The Impact of Evolving SARS-CoV-2 Mutations and Variants on COVID-19 Vaccines

New insights into gold nanoparticles in virology: A review of their applications in the prevention, detection, and treatment of viral infections

Viral infections have led to the deaths of millions worldwide and come with significant economic and social burdens. Emerging viral infections, as witnessed with coronavirus disease 2019 (COVID-19), can profoundly affect all aspects of human life, highlighting the imperative need to develop diagnostic, therapeutic, and effective control strategies in response. Numerous studies highlight the diverse applications of nanoparticles in diagnosing, controlling, preventing, and treating viral infections. Due to favorable and flexible physicochemical properties, small size, immunogenicity, biocompatibility, high surface-to-volume ratio, and the ability to combine with antiviral agents, gold nanoparticles (AuNPs) have shown great potential in the fight against viruses. The physical and chemical properties, the adjustability of characteristics based on the type of application, the ability to cross the blood-brain barrier, the ability to infiltrate cells such as phagocytic and dendritic cells, and compatibility for complexing with various compounds, among other features, transform AuNPs into a suitable tool for combating and addressing pathogenic viral agents through multiple applications. In recent years, AuNPs have been employed in various applications to fight viral infections. However, a comprehensive review article on the applications of AuNPs against viral infections has yet to be available. Given their versatility, AuNPs present an appealing option to address various gaps in combating viral infections. Hence, this review explores the attributes, antiviral properties, contributions to drug delivery, vaccine development, and diagnostic uses of AuNPs.

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.

Evaluation of Genomic Surveillance of SARS-CoV-2 Virus Isolates and Comparison of Mutational Spectrum of Variants in Bangladesh

The SARS-CoV-2-induced disease, COVID-19, remains a worldwide public health concern due to its high rate of transmission, even in vaccinated and previously infected people. In the endemic state, it continues to cause significant pathology. To elu- cidate the viral mutational changes and screen the emergence of new variants of concern, we conducted this study in Bangladesh. The viral RNA genomes extracted from 25 ran- domly collected samples of COVID-19-positive patients from March 2021 to February 2022 were sequenced using Illumina COVID Seq protocol and genomic data processing, as well as evaluations performed in DRAGEN COVID Lineage software. In this study, the percentage of Delta, Omicron, and Mauritius variants identified were 88%, 8%, and 4%, respectively. All of the 25 samples had 23,403 A>G (D614G, S gene), 3037 C>T (nsp3), and 14,408 C>T (nsp12) mutations, where 23,403 A>G was responsible for increased transmis- sion. Omicron had the highest number of unique mutations in the spike protein (i.e., sub- stitutions, deletions, and insertions), which may explain its higher transmissibility and immune-evading ability than Delta. A total of 779 mutations were identified, where 691 substitutions, 85 deletions, and 3 insertion mutations were observed. To sum up, our study will enrich the genomic database of SARS-CoV-2, aiding in treatment strategies along with understanding the virus's preferences in both mutation type and mutation site for predicting newly emerged viruses' survival strategies and thus for preparing to coun- teract them.

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.

Current Advances in Viral Nanoparticles for Biomedicine

Viral nanoparticles (VNPs) have emerged as crucial tools in the field of biomedicine. Leveraging their biological and physicochemical properties, VNPs exhibit significant advantages in the prevention, diagnosis, and treatment of human diseases. Through techniques such as chemical bioconjugation, infusion, genetic engineering, and encapsulation, these VNPs have been endowed with multifunctional capabilities, including the display of functional peptides or proteins, encapsulation of therapeutic drugs or inorganic particles, integration with imaging agents, and conjugation with bioactive molecules. This review provides an in-depth analysis of VNPs in biomedicine, elucidating their diverse types, distinctive features, production methods, and complex design principles behind multifunctional VNPs. It highlights recent innovative research and various applications, covering their roles in imaging, drug delivery, therapeutics, gene delivery, vaccines, immunotherapy, and tissue regeneration. Additionally, the review provides an assessment of their safety and biocompatibility and discusses challenges and future opportunities in the field, underscoring the vast potential and evolving nature of VNP research.

A substitution at the cytoplasmic tail of the spike protein enhances SARS-CoV-2 infectivity and immunogenicity

BACKGROUND

Global dissemination of SARS-CoV-2 Omicron sublineages has provided a sufficient opportunity for natural selection, thus enabling beneficial mutations to emerge. Characterisation of these mutations uncovers the underlying machinery responsible for the fast transmission of Omicron variants and guides vaccine development for combating the COVID-19 pandemic.

METHODS

Through systematic bioinformatics analysis of 496,606 sequences of Omicron variants, we obtained 40 amino acid substitutions that occurred with high frequency in the S protein. Utilising pseudoviruses and a trans-complementation system of SARS-CoV-2, we identified the effect of high-frequency mutations on viral infectivity and elucidated the molecular mechanisms. Finally, we evaluated the impact of a key emerging mutation on the immune protection induced by the SARS-CoV-2 VLP mRNA vaccine in a murine model.

FINDINGS

We identified a proline-to-leucine substitution at the 1263rd residue of the Spike protein, and upon investigating the relative frequencies across multiple Omicron sublineages, we found a trend of increasing frequency for P1263L. The substitution significantly enhances the capacity for S-mediated viral entry and improves the immunogenicity of a virus-like particle mRNA vaccine. Mechanistic studies showed that this mutation is located in the FERM binding motif of the cytoplasmic tail and impairs the interaction between the S protein and the Ezrin/Radixin/Moesin proteins. Additionally, this mutation facilitates the incorporation of S proteins into SARS-CoV-2 virions.

INTERPRETATION

This study offers mechanistic insight into the constantly increasing transmissibility of SARS-CoV-2 Omicron variants and provides a meaningful optimisation strategy for vaccine development against SARS-CoV-2.

FUNDING

This study was supported by grants from the National Key Research and Development Plan of China (2021YFC2302405, 2022YFC2303200, 2021YFC2300200 and 2022YFC2303400), the National Natural Science Foundation of China (32188101, 32200772, 82422049, 82241082, 32270182, 82372254, 82271872, 82341046, 32100755 and 82102389), Shenzhen Medical Research Fund (B2404002, A2303036), the Shenzhen Bay Laboratory Startup Fund (21330111), Shenzhen San-Ming Project for Prevention and Research on Vector-borne Diseases (SZSM202211023), Yunnan Provincial Science and Technology Project at Southwest United Graduate School (202302AO370010). The New Cornerstone Science Foundation through the New Cornerstone Investigator Program, and the Xplorer Prize from Tencent Foundation.

Genomic Diversity and Evolution of Identified SARS-CoV-2 Variants in Iraq

The COVID-19 pandemic caused by the SARS-CoV-2 virus continues to circulate worldwide, causing the deaths of millions of people. The continuous circulation of the virus, its genetic diversity, the emergence of new variants with increased transmissibility, and/or the capacity of the virus to escape from the immune system constitute a major public health concern. In our study, we aimed to characterize SARS-CoV-2 strains in Iraq from the first introduction until the end of 2023, and to identify their variants, lineages, clades, and mutation patterns. All published Iraqi full genome sequences (2020-2023) were obtained from Global Initiative on Sharing All Influenza Data (GISAID) and subjected to molecular characterization along with 19 samples of full genome sequences that were collected during the fifth and sixth waves of the SARS-CoV-2 pandemic in this study. Next-generation sequencing was performed using an Illumina MiSeq system, and phylogenetic analysis was performed for all the Iraqi sequences. Three established global platforms, GISAID, Nextstrain, and PANGO, were used for the classification of isolates into distinct clades, variants, and lineages. Six wave peaks of COVID-19 cases have been identified in Iraq, resulting in approximately 2,400,000 cumulative confirmed cases and more than 25,000 deaths. Our study revealed patterns of circulation and dominance of SARS-CoV-2 clades and their lineages in the pandemic waves in the country.

