SARS-CoV-2 variants and vulnerability at the global level

Epidemiology of bacterial respiratory tract infections during the pre-pandemic, COVID-19 pandemic and post-pandemic era: A retrospective study of hospitalized adults in northern Greece between 2018 and 2023

INTRODUCTION

The COVID-19 pandemic has had impact on global healthcare and respiratory disease patterns. The aim was to evaluate the changes in positive respiratory cultures during the pandemic.

METHODS

A retrospective analysis of respiratory specimens in Papanikolaou Hospital during 2018-2023 was performed. In total, 18,852 samples (12,277 males, 6575 females) of respiratory samples were recorded.

RESULTS

During 2018-2019, 684 BAL samples were received, of which 12.3 % were positive. Positive pharyngeal smears constituted 24.8 %, compared to 18.5 % in pandemic years, and 29.6 % in 2023. In PTC, pre-pandemic, positives were 12.3 %, while in 2021 the maximum percentage of positives (21.9 %) was observed. Positive levels remained high in 2023 (18.3 %). Concerning bronchial secretions, there was an increase (55.3 % in 2022 vs 47.0 % in 2019). The predominant bacteria were Acinetobacter spp, Klebsiella spp and Pseudomonas spp.

CONCLUSION

Except for the bronchial secretions, the rest of the respiratory specimens do not exhibit any definite trends.

Neutralizing antibodies and safety of a COVID-19 vaccine against SARS-CoV-2 wild-type and Omicron variants in solid cancer patients

OBJECTIVE

The aim of this study was to assess the seroconversion rate and percent inhibition of neutralizing antibodies against the wild-type and Omicron variants of SARS-CoV-2 in patients with solid cancer who received two COVID-19 vaccine doses by comparing chemotherapy and nonchemotherapy groups.

METHODS

This prospective cohort study enrolled 115 cancer patients from Maharaj Nakorn Chiang Mai Hospital, Sriphat Medical Center, Faculty of Medicine, Chiang Mai University, and Chiang Mai Klaimor Hospital, Chiang Mai, Thailand, between August 2021 and February 2022, with data from 91 patients who received two COVID-19 vaccine doses analyzed. Participants received vaccines as part of their personal vaccination programs, including various mRNA and non-mRNA vaccine combinations. Blood samples were collected at baseline, on day 28, and at 6 months post-second dose to assess neutralizing antibodies. The primary outcome was the seroconversion rate against the wild-type and Omicron variants on day 28. Secondary outcomes included seroconversion at 6 months, factors associated with seroconversion, and safety.

RESULTS

Among the participants, 45% were receiving chemotherapy. On day 28, seroconversion rates were 77% and 62% for the wild-type and Omicron variants, respectively. Chemotherapy did not significantly affect seroconversion rates (p = 0.789 for wild type, p = 0.597 for Omicron). The vaccine type administered was positively correlated with seroconversion, with an adjusted odds ratio (95% confidence interval) of 25.86 (1.39-478.06) for the wild type and 17.38 (3.65-82.66) for the Omicron variant with the primary heterologous vaccine regimen. Grades 1 and 2 adverse events were observed in 34.0% and 19.7% of participants, respectively.

CONCLUSIONS

Despite the lower seroconversion rate against the Omicron variant, no significant difference was observed between the chemotherapy and nonchemotherapy groups. COVID-19 vaccinations demonstrated good tolerability in this cohort. These findings highlight the importance of vaccine safety and immunogenicity in cancer patients and can inform tailored vaccination strategies for this vulnerable population.

The PDZ domain of the E protein in SARS-CoV induces carcinogenesis and poor prognosis in LUAD

BACKGROUND

In both lung adenocarcinoma (LUAD) and severe acute respiratory syndrome (SARS), uncontrolled inflammation can be detected in lung tissue. The PDZ-binding motif (PBM) in the SARS-CoV-1 E protein has been demonstrated to be a virulence factor that induces a cytokine storm.

METHODS

To identify gene expression fluctuations induced by PBM, microarray sequencing data of lung tissue infected with wild-type (SARS-CoV-1-E-wt) or recombinant virus (SARS-CoV-1-E-mutPBM) were analyzed, followed by functional enrichment analysis. To understand the role of the screened genes in LUAD, overall survival and immune correlation were calculated.

RESULTS

A total of 12 genes might participate in the initial and developmental stages of LUAD through expression variation and mutation. Moreover, dysregulation of a total of 12 genes could lead to a poorer prognosis. In addition, the downregulation of MAMDC2 and ITGA8 by PBM could also affect patient prognosis. Although the conserved PBM (-D-L-L-V-) can be found at the end of the carboxyl terminus in multiple E proteins of coronaviruses, the specific function of each protein depends on the entire amino acid sequence.

CONCLUSIONS

In summary, PBM containing the SARS-CoV-1 E protein promoted the carcinogenesis of LUAD by dysregulating important gene expression profiles and subsequently influencing the immune response and overall prognosis.

Memory T Cells Subpopulations in a Cohort of COVID-19 Vaccinated or Recovered Subjects

Following viral infection, antigen-restricted T lymphocytes are activated and recognize infected cells to eliminate them. A subset of T cells differentiates into memory lymphocytes able to counteract viral rechallenge in a faster and enhanced way. SARS-CoV-2 can escape immune responses leading to a poor clinical outcome. Immune escape can be associated with the failure of the development of T cell memory compartments. The aim of this study is to characterize the T memory subsets and to test the immune response against class I- and II-restricted immunodominant epitopes shared by ancestral and SARS-CoV-2 variants strains. T memory subsets and recognition of SARS-CoV-2S Spike-specific epitopes were analyzed by flow cytometry on 14 fully vaccinated healthy donors (HDV) and 18 COVID-19 recovered patients (CD). The results obtained showed that CD8+ T naïve subset numbers decreased in association with a significant increase of the effector memory T cell subset whereas there was a small increase in the percentage of SARS-CoV-2 antigen-restricted T clones in both CD4+ and CD8+ subset in the CD compared to HDV sample. Collectively, these features may reflect a broader cytotoxic T cell repertoire stimulated by the virus during the natural infection compared to the spike-restricted response activated during vaccination.

Combating Emerging Respiratory Viruses: Lessons and Future Antiviral Strategies

Emerging viral diseases, including seasonal illnesses and pandemics, pose significant global public health risks. Respiratory viruses, particularly coronaviruses and influenza viruses, are associated with high morbidity and mortality, imposing substantial socioeconomic burdens. This review focuses on the current landscape of respiratory viruses, particularly influenza and SARS-CoV-2, and their antiviral treatments. It also discusses the potential for pandemics and the development of new antiviral vaccines and therapies, drawing lessons from past outbreaks to inform future strategies for managing viral threats.

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.

In-silico evaluation of the T-cell based immune response against SARS-CoV-2 omicron variants

During of COVID-19 pandemic, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has continuously evolved, resulting in the emergence of several new variants of concerns (VOCs) with numerous mutations. These VOCs dominate in various regions due to increased transmissibility and antibody evasion, potentially reducing vaccine effectiveness. Nonetheless, it remains uncertain whether the recent SARS-CoV-2 VOCs have the ability to circumvent the T cell immunity elicited by either COVID-19 vaccination or natural infection. To address this, we conducted in-silico analysis to examine the impact of VOC-specific mutations at the epitope level and T cell cross-reactivity with the ancestral SARS-CoV-2. According to the in-silico investigation, T cell responses triggered by immunization or prior infections still recognize the variants in spite of mutations. These variants are expected to either maintain their dominant epitope HLA patterns or bind with new HLAs, unlike the epitopes of the ancestral strain. Our findings indicate that a significant proportion of immuno-dominant CD8 + and CD4 + epitopes are conserved across all the variants, implying that existing vaccines might maintain efficacy against new variations. However, further in-vitro and in-vivo studies are needed to validate the in-silico results and fully elucidate immune sensitivities to VOCs.

