

Antiplatelet therapy prior to COVID-19 infection impacts on patients mortality: a propensity score-matched cohort study

One of the major pathomechanisms of COVID-19 is the interplay of hyperinflammation and disruptions in coagulation processes, involving thrombocytes. Antiplatelet therapy (AP) by anti-inflammatory effect and inhibition of platelet aggregation may affect these pathways. The aim of this study was to investigate if AP has an impact on the in-hospital course and medium-term outcomes in hospitalized COVID-19 patients. The study population (2170 COVID-19 patients: mean ± SD age 60 ± 19 years old, 50% male) was divided into a group of 274 patients receiving any AP prior to COVID-19 infection (AP group), and after propensity score matching, a group of 274 patients without previous AP (non-AP group). Patients from the AP group were less frequently hospitalized in the intensive care unit: 9% vs. 15%, 0.55 (0.33-0.94), developed less often shock: 9% vs. 15%, 0.56 (0.33-0.96), and required less aggressive forms of therapy. The AP group had more coronary revascularizations: 5% vs. 1%, 3.48 (2.19-5.55) and strokes/TIA: 5% vs. 1%, 3.63 (1.18-11.2). The bleeding rate was comparable: 7% vs. 7%, 1.06 (0.54-2.06). The patients from the AP group had lower 3-month mortality: 31% vs. 39%, 0.69 (0.51-0.93) and didn't differ significantly in 6-month mortality: 34% vs. 41%, 0.79 (0.60-1.04). When analyzing the subgroup with a history of myocardial infarction and/or coronary revascularization and/or previous stroke/transient ischemic attack and/or peripheral artery disease, AP had a beneficial effect on both 3-month: 37% vs. 56%, 0.58 (0.40-0.86) and 6-month mortality: 42% vs. 57%, 0.63 (0.44-0.92). Moreover, the favourable effect was highly noticeable in this subgroup where acetylsalicylic acid was continued during hospitalization with reduction of in-hospital: 19% vs. 43%, 0.31 (0.15-0.67), 3-month: 30% vs. 54%, 044 (0.26-0.75) and 6-month mortality: 33% vs. 54%, 0.49 (0.29-0.82) when confronted with the subgroup who had acetylsalicylic acid suspension during hospitalization. The AP may have a beneficial impact on hospital course and mortality in COVID-19 and shouldn't be discontinued, especially in high-risk patients.

Exploring the reported adverse effects of COVID-19 vaccines among vaccinated Arab populations: a multi-national survey study

The coronavirus disease 2019 (COVID-19) pandemic has been a major challenge worldwide for the past years with high morbidity and mortality rates. While vaccination was the cornerstone to control the pandemic and disease spread, concerns regarding safety and adverse events (AEs) have been raised lately. A cross-sectional study was conducted between January 1st and January 22nd, 2022, in six Arabic countries namely Saudi Arabia, Egypt, Syria, Libya, Iraq, and Algeria. We utilized a self-administered questionnaire validated in Arabic which encompassed two main parts. The first was regarding sociodemographic data while the second was about COVID-19 vaccination history, types, doses, and experienced AEs. A multistage sampling was employed in each country, involving the random selection of three governorates from each country, followed by the selection of one urban area and one rural area from each governorate. We included the responses of 1564 participants. The most common AEs after the first and second doses were local AEs (67.9% and 46.6%, respectively) followed by bone pain and myalgia (37.6% and 31.8%, respectively). After the third dose, the most common AEs were local AEs (45.7%) and fever (32.4%). Johnson and Johnson, Sputnik Light, and Moderna vaccines showed the highest frequency of AEs. Factors associated with AEs after the first dose included an increase in age (aOR of 61-75 years compared to the 12-18 years group: 2.60, 95% CI: 1.59-4.25, p = 0.001) and male gender (OR: 0.72, 95% CI: 0.63-0.82, p < 0.001). The cumulative post-vaccination COVID-19 disease was reported with Sinovac (16.1%), Sinopharm (15.8%), and Johnson and Johnson (14.9) vaccines. History of pre-vaccination SARS-CoV-2 infection significantly increases the risk of post-vaccination COVID-19 after the first, second, and booster doses (OR: 3.09, CI: 1.9-5.07, p < 0.0001; OR: 2.56, CI: 1.89-3.47, p < 0.0001; and OR: 2.94, CI: 1.6-5.39, p = 0.0005 respectively). In conclusion, AEs were common among our participants, especially local AEs. Further extensive studies are needed to generate more generalizable data regarding the safety of different vaccines.

