A Comprehensive Review of COVID-19 Virology, Vaccines, Variants, and Therapeutics

Vaccination in post-tuberculosis lung disease management: A review of the evidence

INTRODUCTION AND OBJECTIVES

Post-tuberculosis lung disease (PTLD), as other chronic respiratory disorders, may have infectious complications; some of them can be prevented with vaccinations. So far, no document has discussed the potential role of vaccination in PTLD. Therefore, the objective of this review was to describe vaccination recommendations to prevent infections potentially capable of complicating PTLD.

MATERIALS AND METHODS

A non-systematic review of the literature was conducted. The following keywords were used: tuberculosis, vaccination, vaccines and PTLD. PubMed/MEDLINE and Embase were used as the search engine, focusing on English-language literature only.

RESULTS

We identified 9 vaccines potentially useful in PTLD. Influenza, pneumococcal and anti-COVID-19 vaccinations should be recommended. Patients with PTLD can also benefit from vaccination against shingles. Vaccination against pertussis is mainly relevant during childhood. Diphtheria, tetanus and measles vaccination are recommended for general population and should be considered in patients with PTLD not previously vaccinated. Tdap (Tetanus, diphtheria, and pertussis) booster should be repeated in every adult every ten years. Vaccination against BCG retains its importance during early childhood in countries where TB is endemic.

CONCLUSIONS

Vaccination deserves to be considered among the strategies to prevent and/or mitigate PTLD complications. Further evidence is necessary to better understand which vaccines have the greatest impact and cost-benefit.

Dynamics of COVID-19 based on spontaneous individual behaviors of vaccination

As the COVID-19 vaccine becomes widely available, human self-protection awareness is gradually weakening. However, the epidemic still continue to erupt repeatedly in various areas. Therefore, it is necessary to reveal the relationship between vaccination and individual spontaneous behaviors and their impact on the epidemic. Based on an SVEIR epidemic dynamical model, a novel imitation dynamics model is established by integrating the dynamic changes of individual spontaneous behaviors before and after vaccination. Unvaccinated people are more likely to choose long-term individual spontaneous behavior change strategies to reduce the risk of infection. While the vaccinated individuals are more likely to choose multiple, short-term strategies of individual spontaneous behavior changes. In the case of low vaccine protective efficacy, the changes of individual spontaneous behavior will drive several small-scale outbreaks at the same time. Besides, when the value of R0 is 4.5 and vaccination rate is 0.45, keeping the vaccine protection efficacy above 76.3% can not only complement the epidemic recurrence caused by behavioral changes, but also effectively reduce the epidemic peak and therefore quickly control the epidemic. Our results reveal the underlying mechanisms between vaccination, vaccine protection efficacy, individual spontaneous behaviors of the two groups of people and the COVID-19 epidemic. Vaccination and its protective efficacy effectively have a reciprocal effect with individual behavior changes, so as to control the epidemic quickly and effectively.

Immunologic and inflammatory consequences of SARS-CoV-2 infection and its implications in renal disease

The emergence of the COVID-19 pandemic made it critical to understand the immune and inflammatory responses to the SARS-CoV-2 virus. It became increasingly recognized that the immune response was a key mediator of illness severity and that its mechanisms needed to be better understood. Early infection of both tissue and immune cells, such as macrophages, leading to pyroptosis-mediated inflammasome production in an organ system critical for systemic oxygenation likely plays a central role in the morbidity wrought by SARS-CoV-2. Delayed transcription of Type I and Type III interferons by SARS-CoV-2 may lead to early disinhibition of viral replication. Cytokines such as interleukin-1 (IL-1), IL-6, IL-12, and tumor necrosis factor α (TNFα), some of which may be produced through mechanisms involving nuclear factor kappa B (NF-κB), likely contribute to the hyperinflammatory state in patients with severe COVID-19. Lymphopenia, more apparent among natural killer (NK) cells, CD8+ T-cells, and B-cells, can contribute to disease severity and may reflect direct cytopathic effects of SARS-CoV-2 or end-organ sequestration. Direct infection and immune activation of endothelial cells by SARS-CoV-2 may be a critical mechanism through which end-organ systems are impacted. In this context, endovascular neutrophil extracellular trap (NET) formation and microthrombi development can be seen in the lungs and other critical organs throughout the body, such as the heart, gut, and brain. The kidney may be among the most impacted extrapulmonary organ by SARS-CoV-2 infection owing to a high concentration of ACE2 and exposure to systemic SARS-CoV-2. In the kidney, acute tubular injury, early myofibroblast activation, and collapsing glomerulopathy in select populations likely account for COVID-19-related AKI and CKD development. The development of COVID-19-associated nephropathy (COVAN), in particular, may be mediated through IL-6 and signal transducer and activator of transcription 3 (STAT3) signaling, suggesting a direct connection between the COVID-19-related immune response and the development of chronic disease. Chronic manifestations of COVID-19 also include systemic conditions like Multisystem Inflammatory Syndrome in Children (MIS-C) and Adults (MIS-A) and post-acute sequelae of COVID-19 (PASC), which may reflect a spectrum of clinical presentations of persistent immune dysregulation. The lessons learned and those undergoing continued study likely have broad implications for understanding viral infections' immunologic and inflammatory consequences beyond coronaviruses.

Atomic Insights into pH-Dependent and Water Permeation of mRNA-Lipid Nanoparticles

The exposure of mRNA to water is likely to contribute to the instability of RNA vaccines upon storage under nonfrozen conditions. Using atomistic molecular dynamics (MD) simulations, we investigated the pH-dependent structural transition and water penetration behavior of mRNA-lipid nanoparticles (LNPs) with the compositions of Moderna and Pfizer vaccines against COVID-19 in an aqueous solution. It was revealed that the ionizable lipid (IL) membranes of LNPs were extremely sensitive to pH, and the increased acidity could cause a rapid membrane collapse and hydration swelling of LNP, confirming the high releasing efficiency of both LNP vaccines. The free energy profiles of water penetration showed that the conical structure of IL played a key role in obstructing water from entering the inner core of LNPs: the molecular geometry with more tail chains, lower linearity, and looser packing structure resulted in higher water permeability, leading to lower stability in nonfrozen liquid environment. On the other hand, the geometry of IL also dominated the fusion behavior of LNP with endosomal membrane during the endosomal escape. Thus, for LNP-based vaccines with both high release efficiency and high stability, a suitable molecular structure of ILs should be selected to seek a balance between the packing tightness and fusion rate of membranes.

Large-Scale Screening of CD4+ T-Cell Epitopes From SARS-CoV-2 Proteins and the Universal Detection of SARS-CoV-2 Specific T Cells for Northeast Asian Population

The polymorphism of human leukocyte antigens in the Northeast Asian populations and the lack of broad-spectrum T-cell epitopes covering this cohort markedly limited the development of T cell-directed vaccines against SARS-CoV-2 infection, and also hampered the universal detection of SARS-CoV-2 specific T cells. In this study, 93 CD4+ T-cell epitopes restricted by 12 prevalent HLA-DRB1 allotypes, which covering over 80% Chinese and Northeast Asian populations, were identified from the S, E, M, N and RdRp proteins of SARS-CoV-2 by in silico prediction, DC-peptide-PBL coculture experiment, and immunization in HLA-A2/DR1 transgenic mice. Furthermore, by using validated 215 CD8+ T cell epitope peptides and 123 CD4+ T-cell epitope peptides covering Northeast Asian cohort, the universal ELISpot detection systems of SARS-CoV-2 specific CD8+ T cells and CD4+ T cells were established, for the first time, and followed by the tests for 50 unexposed and 100 convalescent samples. The median of spot-forming units for CD8+ T cells and CD4+ T cells were 68 and 15, respectively, in the unexposed donors, but were 137 and 52 in the convalescent donors 6 months after recovery while 128 and 47 in the convalescent donors 18 months after recovery. This work initially provided the broad-spectrum CD4+ T-cell epitope library of SARS-CoV-2 for the design of T cell-directed vaccines and the universal T cell detection tool tailoring to Northeast Asian population, and confirmed the long-term memory T cell immunity after SARS-CoV-2 infection.

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.