Establishment of national standards of SARS-CoV-2 variants in Taiwan

Objectives

In response to the pandemic, the Taiwan Food and Drug Administration (TFDA) established an initial SARS-CoV-2 RNA national standard based on the original Wuhan strain. However, with the depletion of the first national standard and continued mutation of the virus, the establishment of new national standards was imminent.

Methods

Hence, new candidate national standards were established by heat-inactivation for 30 min for six representative strains of SARS-CoV-2, comprising the original strain and five variants with anticipated concentrations of 7.70 Log10 international units (IU)/mL each. To enhance the credibility of these national standards, the TFDA extended invitations to both domestic and international institutions to participate in a collaborative study. A total of eight participants contributed eleven datasets, incorporating two methods and targeting four distinct genes.

Results

Based on these collective findings, the quantified viral RNA concentrations for each SARS-CoV-2 national standard strain are 7.69, 7.70, 7.69, 7.44, 7.52, and 7.29 Log10 IU/mL with Wuhan, alpha, beta, gamma, delta, and omicron strain, respectively.

Conclusions

These newly established national standards will continue to be made available to the industry, serving as a fundamental reference for the development and quality control of nucleic acid in vitro diagnostic (IVD) reagents in Taiwan.

Adverse drug reactions associated with COVID-19 management

The emergence of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) outbreak, which causes COVID-19, had a devastating impact on both people's lives and the global economy. During the course of the pandemic, the lack of specific drugs or treatments tailored for COVID-19 led to extensive repurposing of existing drugs in the pursuit of effective treatments. Some drug molecules demonstrated efficacy, while others proved ineffective. In this context, the approach of drug repurposing emerged as a novel strategy for combating COVID-19. Repurposed drugs and biologics have shown effectiveness, leading to improved clinical outcomes among patients with COVID-19. Similarly, It is equally important to assess the risk-benefit ratio associated with drugs and biologics adapted for COVID-19 treatment. Herein, we primarily focus on evaluating adverse drug events linked to repurposed COVID-19 medications, repurposed biologics, and COVID-specific drug molecules.

Immuno-inflammatory and organ dysfunction markers in severe COVID-19 patients

Infection with the SARS-CoV-2 virus may induce some complications among people who experience mild to moderate respiratory illness and some of them recover without requiring special treatment. Albeit, some individuals become seriously reached risk points and require special medical attention especially older people and people who suffer from chronic diseases. Serum and whole blood samples were collected from confirmed infected persons with SARS CoV-2 by real-time PCR and the control group. All lab. Investigations were performed using Cobas 6000. Significant differences were noted between patients compared to the control group in the Mean ± SD of IL-6 (76.06 ± 7.60 vs 3.61 ± 0.296 pg/ml), Procalcitonin (0.947 ± 0.117 vs 0.061 ± 0.007 ng/ml), CRP (125.3 ± 7.560 vs 4.027 ± 0.251 mg/dl), ALT (154.8 ± 30.47 vs 49.75 ± 2.977 IU/L) and AST (70.83 ± 9.215 vs 27.23 ± 1.767) respectively. While other parameters were also showed significant differences were noted between patients compared to the control group for D-Dimmer, PT, PTT, LDH, Ferritin, WBC, Lymphocyte and Creatinine. The results reached that the effect of SARS CoV-2 and cytokine storm was clear on the body's organs through vital biomarker investigations that were performed in this study.

Mortality and functional outcomes 18 months after hospitalization for COVID-19 in geriatric patients: a multicentric cohort study

BACKGROUND

Few data are available on the long-term mortality and functional status of geriatric patients surviving after hospitalization for COVID-19. We compared the mortality and functional status 18 months after hospitalization for geriatric patients who were hospitalized for COVID-19 or another diagnosis.

METHODS

This was a multicentric cohort study in Paris from January to June 2021. We included patients aged 75 years and over who were hospitalized with COVID-19 or not during this period and compared their vital and functional status 18 months after hospitalization.

RESULTS

We included 254 patients (63 hospitalized for COVID-19). As compared with patients hospitalized for other reasons, those hospitalized for COVID-19 were younger (mean [SD] age 86 [6.47] vs. 88 [6.41] years, p = 0.03), less frail (median Clinical Frailty Scale score 5 [4-6] vs. 6 [4-6], p 0.007) and more independent at baseline (median activities of daily living score 5.5 [4-6] vs. 5 [3.5-6], p 0.03; instrumental activities of daily living score 3 [1-4] vs. 2 [0-3], p 0.04). At 18 months, 50.8% (n = 32/63) of COVID-19 patients had died versus 66% (n = 126/191) of non-COVID-19 patients (p 0.03). On multivariate analysis, COVID-19 positivity was not significantly associated with 18-month mortality (adjusted hazard ratio 0.67, 95% confidence interval 0.40 to 1.13). At 18 months, the two groups did not differ in activities of daily living or frailty scores.

CONCLUSIONS

In this multicenter study of long-term mortality in geriatric patients discharged alive after hospitalization, positive COVID-19 status was not associated with excess mortality.

Current Progress, Challenges and Prospects in the Development of COVID-19 Vaccines

The COVID-19 pandemic has resulted in over 772 million confirmed cases, including nearly 7 million deaths, according to the World Health Organization (WHO). Leveraging rapid development, accelerated vaccine approval processes, and large-scale production of various COVID-19 vaccines using different technical platforms, the WHO declared an end to the global health emergency of COVID-19 on May 5, 2023. Current COVID-19 vaccines encompass inactivated, live attenuated, viral vector, protein subunit, nucleic acid (DNA and RNA), and virus-like particle (VLP) vaccines. However, the efficacy of these vaccines is diminishing due to the constant mutation of SARS-CoV-2 and the heightened immune evasion abilities of emerging variants. This review examines the impact of the COVID-19 pandemic, the biological characteristics of the virus, and its diverse variants. Moreover, the review underscores the effectiveness, advantages, and disadvantages of authorized COVID-19 vaccines. Additionally, it analyzes the challenges, strategies, and future prospects of developing a safe, broad-spectrum vaccine that confers sufficient and sustainable immune protection against new variants of SARS-CoV-2. These discussions not only offer insight for the development of next-generation COVID-19 vaccines but also summarize experiences for combating future emerging viruses.

Transforming health care systems towards high-performance organizations: qualitative study based on learning from COVID-19 pandemic in the Basque Country (Spain)

BACKGROUND

The COVID-19 pandemic is one of the worst health catastrophes of the last century, which caused severe economic, political, and social consequences worldwide. Despite these devastating consequences, lessons learned provide a great opportunity that can drive the reform of health systems to become high-performing, effective, equitable, accessible, and sustainable organisations. This work identifies areas in which changes must be encouraged that will enable health systems to deal effectively with current and future challenges, beyond COVID-19.

METHODS

A realist design was chosen, based on qualitative data collection techniques, content analysis and triangulation to identify key domains of organizational interventions behind the changes implemented to react to the COVID-19 pandemic in the Basque Country. Twenty key informants were used as an expert source of information. Thematic analysis was done using the Framework Method.

RESULTS

The analysis of the interviews resulted in the identification of 116 codes, which were reviewed and agreed upon by the researchers. Following the process of methodological analysis, these codes were grouped into domains: seven themes and 23 sub-themes. Specifically, the themes are: responsiveness, telehealth, integration, knowledge management, professional roles, digitisation, and organisational communication. The detailed description of each theme and subtheme is presented.