Enhancing Immunological Memory: Unveiling Booster Doses to Bolster Vaccine Efficacy Against Evolving SARS-CoV-2 Mutant Variants

A growing number of re-infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in previously immunized individuals has sparked discussions about the potential need for a booster vaccine dosage to counteract declining antibody levels and new strains. The protective immunity produced by vaccinations, and past illnesses relies on immunological memory. CD4 + T cells, CD8 + T cells, B cells, and long-lasting antibody responses are all components of the adaptive immune system that can generate and maintain this immunological memory. Since novel mutant variants have emerged one after the other, the world has been hit by repeated waves. Various vaccine formulations against SARS-CoV-2 have been administered across the globe. Thus, estimating the efficacy of those vaccines against gradually developed mutant stains is the essential parameter regarding the fate of those vaccine formulations and the necessity of booster doses and their frequency. In this review, focus has also been given to how vaccination stacks up against moderate and severe acute infections in terms of the longevity of the immune cells, neutralizing antibody responses, etc. However, hybrid immunity shows a greater accuracy of re-infection of variants of concern (VOCs) of SARS-CoV-2 than infection and immunization. The review conveys knowledge of detailed information about several marketed vaccines and the status of their efficacy against specific mutant strains of SARS-CoV-2. Furthermore, this review discusses the status of immunological memory after infection, mixed infection, and vaccination.

Profiles of Cough and Associated Risk Factors in Nonhospitalized Individuals With SARS-CoV-2 Omicron Variant Infection: Cross-Sectional Online Survey in China

BACKGROUND

Cough is a common symptom during and after COVID-19 infection; however, few studies have described the cough profiles of COVID-19.

OBJECTIVE

The aim of this study was to investigate the prevalence, severity, and associated risk factors of severe and persistent cough in individuals with COVID-19 during the latest wave of the Omicron variant in China.

METHODS

In this nationwide cross-sectional study, we collected information of the characteristics of cough from individuals with infection of the SARS-CoV-2 Omicron variant using an online questionnaire sent between December 31, 2022, and January 11, 2023.

RESULTS

There were 11,718 (n=7978, 68.1% female) nonhospitalized responders, with a median age of 37 (IQR 30-47) years who responded at a median of 16 (IQR 12-20) days from infection onset to the time of the survey. Cough was the most common symptom, occurring in 91.7% of participants, followed by fever, fatigue, and nasal congestion (68.8%-87.4%). The median cough visual analog scale (VAS) score was 70 (IQR 50-80) mm. Being female (odds ratio [OR] 1.31, 95% CI 1.20-1.43), having a COVID-19 vaccination history (OR 1.71, 95% CI 1.37-2.12), current smoking (OR 0.48, 95% CI 0.41-0.58), chronic cough (OR 2.04, 95% CI 1.69-2.45), coronary heart disease (OR 1.71, 95% CI 1.17-2.52), asthma (OR 1.22, 95% CI 1.02-1.46), and gastroesophageal reflux disease (GERD) (OR 1.21, 95% CI 1.01-1.45) were independent factors for severe cough (VAS>70, 37.4%). Among all respondents, 35.0% indicated having a productive cough, which was associated with risk factors of being female (OR 1.44, 95% CI 1.31-1.57), having asthma (OR 1.84, 95% CI 1.52-2.22), chronic cough (OR 1.44, 95% CI 1.19-1.74), and GERD (OR 1.22, 95% CI 1.01-1.47). Persistent cough (>3 weeks) occurred in 13.0% of individuals, which was associated with the risk factors of having diabetes (OR 2.24, 95% CI 1.30-3.85), asthma (OR 1.70, 95% CI 1.11-2.62), and chronic cough (OR 1.97, 95% CI 1.32-2.94).

CONCLUSIONS

Cough is the most common symptom in nonhospitalized individuals with Omicron SARS-CoV-2 variant infection. Being female, having asthma, chronic cough, GERD, coronary heart disease, diabetes, and a COVID-19 vaccination history emerged as independent factors associated with severe cough, productive cough, and persistent cough.

Targeting the receptor binding domain and heparan sulfate binding for antiviral drug development against SARS-CoV-2 variants

The emergence of SARS-CoV-2 variants diminished the efficacy of current antiviral drugs and vaccines. Hence, identifying highly conserved sequences and potentially druggable pockets for drug development was a promising strategy against SARS-CoV-2 variants. In viral infection, the receptor-binding domain (RBD) proteins are essential in binding to the host receptor. Others, Heparan sulfate (HS), widely distributed on the surface of host cells, is thought to play a central role in the viral infection cycle of SARS-CoV-2. Therefore, it might be a reasonable strategy for antiviral drug design to interfere with the RBD in the HS binding site. In this study, we used computational approaches to analyze multiple sequences of coronaviruses and reveal important information about the binding of HS to RBD in the SARS-CoV-2 spike protein. Our results showed that the potential hot-spots, including R454 and E471, in RBD, exhibited strong interactions in the HS-RBD binding region. Therefore, we screened different compounds in the natural product database towards these hot-spots to find potential antiviral candidates using LibDock, Autodock vina and furthermore applying the MD simulation in AMBER20. The results showed three potential natural compounds, including Acetoside (ACE), Hyperoside (HYP), and Isoquercitrin (ISO), had a strong affinity to the RBD. Our results demonstrate a feasible approach to identify potential antiviral agents by evaluating the binding interaction between viral glycoproteins and host receptors. The present study provided the applications of the structure-based computational approach for designing and developing of new antiviral drugs against SARS-CoV-2 variants.