Antioxidant-Rich Functional Foods and Exercise: Unlocking Metabolic Health Through Nrf2 and Related Pathways

This article reviews the synergistic effects of antioxidant-enriched functional foods and exercise in improving metabolic health, focusing on the underlying molecular mechanisms. The review incorporates evidence from PubMed, SCOPUS, Web of Science, PsycINFO, and reference lists of relevant reviews up to 20 December 2024, highlighting the central role of the Nrf2 pathway. As a critical regulator of oxidative stress and metabolic adaptation, Nrf2 mediates the benefits of these interventions. This article presents an innovative approach to understanding the role of Nrf2 in the regulation of oxidative stress and inflammation, highlighting its potential in the prevention and treatment of various diseases, including cancer, neurodegenerative disorders, cardiovascular and pulmonary diseases, diabetes, inflammatory conditions, ageing, and infections such as COVID-19. The novelty of this study is to investigate the synergistic effects of bioactive compounds found in functional foods (such as polyphenols, flavonoids, and vitamins) and exercise-induced oxidative stress on the activation of the Nrf2 pathway. This combined approach reveals their potential to improve insulin sensitivity and lipid metabolism and reduce inflammation, offering a promising strategy for the management of chronic diseases. However, there are significant gaps in current research, particularly regarding the molecular mechanisms underlying the interaction between diet, physical activity, and Nrf2 activation, as well as their long-term effects in different populations, including those with chronic diseases. In addition, the interactions between Nrf2 and other critical signalling pathways, including AMPK, NF-κB, and PI3K/Akt, and their collective contributions to metabolic health are explored. Furthermore, novel biomarkers are presented to assess the impact of these synergistic strategies, such as the NAD+/NADH ratio, the GSH ratio, and markers of mitochondrial health. The findings provide valuable insights into how the integration of an antioxidant-rich diet and regular exercise can improve metabolic health by activating Nrf2 and related molecular pathways and represent promising strategies for the prevention and treatment of metabolic disorders. Further studies are needed to fully understand the therapeutic potential of these interventions in diseases related to oxidative stress, such as cardiovascular disease, neurodegenerative disease, diabetes, and cancer.

COVID-19 Symptoms Only Minutely Influenced by Genes Among Children in a Nationwide Twin Cohort

BACKGROUND

The World Health Organization classified coronavirus disease (COVID-19) as a pandemic by March 11, 2020. Children had a milder disease than adults, and many were asymptomatic. The pandemic could be seen as a natural experiment with several changes, including time spent at home. The relative influence of genes and environment on the variability of a trait can be studied using twin pairs. We aimed to investigate the occurrence of reported COVID-19 symptoms and to separate the relative influence of genes and environment on these traits by variance decomposition.

METHODS

This was a population-based twin study conducted between November 2020 and March 2023. A survey was sent out to all parents of 9-year-old twins containing questions related to suspected COVID-19, symptoms of cough, fever and rhinorrhea, as well as concerns for their own and others' health. Twin modeling with variance decomposition was used to separate the relative influence of genes and environment.

RESULTS

In total, 3094 individuals from 1547 complete twin pairs were included (618 monozygotic and 929 dizygotic twin pairs). Suspected COVID-19 increased over time and concerns for own and others' health decreased. We found variability to be attributed mainly to shared environment in all traits investigated ranging between 63.0% and 86.2%. The rest of the variance of each trait was attributed to genetic factors (11.6%-33.5%) and nonshared environment (2.1%-9.9%).

CONCLUSIONS

We found results of substantial shared environment in all traits analyzed among 9-year-old twins. Age and timing seem crucial when investigating the possible influence of genes and the environment when a new virus is introduced before herd immunity is reached.

Transfection Potency of Lipid Nanoparticles Containing mRNA Depends on Relative Loading Levels

When formulating mRNA into lipid nanoparticles (LNP), various copy numbers of mRNA are encapsulated, leading to a distribution of mRNA loading levels within the LNPs. It is unclear whether the mRNA loading level affects the functional delivery of the message. Here we show that depending on the mRNA loading level, LNPs exhibit distinct mass densities and can be fractionated via ultracentrifugation. Upon fractionation, we investigated if mRNA loading levels influence LNP sizing, lipid composition, and morphology. We further conducted in vitro and in vivo functional delivery of mRNA and found that the LNP fraction with the highest mRNA loading levels was the least transfection competent.

Advances and Challenges in Antiviral Development for Respiratory Viruses

The development of antivirals for respiratory viruses has advanced markedly in response to the growing threat of pathogens such as Influenzavirus (IAV), respiratory syncytial virus (RSV), and SARS-CoV-2. This article reviews the advances and challenges in this field, highlighting therapeutic strategies that target critical stages of the viral replication cycle, including inhibitors of viral entry, replication, and assembly. In addition, innovative approaches such as inhibiting host cellular proteins to reduce viral resistance and repurposing existing drugs are explored, using advanced bioinformatics tools that optimize the identification of antiviral candidates. The analysis also covers emerging technologies such as nanomedicine and CRISPR gene editing, which promise to improve the stability and efficacy of treatments. While current antivirals offer valuable options, they face challenges such as viral evolution and the need for accessible treatments for vulnerable populations. This article underscores the importance of continued innovation in biotechnology to overcome these limitations and provide safe and effective treatments. Combining traditional and advanced approaches in developing antivirals is essential in order to address respiratory viral diseases that affect global health.

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.

Characterisation of specific responses to three models of viral antigens in immunocompetent older adults

BACKGROUND

Memory responses to the antigens that an individual encounters throughout life may vary with the intensity and duration of antigen contacts or even with changes in immune status over time. This work aims to characterise specific responses to latent CMV, seasonal influenza and novel SARS-CoV-2 infections in immunocompetent individuals over 60 years of age. Specific cellular and humoral responses were identified by IFN-γ and granzyme B release by ELISpot and antibody level measurement. T lymphocyte subpopulation phenotypes were characterised by flow cytometry.

RESULTS

Cellular and humoral responses to these viruses were detected in almost all patients. Influenza and SARS-CoV-2 cellular responses were positively correlated. There was no significant correlation between CMV and influenza or SARS-CoV-2 responses although both were consistently lower in CMV-seropositive patients. CMV responses were negatively correlated with the levels of the least differentiated subsets of T lymphocytes, and positively correlated with the most differentiated ones, contrary to what happened with the influenza responses. Nevertheless, SARS-CoV-2 cellular responses were negatively correlated with the most differentiated CD8+ T lymphocytes, while humoral responses were negatively correlated with the least differentiated T lymphocytes. Responses to the three viruses were correlated with a Th1/Th2/Th17 balance in favour of Th1.

CONCLUSIONS

The results indicate that memory responses differ depending on the durability of the antigen stimulus. Cellular responses to novel pathogens resemble those generated by seasonal but not CMV infection. Subpopulation distribution and the level of specific T lymphocytes against previous pathogens could be used as immunocompetent status biomarkers in older adults reflecting their ability to generate memory responses to new pathogens.

Multimorbidity and COVID-19 Outcomes in the Emergency Department: Is the Association Mediated by the Severity of the Condition at Admission?

Background/Objectives: Charlson Comorbidity Index (CCI) is one of the most reliable indicators to assess the impact of multimorbidity on COVID-19-related outcomes. Moreover, the patient's clinical conditions are associated with SARS-CoV-2 outcomes. This study aimed to analyze the association between multimorbidity and COVID-19-related outcomes, evaluating whether the National Early Warning Score 2 (NEWS2) mediated these associations. Methods: Data were obtained through the platform "EPICLIN". We analyzed all patients who tested positive for COVID-19 after accessing the emergency department (ED) of San Luigi Gonzaga (Orbassano) and Molinette (Turin) hospitals from 1 March to 30 June 2020. Different outcomes were assessed: non-discharge from the ED, 30-day mortality, ICU admission/death among hospitalized patients, and length of hospitalization among surviving patients. Two subgroups of patients (<65 and 65+ years old) were analyzed using logistic regressions, Cox models, and mediation analyses. Results: There was a greater risk of not being discharged or dying among those who were younger and with CCI ≥ 2. Moreover, the higher the CCI, the longer the length of hospitalization. Considering older subjects, a greater CCI was associated with a higher risk of death. Regarding the mediation analyses, multimorbidity significantly impacted the hospitalization length and not being discharged in the younger population. Instead, in the older population, the NEWS2 played a mediation role. Conclusions: This research showed that multimorbidity is a risk factor for a worse prognosis of COVID-19. Moreover, there was a strong direct effect of CCI on not being discharged, and the NEWS2 was found to act as mediator in the association between multimorbidity and COVID-19-related outcomes.

Ion Mobility-Mass Spectrometry Captures the Structural Consequences of Lipid Nanoparticle Encapsulation on Ribonucleic Acid Cargo

Ribonucleic acids (RNAs) are becoming increasingly significant in our search for improved biotherapeutics. RNA-based treatments offer high specificity, targeted delivery, and potentially lower-cost options for various debilitating human diseases. Despite these benefits, there are still relatively few FDA-approved RNA-based therapies, with the notable exceptions being the mRNA (mRNA) COVID-19 vaccines, which are delivered using lipid nanoparticle (LNP) systems. LNPs are distinctive drug delivery systems (DDSs) because of their ability to target specific cells, their biocompatibility, and their efficiency in merging with cellular membranes to enhance treatment effectiveness. While the biophysical landscapes of RNA structures in solution are relatively well understood, the impact of the LNP environment on RNA remains less clear. This study uses native ion mobility-mass spectrometry (IM-MS) and collision-induced unfolding (CIU) techniques to investigate how LNP encapsulation affects RNA structure and stability. We examine how various factors, such as ionization polarity, cofactor binding, lipid types, and lipid ratios, influence LNP-released RNA cargo. Our findings reveal that LNP DDSs induce significant changes in the structures and stabilities of their RNA cargo. However, the extent of these changes strongly depends on the type and composition of the lipids used. We conclude by discussing how IM-MS and CIU can aid in the continued development of more efficient LNP DDSs and improve DDS selection methodologies overall.