CONCLUSIONS

The findings of this work pretend to guide the transformation of health systems into organisations that can improve the health of their populations and provide high quality care. Such a multidimensional and comprehensive reform encompasses both strategic and operational actions in diverse areas and requires a broad and sustained political, technical, and financial commitment.

Analysis of two sequential SARS-CoV-2 outbreaks on a haematology-oncology ward and the role of infection prevention

Two SARS-CoV-2 nosocomial outbreaks occurred on the haematology ward of our hospital. Patients on the ward were at high risk for severe infection because of their immunocompromised status. Whole Genome Sequencing proved transmission of a particular SARS-CoV-2 variant in each outbreak. The first outbreak (20 patients/31 healthcare workers (HCW)) occurred in November 2020 and was caused by a variant belonging to lineage B.1.221. At that time, there were still uncertainties on mode of transmission of SARS-CoV-2, and vaccines nor therapy were available. Despite HCW wearing II-R masks in all patient contacts and FFP-2 masks during aerosol generating procedures (AGP), the outbreak continued. Therefore, extra measures were introduced. Firstly, regular PCR-screening of asymptomatic patients and HCW; positive patients were isolated and positive HCW were excluded from work as a rule and they were only allowed to resume their work if a follow-up PCR CT-value was ≥30 and were asymptomatic or having only mild symptoms. Secondly, the use of FFP-2 masks was expanded to some long-lasting, close-contact, non-AGPs. After implementing these measures, the incidence of new cases declined gradually. Thirty-seven percent of patients died due to COVID-19. The second outbreak (10 patients/2 HCW) was caused by the highly transmissible omicron BA.1 variant and occurred in February 2022, where transmission occurred on shared rooms despite the extra infection control measures. It was controlled much faster, and the clinical impact was low as the majority of patients was vaccinated; no patients died and symptoms were relatively mild in both patients and HCW.

Small-molecule antiviral treatments for COVID-19: A systematic review and network meta-analysis

OBJECTIVE

This study aimed to explore the efficacy and safety of small-molecule antivirals for treating coronavirus disease 2019 (COVID-19).

METHODS

Seven databases were searched from their inception to 01 June 2023. The risk of bias in randomised controlled trials and retrospective studies was evaluated individually using the Cochrane risk-of-bias tool and Newcastle Ottawa Scale.

RESULTS

In total, 160 studies involving 933 409 COVID-19 patients were evaluated. Compared with placebo or standard of care, proxalutamide demonstrated remarkable efficacy in reducing mortality rates, hospitalisation rates, serious adverse events, and the need for mechanical ventilation. Furthermore, it significantly enhanced both the rate of clinical improvement and expedited the duration of clinical recovery when compared with control groups. In patients with mild-to-moderate COVID-19, proxalutamide exhibited the above advantages, except for mortality reduction. Triazavirin was the most effective treatment for reducing the time required for viral clearance and improving the discharge rate. Leritrelvir and VV116 were ranked first in terms of enhancing the viral clearance rate on days 7 and 14, respectively. Molnupiravir was the most effective treatment for reducing the need for oxygen support. Overall, these findings remained consistent across the various subgroups.

CONCLUSIONS

A thorough evaluation of effectiveness, applicable to both mild-to-moderate and unstratified populations, highlights the specific advantages of proxalutamide, nirmatrelvir/ritonavir, triazavirin, azvudine, molnupiravir, and VV116 in combating COVID-19. Additional clinical data are required to confirm the efficacy and safety of simnotrelvir/ritonavir and leritrelvir. The safety profiles of these antivirals were deemed acceptable.

Genetic characteristics of SARS-CoV-2 virus variants observed upon three waves of the COVID-19 pandemic in Ukraine between February 2021-January 2022

The aim

of our study was to identify and characterize the SARS-CoV-2 variants in COVID-19 patients' samples collected from different regions of Ukraine to determine the relationship between SARS-CoV-2 phylogenetics and COVID-19 epidemiology.

Patients and methods

Samples were collected from COVID-19 patients during 2021 and the beginning of 2022 (401 patients). The SARS-CoV-2 genotyping was performed by parallel whole genome sequencing.

Results

The obtained SARS-CoV-2 genotypes showed that three waves of the COVID-19 pandemic in Ukraine were represented by three main variants of concern (VOC), named Alpha, Delta and Omicron; each VOC successfully replaced the earlier variant. The VOC Alpha strain was presented by one B.1.1.7 lineage, while VOC Delta showed a spectrum of 25 lineages that had different prevalence in 19 investigated regions of Ukraine. The VOC Omicron in the first half of the pandemic was represented by 13 lines that belonged to two different clades representing B.1 and B.2 Omicron strains. Each of the three epidemic waves (VOC Alpha, Delta, and Omicron) demonstrated their own course of disease, associated with genetic changes in the SARS-CoV-2 genome. The observed epidemiological features are associated with the genetic characteristics of the different VOCs, such as point mutations, deletions and insertions in the viral genome. A phylogenetic and transmission analysis showed the different mutation rates; there were multiple virus sources with a limited distribution between regions.

Conclusions

The evolution of SARS-CoV-2 virus and high levels of morbidity due to COVID-19 are still registered in the world. Observed multiple virus sourses with the limited distribution between regions indicates the high efficiency of the anti-epidemic policy pursued by the Ministry of Health of Ukraine to prevent the spread of the epidemic, despite the low level of vaccination of the Ukrainian population.

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.

Molecular Epidemiology of Omicron CH.1.1 Lineage: Genomic and Phenotypic Data Perspective

BACKGROUND

The Omicron variant (B.1.1.529 lineage) of SARS-CoV-2 represents a substantial global health challenge due to its high transmissibility and potential resistance to immunity from vaccines or previous infections. Among the rapidly evolving Omicron lineages, the BA.2.75 and the emerging CH.1.1 have garnered attention. While BA.2.75 is marked by mutations that may enhance immune evasion, CH.1.1 is distinguished by the S: L452R mutation, linked to increased pathogenicity and transmission. Initially identified in India by the end of 2021, these variants have exhibited global dissemination, signaling an urgent need to track and analyze their progression.

METHODS

In this study, the genomic and geographical distribution data of CH.1.1 were collected from the Global Initiative on Sharing Avian Influenza Data (GISAID), PANGOLIN, CoV-Spectrum, and NextStrain databases. Due to the unavailability of epidemiological and genomic data of the CH.1.1 lineage, PubMed and ScienceDirect were used as sources of the phenotypic data of the lineage variations. Amino acid variations utilized in the data mining included S: R346T, S: K444T, S: L452R, and S: F486S.

RESULTS

The current epidemiological data indicate that CH.1.1 is more likely to become one of the dominant spreading lineages in the United Kingdom, New Zealand, Australia, and the United States based on a 32% growth advantage, present CH.1.1 lineage cases number, and the amino acid variation's impact.

CONCLUSION

A significant increase in the newly detected lineage CH.1.1 is highly anticipated. The rise in the detected sequences number from 13,231 on January 21, 2023, to 23,181 on February 6, 2023, supports the prediction and growth advantage of the lineage detected cases. Increases in viral transmissibility caused by higher affinity to ACE2 receptors and immune evasion are deduced from amino acid variations analyzed in the study.

COVID-19 Vaccines: Where Did We Stand at the End of 2023?

Vaccine development against SARS-CoV-2 has been highly successful in slowing down the COVID-19 pandemic. A wide spectrum of approaches including vaccines based on whole viruses, protein subunits and peptides, viral vectors, and nucleic acids has been developed in parallel. For all types of COVID-19 vaccines, good safety and efficacy have been obtained in both preclinical animal studies and in clinical trials in humans. Moreover, emergency use authorization has been granted for the major types of COVID-19 vaccines. Although high safety has been demonstrated, rare cases of severe adverse events have been detected after global mass vaccinations. Emerging SARS-CoV-2 variants possessing enhanced infectivity have affected vaccine protection efficacy requiring re-design and re-engineering of novel COVID-19 vaccine candidates. Furthermore, insight is given into preparedness against emerging SARS-CoV-2 variants.