miR-24-3p Is Antiviral Against SARS-CoV-2 by Downregulating Critical Host Entry Factors

Despite all the progress in treating SARS-CoV-2, escape mutants to current therapies remain a constant concern. Promising alternative treatments for current and future coronaviruses are those that limit escape mutants by inhibiting multiple pathogenic targets, analogous to the current strategies for treating HCV and HIV. With increasing popularity and ease of manufacturing of RNA technologies for vaccines and drugs, therapeutic microRNAs represent a promising option. In the present work, miR-24-3p was identified to inhibit SARS-CoV-2 entry, replication, and production; furthermore, this inhibition was retained against common mutations improving SARS-CoV-2 fitness. To determine the mechanism of action, bioinformatic tools were employed, identifying numerous potential effectors promoting infection targeted by miR-24-3p. Of these targets, several key host proteins for priming and facilitating SARS-CoV-2 entry were identified: furin, NRP1, NRP2, and SREBP2. With further experimental analysis, we show that miR-24-3p directly downregulates these viral entry factors to impede infection when producing virions and when infecting the target cell. Furthermore, we compare the findings with coronavirus, HCoV-229E, which relies on different factors strengthening the miR-24-3p mechanism. Taken together, the following work suggests that miR-24-3p could be an avenue to treat current coronaviruses and those likely to emerge.

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.

The epidemiology and phylogenetic trends of Omicron subvariants from BA.5 to XBB.1 in Taiwan

BACKGROUND

Omicron, a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant, entered Taiwan at the end of 2021. The Taiwanese government ended its "zero-COVID" policy in March 2022. Multiple coronavirus disease 2019 (COVID-19) outbreaks began in April 2022. We monitored the replacement of Omicron subvariants after BA.1/BA.2 and analyzed their correlation with COVID-19 outbreaks.

METHODS

We collected SARS-CoV-2 real-time qRTPCR-positive nasopharyngeal swabs from Kaohsiung Medical University Hospital (KMUH), Kaohsiung City, Taiwan, and performed sequencing for specimens exhibiting a cytopathic effect in Vero E6 cells to determine their clades and lineages. We analyzed the medical records of COVID-19 patients and identified hospitalization risk factor(s). We retrieved SARS-CoV-2 sequences identified in Taiwan from GISAID and analyzed their correlation with COVID-19 data from the Taiwan Centers for Disease Control.

RESULTS

We analyzed the phylogenesis of KMUH-47 to KMUH-104 (SARS-CoV-2 isolates identified herein) and all of the Omicron subvariants from BA.5 to XBB.1 (n = 1930). Age and comorbidities were hospitalization risk factors. Men generally exhibited a greater fatality rate than women. COVID-19-related deaths predominantly occurred in individuals over 70 years old. The COVID-19-related case fatality rate increased as nucleotide (NT) and amino acid (AA) substitutions increased. The number of COVID-19-related cases and deaths progressively decreased with each outbreak between August 2022 and October 2023.

CONCLUSION

Hospitalization was associated with age and the presence of comorbidities. COVID-19-related fatality was linked to sex, age, and the accumulation of NT and AA substitutions in emerging Omicron subvariants.

Immunoreactivity Analysis of MHC-I Epitopes Derived from the Nucleocapsid Protein of SARS-CoV-2 via Computation and Vaccination

Background: Since 2019, the SARS-CoV-2 virus has been responsible for the global spread of respiratory illness. As of 1 September 2024, the cumulative number of infections worldwide exceeded 776 million. There are many structural proteins of the virus, among which the SARS-CoV-2 nucleocapsid (N) protein plays a pivotal role in the viral life cycle, participating in a multitude of essential activities following viral invasion. An important antiviral immune response is the major histocompatibility complex (MHC)-restricted differentiation cluster 8 (CD8+) T cell cytotoxicity. Therefore, understanding the immunogenicity of SARS-CoV-2 NP-specific MHC-I-restricted epitopes is highly important. Methods: MHC-I molecules from 11 human leukocyte antigen I (HLA-I) superfamilies with 98% population coverage and 6 mouse H2 alleles were selected. The affinity were screened by IEDB, NetMHCpan, SYFPEITHI, SMMPMBEC and Rankpep. Further immunogenicity and conservative analyses were performed using VaxiJen and BLASTp, respectively. EpiDock was used to simulate molecular docking. Cluster analysis was performed. Selective epitopes were validated by enzyme-linked immunospot (ELISpot) assay and flow cytometry in the mice with pVAX-NPSARS-CoV-2 immunization. Enzyme-Linked Immunosorbent Assay (ELISA) was used to detect whether the preferred epitope induced humoral immunity. Results: There were 64 dominant epitopes for the H-2 haplotype and 238 dominant epitopes for the HLA-I haplotype. Further analysis of immunogenicity and conservation yielded 8 preferred epitopes, and docking simulations were conducted with corresponding MHC-I alleles. The relationships between the NP peptides and MHC-I haplotypes were then determined via two-way hierarchical clustering. ELISA, ELISpot assay, and flow cytometry revealed that the preferred epitope stimulated both humoral and cellular immunity and enhanced cytokine secretion in mice. Conclusions: our study revealed the general patterns among multiple haplotypes within the humans and mice superfamily, providing a comprehensive assessment of the pan-MHC-I immunoreactivity of SARS-CoV-2 NP. Our findings would render prospects for the development and application of epitope-based immunotherapy in lasting viral epidemics.

Cell-based high-content approach for SARS-CoV-2 neutralization identifies unique monoclonal antibodies and PI3K pathway inhibitors

The sudden rise of the SARS-CoV-2 virus and the delay in the development of effective therapeutics to mitigate it made evident a need for ways to screen for compounds that can block infection and prevent further pathogenesis and spread. Yet, identifying effective drugs efficacious against viral infection and replication with minimal toxicity for the patient can be difficult. Monoclonal antibodies were shown to be effective, yet as the SARS-CoV-2 mutated, these antibodies became ineffective. Small molecule antivirals were identified using pseudovirus constructs to recapitulate infection in non-human cells, such as Vero E6 cells. However, the impact was limited due to poor translation of these compounds in the clinical setting. This is partly due to the lack of similarity of screening platforms to the in vivo physiology of the patient and partly because drugs effective in vitro showed dose-limiting toxicities. In this study, we performed two high-throughput screens in human lung adenocarcinoma cells with authentic SARS-CoV-2 virus to identify both monoclonal antibodies that neutralize the virus and clinically useful kinase inhibitors to block the virus and prioritize minimal host toxicity. Using high-content imaging combined with single-cell and multidimensional analysis, we identified antibodies and kinase inhibitors that reduce virus infection without affecting the host. Our screening technique uncovered novel antibodies and overlooked kinase inhibitors (i.e. PIK3i, mTORi, multiple RTKi) that could be effective against SARS-CoV-2 virus. Further characterization of these molecules will streamline the repurposing of compounds for the treatment of future pandemics and uncover novel mechanisms viruses use to hijack and infect host cells.

A potential allosteric inhibitor of SARS-CoV-2 main protease (Mpro) identified through metastable state analysis

Anti-COVID19 drugs, such as nirmatrelvir, have been developed targeting the SARS-CoV-2 main protease, Mpro, based on the critical requirement of its proteolytic processing of the viral polyproteins into functional proteins essential for viral replication. However, the emergence of SARS-CoV-2 variants with Mpro mutations has raised the possibility of developing resistance against these drugs, likely due to therapeutic targeting of the Mpro catalytic site. An alternative to these drugs is the development of drugs that target an allosteric site distant from the catalytic site in the protein that may reduce the chance of the emergence of resistant mutants. Here, we combine computational analysis with in vitro assay and report the discovery of a potential allosteric site and an allosteric inhibitor of SARS-CoV-2 Mpro. Specifically, we identified an Mpro metastable state with a deformed catalytic site harboring potential allosteric sites, raising the possibility that stabilization of this metastable state through ligand binding can lead to the inhibition of Mpro activity. We then performed a computational screening of a library (∼4.2 million) of drug-like compounds from the ZINC database and identified several candidate molecules with high predicted binding affinity. MD simulations showed stable binding of the three top-ranking compounds to the putative allosteric sites in the protein. Finally, we tested the three compounds in vitro using a BRET-based Mpro biosensor and found that one of the compounds (ZINC4497834) inhibited the Mpro activity. We envisage that the identification of a potential allosteric inhibitor of Mpro will aid in developing improved anti-COVID-19 therapy.