Self-assembling peptides: Perspectives regarding biotechnological applications and vaccine development

Self-assembly involves a set of molecules spontaneously interacting in a highly coordinated and dynamic manner to form a specific supramolecular structure having new and clearly defined properties. Many examples of this occur in nature and many more came from research laboratories, with their number increasing every day via ongoing research concerning complex biomolecules and the possibility of harnessing it when developing new applications. As a phenomenon, self-assembly has been described on very different types of molecules (biomolecules including), so this review focuses on what is known about peptide self-assembly, its origins, the forces behind it, how the properties of the resulting material can be tuned in relation to experimental considerations, some biotechnological applications (in which the main protagonists are peptide sequences capable of self-assembly) and what is yet to be tuned regarding their research and development.

COVID-19 cases, vaccination, and SARS-CoV-2 in wastewater: insights from a Brazilian municipality

Vaccines combatting COVID-19 demonstrate the ability to protect against disease and hospitalization, and reduce the likelihood of death caused by SARS-CoV-2. In addition, monitoring viral loads in sewage emerges as another crucial strategy in the epidemiological context, enabling early and collective detection of outbreaks. The study aimed to monitor the viral concentration of SARS-CoV-2 in untreated sewage in a Brazilian municipality. Also, it attempted to correlate these measurements with the number of clinical cases and deaths resulting from COVID-19 between July 2021 and July 2022. SARS-CoV-2 viral RNA was quantified by RT-qPCR. Pearson's correlation was performed to analyze the variables' relationship using the number of cases, deaths, vaccinated individuals, and viral concentration of SARS-CoV-2. The results revealed a significant negative correlation (p < 0.05) between the number of vaccinated individuals and the viral concentration of SARS-CoV-2, suggesting that after vaccination, the RNA viral load concentration was reduced in the sample population by the circulating concentration of wastewater. Consequently, wastewater monitoring, in addition to functioning as an early warning system for the circulation of SARS-CoV-2 and other pathogens, can offer a novel perspective that enhances decision-making, strengthens vaccination campaigns, and contributes to authorities establishing systematic networks for monitoring SARS-CoV-2.

Protein subunit vaccines: Promising frontiers against COVID-19

The emergence of COVID-19 has posed an unprecedented global health crisis, challenging the healthcare systems worldwide. Amidst the rapid development of several vaccine formulations, protein subunit vaccines have emerged as a promising approach. This article provides an in-depth evaluation of the role of protein subunit vaccines in the management of COVID-19. Leveraging viral protein fragments, particularly the spike protein from SARS-CoV-2, these vaccines elicit a targeted immune response without the risk of inducing disease. Notably, the robust safety profile of protein subunit vaccines makes them a compelling candidate in the management of COVID-19. Various innovative approaches, including reverse vaccinology, virus like particles, and recombinant modifications are incorporated to develop protein subunit vaccines. In addition, the utilization of advanced manufacturing techniques facilitates large-scale production, ensuring widespread distribution. Despite these advancements, challenges persist, such as the requirement for cold-chain storage and the necessity for booster doses. This article evaluates the formulation and applications of protein subunit vaccines, providing a comprehensive overview of their clinical development and approvals in the context of COVID-19. By addressing the current status and challenges, this review aims to contribute to the ongoing discourse on optimizing protein subunit vaccines for effective pandemic control.

Antivirals for Broader Coverage against Human Coronaviruses

Coronaviruses (CoVs) are enveloped positive-sense single-stranded RNA viruses with a genome that is 27-31 kbases in length. Critical genes include the spike (S), envelope (E), membrane (M), nucleocapsid (N) and nine accessory open reading frames encoding for non-structural proteins (NSPs) that have multiple roles in the replication cycle and immune evasion (1). There are seven known human CoVs that most likely appeared after zoonotic transfer, the most recent being SARS-CoV-2, responsible for the COVID-19 pandemic. Antivirals that have been approved by the FDA for use against COVID-19 such as Paxlovid can target and successfully inhibit the main protease (MPro) activity of multiple human CoVs; however, alternative proteomes encoded by CoV genomes have a closer genetic similarity to each other, suggesting that antivirals could be developed now that target future CoVs. New zoonotic introductions of CoVs to humans are inevitable and unpredictable. Therefore, new antivirals are required to control not only the next human CoV outbreak but also the four common human CoVs (229E, OC43, NL63, HKU1) that circulate frequently and to contain sporadic outbreaks of the severe human CoVs (SARS-CoV, MERS and SARS-CoV-2). The current study found that emerging antiviral drugs, such as Paxlovid, could target other CoVs, but only SARS-CoV-2 is known to be targeted in vivo. Other drugs which have the potential to target other human CoVs are still within clinical trials and are not yet available for public use. Monoclonal antibody (mAb) treatment and vaccines for SARS-CoV-2 can reduce mortality and hospitalisation rates; however, they target the Spike protein whose sequence mutates frequently and drifts. Spike is also not applicable for targeting other HCoVs as these are not well-conserved sequences among human CoVs. Thus, there is a need for readily available treatments globally that target all seven human CoVs and improve the preparedness for inevitable future outbreaks. Here, we discuss antiviral research, contributing to the control of common and severe CoV replication and transmission, including the current SARS-CoV-2 outbreak. The aim was to identify common features of CoVs for antivirals, biologics and vaccines that could reduce the scientific, political, economic and public health strain caused by CoV outbreaks now and in the future.