Rapid classification of SARS-CoV-2 variant strains using machine learning-based label-free SERS strategy

The spread of COVID-19 over the past three years is largely due to the continuous mutation of the virus, which has significantly impeded global efforts to prevent and control this epidemic. Specifically, mutations in the amino acid sequence of the surface spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have directly impacted its biological functions, leading to enhanced transmission and triggering an immune escape effect. Therefore, prompt identification of these mutations is crucial for formulating targeted treatment plans and implementing precise prevention and control measures. In this study, the label-free surface-enhanced Raman scattering (SERS) technology combined with machine learning (ML) algorithms provide a potential solution for accurate identification of SARS-CoV-2 variants. We establish a SERS spectral database of SARS-CoV-2 variants and demonstrate that a diagnostic classifier using a logistic regression (LR) algorithm can provide accurate results within 10 min. Our classifier achieves 100% accuracy for Beta (B.1.351/501Y.V2), Delta (B.1.617), Wuhan (COVID-19) and Omicron (BA.1) variants. In addition, our method achieves 100% accuracy in blind tests of positive and negative human nasal swabs based on the LR model. This method enables detection and classification of variants in complex biological samples. Therefore, ML-based SERS technology is expected to accurately discriminate various SARS-CoV-2 variants and may be used for rapid diagnosis and therapeutic decision-making.

Immunogenicity of mucosal COVID-19 vaccine candidates based on the highly attenuated vesicular stomatitis virus vector (VSVMT) in golden syrian hamster

COVID-19 is caused by coronavirus SARS-CoV-2. Current systemic vaccines generally provide limited protection against viral replication and shedding within the airway. Recombinant VSV (rVSV) is an effective vector which inducing potent and comprehensive immunities. Currently, there are two clinical trials investigating COVID-19 vaccines based on VSV vectors. These vaccines were developed with spike protein of WA1 which administrated intramuscularly. Although intranasal route is ideal for activating mucosal immunity with VSV vector, safety is of concern. Thus, a highly attenuated rVSV with three amino acids mutations in matrix protein (VSVMT) was developed to construct safe mucosal vaccines against multiple SARS-CoV-2 variants of concern. It demonstrated that spike protein mutant lacking 21 amino acids in its cytoplasmic domain could rescue rVSV efficiently. VSVMT indicated improved safeness compared with wild-type VSV as the vector encoding SARS-CoV-2 spike protein. With a single-dosed intranasal inoculation of rVSVΔGMT-SΔ21, potent SARS-CoV-2 specific neutralization antibodies could be stimulated in animals, particularly in term of mucosal and cellular immunity. Strikingly, the chimeric VSV encoding SΔ21 of Delta-variant can induce more potent immune responses compared with those encoding SΔ21 of Omicron- or WA1-strain. VSVMT is a promising platform to develop a mucosal vaccine for countering COVID-19.

SARS-CoV-2 infection induces expression and secretion of lipocalin-2 and regulates iron in a human lung cancer xenograft model

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection leads to various clinical symptoms including anemia. Lipocalin-2 has various biological functions, including defense against bacterial infections through iron sequestration, and it serves as a biomarker for kidney injury. In a human protein array, we observed increased lipocalin-2 expression due to parental SARS-CoV-2 infection in the Calu-3 human lung cancer cell line. The secretion of lipocalin-2 was also elevated in response to parental SARS-CoV-2 infection, and the SARS-CoV-2 Alpha, Beta, and Delta variants similarly induced this phenomenon. In a Calu-3 implanted mouse xenograft model, parental SARSCoV- 2 and Delta variant induced lipocalin-2 expression and secretion. Additionally, the iron concentration increased in the Calu-3 tumor tissues and decreased in the serum due to infection. In conclusion, SARS-CoV-2 infection induces the production and secretion of lipocalin-2, potentially resulting in a decrease in iron concentration in serum. Because the concentration of iron ions in the blood is associated with anemia, this phenomenon could contribute to developing anemia in COVID-19 patients. [BMB Reports 2023; 56(12): 669-674].

Single-cell transcriptomic atlas of distinct early immune responses induced by SARS-CoV-2 Proto or its variants in rhesus monkey

Immune responses induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection play a critical role in the pathogenesis and outcome of coronavirus disease 2019 (COVID-19). However, the dynamic profile of immune responses postinfection by SARS-CoV-2 variants of concern (VOC) is not fully understood. In this study, peripheral blood mononuclear cells single-cell sequencing was performed to determine dynamic profiles of immune response to Prototype, Alpha, Beta, and Delta in a rhesus monkey model. Overall, all strains induced dramatic changes in both cellular subpopulations and gene expression levels at 1 day postinfection (dpi), which associated function including adaptive immune response, innate immunity, and IFN response. COVID-19-related genes revealed different gene profiles at 1 dpi among the four SARS-CoV-2 strains, including genes reported in COVID-19 patients with increased risk of autoimmune disease and rheumatic diseases. Delta-infected animal showed inhibition of translation pathway. B cells, T cells, and monocytes showed much commonality rather than specificity among the four strains. Monocytes were the major responders to SARS-CoV-2 infection, and the response lasted longer in Alpha than the other strains. Thus, this study reveals the early immune responses induced by SARS-CoV-2 Proto or its variants in nonhuman primates, which is important information for controlling rapidly evolving viruses.

SARS-CoV-2 infection as a model to study the effect of cinnamaldehyde as adjuvant therapy for viral pneumonia

BACKGROUND

The recent pandemic outbursts, due to SARS-CoV-2, have highlighted once more the central role of the inflammatory process in the propagation of viral infection. The main consequence of COVID-19 is the induction of a diffuse pro-inflammatory state, also defined as a cytokine storm, which affects different organs, but mostly the lungs. We aimed to prove the efficacy of cinnamaldehyde, the active compound of cinnamon, as an anti-inflammatory compound, able to reduce SARS-CoV-2 induced cytokine storm.

RESULTS

We enrolled 53 COVID-19 patients hospitalized for respiratory failure. The cohort was composed by 39 males and 13 females, aged 65.0 ± 9.8 years. We reported that COVID-19 patients have significantly higher IL-1β and IL-6 plasma levels compared to non-COVID-19 pneumonia patients. In addition, human mononuclear cells (PBMCs) isolated from SARS-CoV-2 infected patients are significantly more prone to release pro-inflammatory cytokines upon stimuli. We demonstrated, using in vitro cell models, that macrophages are responsible for mediating the pro-inflammatory cytokine storm while lung cells support SARS-CoV-2 replication upon viral infection. In this context, cinnamaldehyde administration significantly reduces SARS-CoV-2-related inflammation by inhibiting NLRP3 mediated IL-1β release in both PBMCs and THP-1 macrophages, as well as viral replication in CaLu-3 epithelial cells. Lastly, aerosol-administered cinnamaldehyde was able to significantly reduce IL-1β release in an in vivo lung-inflammatory model.

CONCLUSION

The obtained results suggest the possible use of cinnamaldehyde as a co-adjuvant preventive treatment for COVID-19 disease together with vaccination, but also as a promising dietary supplement to reduce, more broadly, viral induced inflammation.