Eucalyptus Essential Oil Inhibits Cell Infection by SARS-CoV-2 Spike Pseudotyped Lentivirus

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains a public health concern due to infections with new SARS-CoV-2 variants. Therefore, finding effective preventive and therapeutic treatments against all SARS-CoV-2 variants is of great interest. In this study, we examined the capacity of eucalyptus essential oil (EEO) and eucalyptol (EOL) to prevent SARS-CoV-2 infection, using as a model SARS-CoV-2 Spike pseudotyped lentivirus (SARS-CoV-2 pseudovirus) and 293T cells transfected with human angiotensin-converting enzyme 2 (hACE2-293T cells). First, we determined the cytotoxicity of EEO and EOL using the MTT colorimetric assay, selecting non-cytotoxic concentrations ≤ 0.1% (v/v) for further analysis. Subsequently, we evaluated the capacity of EEO and EOL in cell cultures to preclude infection of hACE2-293T cells by SARS-CoV-2 pseudovirus, using a luciferase-based assay. We found that EEO and EOL significantly reduced SARS-CoV-2 pseudovirus infection, obtaining IC50 values of 0.00895% and 0.0042% (v/v), respectively. Likewise, EEO and EOL also reduced infection by vesicular stomatitis virus (VSV) pseudovirus, although higher concentrations were required. Hence, EEO and EOL may be able to inhibit SARS-CoV-2 infection, at least partially, through a Spike-independent pathway, supporting the implementation of aromatherapy with these agents as a cost-effective antiviral measure.

Multisystem inflammatory syndrome in children: an evolving understanding of a syndrome amid the inflammatory continuum

Multisystem inflammatory syndrome in children (MIS-C) is a rare hyperinflammatory and immunosuppressed condition affecting children exposed to COVID-19. MIS-C has been associated with an over-exaggerated innate and adaptive immune response characterized by a 'selective' cytokine production and T cell suppression. As COVID-19 information has evolved, the knowledge and field surrounding MIS-C is ever evolving. Thus, a comprehensive clinical review that concisely presents current literature findings regarding common clinical presentations and comparisons with similar conditions, associations with the COVID-19 vaccine effects and relevant epigenetic markers and evaluates treatment and long-term outcomes to help guide future studies is needed and provided.

Preparing for future pandemics: frailty associates with mortality in hospitalised older people during the entire COVID-19 pandemic, a Dutch multicentre cohort study

PURPOSE

Viral mutations and improved prevention or treatment options may have changed the association of frailty with mortality throughout the COVID-19 pandemic. We investigated how associations of frailty with in-hospital mortality changed throughout the pandemic in older people hospitalised for COVID-19.

METHODS

The COVID-OLD study included COVID-19 patients aged ≥ 70 years hospitalised during the first (early 2020), second (late 2020), third (late 2021) or fourth wave (early 2022). Based on the clinical frailty scale, patients were categorised as fit (1-3), pre-frail (4-5) or frail (6-9). Associations of frailty with in-hospital mortality were assessed with pairwise comparisons with fit as reference category and modelled using binary logistic regression adjusted for age and sex.

RESULTS

This study included 2362 patients (mean age 79.7 years, 60% men). In the first wave, in-hospital mortality was 46% in patients with frailty and 27% in fit patients. In-hospital mortality decreased in each subsequent wave to 25% in patients with frailty and 11% in fit patients in the fourth wave. After adjustments, an overall higher risk of in-hospital mortality was found in frail (OR 2.26, 95% CI: 1.66-3.07) and pre-frail (OR 1.73, 95% CI: 1.27-2.35) patients compared to fit patients, which did not change over time (p for interaction = 0.74).

CONCLUSIONS

Frailty remained associated with a higher risk of in-hospital mortality throughout the entire COVID-19 pandemic, although overall in-hospital mortality rates decreased. Frailty therefore remains a relevant risk factor in all stages of a pandemic and is important to consider in prevention and treatment guidelines for future pandemics.

NSAIDs for early management of acute respiratory infections

PURPOSE OF REVIEW

To review the rationale for and the potential clinical benefits of an early approach to viral acute respiratory infections with NSAIDs to switch off the inflammatory cascade before the inflammatory process becomes complicated.

RECENT FINDINGS

It has been shown that in COVID-19 as in other viral respiratory infections proinflammatory cytokines are produced, which are responsible of respiratory and systemic symptoms. There have been concerns that NSAIDs could increase susceptibility to SARS-CoV-2 infection or aggravate COVID-19. However, recent articles reviewing experimental research, observational clinical studies, randomized clinical trials, and meta-analyses conclude that there is no basis to limit the use of NSAIDs, which may instead represent effective self-care measures to control symptoms.

SUMMARY

The inflammatory response plays a pivotal role in the early phase of acute respiratory tract infections (ARTIs); a correct diagnosis of the cause and a prompt therapeutic approach with NSAIDs may have the potential to control the pathophysiological mechanisms that can complicate the condition, while reducing symptoms to the benefit of the patient. A timely treatment with NSAIDs may limit the inappropriate use of other categories of drugs, such as antibiotics, which are useless when viral cause is confirmed and whose inappropriate use is responsible for the development of resistance.

Ocular Implications of COVID-19 Infection and Vaccine-Related Adverse Events

The COVID-19 pandemic, caused by SARS-CoV-2, has significantly impacted various organ systems, including the eyes. Initially considered a primarily respiratory disease, it is now evident that COVID-19 can induce a range of ocular symptoms. Recognizing these ocular manifestations is crucial for eye care practitioners as they can serve as early indicators of the disease. This review consolidates current evidence on the ocular effects of COVID-19, identifying manifestations such as conjunctivitis, scleritis, uveitis, and retinopathy. The increasing prevalence of these symptoms highlights the importance of thorough eye examinations and detailed patient histories in COVID-19 cases. Potential routes of viral entry into ocular tissues and the underlying mechanisms, including direct infection, immune responses, and vascular involvement, are explored. Additionally, this review addresses ocular side effects associated with COVID-19 vaccines, such as corneal graft rejection, uveitis, and retinal issues. These findings emphasize the need for ongoing surveillance and research to ensure vaccine safety.

Paxlovid™ reduces the incidence of pneumonia, hospitalization, and death in a cohort of COVID-19 patients from northeast Mexico

BACKGROUND

Information on Paxlovid™ effectiveness must be monitored and updated in real world scenarios. Our research question was what is the effectiveness of Paxlovid™ in adult patients with COVID-19? Therefore, we investigated the effectiveness of Paxlovid™ on reducing the incidence of pneumonia, hospitalization, and mortality in a cohort of COVID-19 positive adult patients from northeast Mexico.

METHODS

A retrospective cohort study of COVID-19 positive adult patients from Nuevo Leon, Mexico from December 2020 to May 2023 (after Omicron BA-5 circulation) was performed. Paxlovid™ use was authorized in September 2022. Therefore, we analyzed effectiveness in patients with confirmed diagnosis who met selection criteria between September 2022 and May 2023 (n = 20,799; 5,673 with and 15,126 without Paxlovid™).

RESULTS

The pneumonia (0.1% vs. 0.4%, p < 0.0001), hospitalization (0.1% vs. 1.2%, p < 0.0001), and death rates (0.04% vs. 0.2%, p < 0.0001) were lower in patients with Paxlovid™ treatment independently of age, sex, comorbidity, and COVID-19 and pneumococcal vaccination history. Effectiveness was 88.2%, 95.9% y 91.9% for pneumonia, hospitalization, and death, respectively.

CONCLUSIONS

Paxlovid™ reduces the presentation of pneumonia, hospitalization, and death secondary to COVID-19. It is recommended to continue monitoring Paxlovid™ effectiveness, as other SARS-CoV-2 variants continue to emerge.

SARS-CoV-2: pathogenesis, therapeutics, variants, and vaccines

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in December 2019 with staggering economic fallout and human suffering. The unique structure of SARS-CoV-2 and its underlying pathogenic mechanism were responsible for the global pandemic. In addition to the direct damage caused by the virus, SARS-CoV-2 triggers an abnormal immune response leading to a cytokine storm, culminating in acute respiratory distress syndrome and other fatal diseases that pose a significant challenge to clinicians. Therefore, potential treatments should focus not only on eliminating the virus but also on alleviating or controlling acute immune/inflammatory responses. Current management strategies for COVID-19 include preventative measures and supportive care, while the role of the host immune/inflammatory response in disease progression has largely been overlooked. Understanding the interaction between SARS-CoV-2 and its receptors, as well as the underlying pathogenesis, has proven to be helpful for disease prevention, early recognition of disease progression, vaccine development, and interventions aimed at reducing immunopathology have been shown to reduce adverse clinical outcomes and improve prognosis. Moreover, several key mutations in the SARS-CoV-2 genome sequence result in an enhanced binding affinity to the host cell receptor, or produce immune escape, leading to either increased virus transmissibility or virulence of variants that carry these mutations. This review characterizes the structural features of SARS-CoV-2, its variants, and their interaction with the immune system, emphasizing the role of dysfunctional immune responses and cytokine storm in disease progression. Additionally, potential therapeutic options are reviewed, providing critical insights into disease management, exploring effective approaches to deal with the public health crises caused by SARS-CoV-2.