Immunomics in one health: understanding the human, animal, and environmental aspects of COVID-19

The coronavirus disease 2019 (COVID-19) pandemic underscores the critical need to integrate immunomics within the One Health framework to effectively address zoonotic diseases across humans, animals, and environments. Employing advanced high-throughput technologies, this interdisciplinary approach reveals the complex immunological interactions among these systems, enhancing our understanding of immune responses and yielding vital insights into the mechanisms that influence viral spread and host susceptibility. Significant advancements in immunomics have accelerated vaccine development, improved viral mutation tracking, and broadened our comprehension of immune pathways in zoonotic transmissions. This review highlights the role of animals, not merely as carriers or reservoirs, but as essential elements of ecological networks that profoundly influence viral epidemiology. Furthermore, we explore how environmental factors shape immune response patterns across species, influencing viral persistence and spillover risks. Moreover, case studies demonstrating the integration of immunogenomic data within the One Health framework for COVID-19 are discussed, outlining its implications for future research. However, linking humans, animals, and the environment through immunogenomics remains challenging, including the complex management of vast amounts of data and issues of scalability. Despite challenges, integrating immunomics data within the One Health framework significantly enhances our strategies and responses to zoonotic diseases and pandemic threats, marking a crucial direction for future public health breakthroughs.

CD147 mediates S protein pseudovirus of SARS-CoV-2 infection and its induction of spermatogonia apoptosis

Male cases diagnosed COVID-19 with more complications and higher mortality compared with females, and the overall consequences of male sex hormones and semen parameters deterioration were observed in COVID-19 patients, whereas the involvement and mechanism for spermatogenic cell remains unclear. The study was aimed to investigate the infection mode of S protein (D614G) pseudovirus (pseu-S-D614G) to spermatogenic cells, as well as the influence on cell growth. Both mouse spermatogonia (GC-1 cell, immortalized spermatogonia) and spermatocyte (GC-2 cell, immortalized spermatocytes) were used to detect the infection of pseu-S-D614G of SARS-CoV-2, and further explored the effect of SARS-CoV-2-spike protein (S-protein) and SARS-CoV-2-spike protein (omicron) (O-protein) on GC-1 cell apoptosis and proliferation. The data showed that the pseu-S-D614G invaded into GC-1 cells through either human ACE2 (hACE2) or human CD147 (hCD147), whereas GC-2 cells were insensitive to viral infection. In addition, the apoptosis and proliferation suppression inflicted by S-protein and O-protein on GC-1 cells was through Bax-Caspase3 signaling rather than arresting cell cycle progression. These findings suggest that CD147, apart from ACE2, may be a potential receptor for SARS-CoV-2 infection in testicular tissues, and that the apoptotic effect was induced in spermatogonia cells by S-protein or O-protein, eventually resulted in the damage to male fertility.

A Single-center Experience With >200 Lung Transplant Recipients With COVID-19 Infection

Background

Although COVID-19 is no longer a declared global health emergency, data remain limited on the impact of COVID-19 in lung transplant recipients.

Methods

We identified lung transplant recipients who were diagnosed with COVID-19 from March 2020 through August 2022 in our institutional database and investigated clinical outcomes. We then analyzed outcomes based on date of COVID-19 diagnosis (first wave March 2020-October 2020; second wave November 2020-2021; third wave December 2021-September 2022) and compared these results.

Results

Of the 210 lung transplant recipients (median age 67; 67% men) enrolled, 140 (67%) required hospital admission. Among admitted recipients, 35 (25%) were intubated and 7 (5%) were placed on extracorporeal membrane oxygenation. Overall survival was 67.1% at 1 y and 59.0% at 2 y post-COVID-19 diagnosis. COVID-19 led to mortality in all 5 patients diagnosed during their index admission for lung transplantation. Although overall survival was significantly better in recipients with COVID-19 during the third wave, in-hospital mortality remained high (first wave 28%, second wave 38%, and 28% third wave). Vaccination (partially vaccinated versus none and fully vaccinated versus none) was the only significant protective factor for hospital admission, and age 70 y and older and partially vaccinated (versus none or fully vaccinated) were independent risk factors for in-hospital mortality.

Conclusions

Overall survival after COVID-19 infection in lung transplant recipients continues to improve; however, in-hospital mortality remains remarkably high. Vaccination appears to have been impactful in preventing hospital admission, but its impact on in-hospital mortality is still unclear. Further research is needed to better identify lung transplant recipients at high risk for mortality from COVID-19.

Hybrid immunity to SARS-CoV-2 arises from serological recall of IgG antibodies distinctly imprinted by infection or vaccination

We describe the molecular-level composition of polyclonal immunoglobulin G (IgG) anti-spike antibodies from ancestral severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, vaccination, or their combination ("hybrid immunity") at monoclonal resolution. Infection primarily triggers S2/N-terminal domain (NTD)-reactive antibodies, whereas vaccination mainly induces anti-receptor-binding domain (RBD) antibodies. This imprint persists after secondary exposures wherein >60% of ensuing hybrid immunity derives from the original IgG pool. Monoclonal constituents of the original IgG pool can increase breadth, affinity, and prevalence upon secondary exposures, as exemplified by the plasma antibody SC27. Following a breakthrough infection, vaccine-induced SC27 gained neutralization breadth and potency against SARS-CoV-2 variants and zoonotic viruses (half-maximal inhibitory concentration [IC50] ∼0.1-1.75 nM) and increased its binding affinity to the protective RBD class 1/4 epitope (dissociation constant [KD] < 5 pM). According to polyclonal escape analysis, SC27-like binding patterns are common in SARS-CoV-2 hybrid immunity. Our findings provide a detailed molecular definition of immunological imprinting and show that vaccination can produce class 1/4 (SC27-like) IgG antibodies circulating in the blood.

Use of a risk assessment tool to determine the origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

The origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is contentious. Most studies have focused on a zoonotic origin, but definitive evidence such as an intermediary animal host is lacking. We used an established risk analysis tool for differentiating natural and unnatural epidemics, the modified Grunow-Finke assessment tool (mGFT) to study the origin of SARS-COV-2. The mGFT scores 11 criteria to provide a likelihood of natural or unnatural origin. Using published literature and publicly available sources of information, we applied the mGFT to the origin of SARS-CoV-2. The mGFT scored 41/60 points (68%), with high inter-rater reliability (100%), indicating a greater likelihood of an unnatural than natural origin of SARS-CoV-2. This risk assessment cannot prove the origin of SARS-CoV-2 but shows that the possibility of a laboratory origin cannot be easily dismissed.