Raman Fingerprints of SARS-CoV-2 Omicron Subvariants: Molecular Roots of Virological Characteristics and Evolutionary Directions

The latest RNA genomic mutation of SARS-CoV-2 virus, termed the Omicron variant, has generated a stream of highly contagious and antibody-resistant strains, which in turn led to classifying Omicron as a variant of concern. We systematically collected Raman spectra from six Omicron subvariants available in Japan (i.e., BA.1.18, BA.2, BA.4, BA.5, XE, and BA.2.75) and applied machine-learning algorithms to decrypt their structural characteristics at the molecular scale. Unique Raman fingerprints of sulfur-containing amino acid rotamers, RNA purines and pyrimidines, tyrosine phenol ring configurations, and secondary protein structures clearly differentiated the six Omicron subvariants. These spectral characteristics, which were linked to infectiousness, transmissibility, and propensity for immune evasion, revealed evolutionary motifs to be compared with the outputs of genomic studies. The availability of a Raman "metabolomic snapshot", which was then translated into a barcode to enable a prompt subvariant identification, opened the way to rationalize in real-time SARS-CoV-2 activity and variability. As a proof of concept, we applied the Raman barcode procedure to a nasal swab sample retrieved from a SARS-CoV-2 patient and identified its Omicron subvariant by coupling a commercially available magnetic bead technology with our newly developed Raman analyses.

Analysis of spike protein variants evolved in a novel in vivo long-term replication model for SARS-CoV-2

Introduction

The spectrum of SARS-CoV-2 mutations have increased over time, resulting in the emergence of several variants of concern. Persistent infection is assumed to be involved in the evolution of the variants. Calu-3 human lung cancer cells persistently grow without apoptosis and release low virus titers after infection.

Methods

We established a novel in vivo long-term replication model using xenografts of Calu-3 human lung cancer cells in immunodeficient mice. Virus replication in the tumor was monitored for 30 days and occurrence of mutations in the viral genome was determined by whole-genome deep sequencing. Viral isolates with mutations were selected after plaque forming assays and their properties were determined in cells and in K18-hACE2 mice.

Results

After infection with parental SARS-CoV-2, viruses were found in the tumor tissues for up to 30 days and acquired various mutations, predominantly in the spike (S) protein, some of which increased while others fluctuated for 30 days. Three viral isolates with different combination of mutations produced higher virus titers than the parental virus in Calu-3 cells without cytopathic effects. In K18-hACE2 mice, the variants were less lethal than the parental virus. Infection with each variant induced production of cross-reactive antibodies to the receptor binding domain of parental SARS-CoV-2 S protein and provided protective immunity against subsequent challenge with parental virus.

Discussion

These results suggest that most of the SARS-CoV-2 variants acquired mutations promoting host adaptation in the Calu-3 xenograft mice. This model can be used in the future to further study SARS-CoV-2 variants upon long-term replication in vivo.

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.

An Overview of SARS-CoV-2 Etiopathogenesis and Recent Developments in COVID-19 Vaccines

The Coronavirus disease-2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has significantly impacted the health and socioeconomic status of humans worldwide. Pulmonary infection of SARS-CoV-2 results in exorbitant viral replication and associated onset of inflammatory cytokine storm and disease pathology in various internal organs. However, the etiopathogenesis of SARS-CoV-2 infection is not fully understood. Currently, there are no targeted therapies available to cure COVID-19, and most patients are treated empirically with anti-inflammatory and/or anti-viral drugs, based on the disease symptoms. Although several types of vaccines are currently implemented to control COVID-19 and prevent viral dissemination, the emergence of new variants of SARS-CoV-2 that can evade the vaccine-induced protective immunity poses challenges to current vaccination strategies and highlights the necessity to develop better and improved vaccines. In this review, we summarize the etiopathogenesis of SARS-CoV-2 and elaborately discuss various types of vaccines and vaccination strategies, focusing on those vaccines that are currently in use worldwide to combat COVID-19 or in various stages of clinical development to use in humans.

Nano-based techniques: A revolutionary approach to prevent covid-19 and enhancing human awareness

In every century of history, there are many new diseases emerged, which are not even cured by many developed countries. Today, despite of scientific development, new deadly pandemic diseases are caused by microorganisms. Hygiene is considered to be one of the best methods of avoiding such communicable diseases, especially viral diseases. Illness caused by SARS-CoV-2 was termed COVID-19 by the WHO, the acronym derived from "coronavirus disease 2019. The globe is living in the worst epidemic era, with the highest infection and mortality rate owing to COVID-19 reaching 6.89% (data up to March 2023). In recent years, nano biotechnology has become a promising and visible field of nanotechnology. Interestingly, nanotechnology is being used to cure many ailments and it has revolutionized many aspects of our lives. Several COVID-19 diagnostic approaches based on nanomaterial have been developed. The various metal NPs, it is highly anticipated that could be viable and economical alternatives for treating drug resistant in many deadly pandemic diseases in near future. This review focuses on an overview of nanotechnology's increasing involvement in the diagnosis, prevention, and therapy of COVID-19, also this review provides readers with an awareness and knowledge of importance of hygiene.

The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2

Over three years' pandemic of 2019 novel coronavirus disease (COVID-19), multiple variants and novel subvariants have emerged successively, outcompeted earlier variants and become predominant. The sequential emergence of variants reflects the evolutionary process of mutation-selection-adaption of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Amino acid substitution/insertion/deletion in the spike protein causes altered viral antigenicity, transmissibility, and pathogenicity of SARS-CoV-2. Early in the pandemic, D614G mutation conferred virus with advantages over previous variants and increased transmissibility, and it also laid a conservative background for subsequent substantial mutations. The role of genomic recombination in the evolution of SARS-CoV-2 raised increasing concern with the occurrence of novel recombinants such as Deltacron, XBB.1.5, XBB.1.9.1, and XBB.1.16 in the late phase of pandemic. Co-circulation of different variants and co-infection in immunocompromised patients accelerate the emergence of recombinants. Surveillance for SARS-CoV-2 genomic variations, particularly spike protein mutation and recombination, is essential to identify ongoing changes in the viral genome and antigenic epitopes and thus leads to the development of new vaccine strategies and interventions.

Assessment of the Immune Response in Patients with Insulin Resistance, Obesity, and Diabetes to COVID-19 Vaccination

The SARS-CoV-19 pandemic overwhelmed multiple healthcare systems across the world. Patients with underlying medical conditions such as obesity or diabetes were particularly vulnerable, had more severe symptoms, and were more frequently hospitalized. To date, there have been many studies on the severity of SARS-CoV-2 in patients with metabolic disorders, but data on the efficiency of vaccines against COVID-19 are still limited. This paper aims to provide a comprehensive overview of the effectiveness of COVID-19 vaccines in individuals with diabetes, insulin resistance, and obesity. A comparison is made between the immune response after vaccination in patients with and without metabolic comorbidities. Additionally, an attempt is made to highlight the mechanisms of immune stimulation affected by SARS-CoV-2 vaccines and how metabolic comorbidities modulate these mechanisms. The focus is on the most common COVID-19 vaccines, which include mRNA vaccines such as Pfizer-BioNTech and Moderna, as well as viral vector vaccines such as AstraZeneca and Johnson & Johnson. Furthermore, an effort is made to clarify how the functional differences between these vaccines may impact the response in individuals with metabolic disorders, drawing from available experimental data. This review summarizes the current knowledge regarding the post-vaccination response to COVID-19 in the context of metabolic comorbidities such as diabetes, insulin resistance, and obesity.