Impact of the COVID-19 pandemic on lung transplant patients and on a cohort of patients with rare lung disease: A single-center study

INTRODUCTION

Due to the COVID-19 pandemic, France underwent several lockdown periods during 2020. Our aim was to evaluate its clinical and social impact on lung transplant (LT) patients treated at Strasbourg University Hospital, by comparing three periods: first lockdown (T1: March-May 2020), end of the first lockdown (T2: May-October 2020), and second lockdown (T3: November-December 2020) and the incidence of COVID-19 infections. A cohort of patients with rare lung disease (RLD) was also studied during T2.

METHODS

We used clinical and paraclinical data collected during routine follow-up. A questionnaire was submitted to each patient at each period to assess their lifestyle, adherence to protective measures against COVID-19, contacts with their family and friends, and contagion risk. The incidence of new COVID-19 cases was also assessed.

RESULTS

Overall, 283 LT and 57 RLD patients were included. We observed only eight COVID-19 cases over the three periods (n = 4 during T1, n = 0 during T2, and n = 4 during T3) in LT patients, with 37.5 % of patients hospitalized, no ICU transfers, and 100 % favorable outcomes. No case of COVID-19 was diagnosed in the RLD cohort. When comparing the three periods in the LT group, fewer patients limited their out-of-home activities during T2 (p < 0.0001). The frequency of these activities increased after the first lockdown, for the purchase of basic necessities (p < 0.0001), and professional activity continued (p = 0.008). We observed a significant increase in unscheduled medical consultations and in the prescription of anti-infective treatments during the end of the lockdown (p = 0.0002 and p = 0.005, respectively). Adherence to lockdown and to protective measures was high in both groups of patients.

CONCLUSION

COVID-19 incidence remained low in both groups and there were significant lifestyle evolutions in LT patients and in those with RLD between first and second lockdown.

High Levels of NfL, GFAP, TAU, and UCH-L1 as Potential Predictor Biomarkers of Severity and Lethality in Acute COVID-19

Few studies showed that neurofilament light chain (NfL), glial fibrillary acidic protein (GFAP), total tubulin-associated unit (TAU), and ubiquitin carboxy-terminal hydrolase-L1 (UCH-L1) may be related to neurological manifestations and severity during and after SARS-CoV-2 infection. The objective of this work was to investigate the relationship among nervous system biomarkers (NfL, TAU, GFAP, and UCH-L1), biochemical parameters, and viral loads with heterogeneous outcomes in a cohort of severe COVID-19 patients admitted in Intensive Care Unit (ICU) of a university hospital. For that, 108 subjects were recruited within the first 5 days at ICU. In parallel, 16 mild COVID-19 patients were enrolled. Severe COVID-19 group was divided between "deceased" and "survivor." All subjects were positive for SARS-CoV-2 detection. NfL, total TAU, GFAP, and UCH-L1 quantification in plasma was performed using SIMOA SR-X platform. Of 108 severe patients, 36 (33.33%) presented neurological manifestation and 41 (37.96%) died. All four biomarkers - GFAP, NfL, TAU, and UCH-L1 - were significantly higher among deceased patients in comparison to survivors (p < 0.05). Analyzing biochemical biomarkers, higher Peak Serum Ferritin, D-Dimer Peak, Gamma-glutamyltransferase, and C-Reactive Protein levels were related to death (p < 0.0001). In multivariate analysis, GFAP, NfL, TAU, UCH-L1, and Peak Serum Ferritin levels were correlated to death. Regarding SARS-CoV-2 viral load, no statistical difference was observed for any group. Thus, Ferritin, NFL, GFAP, TAU, and UCH-L1 are early biomarkers of severity and lethality of SARS-COV-2 infection and may be important tools for therapeutic decision-making in the acute phase of disease.

Management of immunosuppression in lung transplant recipients and COVID-19 outcomes: an observational retrospective cohort-study

BACKGROUND

The aim of this study was to assess the impact of immunosuppression management on coronavirus disease 2019 (COVID-19) outcomes.

METHODS

We performed a single-center retrospective study in a cohort of 358 lung transplant recipients (LTx) over the period from March 2020 to April 2022. All included symptomatic patients had at least one positive SARS-CoV-2 rt-PCR. We used a composite primary outcome for COVID-19 including increased need for oxygen since the hospital admission, ICU transfer, and in-hospital mortality. We assessed by univariate and multivariate analyses the risk factors for poor outcomes.

RESULTS

Overall, we included 91 LTx who contracted COVID-19. The COVID-19 in-hospital mortality rate reached 4.4%. By hierarchical clustering, we found a strong and independent association between the composite poor outcome and the discontinuation of at least one immunosuppressive molecule among tacrolimus, cyclosporine, mycophenolate mofetil, and everolimus. Obesity (OR = 16, 95%CI (1.96; 167), p = 0.01) and chronic renal failure (OR = 4.6, 95%CI (1.4; 18), p = 0.01) were also independently associated with the composite poor outcome. Conversely, full vaccination was protective (OR = 0.23, 95%CI (0.046; 0.89), p = 0.047).

CONCLUSION

The administration of immunosuppressive drugs such as tacrolimus, cyclocporine or everolimus can have a protective effect in LTx with COVID-19, probably related to their intrinsic antiviral capacity.

Status of COVID-19 Patients Treated With Extracorporeal Membrane Oxygenation in Japan: Nationwide Database Analysis

Background The report of epidemiological data on coronavirus disease 2019 (COVID-19) patients treated using extracorporeal membrane oxygenation (ECMO) in Japan has been limited. Our study seeks to fill the existing gap in knowledge by providing an in-depth analysis of the clinical epidemiological characteristics and diverse medical outcomes of COVID-19 patients treated with ECMO in Japan. Methods This study used the COVID-19 Registry Japan nationwide database. We included patients aged 18 years or older enrolled between March 17, 2020, and February 1, 2022, with traceable ECMO data. The items on clinical epidemiological characteristics and various medical outcomes were collected. Statistical analysis included a median and interquartile range (IQR) for continuous variables and frequencies for categorical variables. Results The number of participating hospitals was 731, and the number of patients enrolled for analysis was 49,590. Of these, 196 (0.4%) patients received ECMO. Hospital mortality was 33.2%, and discharge to home was 23.0% in the ECMO group. The complications during hospitalization included pneumothorax (9.7%), seizures (4.1%), stroke (4.6%), and pulmonary thromboembolism (2.0%). At discharge, 38.3% had worsened self-care ability, and 38.8% had worsened ambulatory function. Conclusions The results of ECMO treatment in Japan showed that the mortality and complication rates were well-controlled compared with those worldwide.

Vaccines and the Eye: Current Understanding of the Molecular and Immunological Effects of Vaccination on the Eye

Vaccination is a public health cornerstone that protects against numerous infectious diseases. Despite its benefits, immunization implications on ocular health warrant thorough investigation, particularly in the context of vaccine-induced ocular inflammation. This review aimed to elucidate the complex interplay between vaccination and the eye, focusing on the molecular and immunological pathways implicated in vaccine-associated ocular adverse effects. Through an in-depth analysis of recent advancements and the existing literature, we explored various mechanisms of vaccine-induced ocular inflammation, such as direct infection by live attenuated vaccines, immune complex formation, adjuvant-induced autoimmunity, molecular mimicry, hypersensitivity reactions, PEG-induced allergic reactions, Type 1 IFN activation, free extracellular RNA, and specific components. We further examined the specific ocular conditions associated with vaccination, such as uveitis, optic neuritis, and retinitis, and discussed the potential impact of novel vaccines, including those against SARS-CoV-2. This review sheds light on the intricate relationships between vaccination, the immune system, and ocular tissues, offering insights into informed discussions and future research directions aimed at optimizing vaccine safety and ophthalmological care. Our analysis underscores the importance of vigilance and further research to understand and mitigate the ocular side effects of vaccines, thereby ensuring the continued success of vaccination programs, while preserving ocular health.

Immune response stability to the SARS-CoV-2 mRNA vaccine booster is influenced by differential splicing of HLA genes

Many molecular mechanisms that lead to the host antibody response to COVID-19 vaccines remain largely unknown. In this study, we used serum antibody detection combined with whole blood RNA-based transcriptome analysis to investigate variability in vaccine response in healthy recipients of a booster (third) dose schedule of the mRNA BNT162b2 vaccine against COVID-19. The cohort was divided into two groups: (1) low-stable individuals, with antibody concentration anti-SARS-CoV IgG S1 below 0.4 percentile at 180 days after boosting vaccination; and (2) high-stable individuals, with antibody values greater than 0.6 percentile of the range in the same period (median 9525 [185-80,000] AU/mL). Differential gene expression, expressed single nucleotide variants and insertions/deletions, differential splicing events, and allelic imbalance were explored to broaden our understanding of the immune response sustenance. Our analysis revealed a differential expression of genes with immunological functions in individuals with low antibody titers, compared to those with higher antibody titers, underscoring the fundamental importance of the innate immune response for boosting immunity. Our findings also provide new insights into the determinants of the immune response variability to the SARS-CoV-2 mRNA vaccine booster, highlighting the significance of differential splicing regulatory mechanisms, mainly concerning HLA alleles, in delineating vaccine immunogenicity.