Equal Maintenance of Anti-SARS-CoV-2 Antibody Levels Induced by Heterologous and Homologous Regimens of the BNT162b2, ChAdOx1, CoronaVac and Ad26.COV2.S Vaccines: A Longitudinal Study Up to the 4th Dose of Booster

Several technological approaches have been used to develop vaccines against COVID-19, including those based on inactivated viruses, viral vectors, and mRNA. This study aimed to monitor the maintenance of anti-SARS-CoV-2 antibodies in individuals from Brazil according to the primary vaccination regimen, as follows: BNT162b2 (group 1; 22) and ChAdOx1 (group 2; 18). Everyone received BNT162b2 in the first booster while in the second booster CoronaVac, Ad26.COV2.S, or BNT162b2. Blood samples were collected from 2021 to 2023 to analyze specific RBD (ELISA) and neutralizing antibodies (PRNT50). We observed a progressive increase in anti-RBD and neutralizing antibodies in each subsequent dose, remaining at high titers until the end of follow-up. Group 1 had higher anti-RBD antibody titers than group 2 after beginning the primary regimen, with significant differences after the 2nd and 3rd doses. Group 2 showed a more expressive increase after the first booster with BNT162B2 (heterologous booster). Group 2 also presented high levels of neutralizing antibodies against the Gamma and Delta variants until five months after the second booster. In conclusion, the circulating levels of anti-RBD and neutralizing antibodies against the two variants of SARS-CoV-2 were durable even five months after the 4th dose, suggesting that periodic booster vaccinations (homologous or heterologous) induced long-lasting immunity.

Usefulness of aircraft and airport wastewater for monitoring multiple pathogens including SARS-CoV-2 variants

BACKGROUND

As global travel resumed in coronavirus disease 2019 (COVID-19) endemicity, the potential of aircraft wastewater monitoring to provide early warning of disease trends for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and other infectious diseases, particularly at international air travel hubs, was recognized. We therefore assessed and compared the feasibility of testing wastewater from inbound aircraft and airport terminals for 18 pathogens including SARS-CoV-2 in Singapore, a popular travel hub in Asia.

METHODS

Wastewater samples collected from inbound medium- and long-haul flights and airport terminals were tested for SARS-CoV-2. Next Generation Sequencing was carried out on positive samples to identify SARS-CoV-2 variants. Airport and aircraft samples were further tested for 17 other pathogens through quantitative reverse transcription polymerase chain reaction.

RESULTS

The proportion of SARS-CoV-2-positive samples and the average virus load was higher for wastewater samples from aircraft as compared with airport terminals. Cross-correlation analyses indicated that viral load trends from airport wastewater led local COVID-19 case trends by 2-5 days. A total of 10 variants (44 sub-lineages) were successfully identified from aircraft wastewater and airport terminals, and four variants of interest and one variant under monitoring were detected in aircraft and airport wastewater 18-31 days prior to detection in local clinical cases. The detection of five respiratory and four enteric viruses in aircraft wastewater samples further underscores the potential to expand aircraft wastewater to monitoring pathogens beyond SARS-CoV-2.

CONCLUSION

Our findings demonstrate the feasibility of aircraft wastewater testing for monitoring infectious diseases threats, potentially detecting signals before clinical cases are reported. The triangulation of similar datapoints from aircraft wastewater of international travel nodes could therefore serve as a useful early warning system for global health threats.

Design, Synthesis, and Biological Evaluation of 1,2,4-Oxadiazole Derivatives Containing an Aryl Carboxylic Acid Moiety as Potent Sarbecovirus Papain-like Protease Inhibitors

Papain-like protease (PLpro) is a promising therapeutic target for its pivotal role in the life cycle of SARS-CoV-2. A series of 1,2,4-oxadiazole derivatives was designed and synthesized via a ring formation strategy based on SARS-CoV-2 PLpro-GRL0617 complex structure. Systematic structure-activity relationship studies revealed that introducing oxadiazole and aryl carboxylic acid moieties to GRL0617 enhanced the enzymatic inhibition activity, affinity, and deubiquitination capacity toward PLpro. 1,2,4-Oxadiazole compounds 13f and 26r, which had PLpro inhibition activity (IC50 = 1.8 and 1.0 μM) and antiviral activity against SARS-CoV-2 (EC50 = 5.4 and 4.3 μM), exhibited good metabolic stability (t1/2 > 93.2 min) and higher plasma exposure (AUC0-t = 17,380.08 and 24,289.76 ng·h/mL) in mice. Especially, compound 26r with moderate oral bioavailability of 39.1% and potent antiviral activity is worthy of further studies in vivo. Our findings provide a new insight for the discovery of antiviral agents targeting PLpro.

The landscape of the COVID-19 pandemic in Poland emerging from epidemiological and genomic data

The COVID-19 pandemic has profoundly affected all aspects of our lives. Through real-time monitoring and rapid vaccine implementation, we succeeded in suppressing the spread of the disease and mitigating its consequences. Finally, conclusions can be summarized and drawn. Here, we use the example of Poland, which was seriously affected by the pandemic. Compared to other countries, Poland has not achieved impressive results in either testing or vaccination, which may explain its high mortality (case fatality rate, CFR 1.94%). Through retrospective analysis of data collected by the COVID-19 Data Portal Poland, we found significant regional differences in the number of tests performed, number of cases detected, number of COVID-19-related deaths, and vaccination rates. The Masovian, Greater Poland, and Pomeranian voivodeships, the country's leaders in vaccination, reported high case numbers but low death rates. In contrast, the voivodeships in the eastern and southern parts of Poland (Subcarpathian, Podlaskie, Lublin, Opole), which documented low vaccination levels and low case numbers, had higher COVID-19-related mortality rates. The strong negative correlation between the CFR and the percentage of the population that was vaccinated in Poland supports the validity of vaccination. To gain insight into virus evolution, we sequenced more than 500 genomes and analyzed nearly 80 thousand SARS-CoV-2 genome sequences deposited in GISAID by Polish diagnostic centers. We showed that the SARS-CoV-2 variant distribution over time in Poland reflected that in Europe. Haplotype network analysis allowed us to follow the virus transmission routes and identify potential superspreaders in each pandemic wave.

The alarmin IL-33 exacerbates pulmonary inflammation and immune dysfunction in SARS-CoV-2 infection

Dysregulated host immune responses contribute to disease severity and worsened prognosis in COVID-19 infection and the underlying mechanisms are not fully understood. In this study, we observed that IL-33, a damage-associated molecular pattern molecule, is significantly increased in COVID-19 patients and in SARS-CoV-2-infected mice. Using IL-33-/- mice, we demonstrated that IL-33 deficiency resulted in significant decreases in bodyweight loss, tissue viral burdens, and lung pathology. These improved outcomes in IL-33-/- mice also correlated with a reduction in innate immune cell infiltrates, i.e., neutrophils, macrophages, natural killer cells, and activated T cells in inflamed lungs. Lung RNA-seq results revealed that IL-33 signaling enhances activation of inflammatory pathways, including interferon signaling, pathogen phagocytosis, macrophage activation, and cytokine/chemokine signals. Overall, these findings demonstrate that the alarmin IL-33 plays a pathogenic role in SARS-CoV-2 infection and provides new insights that will inform the development of effective therapeutic strategies for COVID-19.

Lingering effects of COVID-19 in the care of perioperative patients

PURPOSE OF REVIEW

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), can lead to organ dysfunction and clinical symptoms beyond the acute infection phase. These effects may have significant implications for the management of perioperative patients. The purpose of this article is to provide a systems-based approach to the subacute and chronic effects of SARS-CoV-2 that are most relevant to anesthesiology practice.

RECENT FINDINGS

In 2024, COVID-19 remains a concern for anesthesiologists due ongoing new infections, evolving viral strains, and relatively low rates of booster vaccination in the general population. A growing body of literature describes the post-COVID-19 syndrome in which patients experience symptoms more than 12 weeks after acute infection. Recent literature describes the lingering effects of SARS-CoV-2 infection on all major organ systems, including neurologic, pulmonary, cardiovascular, renal, hematologic, and musculoskeletal, and suggests an increased perioperative mortality risk in some populations.

SUMMARY

This review offers anesthesiologists an organ system-based approach to patients with a history of COVID-19. Recognizing the long-term sequelae of SARS-CoV-2 infection can help anesthesiologists to better evaluate perioperative risk, anticipate clinical challenges, and thereby optimize patient care.

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.