The anti-SARS-CoV-2 effect and mechanism of Chiehyuan herbal oral protection solution

The Chiehyuan herbal oral protection solution (GB-2) is a herbal mixture commonly utilized in Taiwan for combating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as per traditional Chinese medicine practices. This study assessed the clinical impact of GB-2 through prospective clinical trials. With twice-daily use for a week, GB-2 was shown to diminish the expression of angiotensin-converting enzyme 2 (ACE2) in oral mucosal cells. Moreover, after two weeks of use, it could reduce transmembrane protease, serine 2 (TMRPSS2) expression in these cells. Additionally, in vitro experiments demonstrated that GB-2 lessened the entry efficiency of the Omicron, L452R-D614G, T478K-D614G, and L452R-T478K-D614G variants of the SARS-CoV-2 pseudotyped lentivirus. It also impeded the interaction between ACE2 and the receptor-binding domain (RBD) presenting N501Y-K417N-E484A-G339D-Q493R-G496S-Q498R and L452R-T478K mutations. Glycyrrhizic acid, a major compound in GB-2, also hindered the entry of the Omicron variant (BA.1) of the SARS-CoV-2 pseudotyped lentivirus by obstructing the binding between ACE2 and the RBD presenting the N501Y-K417N-E484A-G339D-Q493R-G496S-Q498R mutation. To sum up, these findings suggest that GB-2 can decrease ACE2 and TMPRSS2 expression in oral mucosal cells. Both glycyrrhizic acid and GB-2 were found to reduce the entry efficiency of the Omicron variant (BA.1) of the SARS-CoV-2 pseudotyped lentivirus and block the binding between ACE2 and the RBD with the N501Y-K417N-E484A-G339D-Q493R-G496S-Q498R mutation. This evidence implies that GB-2 might be a potential candidate for further study as a preventative measure against SARS-CoV-2 infection.

Association between SUMF1 polymorphisms and COVID-19 severity

BACKGROUND

Evidence shows that genetic factors play important roles in the severity of coronavirus disease 2019 (COVID-19). Sulfatase modifying factor 1 (SUMF1) gene is involved in alveolar damage and systemic inflammatory response. Therefore, we speculate that it may play a key role in COVID-19.

RESULTS

We found that rs794185 was significantly associated with COVID-19 severity in Chinese population, under the additive model after adjusting for gender and age (for C allele = 0.62, 95% CI = 0.44-0.88, P = 0.0073, logistic regression). And this association was consistent with this in European population Genetics Of Mortality In Critical Care (GenOMICC: OR for C allele = 0.94, 95% CI = 0.90-0.98, P = 0.0037). Additionally, we also revealed a remarkable association between rs794185 and the prothrombin activity (PTA) in subjects (P = 0.015, Generalized Linear Model).

CONCLUSIONS

In conclusion, our study for the first time identified that rs794185 in SUMF1 gene was associated with the severity of COVID-19.

The importance of equally accessible genomic surveillance in the age of pandemics

Genomic epidemiology is now a core component in investigating the spread of a disease during an outbreak and for future preparedness to tackle emerging zoonoses. During the last decades, several viral diseases arose and emphasized the importance of molecular epidemiology in tracking the dispersal route, supporting proper mitigation measures, and appropriate vaccine development. In this perspective article, we summarized what has been done so far in the genomic epidemiology field and what should be considered in the future. We traced back the methods and protocols employed over time for zoonotic disease response. Either to small outbreaks such as the severe acute respiratory syndrome (SARS) outbreak identified first in 2002 in Guangdong, China, or to a global pandemic like the one that we are experiencing now since 2019 when the severe acute respiratory syndrome 2 (SARS-CoV-2) virus emerged in Wuhan, China, following several pneumonia cases, and subsequently spread worldwide. We explored both the benefits and shortages encountered when relying on genomic epidemiology, and we clearly present the disadvantages of inequity in accessing these tools around the world, especially in countries with less developed economies. For effectively addressing future pandemics, it is crucial to work for better sequencing equity around the globe.

Post-Acute SARS-CoV-2 Symptoms are Fewer, Less Intense Over Time in People Treated with Mono-Clonal Antibodies for Acute Infection

Introduction

Many with post-acute SARS-CoV-2 (PASC) have persistent symptoms impacting physical and cognitive function, decreased health and health-related life quality. Monoclonal antibody (mAb) treatment was available to acutely infected patients which might improve these outcomes.

Purpose

To compare patient perception of PASC symptoms for those receiving bamlanivimab or casirivimab and imdevimab (mAbs) to those not receiving this treatment (non-mAbs). To compare changes between these groups in symptoms, function and quality of life over a 6-month follow-up.

Patients and Methods

Consented adults >28 days post-infection with positive SARS-CoV-2 qPCR or antigen test and SARS-CoV-2 infection between March of 2020 and July of 2022 were enrolled. This prospective, repeated measure observational study reports baseline through 6-month follow-up. Extensive sociodemographic data, detailed medical history, COVID-19 symptom history, and standardized measures of well-being, depression, anxiety, stigma, cognition, symptom assessment, distress, and health status were collected.

Results

323 participants [101 mAb, 221 non-mAb, 52.7±15.5 years, 47.7% male, body mass index (BMI) 31.4±8.4] were analyzed. Fewer symptoms at baseline were reported in mAb versus non-mAb participants (1.06±1.31 vs 1.78±2.15, respectively p=0.0177) 6 months: (0.911±1.276 mAb vs.1.75±2.22 non-mAb, p=0.0427). Both groups showed significant within-group decreases in symptom number (52 to 21 mAb, 126 to 63 non-mAb) and symptom burden (p=0.0088 mAb, p<0.00001 non-mAb). mAb patients had significantly shorter infection-to-baseline interval (days) (120.4±55.3 mAb vs 194.0±89.3 non-mAb, p<0.00001); less frequent history of myocardial infarction (0.0 vs 3.9%, p=0.0464); headache (2.0% vs.11.8%, p=0.0046), rash (3.1% vs 9.9%, p=0.0377), and miscellaneous muscle complaints (2.0% vs 12.3%, p=0.0035), plus significantly better 6-month mood. (2.2% vs 13.2%, p=0.0390).

Conclusion

mAb treated participants had reduced symptom burden and consistently reported fewer symptoms than non-mAb at all time points despite less time since acute illness. Both groups reported a statistically significant decrease in symptoms by 6-month visit with no statistically significant differences between them at follow-up.

SARS-CoV-2 RBD Conjugated to Polyglucin, Spermidine, and dsRNA Elicits a Strong Immune Response in Mice

Despite the rapid development and approval of several COVID vaccines based on the full-length spike protein, there is a need for safe, potent, and high-volume vaccines. Considering the predominance of the production of neutralizing antibodies targeting the receptor-binding domain (RBD) of S-protein after natural infection or vaccination, it makes sense to choose RBD as a vaccine immunogen. However, due to its small size, RBD exhibits relatively poor immunogenicity. Searching for novel adjuvants for RBD-based vaccine formulations is considered a good strategy for enhancing its immunogenicity. Herein, we assess the immunogenicity of severe acute respiratory syndrome coronavirus 2 RBD conjugated to a polyglucin:spermidine complex (PGS) and dsRNA (RBD-PGS + dsRNA) in a mouse model. BALB/c mice were immunized intramuscularly twice, with a 2-week interval, with 50 µg of RBD, RBD with Al(OH)₃, or conjugated RBD. A comparative analysis of serum RBD-specific IgG and neutralizing antibody titers showed that PGS, PGS + dsRNA, and Al(OH)₃ enhanced the specific humoral response in animals. There was no significant difference between the groups immunized with RBD-PGS + dsRNA and RBD with Al(OH)₃. Additionally, the study of the T-cell response in animals showed that, unlike adjuvants, the RBD-PGS + dsRNA conjugate stimulates the production of specific CD4+ and CD8+ T cells in animals.