Determinants of health as predictors for differential antibody responses following SARS-CoV-2 primary and booster vaccination in an at-risk, longitudinal cohort

Post vaccine immunity following COVID-19 mRNA vaccination may be driven by extrinsic, or controllable and intrinsic, or inherent health factors. Thus, we investigated the effects of extrinsic and intrinsic on the peak antibody response following COVID-19 primary vaccination and on the trajectory of peak antibody magnitude and durability over time. Participants in a longitudinal cohort attended visits every 3 months for up to 2 years following enrollment. At baseline, participants provided information on their demographics, recreational behaviors, and comorbid health conditions which guided our model selection process. Blood samples were collected for serum processing and spike antibody testing at each visit. Cross-sectional and longitudinal models (linear-mixed effects models) were generated to assess the relationship between selected intrinsic and extrinsic health factors on peak antibody following vaccination and to determine the influence of these predictors on antibody over time. Following cross-sectional analysis, we observed higher peak antibody titers after primary vaccination in females, those who reported recreational drug use, younger age, and prior COVID-19 history. Following booster vaccination, females and Hispanics had higher peak titers after the 3rd and 4th doses, respectively. Longitudinal models demonstrated that Moderna mRNA-1273 recipients, females, and those previously vaccinated had increased peak titers over time. Moreover, drug users and half-dose Moderna mRNA-1273 recipients had higher peak antibody titers over time following the first booster, while no predictive factors significantly affected post-second booster antibody responses. Overall, both intrinsic and extrinsic health factors play a significant role in shaping humoral immunogenicity after initial vaccination and the first booster. The absence of predictive factors for second booster immunogenicity suggests a more robust and consistent immune response after the second booster vaccine administration.

Preexisting renal graft dysfunction as a major risk factor for SARS-CoV-2 Omicron variant pneumonia: A postinfection cross-sectional study of 312 immunosuppressed renal transplant recipients

OBJECTIVES

SARS-CoV-2 pneumonia poses significant challenges to health systems worldwide, particularly, in severe and critical cases. Immunosuppressed renal transplant recipients appear to be at a particularly high risk for severe or critical COVID-19 illness. However, few studies elucidated the risk factors of SARS-CoV-2 pneumonia in renal transplant recipients with COVID-19.

METHODS

A postinfection cross-sectional survey was conducted in 312 renal transplant recipients and 503 age- and sex-matched controls to explore risk factors for SARS-CoV-2 pneumonia in immunosuppressed renal transplant recipients.

RESULTS

The results showed that renal transplant recipients had a much higher incidence of SARS-CoV-2 pneumonia (48.1%) after infection with the SARS-CoV-2 Omicron variant than controls (5.6%). The multivariate binary logistic regression analysis identified older age, lower creatinine clearance before infection, and higher dose of prednisone before infection as risk factors for SARS-CoV-2 pneumonia in renal transplant recipients. Preexisting renal dysfunction was a major risk factor for SARS-CoV-2 pneumonia, with an odds ratio of 3.27 (1.01-10.61).

CONCLUSIONS

Preexisting renal graft dysfunction was a major risk factor for SARS-CoV-2 Omicron variant pneumonia. It is suggested that high-risk renal transplant recipients should undergo computed tomography scanning within 14 days after infection with SARS-CoV-2.

An Evaluation of Type 1 Interferon Related Genes in Male and Female-Matched, SARS-CoV-2 Infected Individuals Early in the COVID-19 Pandemic

SARS-CoV-2 infection has claimed just over 1.1 million lives in the US since 2020. Globally, the SARS-CoV-2 respiratory infection spread to 771 million people and caused mortality in 6.9 million individuals to date. Much of the early literature showed that SARS-CoV-2 immunity was defective in the early stages of the pandemic, leading to heightened and, sometimes, chronic inflammatory responses in the lungs. This lung-associated 'cytokine storm' or 'cytokine release syndrome' led to the need for oxygen supplementation, respiratory distress syndrome, and mechanical ventilation in a relatively high number of people. In this study, we evaluated circulating PBMC from non-hospitalized, male and female, COVID-19+ individuals over the course of infection, from the day of diagnosis (day 0) to one-week post diagnosis (day 7), and finally 4 weeks after diagnosis (day 28). In our early studies, we included hospitalized and critically care patient PBMC; however, most of these individuals were lymphopenic, which limited our assessments of their immune integrity. We chose a panel of 30 interferon-stimulated genes (ISG) to evaluate by PCR and completed flow analysis for immune populations present in those PBMC. Lastly, we assessed immune activation by stimulating PBMC with common TLR ligands. We identified changes in innate cells, primarily the innate lymphoid cells (ILC, NK cells) and adaptive immune cells (CD4+ and CD8+ T cells) over this time course of infection. We found that the TLR-7 agonist, Resiquimod, and the TLR-4 ligand, LPS, induced significantly better IFNα and IFNγ responses in the later phase (day 28) of SARS-CoV-2 infection in those non-hospitalized COVID-19+ individuals as compared to early infection (day 0 and day 7). We concluded that TLR-7 and TLR-4 agonists may be effective adjuvants in COVID-19 vaccines for mounting immunity that is long-lasting against SARS-CoV-2 infection.

Multicentre, randomised, double-blind, placebo-controlled, proof of concept study of LSALT peptide as prevention of acute respiratory distress syndrome and acute kidney injury in patients infected with SARS-CoV-2 (COVID-19)

OBJECTIVE

Dipeptidase-1 (DPEP-1) is a recently discovered leucocyte adhesion receptor for neutrophils and monocytes in the lungs and kidneys and serves as a potential therapeutic target to attenuate inflammation in moderate-to-severe COVID-19. We aimed to evaluate the safety and efficacy of the DPEP-1 inhibitor, LSALT peptide, to prevent specific organ dysfunction in patients hospitalised with COVID-19.

DESIGN

Phase 2a randomised, placebo-controlled, double-blinded, trial.

SETTING

Hospitals in Canada, Turkey and the USA.

PARTICIPANTS

A total of 61 subjects with moderate-to-severe COVID-19.

INTERVENTIONS

Randomisation to LSALT peptide 5 mg intravenously daily or placebo for up to 14 days.

PRIMARY AND SECONDARY OUTCOME MEASURES

The primary endpoint was the proportion of subjects alive and free of respiratory failure and/or the need for renal replacement therapy (RRT). Numerous secondary and exploratory endpoints were assessed including ventilation-free days, and changes in kidney function or serum biomarkers.

RESULTS

At 28 days, 27 (90.3%) and 28 (93.3%) of subjects in the placebo and LSALT groups were free of respiratory failure and the need for RRT (p=0.86). On days 14 and 28, the number of patients still requiring more intensive respiratory support (O2 ≥6 L/minute, non-invasive or invasive mechanical ventilation or extracorporeal membrane oxygenation) was 6 (19.4%) and 3 (9.7%) in the placebo group versus 2 (6.7%) and 2 (6.7%) in the LSALT group, respectively (p=0.14; p=0.67). Unadjusted analysis of ventilation-free days demonstrated 22.8 days for the LSALT group compared with 20.9 in the placebo group (p=0.4). LSALT-treated subjects had a significant reduction in the fold expression from baseline to end of treatment of serum CXCL10 compared with placebo (p=0.02). Treatment-emergent adverse events were similar between groups.

CONCLUSION

In a Phase 2 study, LSALT peptide was demonstrated to be safe and tolerated in patients hospitalised with moderate-to-severe COVID-19.

TRIAL REGISTRATION NUMBER

NCT04402957.

Calpain-2 mediates SARS-CoV-2 entry via regulating ACE2 levels

Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, much effort has been dedicated to identifying effective antivirals against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A number of calpain inhibitors show excellent antiviral activities against SARS-CoV-2 by targeting the viral main protease (Mpro), which plays an essential role in processing viral polyproteins. In this study, we found that calpain inhibitors potently inhibited the infection of a chimeric vesicular stomatitis virus (VSV) encoding the SARS-CoV-2 spike protein but not Mpro. In contrast, calpain inhibitors did not exhibit antiviral activities toward the wild-type VSV with its native glycoprotein. Genetic knockout of calpain-2 by CRISPR/Cas9 conferred resistance of the host cells to the chimeric VSV-SARS-CoV-2 virus and a clinical isolate of wild-type SARS-CoV-2. Mechanistically, calpain-2 facilitates SARS-CoV-2 spike protein-mediated cell attachment by positively regulating the cell surface levels of ACE2. These results highlight an Mpro-independent pathway targeted by calpain inhibitors for efficient viral inhibition. We also identify calpain-2 as a novel host factor and a potential therapeutic target responsible for SARS-CoV-2 infection at the entry step.

