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This document is an editorial from the journal Biomedicines, discussing a special issue on the latest research in post-COVID conditions. The COVID-19 pandemic has led to a significant increase in research, with a focus on managing acute cases and preventing the spread of the virus. However, there is now a growing concern about the development of long-lasting symptoms after the acute infection, known as long-COVID or post-COVID-19 condition. This special issue includes fourteen papers covering topics such as the treatment of post-COVID-19 condition, the impact of SARS-CoV-2 infection on neonates, risk factors for severe COVID-19, and the phenotyping of post-COVID pain. The papers discuss various treatment strategies, the potential transmission of the virus during pregnancy, risk factors for severe disease, and different types of post-COVID pain. Overall, this special issue provides valuable insights into the understanding and management of post-COVID conditions. [Extracted from the article]

This document is a summary of a special issue of the journal Brain Sciences titled "Neurological and Psychiatric Disorders in the COVID-19 Era." The issue aims to expand knowledge about the impact of COVID-19 on neurological and psychiatric disorders and how the outbreak has affected their management. The issue includes six original scientific papers. One study found an association between pulmonary embolism in COVID-19 patients and neurological complications such as stroke and seizures. Another study reviewed the possible mechanisms of SARS-CoV-2 damage in the body, including neurological disorders. A systematic review identified risk factors for depressive symptoms during COVID-19-related restrictions. Another study evaluated long-term neuropsychiatric sequelae in COVID-19 survivors and found that a significant portion still experienced symptoms. A review focused on the impact of COVID-19 on neurology training, and the final paper examined emotional distress in COVID-19 patients admitted to a rehabilitation unit. The special issue aims to provide new insights for future research initiatives. [Extracted from the article]

In this paper, we construct an infectious disease model with a testing compartment and analyze the existence and stability of its endemic states. We obtain the basic reproduction number, R 0 , and demonstrate the existence of one endemic equilibrium without testing and one endemic equilibrium with testing and prove their local and global stabilities based on the value of the basic reproduction number, R 0 . We then apply our model to the US COVID-19 pandemic and find that, for a large parameter set, including those relevant to the SARS-CoV-2 virus, our analytic and numerical results suggest that the trajectories will be trapped to the testing-free state when the testing number is small enough. This indicates that the pandemic may end with a testing-free endemic state through a novel and surprising mechanism called stochastic trapping. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic has resulted in millions of fatalities worldwide. The case of pediatric cancer patients stands out since, despite being considered a population at risk, few studies have been carried out concerning symptom detection or the description of the mechanisms capable of modifying the course of the COVID-19 disease, such as the interaction and response between the virus and the treatment given to cancer patients. By synthesizing existing studies, this paper aims to expose the treatment challenges for pediatric patients with COVID-19 in an oncology context. Additionally, this updated review includes studies that utilized the antiviral agents Remdesivir and PaxlovidTM in pediatric cancer patients. There is no specific treatment designed exclusively for pediatric cancer patients dealing with COVID-19, and it is advisable to avoid self-medication to prevent potential side effects. Managing COVID-19 in pediatric cancer patients is indeed a substantial challenge. New strategies, such as chemotherapy application rooms, have been implemented for children with cancer who were positive for COVID-19 but asymptomatic since the risk of disease progression is greater than the risk of complications from SARS-CoV-2. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic represented a huge obstacle for public health and demonstrated weaknesses in surveillance and health promotion systems around the world. Its etiological agent, SARS-CoV-2, of zoonotic origin, has been the target of several studies related to the control and prevention of outbreaks and epidemics of COVID-19 not only for humans but also for animals. Domestic animals, such as dogs and cats, have extensive contact with humans and can acquire the infection both naturally and directly from humans. The objective of this article was to summarize the seroprevalence findings of SARS-CoV-2 in dogs and cats and correlate them with the strength of infection risk between each of them. This is a systematic review and meta-analysis following the recommendations of PRISMA 2020. The search and selection of papers was carried out using in vivo experimental works with animals using the descriptors (MeSH/DeCS) "Animal", "Public Health", "SARS-CoV-2" and "Pandemic" (together with AND) in English, Portuguese or Spanish for Science Direct, PUBMED, LILACS and SciELO databases. The ARRIVE checklist was used for methodological evaluation and the Comprehensive Meta-Analysis v2.2 software with the Difference Risk (RD) test to evaluate statistical inferences (with subgroups by continent). Cats showed greater susceptibility to SARS-CoV-2 compared to dogs both in a joint analysis of studies (RD = 0.017; 95% CI = 0.008–0.025; p < 0.0001) and in the American subgroup (RD = 0.053; 95% CI = 0.032–0.073; p < 0.0001), unlike the lack of significant difference on the European continent (RD = 0.009; 95% CI = −0.001–0.018; p = 0.066). Therefore, it was observed that cats have a greater interest in health surveillance due to the set of biological and ecological aspects of these animals, but also that there are a set of factors that can influence the spread and possible spillover events of the virus thanks to the anthropozoonotic context. [ABSTRACT FROM AUTHOR]