Characteristics, outcome, duration of hospitalization, and cycle threshold of patients with COVID-19 referred to four hospitals in Babol City: a multicenter retrospective observational study on the fourth, fifth, and sixth waves

BACKGROUND

The aim of the present study was to compare the epidemiological patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) infections, hospitalizations, deaths, and duration of hospitalization during the fourth, fifth and sixth epidemic waves of coronavirus disease 2019 (COVID-19) in Iran.

METHODS

A multicenter retrospective observational study was conducted on hospitalized patients in four hospitals in the Babol district of northern Iran. The study periods were during the fourth, fifth, and sixth waves of the epidemic in Iran, (March 2021 to March 2022). A total of 13,312 patients with suspected COVID-19 were included. Patient demographics, medical history, length of hospital stay, and clinical outcomes were obtained from the hospital information system. Data on the cycle threshold (Ct) and SARS-CoV2 variant were collected for SARS-CoV2-positive cases.

RESULTS

The highest number of hospitalized patients was reported during the fifth (Delta) wave (5231; 39.3%), while the lowest number of hospitalized patients was reported during the sixth (Omicron) wave (2143; 16.1%). In total, 6459 (48.5%) out of 13,312 hospitalized patients with suspected COVID-19 had a positive rRT-PCR result. The fifth (Delta) wave had the highest number of SARS-CoV2 rRT-PCR-positive hospitalized patients (3573, 55.3%), while the sixth (Omicron) wave had the lowest number (835, 12.9%). Moreover, 238 (3.7%) patients with laboratory-confirmed COVID-19 died. The hospital mortality rate was 6.8% in the fourth (Alpha) wave, which reduced to 2.7 and 3.5% in the fifth (Delta) and sixth (Omicron) waves, respectively (p < 0.001).

CONCLUSIONS

This is the most comprehensive study evaluating the epidemiologic characteristics of laboratory-confirmed SARS-CoV2 cases in Iran during the Alpha, Delta, and Omicron waves. The highest number of SARS-CoV2-positive hospitalized patients was in the fifth wave of COVID-19 (dominance of the Delta variant), while the sixth wave (dominance of the Omicron variant) had the lowest number. Comorbidities were similar, and cardiovascular disease, diabetes, kidney disease, and hypertension were the main risk factors in all waves.

Effectiveness and safety of azvudine in older adults with mild and moderate COVID-19: a retrospective observational study

BACKGROUND

Azvudine has clinical benefits and acceptable safety against COVID-19, including in patients with comorbidities, but there is a lack of available data for its use in older adult patients. This study explored the effectiveness and safety of azvudine in older adults with mild or moderate COVID-19.

METHODS

This retrospective cohort study included patients aged ≥80 diagnosed with COVID-19 at the Central Hospital of Shaoyang between October and November 2022. According to the therapies they received, the eligible patients were divided into the azvudine, nirmatrelvir/ritonavir, and standard-of-care (SOC) groups. The outcomes were the proportion of patients progressing to severe COVID-19, time to nucleic acid negative conversion (NANC), and the 5-, 7-, 10-, and 14-day NANC rates from admission.

RESULTS

The study included 55 patients treated with azvudine (n = 14), nirmatrelvir/ritonavir (n = 18), and SOC (n = 23). The median time from symptom onset to NANC of the azvudine, nirmatrelvir/ritonavir, and SOC groups was 14 (range, 6-25), 15 (range, 11-24), and 19 (range, 18-23) days, respectively. The median time from treatment initiation to NANC of the azvudine and nirmatrelvir/ritonavir groups was 8 (range, 4-20) and 9 (range, 5-16) days, respectively. The median length of hospital stay in the three groups was 10.5 (range, 5-23), 13.5 (range, 10-21), and 17 (range, 10-23) days, respectively. No treatment-related adverse events or serious adverse events were reported.

CONCLUSION

Azvudine showed satisfactory effectiveness and acceptable safety in older adults with mild or moderate COVID-19. Therefore, azvudine could be a treatment option for this special patient population.