IMPORTANCE

Many efforts in small-molecule screens have been made to counter SARS-CoV-2 infection by targeting the viral main protease, the major element that processes viral proteins after translation. Here, we discovered that calpain inhibitors further block SARS-CoV-2 infection in a main protease-independent manner. We identified the host cysteine protease calpain-2 as an important positive regulator of the cell surface levels of SARS-CoV-2 cellular receptor ACE2 and, thus, a facilitator of viral infection. By either pharmacological inhibition or genetic knockout of calpain-2, the SARS-CoV-2 binding to host cells is blocked and viral infection is decreased. Our findings highlight a novel mechanism of ACE2 regulation, which presents a potential new therapeutic target. Since calpain inhibitors also potently interfere with the viral main protease, our data also provide a mechanistic understanding of the potential use of calpain inhibitors as dual inhibitors (entry and replication) in the clinical setting of COVID-19 diseases. Our findings bring mechanistic insights into the cellular process of SARS-CoV-2 entry and offer a novel explanation to the mechanism of activities of calpain inhibitors.

Meta-analysis of KAP toward COVID-19 in Chinese residents

Background

During the coronavirus disease-2019 (COVID-19) pandemic, there have been many studies on knowledge, attitudes, and practices (KAP) toward prevention of COVID-19 infection in China. Except for symptomatic treatment and vaccination, KAP toward COVID-19 plays an important role in the prevention of COVID-19. There is no systematic evaluation and meta-analysis of KAP toward COVID-19 in China. This study is the earliest meta-analysis of KAP toward COVID-19 in China's general population. Hence, this systematic review aimed to summarize the knowledge, attitudes, and practices (KAP) of Chinese residents toward COVID-19 during the pandemic.

Methodology

Following the PRISMA guidelines, articles relevant to COVID-19 KAP that were conducted among the Chinese population were found in databases such as Scopus, ProQuest, PubMed, EMbase, Web of Science, Cochrane Library, China Biology Medicine, China National Knowledge Infrastructure, CQVIP, Wanfang and Google Scholar. A random-effect meta-analysis is used to summarize studies on knowledge, attitudes, and practice levels toward COVID-19 infection in China's general population.

Results

Fifty-seven articles published between August 2020 and November 2022 were included in this review. Overall, 75% (95% CI: 72-79%) of Chinese residents had good knowledge about COVID-19, 80% (95% CI: 73-87%) of Chinese residents had a positive attitude toward COVID-19 pandemic control and prevention (they believe that Chinese people will win the battle against the epidemic), and the aggregated proportion of residents with a correct practice toward COVID-19 was 84% (95% CI: 82-87%, I2 = 99.7%).In the gender subgroup analysis, there is no significant difference between Chinese men and Chinese women in terms of their understanding of COVID-19. However, Chinese women tend to have slightly higher levels of knowledge and a more positive attitude toward the virus compared to Chinese men. When considering the urban and rural subgroup analysis, it was found that Chinese urban residents have a better understanding of COVID-19 compared to Chinese rural residents. Interestingly, the rural population displayed higher rates of correct behavior and positive attitudes toward COVID-19 compared to the urban population. Furthermore, in the subgroup analysis based on different regions in China, the eastern, central, and southwestern regions exhibited higher levels of knowledge awareness compared to other regions. It is worth noting that all regions in China demonstrated good rates of correct behavior and positive attitudes toward COVID-19.

Conclusion

This study reviews the level of KAP toward COVID-19 during the pandemic period in China. The results show that the KAP toward COVID-19 in Chinese residents was above a favorable level, but the lack of translation of knowledge into practice should be further reflected on and improved. A subgroup analysis suggests that certain groups need more attention, such as males and people living in rural areas. Policy makers should pay attention to the results of this study and use them as a reference for the development of prevention and control strategies for major public health events that may occur in the future.

Systematic Review Registration

https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=348246, CRD42022348246.

Immunomodulatory effect of Unani polyherbal formulation - Tiryaq Wabai in mild to moderate COVID-19 patients - A randomized placebo-controlled clinical trial

BACKGROUND

The pathogenesis of COVID-19 includes an integrated immune-inflammatory response. Modulation of host immune responses against the SARS-CoV-2 virus might be effective therapeutic management. Various Unani formulations have an immunomodulatory effect.

OBJECTIVE

To explore the immunomodulatory effect and safety of Unani polyherbal drug (Tiryaq Wabai) in COVID-19 patients.

MATERIALS AND METHODS

The current study was a randomized placebo-controlled clinical trial that included 92 mild to moderate COVID-19 patients randomized into two groups. The Unani formulation Tiryaq Wabai (2 gm orally once a day) was used as an intervention for 45 days, while the control group received a placebo. Both groups received standard care treatment. The primary outcome was 50% increment in absolute lymphocyte count (ALC). The secondary outcome was 50% increment in mean lymphocyte percentage, CD4 cells, and CD8 cell count. The mean increase in all the above parameters has also been studied. Relevant statistical tests were used to analyze the effect.

RESULTS

A statistically significant improvement in a 50% increase in ALC (p-value, 0.004), lymphocyte percentage (p-value, 0.056), CD4 (p-value, 0.005), and CD8 cell count (p-value, 0.050) was reported. Also, a significant improvement in the mean value of the lymphocyte percentage (p-value 0.0007), ALC (p-value 0.0022), CD4 cell count (p-value 0.0025), and CD8 cell count (p-value 0.0093) was observed after the treatment. One adverse event of mild grade was reported in the placebo group. The analysis of safety parameters (LFT and KFT) was normal for both groups.

CONCLUSION

In mild to moderate COVID-19 patients, Tiryaq Wabai effectively showed immunomodulatory activity by improving ALC count, lymphocyte percentage, CD4, and CD8 cell count.

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.

Epidemiological contemplation for a currently pragmatic COVID-19 health passport: a perspective

The coronavirus disease 2019 (COVID-19) has caused a global pandemic that has wreaked havoc on the lives of millions of people around the world. Confinement measures aim to reduce the epidemic's spread and minimize the burden of morbidity and mortality. In response to the challenges caused by the pandemic, digital health passports have been developed exponentially. We highlight the latent epidemiological barriers to health passports to achieve standardized digital care platforms. This review paper not only highlights the epidemiological barriers but also articulates the possible infrastructure required to make the International Standard for a multi-factor authenticated and validated health passport.

Serological surveillance reveals a high exposure to SARS-CoV-2 and altered immune response among COVID-19 unvaccinated Cameroonian individuals

Surveillance of COVID-19/SARS-CoV-2 dynamics is crucial to understanding natural history and providing insights into the population's exposure risk and specific susceptibilities. This study investigated the seroprevalence of SARS-CoV-2 antibodies, its predictors, and immunological status among unvaccinated patients in Cameroon. A multicentre cross-sectional study was conducted between January and September 2022 in the town of Douala. Patients were consecutively recruited, and data of interest were collected using a questionnaire. Blood samples were collected to determine Immunoglobin titres (IgM and IgG), interferon gamma (IFN- γ) and interleukin-6 (IL-6) by ELISA, and CD4+ cells by flow cytometry. A total of 342 patients aged 41.5 ± 13.9 years were included. Most participants (75.8%) were asymptomatic. The overall crude prevalence of IgM and IgG was 49.1% and 88.9%, respectively. After adjustment, the seroprevalence values were 51% for IgM and 93% for IgM. Ageusia and anosmia have displayed the highest positive predictive values (90.9% and 82.4%) and specificity (98.9% and 98.3%). The predictors of IgM seropositivity were being diabetic (aOR = 0.23, p = 0.01), frequently seeking healthcare (aOR = 1.97, p = 0.03), and diagnosed with ageusia (aOR = 20.63, p = 0.005), whereas those of IgG seropositivity included health facility (aOR = 0.15, p = 0.01), age of 40-50 years (aOR = 8.78, p = 0.01), married (aOR = 0.21, p = 0.02), fever (aOR = 0.08, p = 0.01), and ageusia (aOR = 0.08, p = 0.01). CD4+, IFN-γ, and IL-6 were impaired in seropositive individuals, with a confounding role of socio-demographic factors or comorbidities. Although the WHO declared the end of COVID-19 as a public health emergency, the findings of this study indicate the need for continuous surveillance to adequately control the disease in Cameroon.

Regional geographies and public health lessons of the COVID-19 pandemic in the Arctic

Objectives

This study examines the COVID-19 pandemic's spatiotemporal dynamics in 52 sub-regions in eight Arctic states. This study further investigates the potential impact of early vaccination coverage on subsequent COVID-19 outcomes within these regions, potentially revealing public health insights of global significance.

Methods

We assessed the outcomes of the COVID-19 pandemic in Arctic sub-regions using three key epidemiological variables: confirmed cases, confirmed deaths, and case fatality ratio (CFR), along with vaccination rates to evaluate the effectiveness of the early vaccination campaign on the later dynamics of COVID-19 outcomes in these regions.