Peripheral helper T cells in human diseases

Peripheral helper T cells (Tph) are a specialized subset of CD4+ T cells with the ability to help B cells and induce antibody production. Although usually located in ectopic lymphoid-like structures (ELS), inside the peripheral blood, Tph cells can also be identified. The aberrant proliferation and functions of Tph cells are commonly found in the patients with disease. In this review, first we will summarize the biological characteristics of Tph cells, such as the expression of surface molecules, transcription factors and cytokines, and discuss its B cell help functions. Tph cells also have roles in a wide range of human diseases, including autoimmune diseases, infectious diseases, malignancies etc. Therefore, there is a strong interest in targeting Tph cells to improve treat strategies of human diseases.

COVID-19: From emerging variants to vaccination

The vigorous spread of SARS-CoV-2 resulted in the rapid infection of millions of people worldwide and devastation of not only public healthcare, but also social, educational, and economic infrastructures. The evolution of SARS-CoV-2 over time is due to the mutations that occurred in the genome during each replication. These mutated forms of SARS-CoV-2, otherwise known as variants, were categorized as variants of interest (VOI) or variants of concern (VOC) based on the increased risk of transmissibility, disease severity, immune escape, decreased effectiveness of current social measures, and available vaccines and therapeutics. The swift development of COVID-19 vaccines has been a great success for biomedical research, and billions of vaccine doses, including boosters, have been administered worldwide. BNT162b2 vaccine (Pfizer-BioNTech), mRNA-1273 (Moderna), ChAdOx1 nCoV-19 (AstraZeneca), and Janssen (Johnson & Johnson) are the four major COVID-19 vaccines that received early regulatory authorization based on their efficacy. However, some SARS-CoV-2 variants resulted in higher resistance to available vaccines or treatments. It has been four years since the first reported infection of SARS-CoV-2, yet the Omicron variant and its subvariants are still infecting people worldwide. Despite this, COVID-19 vaccines are still expected to be effective at preventing severe disease, hospitalization, and death from COVID. In this review, we provide a comprehensive overview of the COVID-19 pandemic focused on evolution of VOC and vaccination strategies against them.

Multivalent and Sequential Heterologous Spike Protein Vaccinations Effectively Induce Protective Humoral Immunity against SARS-CoV-2 Variants

The emergence of new SARS-CoV-2 variants continues to cause challenging problems for the effective control of COVID-19. In this study, we tested the hypothesis of whether a strategy of multivalent and sequential heterologous spike protein vaccinations would induce a broader range and higher levels of neutralizing antibodies against SARS-CoV-2 variants and more effective protection than homologous spike protein vaccination in a mouse model. We determined spike-specific IgG, receptor-binding inhibition titers, and protective efficacy in the groups of mice that were vaccinated with multivalent recombinant spike proteins (Wuhan, Delta, Omicron), sequentially with heterologous spike protein variants, or with homologous spike proteins. Trivalent (Wuhan + Delta + Omicron) and sequential heterologous spike protein vaccinations were more effective in inducing serum inhibition activities of receptor binding to spike variants and virus neutralizing antibody titers than homologous spike protein vaccination. The higher efficacy of protection was observed in mice with trivalent and sequential heterologous spike protein vaccination after a challenge with a mouse-adapted SARS-CoV-2 MA10 strain compared to homologous spike protein vaccination. This study provides evidence that a strategy of multivalent and sequential heterologous variant spike vaccination might provide more effective protection against emerging SARS-CoV-2 variants than homologous spike vaccination and significantly alleviate severe inflammation due to COVID-19.

Prebiotic inulin ameliorates SARS-CoV-2 infection in hamsters by modulating the gut microbiome

Current treatment options for COVID-19 are limited, with many antivirals and immunomodulators restricted to the most severe cases and preventative care limited to vaccination. As the SARS-CoV-2 virus and its increasing variants threaten to become a permanent fixture of our lives, this new reality necessitates the development of cost-effective and accessible treatment options for COVID-19. Studies have shown that there are correlations between the gut microbiome and severity of COVID-19, especially with regards to production of physiologically beneficial short-chain fatty acids (SCFAs) by gut microbes. In this study, we used a Syrian hamster model to study how dietary consumption of the prebiotic inulin affected morbidity and mortality resulting from SARS-CoV-2 infection. After two weeks of observation, we discovered that inulin supplementation attenuated morbid weight loss and increased survival rate in hamster subjects. An analysis of microbiome community structure showed significant alterations in 15 genera. Notably, there were also small increases in fecal DCA and a significant increase in serum DCA, perhaps highlighting a role for this secondary bile acid in conferring protection against SARS-CoV-2. In light of these results, inulin and other prebiotics are promising targets for future investigation as preventative treatment options for COVID-19.

Flublok Quadrivalent Vaccine Adjuvanted with R-DOTAP Elicits a Robust and Multifunctional CD4 T Cell Response That Is of Greater Magnitude and Functional Diversity Than Conventional Adjuvant Systems

It is clear that new approaches are needed to promote broadly protective immunity to viral pathogens, particularly those that are prone to mutation and escape from antibody-mediated immunity. CD4+ T cells, known to target many viral proteins and highly conserved peptide epitopes, can contribute greatly to protective immunity through multiple mechanisms. Despite this potential, CD4+ T cells are often poorly recruited by current vaccine strategies. Here, we have analyzed a promising new adjuvant (R-DOTAP), as well as conventional adjuvant systems AddaVax with or without an added TLR9 agonist CpG, to promote CD4+ T cell responses to the licensed vaccine Flublok containing H1, H3, and HA-B proteins. Our studies, using a preclinical mouse model of vaccination, revealed that the addition of R-DOTAP to Flublok dramatically enhances the magnitude and functionality of CD4+ T cells specific for HA-derived CD4+ T cell epitopes, far outperforming conventional adjuvant systems based on cytokine EliSpot assays and multiparameter flow cytometry. The elicited CD4+ T cells specific for HA-derived epitopes produce IL-2, IFN-γ, IL-4/5, and granzyme B and have multifunctional potential. Hence, R-DOTAP, which has been verified safe by human studies, can offer exciting opportunities as an immune stimulant for next-generation prophylactic recombinant protein-based vaccines.

A semi-quantitative visual lateral flow immunoassay for SARS-CoV-2 antibody detection for the follow-up of immune response to vaccination or recovery

The lateral flow immunoassay (LFIA) technique is largely employed for the point-of-care detection of antibodies especially for revealing the immune response in serum. Visual LFIAs usually provide the qualitative yes/no detection of antibodies, while quantification requires some equipment, making the assay more expensive and complicated. To achieve visual semi-quantification, the alignment of several lines (made of the same antigen) along a LFIA strip has been proposed. The numbering of the reacting lines has been used to correlate with the quantity of some biomarkers in serum. Here, we designed the first semiquantitative LFIA for detecting antibodies and applied it to classify the immune response to SARS-CoV-2 raised by vaccination or natural infection. We used a recombinant spike receptor-binding domain (RBD) as the specific capture reagent to draw two test lines. The detection reagent was selected among three possible ligands that are able to bind to anti-spike human antibodies: the same RBD, staphylococcal protein A, and anti-human immunoglobulin G antibodies. The most convenient detector, adsorbed on gold nanoparticles, was chosen based on the highest correlation with an antibody titre of 171 human sera, measured by a reference serological method, and was the RBD (Spearman's rho = 0.84). Incorporated into the semiquantitative LFIA, it confirmed the ability to discriminate high- and low-titre samples and to classify them into two classes (Dunn's test, P < 0.05). The proposed approach enabled the semiquantification of the immune response to SARS-CoV-2 by the unaided eye observation, thus overcoming the requirement of costly and complicated equipment, and represents a general strategy for the development of semiquantitative serological LFIAs.

Head CT Scans in the Emergency Department during the COVID-19 Pandemic: Use or Overuse?