Ethanol Inhalation as a Method to Denature the Spike Protein of SARS-CoV-2

The SARS-CoV-2 virus caused the 2019 COVID pandemic by infecting almost eight hundred million people worldwide. Because it was a new viral infection, there were no vaccines or small molecule medications that could prevent or treat the disease.  This chapter provides some details for an obscure treatment for COVID-19, that has decades of anti-viral activity data both in vitro and in vivo in the literature. The medicinal molecules are compared to other small molecules that were identified as possible medications for COVID-19.  We developed a computational method that ranks small molecules and their ability to penetrate mucus in the lungs of a COVID-19 patient. Our focus is ethanol as a COVID-19 treatment. The results discussed here are based on Lipinski Rules and QSAR computational methods as well as in vitro and in vivo data. These parameters indicate that ethanol should be a strong candidate for future evaluations.

Inhibitory effects of SARS-CoV-2 spike protein and BNT162b2 vaccine on erythropoietin-induced globin gene expression in erythroid precursor cells from patients with β-thalassemia

During the recent coronavirus disease 2019 (COVID-19) pandemic several patients with β-thalassemia have been infected by severe acute respiratory syndrome coronavirus (SARS-CoV-2), and most patients were vaccinated against SARS-CoV-2. Recent studies demonstrate an impact of SARS-CoV-2 infection on the hematopoietic system. The main objective of this study was to verify the effects of exposure of erythroid precursor cells (ErPCs) from patients with β-thalassemia to SARS-CoV-2 spike protein (S-protein) and the BNT162b2 vaccine. Erythropoietin (EPO)-cultured ErPCs have been either untreated or treated with S-protein or BNT162b2 vaccine. The employed ErPCs were from a β-thalassemia cellular Biobank developed before the COVID-19 pandemic. The genotypes were β+-IVSI-110/β+-IVSI-110 (one patient),  β039/β+-IVSI-110 (3 patients), and β039/ β039 (2 patients). After treatment with S-protein or BNT162b2 for 5 days, lysates were analyzed by high performance liquid chromatography (HPLC), for hemoglobin production, and isolated RNA was assayed by RT-qPCR, for detection of globin gene expression. The main conclusions of the results obtained are that SARS-CoV-2 S-protein and BNT162b2 vaccine (a) inhibit fetal hemoglobin (HbF) production by β-thalassemic ErPCs and (b) inhibit γ-globin mRNA accumulation. In addition, we have performed in silico studies suggesting a high affinity of S-protein to HbF. Remarkably, the binding interaction energy of fetal hemoglobin to S-protein was comparable with that of angiotensin-converting enzyme 2 (ACE2). Our results are consistent with the hypothesis of a relevant impact of SARS-CoV-2 infection and COVID-19 vaccination on the hematopoietic system.

Quantitative Synthesis of Factors Associated with COVID-19 Vaccine Acceptance and Vaccine Hesitancy in 185 Countries

Mass vaccination against COVID-19 is the best method to ensure herd immunity in order to curb the effect of the pandemic on the global economy. It is therefore important to assess the determinants of COVID-19 vaccine acceptance and hesitancy on a global scale. Factors were recorded from cross-sectional studies analyzed with t-Test, ANOVA, correlation, and meta-regression analyses and synthesized to identify global trends in order to inform policy. We registered the protocol (ID: CRD42022350418) and used standard Cochrane methods and PRISMA guidelines to collect and synthesize cross-sectional articles published between January 2020 and August 2023. A total of 67 articles with 576 studies from 185 countries involving 3081,766 participants were included in this synthesis. Global COVID-19 vaccine acceptance was 65.27% (95% CI; 62.72-67.84%), while global vaccine hesitancy stood at 32.1% (95% CI; 29.05-35.17%). One-Way ANOVA showed that there was no significant difference in the percentage Gross Domestic Product spent on vaccine procurement across the World Bank income levels (p < 0.187). There was a significant difference of vaccine acceptance (p < 0.001) and vaccine hesitancy (p < 0.005) across the different World Bank Income levels. World Bank income level had a strong influence on COVID-19 vaccine acceptance (p < 0.0004) and hesitancy (p < 0.003) but percentage Gross Domestic Product spent on vaccine procurement did not. There was no correlation between percentage Gross Domestic Product spent on vaccine procurement and COVID-19 vaccine acceptance (r = -0.11, p < 0.164) or vaccine hesitancy (r = -0.09, p < 0.234). Meta-regression analysis showed that living in an urban setting (OR = 4.83, 95% CI; 0.67-212.8), rural setting (OR = 2.53, 95% CI; 0.29-119.33), older (OR = 1.98, 95% CI; 0.99-4.07), higher education (OR = 1.76, 95% CI; 0.85-3.81), and being a low income earner (OR = 2.85, 95% CI; 0.45-30.63) increased the odds of high COVID-19 vaccine acceptance. Factors that increased the odds of high COVID-19 vaccine hesitancy were no influenza vaccine (OR = 33.06, 95% CI; 5.03-1395.01), mistrust for vaccines (OR = 3.91, 95% CI; 1.92-8.24), complacency (OR = 2.86, 95% CI; 1.02-8.83), pregnancy (OR = 2.3, 95% CI; 0.12-141.76), taking traditional herbs (OR = 2.15, 95% CI; 0.52-10.42), being female (OR = 1.53, 95% CI; 0.78-3.01), and safety concerns (OR = 1.29, 95% CI; 0.67-2.51). We proposed a number of recommendations to increase vaccine acceptance and ensure global herd immunity against COVID-19.