Results

From February 2020 to February 2023, the Arctic experienced five distinct waves of COVID-19 infections and fatalities. However, most Arctic regions consistently maintained Case Fatality Ratios (CFRs) below their respective national levels throughout these waves. Further, the regression analysis indicated that the impact of initial vaccination coverage on subsequent cumulative mortality rates and Case Fatality Ratio (CFR) was inverse and statistically significant. A common trend was the delayed onset of the pandemic in the Arctic due to its remoteness. A few regions, including Greenland, Iceland, the Faroe Islands, Northern Canada, Finland, and Norway, experienced isolated spikes in cases at the beginning of the pandemic with minimal or no fatalities. In contrast, Alaska, Northern Sweden, and Russia had generally high death rates, with surges in cases and fatalities.

Conclusion

Analyzing COVID-19 data from 52 Arctic subregions shows significant spatial and temporal variations in the pandemic's severity. Greenland, Iceland, the Faroe Islands, Northern Canada, Finland, and Norway exemplify successful pandemic management models characterized by low cases and deaths. These outcomes can be attributed to successful vaccination campaigns, and proactive public health initiatives along the delayed onset of the pandemic, which reduced the impact of COVID-19, given structural and population vulnerabilities. Thus, the Arctic experience of COVID-19 informs preparedness for future pandemic-like public health emergencies in remote regions and marginalized communities worldwide that share similar contexts.

Management of COVID-19 in Ophthalmology

From its outbreak in early 2020, the new SARS-CoV-2 infection has deeply affected the entire eye care system for several reasons. Since the beginning of the COVID-19 pandemic, ophthalmologists were among the "high-risk category" for contracting the SARS-CoV-2 infection based on the notion that the eye was suspected to be a site of inoculation, infection, and transmission. Clinical ophthalmologists have been required to learn and promptly recognize the ocular manifestations associated with the COVID-19 disease, with its treatments and vaccinations. Restriction measures, lockdown periods, guidelines to prevent SARS-CoV-2 infection transmission, and the use of telemedicine and artificial intelligence modalities have induced profound modifications. These changes, which are most likely to be irreversible, influence routine clinical practice, education, and research, thus giving rise to a "new ophthalmology in the COVID era". This book chapter aims to provide several notions regarding COVID-19 in ophthalmology, including the SARS-CoV-2 virus infection and transmission modalities; the ocular manifestation associated with the COVID-19 disease; the drugs and vaccines used for COVID-19; the precautions adopted in the ophthalmic practice to limit the spread of the virus; the consequences of the pandemic on the ophthalmic patients, clinicians, and the entire eye care system; and, the future of ophthalmology in the era of "COVID new normal".

The Interrelationship between HIV Infection and COVID-19: A Review of the Literature

The Corona Virus Disease 2019 (COVID-19) pandemic resulting from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to significant morbidity and mortality in patients and put a strain on healthcare systems worldwide. The clinical characteristics and results of COVID-19 in immunosuppressed patients, such as people living with human immunodeficiency virus (PLWH), considered at higher risk of severe disease, are not well-characterized. Accumulated evidence indicates that COVID-19 and the human immunodeficiency virus (HIV) can interact in various ways. This review explored the similarities and differences in virology between SARS-CoV-2 and HIV, the effect of the COVID-19 vaccine on PLWH, the impact of the COVID-19 pandemic on PLWH care and prevention, and the influence of HIV-related factors on COVID-19. Discovering the potential link between HIV and COVID-19 may provide a novel way to avoid the factors of HIV and SARS-CoV-2 co-infection and advance future research.

A Profound Insight into the Structure-activity Relationship of Ubiquitous Scaffold Piperazine: An Explicative Review

Despite extensive research in the field of drug discovery and development, still there is a need to develop novel molecular entities. Literature reveals a substantial heterocyclic nucleus named, piperazine, which shows an immense therapeutic voyage. For several decades, molecules having the piperazine nucleus have entered the market as a drug exhibiting biological potential. It was known to possess antipsychotic, antihistamine, antianginal, antidepressant, anticancer, antiviral, cardioprotective, and anti-inflammatory activity with a specific basis for structural activity relationship. Thus, it is regarded as a key structural feature in most of the already available therapeutic drugs in the market. Reports also suggest that the extensive utilization of these currently available drugs having a piperazine nucleus shows increasing tolerance significantly day by day. In addition to this, various other factors like solubility, low bioavailability, cost-effectiveness, and imbalance between pharmacokinetics and pharmacodynamics profile limit their utilization. Focusing on that issues, various structural modification studies were performed on the piperazine moiety to develop new derivatives/analogs to overcome the problems associated with available marketed drugs. Thus, this review article aims to gain insight into the number of structural modifications at the N-1 and N-4 positions of the piperazine scaffold. This SAR approach may prove to be the best way to overcome the above-discussed drawbacks and lead to the design of drug molecules with better efficacy and affinity. Hence, there is an urgent need to focus on the structural features of this scaffold which paves further work for deeper exploration and may help medicinal chemists as well as pharmaceutical industries.

How predictive of SARS-CoV-2 infection are clinical characteristics at presentation among individuals with COVID-like symptoms treated at the Mexican Institute of Social Security

BACKGROUND

The COVID-19 pandemic has progressed rapidly, with the emergence of new virus variants that pose challenges in treating infected individuals. In Mexico, four epidemic waves have been recorded with varying disease severity. To understand the heterogeneity in clinical presentation over time and the sensitivity and specificity of signs and symptoms in identifying COVID-19 cases, an analysis of the changes in the clinical presentation of the disease was conducted.

AIM

To analyze the changes in the clinical presentation of COVID-19 among 3.38 million individuals tested for SARS-CoV-2 at the Mexican Social Security Institute (IMSS) from March 2020 to October 2021 and evaluate the predictivity of signs and symptoms in identifying COVID-19 cases.

METHODS

A retrospective analysis of clinical presentation patterns of COVID-19 among individuals treated at IMSS was performed, contrasting the signs and symptoms among SARS-CoV-2-positive individuals with those who tested negative for the virus but had respiratory infection symptoms. The sensitivity and specificity of each sign and symptom in identifying SARS-CoV-2 infection were estimated.

RESULTS

The set of signs and symptoms reported for COVID-19-suspected patients treated at IMSS were not highly specific for SARS-CoV-2 positivity. The signs and symptoms exhibited variability based on age and epidemic wave. The area under the receiver operating characteristic (ROC) curve was 0.62 when grouping the five main symptoms (headache, dyspnea, fever, arthralgia, and cough). Most of the individual symptoms had ROC values close to 0.5 (16 out of 22 between 0.48 and 0.52), indicating non-specificity.

CONCLUSIONS

The results highlight the difficulty in making a clinical diagnosis of COVID-19 due to the lack of specificity of signs and symptoms. The variability of clinical presentation over time and among age groups highlights the need for further research to differentiate whether the changes are due to changes in the virus, who is becoming infected, or the population, particularly with respect to prior infection and vaccination status.

Novel S2 subunit-specific antibody with broad neutralizing activity against SARS-CoV-2 variants of concern

Introduction

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), had a major impact on both the global health and economy. Numerous virus-neutralizing antibodies were developed against the S1 subunit of SARS-CoV-2 spike (S) protein to block viral binding to host cells and were authorized for control of the COVID-19 pandemic. However, frequent mutations in the S1 subunit of SARS-CoV-2 enabled the emergence of immune evasive variants. To address these challenges, broadly neutralizing antibodies targeting the relatively conserved S2 subunit and its epitopes have been investigated as antibody therapeutics and universal vaccines.

Methods

We initiated this study by immunizing BALB/c mice with β-propiolactone-inactivated SARS-CoV-2 (IAV) to generate B-cell hybridomas. These hybridomas were subsequently screened using HEK293T cells expressing the S2-ECD domain. Hybridomas that produced anti-S2 antibodies were selected, and we conducted a comprehensive evaluation of the potential of these anti-S2 antibodies as antiviral agents and versatile tools for research and diagnostics.

Results

In this study, we present a novel S2-specific antibody, 4A5, isolated from BALB/c mice immunized with inactivated SARS-CoV-2. 4A5 exhibited specific affinity to SARS-CoV-2 S2 subunits compared with those of other β-CoVs. 4A5 bound to epitope segment F1109-V1133 between the heptad-repeat1 (HR1) and the stem-helix (SH) region. The 4A5 epitope is highly conserved in SARS-CoV-2 variants, with a significant conformational feature in both pre- and postfusion S proteins. Notably, 4A5 exhibited broad neutralizing activity against variants and triggered Fc-enhanced antibody-dependent cellular phagocytosis.

Discussion

These findings offer a promising avenue for novel antibody therapeutics and insights for next-generation vaccine design. The identification of 4A5, with its unique binding properties and broad neutralizing capacity, offers a potential solution to the challenge posed by SARS-CoV-2 variants and highlights the importance of targeting the conserved S2 subunit in combating the COVID-19.