BACKGROUND

The COVID-19 pandemic seemed to mainly involve the respiratory system, but it was realized that it could affect any organ, including the CNS. The pandemic has followed a wave-like trend, with its peaks being due to the COVID-19 different variants and the introduction of the vaccine, which led to an apparent reduction in hospitalizations but also brought about perplexities related to its adverse effects. The aim of this study was to analyze the changes in the use of head CT/contrast CT and their impacts on the onset of cerebrovascular disease in our emergency department during the COVID-19 period and the vaccine rollout.

METHODS

Patients ≥ 18 years old admitted to our emergency department from January 2018 to September 2021 were enrolled. The patients were divided into three groups. The COVID-19 period included patients who visited our emergency department from 1 March 2020 to 31 January 2021; the vaccine period was considered to range from 1 February 2021 to 30 September 2021. The patients who visited the emergency department from 1 January 2018 to 31 January 2020 were considered the controls.

RESULTS

We found an increase in head CT/contrast CT requests during the COVID-19 period and increase in head contrast CT during the vaccine period, without an increase in the incidence of cerebrovascular disease.

CONCLUSIONS

The uncertainty regarding the possible thrombotic events associated with COVID-19 and its vaccine increased the relative use of head CT/contrast CT by about 20% compared to the control period.

Spike S2 Subunit: Possible Target for Detecting Novel SARS-CoV-2 Variants with Multiple Mutations

Novel SARS-CoV-2 variants have multiple mutations that may impact molecular diagnostics. The markedly conserved S2 subunit may be utilized to detect new variants. A comparison of 694 specimens (2019-2022) in Thailand using a commercial RT-PCR kit and the kit in combination with S2 primers and a probe was performed. Delayed amplification in ORF1ab was detected in one BA.4 omicron, whereas no amplification problem was encountered in the S2 target. There were no statistically significant differences in mean Ct value between the target genes (E, N, ORF1ab, and S2) and no significant differences in mean Ct value between the reagents. Furthermore, 230,821 nucleotide sequences submitted by 20 representative counties in each region (Jan-Oct 2022) have been checked for mutations in S2 primers and probe using PrimerChecker; there is a very low chance of encountering performance problems. The S2 primers and probe are still bound to the top five currently circulating variants in all countries and Thailand without mismatch recognition (Jun-Nov 2023). This study shows the possible benefits of detecting S2 in combination with simultaneously detecting three genes in a kit without affecting the Ct value of each target. The S2 subunit may be a promising target for the detection of SARS-CoV-2 variants with multiple mutations.

Unraveling the Dynamics of SARS-CoV-2 Mutations: Insights from Surface Plasmon Resonance Biosensor Kinetics

Surface Plasmon Resonance (SPR) technology is known to be a powerful tool for studying biomolecular interactions because it offers real-time and label-free multiparameter analysis with high sensitivity. This article summarizes the results that have been obtained from the use of SPR technology in studying the dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations. This paper will begin by introducing the working principle of SPR and the kinetic parameters of the sensorgram, which include the association rate constant (ka), dissociation rate constant (kd), equilibrium association constant (KA), and equilibrium dissociation constant (KD). At the end of the paper, we will summarize the kinetic data on the interaction between angiotensin-converting enzyme 2 (ACE2) and SARS-CoV-2 obtained from the results of SPR signal analysis. ACE2 is a material that mediates virus entry. Therefore, understanding the kinetic changes between ACE2 and SARS-CoV-2 caused by the mutation will provide beneficial information for drug discovery, vaccine development, and other therapeutic purposes.

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.

Vaccination and its impact on healthcare utilization in two groups of vaccinated and unvaccinated patients with COVID-19: A cross-sectional study in Iran between 2021 and 2022

Background and Aims

One of the main responsibilities of health systems impacted by the global Coronavirus disease 2019 (COVID-19) pandemic, where the first case was discovered in Wuhan, China, in December 2019, is the provision of medical services. The current study looked into the impact of vaccination on the utilization of services provided to COVID-19 patients.

Methods

This study was conducted in Iran between 2021 and 2022, utilizing a cross-sectional research design. The research team collected data on the utilization of provided services and the number of COVID-19 vaccines administered to 1000 patients in Iran through a random sampling approach. The data were analyzed with statistical methods, including the mean difference test, and multiple linear regression.

Results

Regression estimates show that after controlling for confounding variables like age, type of admission, and comorbidities, vaccination reduces the utilization of healthcare services in the general majority of services. The study's results reveal a fall in COVID-19 patients' utilization of services, specifically in patients administered two or three doses of the vaccine. However, the reduction is not statistically significant. Regression models are in contrast to univariate analysis findings that vaccination increases the mean utilization of healthcare services for COVID-19 patients in general. Comorbidities are a crucial factor in determining the utilization of diagnostic and treatment services for COVID-19 patients.

Conclusion

Full COVID-19 vaccination and other implementations, including investing in public health, cooperating globally, and vaccinating high-risk groups for future pandemics, are essential as a critical response to this pandemic as they reduce healthcare service utilization to alleviate the burden on healthcare systems and allocate resources more efficiently.

Dynamics of humoral and cellular response to three doses of anti-SARS-CoV-2 BNT162b2 vaccine in patients with hematological malignancies and older subjects

Background

Few data are available about the durability of the response, the induction of neutralizing antibodies, and the cellular response upon the third dose of the anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine in hemato-oncological patients.

Objective

To investigate the antibody and cellular response to the BNT162b2 vaccine in patients with hematological malignancy.

Methods

We measured SARS-CoV-2 anti-spike antibodies, anti-Omicron neutralizing antibodies, and T-cell responses 1 month after the third dose of vaccine in 93 fragile patients with hematological malignancy (FHM), 51 fragile not oncological subjects (FNO) aged 80-92, and 47 employees of the hospital (healthcare workers, (HW), aged 23-66 years. Blood samples were collected at day 0 (T0), 21 (T1), 35 (T2), 84 (T3), 168 (T4), 351 (T pre-3D), and 381 (T post-3D) after the first dose of vaccine. Serum IgG antibodies against S1/S2 antigens of SARS-CoV-2 spike protein were measured at every time point. Neutralizing antibodies were measured at T2, T3 (anti-Alpha), T4 (anti-Delta), and T post-3D (anti-Omicron). T cell response was assessed at T post-3D.

Results

An increase in anti-S1/S2 antigen antibodies compared to T0 was observed in the three groups at T post-3D. After the third vaccine dose, the median antibody level of FHM subjects was higher than after the second dose and above the putative protection threshold, although lower than in the other groups. The neutralizing activity of antibodies against the Omicron variant of the virus was tested at T2 and T post-3D. 42.3% of FHM, 80,0% of FNO, and 90,0% of HW had anti-Omicron neutralizing antibodies at T post-3D. To get more insight into the breadth of antibody responses, we analyzed neutralizing capacity against BA.4/BA.5, BF.7, BQ.1, XBB.1.5 since also for the Omicron variants, different mutations have been reported especially for the spike protein. The memory T-cell response was lower in FHM than in FNO and HW cohorts. Data on breakthrough infections and deaths suggested that the positivity threshold of the test is protective after the third dose of the vaccine in all cohorts.

Conclusion

FHM have a relevant response to the BNT162b2 vaccine, with increasing antibody levels after the third dose coupled with, although low, a T-cell response. FHM need repeated vaccine doses to attain a protective immunological response.