Demographics, clinical characteristics, and outcomes in hospitalized patients during six waves of COVID‑19 in Northern Iran: a large cohort study

Since the first report of coronavirus disease 2019 (COVID-19) in Iran, our country has experienced several waves of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Northern Iran was one of the most affected regions of the country by COVID-19. In the current study, the demographic and clinical characteristics and outcomes of hospitalized patients were determined over a 2-year period (during six waves of SARS-CoV-2). This is a large cohort study investigating hospitalized patients with suspected and probable, and confirmed SARS-CoV-2 infection in Babol district, northern Iran, during the two years of COVID-19. The study population included patients admitted to four hospitals affiliated with Babol University of Medical Sciences between March 7, 2020 (start of the first wave) and March 20, 2022 (end of the sixth wave). Epidemiological and demographic characteristics, real-time PCR, cycle thresholds, clinical data and outcomes of COVID-19 were analyzed in 24,287 hospitalized patients. A total of 24,287 hospitalized patients were included in the study: 13,250 (46.6%) patients were suspected of having COVID-19, 11037(45.4%) were confirmed COVID-19 cases. The mean age of confirmed COVID-19 patients was 54.5 ± 18.9 years and 5961 (54%) were female. The median length of hospitalization for COVID-19 survivors and non-survivors was 5 (interquartile range [IQR] 4-8) and 7 (IQR 3-15) days, respectively. Of the patients with confirmed COVID-19, 714 (6.5%) died during hospitalization. In addition, the mortality rate from the first to the sixth wave was 22.9%, 8.1%, 9.9%, 6.8%, 2.7% and 3.5% in confirmed COVID-19 patients. The patients in the fifth wave were significantly younger than the others (mean age and SD of 51.1 ± 17.4 versus 59.2 ± 16.9, 54.7 ± 19.9, 58.4 ± 17.9, 53.5 ± 16.8 and 58.5 ± 25.1 years; p<0.001). The highest in-hospital mortality rate was 22.9% (126/551) in the first wave and the lowest in the fifth wave was 2.7% (96/3573) of cases. In conclusion, in the present study, the in-hospital mortality rate was 6.5% and more than half of the deceased patients were ≥65 years old. Male gender, advanced age and comorbidities significantly increased the mortality rate. The patients in the fifth wave were significantly younger than those in the other waves, and the lowest mortality rate and intensive care unit admission were also observed in the fifth wave.

Modulating SARS-CoV-2 Spike Protein Reactivity through Moderate Electric Fields: A Pathway to Innovative Therapies

In the quest for effective COVID-19 treatments and vaccines, traditional biochemical methods have been paramount, yet the challenge of accommodating diverse viral mutants persists. Recent simulations propose an innovative physical strategy involving an external electric field applied to the SARS-CoV-2 spike protein, demonstrating a reduced viral binding potential. However, limited empirical knowledge exists regarding the characteristics of the spike protein after E-field treatment. Our study addresses this gap by employing diverse analytical techniques to elucidate the impact of low/moderate E-field intensity on the binding of the SARS-CoV-2 spike protein to the ACE2 receptor. Through comprehensive analysis, we unveil a substantial reduction in the spike protein binding capacity validated via enzyme-linked immunosorbent assay and quartz crystal microbalance experiments. Remarkably, the E-field exposure induces significant protein structure rearrangement, leading to an enhanced negative surface zeta potential confirmed by dynamic light scattering. Circular dichroism spectroscopy corroborates these structural changes, showing alterations in the secondary protein structures. This study provides insights into SARS-CoV-2 spike protein modification under an E-field pulse, potentially paving the way for nonbiochemical strategies to mitigate viral reactivity and opening avenues for innovative therapeutic and preventive approaches against COVID-19 and its evolving variants.

Adhatoda vasica and Tinospora cordifolia extracts ameliorate clinical and molecular markers in mild COVID-19 patients: a randomized open-label three-armed study

BACKGROUND

SARS-CoV-2 infections caused mild-to-moderate illness. However, a sizable portion of infected people experience a rapid progression of hyper-inflammatory and hypoxic respiratory illness that necessitates an effective and safer remedy to combat COVID-19.