Convalescent plasma (hyperimmune immunoglobulin) for COVID-19 management: An update

The pandemic COVID-19 has spread widely throughout the globe and has been responsible for millions of deaths worldwide. Recently, it has been identified that there is no specific and 100% effective treatment available to manage the infection especially for the severe cases. A significant amount of research efforts and clinical trials have been undertaken globally and many more are underway to find the potential treatment option. Earlier, convalescent plasma or hyperimmune immunoglobulin was effectively used in the treatment of many endemic or epidemic viral infections as a part of passive immunization. In this article, we have touched upon the immunopathology of COVID-19 infection, a basic understanding of convalescent plasma, it's manufacturing as well as evaluation, and have reviewed the scientific developments focussing on the potential of convalescent plasma vis-à-vis other modalities for the management of COVID-19. The article also covers various research approaches, clinical trials conducted globally, and the clinical trials which are at various stages for exploring the efficacy and safety of the convalescent plasma therapy (CPT) to predict its future perspective to manage COVID-19.

The Emergence of Hybrid Variants of SARS-CoV-2: Towards Hybrid Immunity

In this review work, the authors emphasize the discussion on different emerging variants of SARS-CoV-2 and vaccine effectiveness against them [...]

Molnupiravir: A Versatile Prodrug against SARS-CoV-2 Variants

The nucleoside analog β-D-N4-hydroxycytidine is the active metabolite of the prodrug molnupiravir and is accepted as an efficient drug against COVID-19. Molnupiravir targets the RNA-dependent RNA polymerase (RdRp) enzyme, which is responsible for replicating the viral genome during the replication process of certain types of viruses. It works by disrupting the normal function of the RdRp enzyme, causing it to make mistakes during the replication of the viral genome. These mistakes can prevent the viral RNA from being transcribed, converted into a complementary DNA template, translated, or converted into a functional protein. By disrupting these crucial steps in the viral replication process, molnupiravir can effectively inhibit the replication of the virus and reduce its ability to cause disease. This review article sheds light on the impact of molnupiravir and its metabolite on SARS-CoV-2 variants of concern, such as delta, omicron, and hybrid/recombinant variants. The detailed mechanism and molecular interactions using molecular docking and dynamics have also been covered. The safety and tolerability of molnupiravir in patients with comorbidities have also been emphasized.

Real-World Effectiveness of SARS-CoV-2 Vaccine Booster in Hemodialysis Patients with COVID-19 Receiving Molnupiravir

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine booster is one of the most essential strategies against coronavirus disease 2019 (COVID-19) in the era of emerging variants. However, the effectiveness of SARS-CoV-2 vaccine boosters has not much been investigated in hemodialysis (HD) patients receiving oral antiviral agents. In this retrospective study involving 258 HD patients with COVID-19 receiving molnupiravir, we stratified the study cohort according to vaccination status and compared the baseline characteristics and risks of 30-day composite events (COVID-19-related acute care visits, hospitalization, or mortality) among groups. Our analysis demonstrated that the SARS-CoV-2 vaccine boosters markedly decreased the risk of composite events in HD patients (hazard ratio (95% confidence interval), 0.163 (0.063-0.423) for three vs. ≤ two doses of vaccination, p < 0.001; 0.309 (0.115-0.830) for four vs. ≤ two doses of vaccination, p = 0.020). The benefits of vaccine boosters were similar between patients receiving mRNA-based and protein-based boosters and between those with post-booster intervals of ≤ 120 and > 120 days. In conclusion, for HD patients with initially mild or asymptomatic COVID-19 receiving molnupiravir, the benefits of SARS-CoV-2 vaccine boosters are prominent, irrespective of booster vaccine types.

Adenoviral Vector-Based Vaccine Platform for COVID-19: Current Status

The coronavirus disease (COVID-19) breakout had an unimaginable worldwide effect in the 21st century, claiming millions of lives and putting a huge burden on the global economy. The potential developments in vaccine technologies following the determination of the genetic sequence of SARS-CoV-2 and the increasing global efforts to bring potential vaccines and therapeutics into the market for emergency use have provided a small bright spot to this tragic event. Several intriguing vaccine candidates have been developed using recombinant technology, genetic engineering, and other vaccine development technologies. In the last decade, a vast amount of the vaccine development process has diversified towards the usage of viral vector-based vaccines. The immune response elicited by such vaccines is comparatively higher than other approved vaccine candidates that require a booster dose to provide sufficient immune protection. The non-replicating adenoviral vectors are promising vaccine carriers for infectious diseases due to better yield, cGMP-friendly manufacturing processes, safety, better efficacy, manageable shipping, and storage procedures. As of April 2022, the WHO has approved a total of 10 vaccines around the world for COVID-19 (33 vaccines approved by at least one country), among which three candidates are adenoviral vector-based vaccines. This review sheds light on the developmental summary of all the adenoviral vector-based vaccines that are under emergency use authorization (EUA) or in the different stages of development for COVID-19 management.

Conventional and Novel Diagnostic Tools for the Diagnosis of Emerging SARS-CoV-2 Variants

Accurate identification at an early stage of infection is critical for effective care of any infectious disease. The "coronavirus disease 2019 (COVID-19)" outbreak, caused by the virus "Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)", corresponds to the current and global pandemic, characterized by several developing variants, many of which are classified as variants of concern (VOCs) by the "World Health Organization (WHO, Geneva, Switzerland)". The primary diagnosis of infection is made using either the molecular technique of RT-PCR, which detects parts of the viral genome's RNA, or immunodiagnostic procedures, which identify viral proteins or antibodies generated by the host. As the demand for the RT-PCR test grew fast, several inexperienced producers joined the market with innovative kits, and an increasing number of laboratories joined the diagnostic field, rendering the test results increasingly prone to mistakes. It is difficult to determine how the outcomes of one unnoticed result could influence decisions about patient quarantine and social isolation, particularly when the patients themselves are health care providers. The development of point-of-care testing helps in the rapid in-field diagnosis of the disease, and such testing can also be used as a bedside monitor for mapping the progression of the disease in critical patients. In this review, we have provided the readers with available molecular diagnostic techniques and their pitfalls in detecting emerging VOCs of SARS-CoV-2, and lastly, we have discussed AI-ML- and nanotechnology-based smart diagnostic techniques for SARS-CoV-2 detection.

A bibliometric analysis of inflammatory bowel disease and COVID-19 researches

Background

Patients with inflammatory bowel disease (IBD) often require immunosuppressive therapy and are hence susceptible to various opportunistic viral and bacterial infections. In this regard, many studies on IBD and COVID-19 have been conducted. However, no bibliometric analysis has been performed. This study provides a general overview of IBD and COVID-19.

Methods

Publications about IBD and COVID-19 from 2020 to 2022 were retrieved from the Web of Science Core Collection (WoSCC) database. Bibliometric analysis was performed using VOSviewer, CiteSpace, and HistCite.

Results

A total of 396 publications were retrieved and considered in this study. The maximum number of publications were from the United States, Italy, and England, and the contributions of these countries were significant. Kappelman ranked first in article citations. The Icahn School of Medicine at Mount Sinai and Inflammatory Bowel Diseases were the most prolific affiliation and journal, respectively. The most influential research topics were "management", "impact", "vaccination", and "receptor". The following keywords represented research frontiers: "depression", "the quality of life of IBD patients", "infliximab", "COVID-19 vaccine", and "second vaccination".

Conclusions

Over the past 3 years, most studies on IBD and COVID-19 have focused on clinical research. In particular, topics such as "depression", "the quality of life of IBD patients", "infliximab", "COVID-19 vaccine", and "second vaccination" were noted to have received much attention recently. Future research should focus on our understanding of the immune response to COVID-19 vaccination in biologically treated patients, the psychological impact of COVID-19, IBD management guidelines, and the long-term impact of COVID-19 in IBD patients. This study will provide researchers with a better understanding of research trends on IBD during COVID-19.