Hybrid immunity to SARS-CoV-2 arises from serological recall of IgG antibodies distinctly imprinted by infection or vaccination

We used plasma IgG proteomics to study the molecular composition and temporal durability of polyclonal IgG antibodies triggered by ancestral SARS-CoV-2 infection, vaccination, or their combination ("hybrid immunity"). Infection, whether primary or post-vaccination, mainly triggered an anti-spike antibody response to the S2 domain, while vaccination predominantly induced anti-RBD antibodies. Immunological imprinting persisted after a secondary (hybrid) exposure, with >60% of the ensuing serological response originating from the initial antibodies generated during the first exposure. We highlight one instance where hybrid immunity arising from breakthrough infection resulted in a marked increase in the breadth and affinity of a highly abundant vaccination-elicited plasma IgG antibody, SC27. With an intrinsic binding affinity surpassing a theoretical maximum (K D < 5 pM), SC27 demonstrated potent neutralization of various SARS-CoV-2 variants and SARS-like zoonotic viruses (IC 50 ∼0.1-1.75 nM) and provided robust protection in vivo . Cryo-EM structural analysis unveiled that SC27 binds to the RBD class 1/4 epitope, with both VH and VL significantly contributing to the binding interface. These findings suggest that exceptionally broad and potent antibodies can be prevalent in plasma and can largely dictate the nature of serological neutralization.

HIGHLIGHTS

▪ Infection and vaccination elicit unique IgG antibody profiles at the molecular level▪ Immunological imprinting varies between infection (S2/NTD) and vaccination (RBD)▪ Hybrid immunity maintains the imprint of first infection or first vaccination▪ Hybrid immune IgG plasma mAbs have superior neutralization potency and breadth.

Baricitinib statistically significantly reduced COVID-19-related mortality: a systematic review and meta-analysis of five phase III randomized, blinded and placebo-controlled clinical trials

Due to high heterogeneity and risk of bias (RoB) found in previously published meta-analysis (MA), a concrete conclusion on the efficacy of baricitinib in reducing mortality in coronavirus disease 2019 (COVID-19) patients was unable to form. Hence, this systematic review and MA were conducted to analyse whether RoB, heterogeneity, and optimal sample size from placebo-controlled randomized controlled trials (RCTs) are still the problems to derive a concrete conclusion. Search engines PubMed/MEDLINE, ScienceDirect, and other sources like preprints and reference lists were searched with appropriate keywords. The RoB and MA were conducted using RevMan 5.4. The grading of the articles was conducted using the GRADEPro Guideline Development Tool. Ten RCTs were included in the current systematic review. Only five low RoB articles are Phase III placebo-controlled RCTs with a high certainty level based on the GRADE grading system. For the MA, based on five low RoB articles, baricitinib statistically significantly reduced mortality where the risk ratio (RR) = 0.68 [95% confidence interval (95% CI) 0.56-0.82; P < 0.0001; I2 = 0%; P = 0.85]. The absolute mortality effect (95% CI) based on the grading system was 35 fewer mortalities per 1000 COVID-19 patients, whereas in the baricitinib and control groups, the mortality was 7.4% and 10.9%, respectively. With the presence of an optimal sample size of 3944 from five low RoB-placebo-controlled RCTs, which represent a minimum of 300 million population of people and with the presence of 0% heterogeneity from MA, the effectiveness of baricitinib in reducing the mortality in COVID-19 patients is concretely proven.

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.

A multifaceted approach for identification, validation, and immunogenicity of naturally processed and in silico-predicted highly conserved SARS-CoV-2 peptides

SARS-CoV-2 remains a major global public health concern. Antibody waning and immune escape variant emergence necessitate the development of next generation vaccines that induce cross-reactive durable immune responses. T cell responses to SARS-CoV-2 demonstrate higher conservation, antigenic breadth, and longevity than antibody responses. Therefore, we sought to identify pathogen-derived T cell epitopes for a potential peptide-based vaccine. We pursued an approach leveraging: 1) liquid chromatography and tandem mass spectrometry (LC-MS/MS)-based identification of peptides from ancestral SARS-CoV-2-infected cell lines, 2) epitope prediction algorithms, and 3) overlapping peptide libraries. From this strategy, we identified 380 unique SARS-CoV-2-derived peptide sequences, including 53 antigenic HLA class I and class II peptides from multiple structural and non-structural/accessory viral proteins. These peptide sequences were highly conserved across variants of concern/interest (VoC/VoIs), and are estimated to achieve coverage of >96% of the world population. Our findings validate this discovery pipeline for peptide identification and immunogenicity testing, and are a crucial step toward the development of a next-generation multi-epitope SARS-CoV-2 peptide vaccine, and a novel vaccine platform methodology.

Tracking SARS-CoV-2 variants during the 2023 flu season and beyond in Lebanon

BACKGROUND

Early SARS-CoV-2 variant detection relies on testing and genomic surveillance. The Omicron variant (B.1.1.529) has quickly become the dominant type among the previous circulating variants worldwide. Several subvariants have emerged exhibiting greater infectivity and immune evasion. In this study we aimed at studying the prevalence of the Omicron subvariants during the flu season and beyond in Lebanon through genomic screening and at determining the overall standing and trajectory of the pandemic in the country.

METHODS

A total of 155 SARS-CoV-2 RNA samples were sequenced, using Nanopore sequencing technology.

RESULTS

Nanopore sequencing of 155 genomes revealed their distribution over 39 Omicron variants. XBB.1.5 (23.29 %) was the most common, followed by XBB.1.9.1 (10.96 %) and XBB.1.42 (7.5 %). The first batch collected between September and November 2022, included the BA.2.75.2, BA.5.2, BA.5.2.20, BA.5.2.25 and BQ.1.1.5 lineages. Between December 2022 and January 2023, those lineages were replaced by BA.2.75.5, BN.1, BN.1.4, BQ.1, BQ.1.1, BQ.1.1.23, CH.1.1, CM.4 and XBK. Starting February 2023, we observed a gradual emergence and dominance of the recombinant XBB and its sub-lineages (XBB.1, XBB.1.5, XBB.1.5.2, XBB.1.5.3, XBB.1.9, XBB.1.9.1, XBB.1.9.2, XBB.1.16, XBB.1.22 and XBB.1.42).

CONCLUSIONS

The timely detection and characterization of SARS-CoV-2 variants is important to reduce transmission through established disease control measures and to avoid introductions into animal populations that could lead to serious public health implications.

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.

Plant-Derived Natural Compounds as an Emerging Antiviral in Combating COVID-19

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a human virus that burst at Wuhan in China and spread quickly over the world, leading to millions of deaths globally. The journey of this deadly virus to different mutant strains is still ongoing. The plethora of drugs and vaccines have been tested to cope up this pandemic. The herbal plants and different spices have received great attention during pandemic, because of their anti-inflammatory, and immunomodulatory properties in treating viruses and their symptoms. Also, it has been shown that nano-formulation of phytochemicals has potential therapeutic effect against COVID-19. Furthermore, the plant derived compound nano-formulation specifically increases its antiviral property by enhancing its bioavailability, solubility, and target-specific delivery system. This review highlights the potentiality of herbal plants and their phytochemical against SARS-CoV-2 utilizing different mechanisms such as blocking the ACE-2 receptors, inhibiting the main proteases, binding spike proteins and reducing the cytokine storms.

Dynamics of water-mediated interaction effects on the stability and transmission of Omicron

SARS-Cov-2 Omicron variant and its highly transmissible sublineages amidst news of emerging hybrid variants strengthen the evidence of its ability to rapidly spread and evolve giving rise to unprecedented future waves. Owing to the presence of isolated RBD, monomeric and trimeric Cryo-EM structures of spike protein in complex with ACE2 receptor, comparative analysis of Alpha, Beta, Gamma, Delta, and Omicron assist in a rational assessment of their probability to evolve as new or hybrid variants in future. This study proposes the role of hydration forces in mediating Omicron function and dynamics based on a stronger interplay between protein and solvent with each Covid wave. Mutations of multiple hydrophobic residues into hydrophilic residues underwent concerted interactions with water leading to variations in charge distribution in Delta and Omicron during molecular dynamics simulations. Moreover, comparative analysis of interacting moieties characterized a large number of mutations lying at RBD into constrained, homologous and low-affinity groups referred to as mutational drivers inferring that the probability of future mutations relies on their function. Furthermore, the computational findings reveal a significant difference in angular distances among variants of concern due 3 amino acid insertion (EPE) in Omicron variant that not only facilitates tight domain organization but also seems requisite for characterization of mutational processes. The outcome of this work signifies the possible relation between hydration forces, their impact on conformation and binding affinities, and viral fitness that will significantly aid in understanding dynamics of drug targets for Covid-19 countermeasures. The emerging scenario is that hydration forces and hydrophobic interactions are crucial variables to probe in mutational analysis to explore conformational landscape of macromolecules and reveal the molecular origins of protein behaviors.