METHODS

A total of 150 COVID-19-positive patients with no to mild symptoms, between the age groups 19-65 years were enrolled in this randomized, open-labeled three-armed clinical trial. Among them, 136 patients completed the study with RT-PCR negative reports. The patients received herbal drugs orally (Group A (Adhatoda vasica; AV; 500 mg; n = 50); Group B (Tinospora cordifolia; TC; 500 mg; n = 43), and Group C (AV + TC; 250 mg each; n = 43)) for 14 days. Clinical symptoms, vital parameters, and viral clearance were taken as primary outcomes, and biochemical, hematological parameters, cytokines, and biomarkers were evaluated at three time points as secondary outcomes.

RESULTS

We found that the mean viral clearance time was 13.92 days (95% confidence interval [CI] 12.85-14.99) in Group A, 13.44 days (95% confidence interval [CI] 12.14-14.74) in Group B, and 11.86 days (95% confidence interval [CI] 10.62-13.11) days in Group C. Over a period of 14 days, the mean temperature in Groups A, and B significantly decreased linearly. In Group A, during the trial period, eosinophils, and PT/INR increased significantly, while monocytes, SGOT, globulin, serum ferritin, and HIF-1α, a marker of hypoxia reduced significantly. On the other hand, in Group B hsCRP decreased at mid-treatment. Eosinophil levels increased in Group C during the treatment, while MCP-3 levels were significantly reduced.

CONCLUSIONS

All the patients of the three-armed interventions recovered from COVID-19 and none of them reported any adverse effects from the drugs. Group C patients (AV + TC) resulted in a quicker viral clearance as compared to the other two groups. We provide the first clinical report of AV herbal extract acting as a modifier of HIF-1α in COVID-19 patients along with a reduction in levels of ferritin, VEGF, and PT/INR as the markers of hypoxia, inflammation, and thrombosis highlighting the potential use in progression stages, whereas the TC group showed immunomodulatory effects. Trial registration Clinical Trials Database -India (ICMR-NIMS), CTRI/2020/09/028043. Registered 24th September 2020, https://www.ctri.nic.in/Clinicaltrials/pdf_generate.php?trialid=47443&EncHid=&modid=&compid=%27,%2747443det%27.

A review of SARS-CoV-2 variants and vaccines: Viral properties, mutations, vaccine efficacy, and safety

The severe acute respiratory syndrome coronavirus disease 2 instigated by coronavirus disease of 2019 (COVID-19) has delivered an unfathomable obstruction that has touched all sectors worldwide. Despite new vaccine technologies and mass administration of booster doses, the virus persists, and unknown the ending of the pandemic for new variants and sub-variants. Moreover, whether leaning on home medications or using plant extracts is sufficient often to combat the virus has generated tremendous interest in the scientific fraternity. Different databases including PubMed, Scopus, Web of Science, and Google Scholar used to find published articles linked with related topics. Currently, COVID-19 third and fourth shots of vaccines are progressively administered worldwide, where some countries trail others by a significant margin. Many proteins related to viral activity have changed, possibly boosting the virus infectivity and making antibodies ineffective. This study will reminisce the viral genome, associated pathways for viral protein functions, variants, and their mutations. The current, comprehensive review will also provide information on vaccine technologies developed by several biotech companies and the efficacy of their doses, costs including boosters on a mass level. As no vaccine is working to protect fully against all the variants, the new proactive vaccine research needs to be conducted based on all variants, their sub-lineage, and mutations.

LAMPPrimerBank, a manually curated database of experimentally validated loop-mediated isothermal amplification primers for detection of respiratory pathogens

PURPOSE AND METHODS

The emergence of coronavirus disease 2019 (COVID-19) has once again affirmed the significant threat of respiratory infections to global public health and the utmost importance of prompt diagnosis in managing and mitigating any pandemic. The nucleic acid amplification test (NAAT) is the primary detection method for most pathogens. Loop-mediated isothermal amplification (LAMP) is a rapid, simple, sensitive, and specific epitome of isothermal NAAT performed using a set of four to six primers. Primer design is a fundamental step in LAMP assays, with several complexities and experimental screening requirements. To address this challenge, an online database is presented here. Its workflow comprises three steps: literature aggregation, data curation, and database and website implementation.

RESULTS

LAMPPrimerBank ( https://lampprimerbank.mathematik.uni-marburg.de ) is a manually curated database dedicated to experimentally validated LAMP primers, their peculiarities of assays, and accompanying literature, with a primary emphasis on respiratory pathogens. LAMPPrimerBank, with its user-friendly web interface and an open application programming interface, enables the accelerated and facile exploration, comparison, and exportation of LAMP primer sequences and their respective information from the massively scattered literature. LAMPPrimerBank currently comprises LAMP primers for diagnosing viral, bacterial, and fungal respiratory pathogens. Additionally, to address the challenge of false-positive results generated by nonspecific amplifications, LAMPPrimerBank computationally predicted and visualized the sizes of LAMP products for recorded primer sets in the database.

CONCLUSION

LAMPPrimerBank, as a pioneering database in the rapidly expanding field of isothermal NAAT, endeavors to confront the two challenges of the LAMP: primer design and discrimination of false-positive results.