The evolutionary dynamics of viruses, particularly exemplified by SARS-CoV-2 during the ongoing COVID-19 pandemic, underscore the intricate interplay between genetics, host adaptation, and viral spread. This paper delves into the genetic evolution of SARS-CoV-2, emphasizing the implications of viral variants on global health. Initially emerging from the Wuhan-Hu-1 lineage, SARS-CoV-2 rapidly diversified into numerous variants, each characterized by distinct mutations in the spike protein and other genomic regions. Notable variants such as B.1.1.7 (α), B.1.351 (β), P.1 (γ), B.1.617.2 (δ), and the Omicron variant have garnered significant attention due to their heightened transmissibility and immune evasion capabilities. In particular, the Omicron variant has presented a myriad of subvariants, raising concerns about its potential impact on public health. Despite the emergence of numerous variants, the vast majority have exhibited limited expansion capabilities and have not posed significant threats akin to early pandemic strains. Continued genomic surveillance is imperative to identify emerging variants of concern promptly. While genetic adaptation is intrinsic to viral evolution, effective public health responses must be grounded in empirical evidence to navigate the evolving landscape of the pandemic with resilience and precision. [ABSTRACT FROM AUTHOR]

The novel coronavirus outbreak has significantly heightened environmental costs and operational challenges for civil aviation airlines, prompting emergency airport closures in affected regions and a substantial decline in ridership. The consequential need to reassess, delay, or cancel flight itineraries has led to disruptions at airports, amplifying the risk of disease transmission. In response, this paper proposes a spatial approach to efficiently address pandemic spread in the civil aviation network. The methodology prioritizes the use of a static gravity model for calculating route-specific infection pressures, enabling strategic flight rescheduling to control infection levels at airports (nodes) and among airlines (edges). Temporally, this study considers intervals between takeoffs and landings to minimize crowd gatherings, mitigating the novel coronavirus transmission rate. By constructing a discrete space–time network for irregular flights, this research generates a viable set of routes for aircraft operating in special circumstances, minimizing both route-specific infection pressures and operational costs for airlines. Remarkably, the introduced method demonstrates substantial savings, reaching almost 53.4%, compared to traditional plans. This showcases its efficacy in optimizing responses to pandemic-induced disruptions within the civil aviation network, offering a comprehensive solution that balances operational efficiency and public health considerations in the face of unprecedented challenges. [ABSTRACT FROM AUTHOR]

During the COVID-19 pandemic, microbiological controls neglected the spread of viruses through the air. Techniques to identify this threat required additional research to enable control measures to be introduced to protect against the spread of disease through this route. Due to the very high level of risk occurring during research on the COVID-19 and SARS-CoV-2 viruses, it seems necessary to use analogous microorganisms that will allow, through an experiment, to validate or challenge a method that stops the spread of infectious microorganisms, without unnecessary risk to research staff. The presented work was carried out to assess the possibility of using airborne microorganisms that are safe for humans for this type of research. The work presents the selection process of bacteria and viruses (bacteriophages) that have the greatest potential for use in experimental studies on airborne-droplet transmission indoors, especially in hospital facilities. In the study, it was assumed that determining the survival rates of groups of organisms would allow them to be used as a proxy for studying more dangerous bacteria and viruses. Survival studies of selected microorganisms were carried out, and the paper selected microorganisms with the highest survival rate in a given environment. [ABSTRACT FROM AUTHOR]