Transient Expression in HEK-293 Cells in Suspension Culture as a Rapid and Powerful Tool: SARS-CoV-2 N and Chimeric SARS-CoV-2N-CD154 Proteins as a Case Study

In a previous work, we proposed a vaccine chimeric antigen based on the fusion of the SARS-CoV-2 N protein to the extracellular domain of the human CD40 ligand (CD154). This vaccine antigen was named N-CD protein and its expression was carried out in HEK-293 stably transfected cells, grown in adherent conditions and serum-supplemented medium. The chimeric protein obtained in these conditions presented a consistent pattern of degradation. The immunization of mice and monkeys with this chimeric protein was able to induce a high N-specific IgG response with only two doses in pre-clinical experiments. In order to explore ways to diminish protein degradation, in the present work, the N and N-CD proteins were produced in suspension cultures and serum-free media following transient transfection of the HEK-293 clone 3F6, at different scales, including stirred-tank controlled bioreactors. The results showed negligible or no degradation of the target proteins. Further, clones stably expressing N-CD were obtained and adapted to suspension culture, obtaining similar results to those observed in the transient expression experiments in HEK-293-3F6. The evidence supports transient protein expression in suspension cultures and serum-free media as a powerful tool to produce in a short period of time high levels of complex proteins susceptible to degradation, such as the SARS-CoV-2 N protein.

Structural understanding of SARS-CoV-2 virus entry to host cells

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a major global health concern associated with millions of fatalities worldwide. Mutant variants of the virus have further exacerbated COVID-19 mortality and infection rates, emphasizing the urgent need for effective preventive strategies. Understanding the viral infection mechanism is crucial for developing therapeutics and vaccines. The entry of SARS-CoV-2 into host cells is a key step in the infection pathway and has been targeted for drug development. Despite numerous reviews of COVID-19 and the virus, there is a lack of comprehensive reviews focusing on the structural aspects of viral entry. In this review, we analyze structural changes in Spike proteins during the entry process, dividing the entry process into prebinding, receptor binding, proteolytic cleavage, and membrane fusion steps. By understanding the atomic-scale details of viral entry, we can better target the entry step for intervention strategies. We also examine the impacts of mutations in Spike proteins, including the Omicron variant, on viral entry. Structural information provides insights into the effects of mutations and can guide the development of therapeutics and vaccines. Finally, we discuss available structure-based approaches for the development of therapeutics and vaccines. Overall, this review provides a detailed analysis of the structural aspects of SARS-CoV-2 viral entry, highlighting its significance in the development of therapeutics and vaccines against COVID-19. Therefore, our review emphasizes the importance of structural information in combating SARS-CoV-2 infection.

Impact of Sars-CoV-2 Prophylaxis with Tixagevimab-Cilgavimab in High-Risk Patients with B-Cell Malignancies: A Single-Center Retrospective Study

Severe Acute Respiratory Syndrome CoronaVirus‐2 (SARS‐CoV‐2) infection can result in different clinical manifestations (COVID-19), starting from asymptomatic disease to life threatening respiratory insufficiency. Onco-haematologic patients are at higher risk to develop severe COVID-19. In particular, patients affected by lymphoproliferative diseases, given the impaired cell-mediated and antibody-mediated immunity and treatment toxicity, develop more often a symptomatic and a more serious disease of Covid-19. Various therapeutic and prophylactic agents are being used against COVID‐19 such as antiviral drugs, vaccines and antiviral S‐protein monoclonal antibodies. Pre-exposure prophylaxis with AZD442/Evusheld (tixagevimab-cilgavimab) may be a complementary strategy to decrease the incidence or severity of COVID-19 for patients with B-cell malignancies. Tixagevimab-cilgavimab is a combination of two monoclonal antibodies that bind SARS-CoV-2 spike protein and inhibits the attachment to the surface of cells, preventing viral entry in the cell and COVID-19 development. In the setting of hematology real-life, few data are available on the impact of pre-exposure prophylaxis, given the multiple factors involved in the clinical behavior of SARS-CoV-2 . Our aim was to evaluate the clinical benefit and the safety of this strategy at our center.

Covalent Inhibitors from Saudi Medicinal Plants Target RNA-Dependent RNA Polymerase (RdRp) of SARS-CoV-2

COVID-19, a disease caused by SARS-CoV-2, has caused a huge loss of human life, and the number of deaths is still continuing. Despite the lack of repurposed drugs and vaccines, the search for potential small molecules to inhibit SARS-CoV-2 is in demand. Hence, we relied on the drug-like characters of ten phytochemicals (compounds 1-10) that were previously isolated and purified by our research team from Saudi medicinal plants. We computationally evaluated the inhibition of RNA-dependent RNA polymerase (RdRp) by compounds 1-10. Non-covalent (reversible) docking of compounds 1-10 with RdRp led to the formation of a hydrogen bond with template primer nucleotides (A and U) and key amino acid residues (ASP623, LYS545, ARG555, ASN691, SER682, and ARG553) in its active pocket. Covalent (irreversible) docking revealed that compounds 7, 8, and 9 exhibited their irreversible nature of binding with CYS813, a crucial amino acid in the palm domain of RdRP. Molecular dynamic (MD) simulation analysis by RMSD, RMSF, and Rg parameters affirmed that RdRP complexes with compounds 7, 8, and 9 were stable and showed less deviation. Our data provide novel information on compounds 7, 8, and 9 that demonstrated their non-nucleoside and irreversible interaction capabilities to inhibit RdRp and shed new scaffolds as antivirals against SARS-CoV-2.

Some common deleterious mutations are shared in SARS-CoV-2 genomes from deceased COVID-19 patients across continents

The identification of deleterious mutations in different variants of SARS-CoV-2 and their roles in the morbidity of COVID-19 patients has yet to be thoroughly investigated. To unravel the spectrum of mutations and their effects within SARS-CoV-2 genomes, we analyzed 5,724 complete genomes from deceased COVID-19 patients sourced from the GISAID database. This analysis was conducted using the Nextstrain platform, applying a generalized time-reversible model for evolutionary phylogeny. These genomes were compared to the reference strain (hCoV-19/Wuhan/WIV04/2019) using MAFFT v7.470. Our findings revealed that SARS-CoV-2 genomes from deceased individuals belonged to 21 Nextstrain clades, with clade 20I (Alpha variant) being the most predominant, followed by clade 20H (Beta variant) and clade 20J (Gamma variant). The majority of SARS-CoV-2 genomes from deceased patients (33.4%) were sequenced in North America, while the lowest percentage (0.98%) came from Africa. The 'G' clade was dominant in the SARS-CoV-2 genomes of Asian, African, and North American regions, while the 'GRY' clade prevailed in Europe. In our analysis, we identified 35,799 nucleotide (NT) mutations throughout the genome, with the highest frequency (11,402 occurrences) found in the spike protein. Notably, we observed 4150 point-specific amino acid (AA) mutations in SARS-CoV-2 genomes, with D614G (20%) and N501Y (14%) identified as the top two deleterious mutations in the spike protein on a global scale. Furthermore, we detected five common deleterious AA mutations, including G18V, W45S, I33T, P30L, and Q418H, which play a key role in defining each clade of SARS-CoV-2. Our novel findings hold potential value for genomic surveillance, enabling the monitoring of the evolving pattern of SARS-CoV-2 infection, its emerging variants, and their impact on the development of effective vaccination and control strategies.