Vaccination reduces viral load and accelerates viral clearance in SARS-CoV-2 Delta variant-infected patients

OBJECTIVE

The purpose of this study was to investigate vaccine effectiveness in relieving symptoms in patients with the SARS-CoV-2 delta (B.1.617.2) variant.

METHODS

In this retrospective study, 31 patients did not receive any vaccine (non-vaccination, NV), 21 patients received 1-dose of inactivated vaccine (one-dose vaccination, OV), and 60 patients received at least 2-dose inactivated vaccine (two-dose vaccination, TV). The baseline data, clinical outcomes and vaccination information were collected and analyzed.

RESULTS

Patients in the OV group were younger than those in the other two groups (p = 0.001), but there was no significant difference in any of the other baseline data among the three groups. The TV group showed higher IgG antibody levels and cycle threshold values of SARS-CoV-2 than the NV and OV groups (p < 0.01), and time to peak viral load was shorter in the TV group (3.5 ± 2.3 d) than in the NV (4.8 ± 2.8 d) and OV groups (4.8 ± 2.9 d, p = 0.03). The patients in the TV group (18%) showed a higher recovery rate without drug therapy (p < 0.001). Viral clearance time and hospital stay were significantly shorter in the TV group than in the NV and OV groups (p < 0.01), and there were no significant differences in these parameters between the OV and NV groups, but IgG values were higher in the OV group (p = 0.025). No severe complications occurred in this study.

CONCLUSIONS

Our results suggest that 2-dose vaccination can reduce viral load and accelerate viral clearance in patients with the delta variant and enhance the protection afforded by IgG antibodies in vivo.Key MessagesIn this study, our results shows that two-dose vaccination can reduce viral loads and accelerate viral clearance, and two-dose vaccination enhance the protection of IgG antibodies in vivo; however, one-dose vaccination did not confer protective effectiveness.

Unraveling the association between vaccine attitude, vaccine conspiracies and self-reported side effects following COVID-19 vaccination among nurses and physicians in Jordan

BACKGROUND

The negative impact of vaccine conspiracies is linked with negative health behavior. The aim of the current study was to examine the association between attitudes toward booster COVID-19, influenza, and monkeypox (mpox) vaccinations with post-COVID-19 vaccine side effects, vaccine conspiracies, and attitude towards mandatory vaccination among nurses and physicians in Jordan.

METHODS

A structured closed-ended questionnaire was used to collect data on demographics, COVID-19 history, COVID-19 vaccine type and doses received, self-reported side effects post-COVID-19 vaccination, acceptance of booster COVID-19, seasonal influenza, and mpox vaccinations, attitudes towards mandatory vaccination, and beliefs in vaccine conspiracies.

RESULTS

The study sample comprised a total of 341 participants. Acceptance of yearly booster COVID-19 vaccination was expressed by 46.6% of the sample, while 73.3% accepted seasonal influenza vaccination, and only 37.0% accepted mpox vaccination. A higher frequency of self-reported side effects following the first COVID-19 vaccine dose was associated with embrace of vaccine conspiracies and vaccine type. For the second vaccine dose, a higher frequency of self-reported side effects was associated with the embrace of vaccine conspiracies, older age, and affiliation to private sector. In multinomial logistic regression analyses, the lower embrace of vaccine conspiracies was associated with lower odds of reporting side effects post-COVID-19 vaccination. The lower embrace of vaccine conspiracies and favorable attitude towards mandatory vaccination were associated with the willingness to get COVID-19, influenza, and mpox vaccinations.

CONCLUSION

The study findings highlighted the negative impact of embracing vaccine conspiracies on health-seeking behavior among nurses and physicians. The findings indicated that the willingness to get vaccinated was associated with lower endorsement of vaccine conspiracies. Additionally, the lower embrace of vaccine conspiracies was associated with a lower frequency of self-reported side effects following COVID-19 vaccination. These results emphasize the importance of addressing vaccine misinformation and promoting accurate information to ensure optimal vaccine uptake and public health outcomes.

Targeting the Spike: Repurposing Mithramycin and Dihydroergotamine to Block SARS-CoV-2 Infection

The urgency to find complementary therapies to current SARS-CoV-2 vaccines, whose effectiveness is preserved over time and not compromised by the emergence of new and emerging variants, has become a critical health challenge. We investigate the possibility of jamming the opening of the Receptor Binding Domain (RBD) of the spike protein of SARS-CoV-2 with small compounds. Through in silico screening, we identified two potential candidates that would lock the Receptor Binding Domain (RBD) in a closed configuration, preventing the virus from infecting the host cells. We show that two drugs already approved by the FDA, mithramycin and dihydroergotamine, can block infection using concentrations in the μM range in cell-based assays. Further STD-NMR experiments support dihydroergotamine's direct interaction with the spike protein. Overall, our results indicate that repurposing of these compounds might lead to potential clinical drug candidates for the treatment of SARS-CoV-2 infection.