Detection of Circulating SARS-CoV-2 Variants of Concern (VOCs) Using a Multiallelic Spectral Genotyping Assay

Throughout the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously evolved, resulting in new variants, some of which possess increased infectivity, immune evasion, and virulence. Such variants have been denoted by the World Health Organization as variants of concern (VOC) because they have resulted in an increased number of cases, posing a strong risk to public health. Thus far, five VOCs have been designated, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529), including their sublineages. Next-generation sequencing (NGS) can produce a significant amount of information facilitating the study of variants; however, NGS is time-consuming and costly and not efficient during outbreaks, when rapid identification of VOCs is urgently needed. In such periods, there is a need for fast and accurate methods, such as real-time reverse transcription PCR in combination with probes, which can be used for monitoring and screening of the population for these variants. Thus, we developed a molecular beacon-based real-time RT-PCR assay according to the principles of spectral genotyping. This assay employs five molecular beacons that target ORF1a:ΔS3675/G3676/F3677, S:ΔH69/V70, S:ΔE156/F157, S:ΔΝ211, S:ins214EPE, and S:ΔL242/A243/L244, deletions and an insertion found in SARS-CoV-2 VOCs. This assay targets deletions/insertions because they inherently provide higher discrimination capacity. Here, the design process of the molecular beacon-based real-time RT-PCR assay for detection and discrimination of SARS-CoV-2 is presented, and experimental testing using SARS-CoV-2 VOC samples from reference strains (cultured virus) and clinical patient samples (nasopharyngeal samples), which have been previously classified using NGS, were evaluated. Based on the results, it was shown that all molecular beacons can be used under the same real-time RT-PCR conditions, consequently improving the time and cost efficiency of the assay. Furthermore, this assay was able to confirm the genotype of each of the tested samples from various VOCs, thereby constituting an accurate and reliable method for VOC detection and discrimination. Overall, this assay is a valuable tool that can be used for screening and monitoring the population for VOCs or other emerging variants, contributing to limiting their spread and protecting public health.

Omicron Variant of SARS-CoV-2: An Indian Perspective of Vaccination and Management

Omicron variants have highly influenced the entire globe. It has a high rate of transmissibility, which makes its management tedious. There are various subtypes of omicron, namely BA.1, BA.2, BA.3, BA.4, and BA.5. Currently, one omicron subvariant BF.7 is also immersed in some parts of India. Further studies are required for a better understanding of the new immersing SARS-CoV-2 subvariant of the omicron. They differ in the mutation of the spike proteins, which alters their attachment to the host receptor and hence modifies their virulence and adaptability. Delta variants have a great disastrous influence on the entire world, especially in India. While overcoming it, another mutant catches the pace. The Indian population is highly affected by omicron variants. It alters the entire management and diagnosis system against COVID-19. It demanded forcemeat in the health care system, both qualitatively and quantitively, to cope with the omicron wave. The alteration in spike protein, which is the major target of vaccines, leads to varied immunization against the subvariants. The efficacy of vaccines against the new variant was questioned. Every vaccine had a different shielding effect on the new variant. The hesitancy of vaccination was a prevalent factor in India that might have contributed to its outbreak. The prevalence of omicron, monkeypox, and tomato flu shared some similarities and distinct features when compared to their influence on the Indian population. This review emphasizes the changes omicron brings with it and how the Indian health care system outrage this dangerous variant.

COVID-19 vaccines adverse events: potential molecular mechanisms

COVID-19 is an infectious disease caused by a single-stranded RNA (ssRNA) virus, known as SARS-CoV-2. The disease, since its first outbreak in Wuhan, China, in December 2019, has led to a global pandemic. The pharmaceutical industry has developed several vaccines, of different vector technologies, against the virus. Of note, among these vaccines, seven have been fully approved by WHO. However, despite the benefits of COVID-19 vaccination, some rare adverse effects have been reported and have been associated with the use of the vaccines developed against SARS-CoV-2, especially those based on mRNA and non-replicating viral vector technology. Rare adverse events reported include allergic and anaphylactic reactions, thrombosis and thrombocytopenia, myocarditis, Bell's palsy, transient myelitis, Guillen-Barre syndrome, recurrences of herpes-zoster, autoimmunity flares, epilepsy, and tachycardia. In this review, we discuss the potential molecular mechanisms leading to these rare adverse events of interest and we also attempt an association with the various vaccine components and platforms. A better understanding of the underlying mechanisms, according to which the vaccines cause side effects, in conjunction with the identification of the vaccine components and/or platforms that are responsible for these reactions, in terms of pharmacovigilance, could probably enable the improvement of future vaccines against COVID-19 and/or even other pathological conditions.

A China-developed adenovirus vector-based COVID-19 vaccine: review of the development and application of Ad5-nCov

INTRODUCTION

The global spread of COVID-19 has prompted the development of vaccines. A recombinant adenovirus type-5 vectored COVID-19 vaccine (Ad5-nCoV) developed by Chinese scientists has been authorized for use as a prime and booster dose in China and several other countries.

AREAS COVERED

We searched published articles as of 4 May 2023, on PubMed using keywords related to Adenovirus vector, vaccine, and SARS-CoV-2. We reported the progress and outcomes of Ad5-nCov, including vaccine efficacy, safety, immunogenicity based on pre-clinical trials, clinical trials, and real-world studies for primary and booster doses.

EXPERT OPINION

Ad5-nCoV is a significant advancement in Chinese vaccine development technology. Evidence from clinical trials and real-world studies has demonstrated well-tolerated, highly immunogenic, and efficacy of Ad5-nCoV in preventing severe/critical COVID-19. Aerosolized Ad5-nCoV, given via a novel route, could elicit mucosal immunity and improve the vaccine efficacy, enhance the production capacity and availability, and reduce the potential negative impact of preexisting antibodies. However, additional research is necessary to evaluate the long-term safety and immunogenicity of Ad5-nCoV, its efficacy against emerging variants, its effectiveness in a real-world context of hybrid immunity, and its cost-effectiveness, particularly with respect to aerosolized Ad5-nCoV.

Acute liver injury in COVID-19 patients hospitalized in the intensive care unit: Narrative review

In recent years, humanity has been confronted with a global pandemic due to coronavirus disease 2019 (COVID-19), which has caused an unprecedented health and economic crisis worldwide. Apart from the respiratory symptoms, which are considered the principal manifestations of COVID-19, it has been recognized that COVID-19 constitutes a systemic inflammatory process affecting multiple organ systems. Across the spectrum of organ involvement in COVID-19, acute liver injury (ALI) has been gradually gaining increasing attention by the international scientific community. COVID-19 associated liver impairment can affect a considerable proportion of COVID-19 patients and seems to correlate with the severity of the disease course. Indeed, COVID-19 patients hospitalized in the intensive care unit (ICU) run a greater risk of developing ALI due to the severity of their clinical condition and in the context of multi-organ failure. The putative pathophysiological mechanisms of COVID-19 induced ALI in ICU patients remain poorly understood and appear to be multifactorial in nature. Several theories have been proposed to explain the occurrence of ALI in the ICU setting, such as hypoperfusion and ischemia due to hemodynamic instability, passive liver congestion as a result of congestive heart failure, ischemia-reperfusion injury, hypoxia due to respiratory failure, mechanical ventilation itself, sepsis and septic shock, cytokine storm, endotheliitis with concomitant coagulopathy, drug-induced liver injury, parenteral nutrition and direct cytopathic viral effect. It should be noted that no specific therapy for COVID-19 induced ALI exists. Therefore, the therapeutic approach lies in preventive measures and is exclusively supportive once ALI ensues. The aim of the current review is to scrutinize the existing evidence on COVID-19 associated ALI in ICU patients, explore its clinical implications, shed light on the underlying pathophysiological mechanisms and propose potential therapeutic approaches. Ongoing research on the particular scientific field will further elucidate the pathophysiology behind ALI and address unresolved issues, in the hope of mitigating the tremendous health consequences imposed by COVID-19 on ICU patients.