ACE2 knockout hinders SARS-CoV-2 propagation in iPS cell-derived airway and alveolar epithelial cells

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, continues to spread around the world with serious cases and deaths. It has also been suggested that different genetic variants in the human genome affect both the susceptibility to infection and severity of disease in COVID-19 patients. Angiotensin-converting enzyme 2 (ACE2) has been identified as a cell surface receptor for SARS-CoV and SARS-CoV-2 entry into cells. The construction of an experimental model system using human iPS cells would enable further studies of the association between viral characteristics and genetic variants. Airway and alveolar epithelial cells are cell types of the lung that express high levels of ACE2 and are suitable for in vitro infection experiments. Here, we show that human iPS cell-derived airway and alveolar epithelial cells are highly susceptible to viral infection of SARS-CoV-2. Using gene knockout with CRISPR-Cas9 in human iPS cells we demonstrate that ACE2 plays an essential role in the airway and alveolar epithelial cell entry of SARS-CoV-2 in vitro. Replication of SARS-CoV-2 was strongly suppressed in ACE2 knockout (KO) lung cells. Our model system based on human iPS cell-derived lung cells may be applied to understand the molecular biology regulating viral respiratory infection leading to potential therapeutic developments for COVID-19 and the prevention of future pandemics.

The effect of SARS-CoV-2 variants on the plasma oxylipins and PUFAs of COVID-19 patients

Oxylipins are important signalling compounds that are significantly involved in the regulation of the immune system and the resolution of inflammation. Lipid metabolism is strongly activated upon SARS-CoV-2 infection, however the modulating effects of oxylipins induced by different variants remain unexplored. Here, we compare the plasma profiles of thirty-seven oxylipins and four PUFAs in subjects infected with Wild-type, Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (B.1.1.529) variants. The results suggest that oxidative stress and inflammation resulting from COVID-19 were highly dependent on the SARS-CoV-2 variant, and that the Wild-type elicited the strongest inflammatory storm. The Alpha and Delta variants induced a comparable lipid profile alteration upon infection, which differed significantly from Omicron. The latter variant increased the levels of pro-inflammatory mediators and decreased the levels of omega-3 PUFA in infected patients. We speculate that changes in therapeutics, vaccination, and prior infections may have a role in the alteration of the oxylipin profile besides viral mutations. The results shed new light on the evolution of the inflammatory response in COVID-19.

Incidence and severity of pulmonary embolism in COVID-19 infection: Ancestral, Alpha, Delta, and Omicron variants

Little information is available regarding incidence and severity of pulmonary embolism (PE) across the periods of ancestral strain, Alpha, Delta, and Omicron variants. The aim of this study is to investigate the incidence and severity of PE over the dominant periods of ancestral strain and Alpha, Delta, and Omicron variants. We hypothesized that the incidence and the severity by proximity of PE in patients with the newer variants and vaccination would be decreased compared with those in ancestral and earlier variants. Patients with COVID-19 diagnosis between March 2020 and February 2022 and computed tomography pulmonary angiogram performed within a 6-week window around the diagnosis (-2 to +4 weeks) were studied retrospectively. The primary endpoints were the associations of the incidence and location of PE with the ancestral strain and each variant. Of the 720 coronavirus disease 2019 patients with computed tomography pulmonary angiogram (58.6 ± 17.2 years; 374 females), PE was diagnosed among 42/358 (12%) during the ancestral strain period, 5/60 (8%) during the Alpha variant period, 16/152 (11%) during the Delta variant period, and 13/150 (9%) during the Omicron variant period. The most proximal PE (ancestral strain vs variants) was located in the main/lobar arteries (31% vs 6%-40%), in the segmental arteries (52% vs 60%-75%), and in the subsegmental arteries (17% vs 0%-19%). There was no significant difference in both the incidence and location of PE across the periods, confirmed by multivariable logistic regression models. In summary, the incidence and severity of PE did not significantly differ across the periods of ancestral strain and Alpha, Delta, and Omicron variants.

Knowledge, attitude and practices towards SARS-CoV-2 genetic mutations and emerging variants among the population in Bangladesh: a cross-sectional study

OBJECTIVES

The coronavirus is continuously mutating and creating new SARS-CoV-2 variants. Public awareness about SARS-CoV-2 mutation is essential for effective preventive measures. The present study aimed to assess the knowledge, attitude and practices (KAP) towards SARS-CoV-2 variants among the general population in Bangladesh.

DESIGN

We conducted this online survey between 9 April 2021 and 10 May 2021 using structured questionnaires to collect the information.

SETTING

We distributed the survey link among the participants from all 64 districts of Bangladesh using social media platforms.

PARTICIPANTS

A total of 1,090 respondents completed this survey. After careful evaluation, we excluded 18 responses due to partial or incomplete information, and 1,072 responses entered into the final analysis.

PRIMARY OUTCOME

The KAP of participants towards SARS-CoV-2 variants depends on their demographic backgrounds. Associations between demographic characteristics and the likelihood of having adequate KAP were estimated using adjusted logistic regressions.

RESULTS

Among the participants, 42% had a poor knowledge level, 4% had a low attitude level and 14% had a poor practice score. The average knowledge, attitude and practice score were 2.65, 4.194 and 4.464 on a scale of 5, respectively. Only 51.8% of the participants knew about mutant strains, and only 47.6% knew about the effectiveness of vaccines against new variants. The key factors associated with poor knowledge levels were educational levels, area of residence, geographic location, and concern regarding COVID-19. Sociodemographic factors for poor attitude levels were geographic location, vaccination and concern regarding COVID-19. The pivotal factors in determining poor practice scores were the residence area of people and concern regarding COVID-19.

CONCLUSIONS

The knowledge level and positive attitude are associated with better preventive measures against SARS-CoV-2 variants. Based on these findings, we recommended several awareness programmes on SARS-CoV-2 mutations and variants for the rural population in Bangladesh to increase overall awareness levels.

The Promotion of Humoral Immune Responses in Humans via SOCS1-Mediated Th2-Bias Following SARS-CoV-2 Vaccination

The effectiveness of SARS-CoV-2 vaccines varies among individuals. During the COVID-19 global pandemic, SARS-CoV-2 infection showed significant Th1 characteristics, suggesting that the immune disorder and production of SARS-CoV-2 antibodies may be related to Th1/Th2 bias. However, the molecular mechanisms underlying Th1/Th2 bias effects on host immune responses to viruses remain unclear. In this study, the top three subjects with the highest and lowest changes in anti-SARS-CoV-2 antibodies after receiving three doses of SARS-CoV-2 vaccination were selected and defined as the elevated group (E) and the control group (C), respectively. Peripheral blood was collected, single-cell sequencing was performed before and after the third dose of the SARS-CoV-2 vaccine, and the changes in T cell clusters were analyzed. Compared with the C group, the Treg pre-vaccination proportion was lower in E, while the post-vaccination proportion was higher, suggesting that Tregs may be crucial in this process. Differential analysis results of Tregs between the two groups revealed that differentially expressed genes (DEGs) were significantly enriched in the IL4 pathway. Correlation analysis between DEGs and serum antibody showed that the expression of NR4A2, SOCS1, and SOCS3 in Tregs was significantly correlated with serum antibodies, suggesting that the immune response in E group changed to Th2 bias, thereby promoting host humoral immune responses. On the other hand, antibody-related genes SOCS1 and NR4A2, as well as lnc-RNA MALAT1 and NEAT1, were highly expressed in the CD4-MALAT1 subclusters. In summary, our study revealed that Th2 bias promotes humoral immune responses in humans by increasing SOCS1 in T cells after SARS-CoV-2 vaccination. Moreover, NR4A2, SOCS1, MALAT1, and NEAT1 were identified as the potential key biomarkers or treatment targets for enhanced SARS-CoV-2 antibody production by influencing the Th1/Th2 balance in T cells. Our findings have important implications for population stratification and tailored therapeutics for more effective SARS-CoV-2 vaccines.

Characterization of SARS-CoV-2 Variants in Military and Civilian Personnel of an Air Force Airport during Three Pandemic Waves in Italy

We investigated SARS-CoV-2 variants circulating, from November 2020 to March 2022, among military and civilian personnel at an Air Force airport in Italy in order to classify viral isolates in a potential hotspot for virus spread. Positive samples were subjected to Next-Generation Sequencing (NGS) of the whole viral genome and Sanger sequencing of the spike coding region. Phylogenetic analysis classified viral isolates and traced their evolutionary relationships. Clusters were identified using 70% cut-off. Sequencing methods yielded comparable results in terms of variant classification. In 2020 and 2021, we identified several variants, including B.1.258 (4/67), B.1.177 (9/67), Alpha (B.1.1.7, 9/67), Gamma (P.1.1, 4/67), and Delta (4/67). In 2022, only Omicron and its sub-lineage variants were observed (37/67). SARS-CoV-2 isolates were screened to detect naturally occurring resistance in genomic regions, the target of new therapies, comparing them to the Wuhan Hu-1 reference strain. Interestingly, 2/30 non-Omicron isolates carried the G15S 3CLpro substitution responsible for reduced susceptibility to protease inhibitors. On the other hand, Omicron isolates carried unusual substitutions A1803V, D1809N, and A949T on PLpro, and the D216N on 3CLpro. Finally, the P323L substitution on RdRp coding regions was not associated with the mutational pattern related to polymerase inhibitor resistance. This study highlights the importance of continuous genomic surveillance to monitor SARS-CoV-2 evolution in the general population, as well as in restricted communities.