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for coronavirus disease-19 (COVID-19). This virus has caused a global pandemic, marked by several mutations leading to multiple waves of infection. This paper proposes a comprehensive and integrative mathematical approach to the third wave of COVID-19 (Omicron) in the Kingdom of Saudi Arabia (KSA) for the period between 16 December 2022 and 8 February 2023. It may help to implement a better response in the next waves. For this purpose, in this article, we generate a new mathematical transmission model for coronavirus, particularly during the third wave in the KSA caused by the Omicron variant, factoring in the impact of vaccination. We developed this model using a fractal-fractional derivative approach. It categorizes the total population into six segments: susceptible, vaccinated, exposed, asymptomatic infected, symptomatic infected, and recovered individuals. The conventional least-squares method is used for estimating the model parameters. The Perov fixed point theorem is utilized to demonstrate the solution's uniqueness and existence. Moreover, we investigate the Ulam–Hyers stability of this fractal–fractional model. Our numerical approach involves a two-step Newton polynomial approximation. We present simulation results that vary according to the fractional orders (γ) and fractal dimensions (θ), providing detailed analysis and discussion. Our graphical analysis shows that the fractal-fractional derivative model offers more biologically realistic results than traditional integer-order and other fractional models. [ABSTRACT FROM AUTHOR]

During the SARS-CoV-2 pandemic, the air quality and infection risk in classrooms were the focus of many investigations. Despite general recommendations for sufficient ventilation, quantitative analyses were often lacking due to the large number of combinations of boundary conditions. Hence, in this paper, we describe a computational fluid dynamics model that predicts the time-resolved airflow for a typical 45 min classroom scenario. We model 28 students and a teacher, each emitting CO2 and an individual aerosol. We investigated 13 ventilation setups with window or mechanical ventilation and different positions and operating conditions of an additional air purifier. The ventilation performance is assessed by evaluating the ventilation effectiveness, aerosol removal effectiveness, local air exchange efficiency and overall inhaled aerosol mass of the occupants, which is a measure of the infection risk. If the window is opened according to the "20-5-20" recommendation, the incoming airflow reduces both the CO2 and aerosol concentration whilst decreasing the thermal comfort at low ambient temperatures. An active air purifier enhances aerosol removal, but, depending on the position, the local air exchange efficiency and individual aerosol inhalation vary. If mechanical ventilation with 700 m3/h is utilised, the CO2 concentration is kept below 1250 ppm while also effectively removing aerosol from the classroom. [ABSTRACT FROM AUTHOR]

COVID-19 made explicit the need for rethinking the way in which we conduct testing for epidemic emergencies. During the COVID-19 pandemic, the dependence on centralized lab facilities and resource-intensive methodologies (e.g., RT-qPCR methods) greatly limited the deployment of widespread testing efforts in many developed and underdeveloped countries. Here, we illustrate the development of a simple and portable diagnostic kit that enables self-diagnosis of COVID-19 at home from saliva samples. We describe the development of a do-it-yourself (DIY) incubator for Eppendorf tubes that can be used to conduct SARS-CoV-2 detection with competitive sensitivity and selectivity from saliva at home. In a proof-of-concept experiment, we assembled Eppendorf-tube incubators at our home shop, prepared a single-tube mix of reagents and LAMP primers in our lab, and deployed these COVID-19 detection kits using urban delivery systems (i.e., Rappifavor or Uber) to more than 15 different locations in Monterrey, México. This straightforward strategy enabled rapid and cost-effective at-home molecular diagnostics of SARS-CoV-2 from real saliva samples with a high sensitivity (100%) and high selectivity (87%). [ABSTRACT FROM AUTHOR]

Wastewater-based epidemiology (WBE) is useful for detecting pathogen prevalence and may serve to effectively monitor diseases across broad scales. WBE has been used throughout the COVID-19 pandemic to track disease burden through quantifying SARS-CoV-2 RNA present in wastewater. Aside from case load estimation, WBE is being used to assay viral genomic diversity and emerging potential SARS-CoV-2 variants. Here, we present a study in which we sequenced RNA extracted from sewage influent obtained from eight wastewater treatment plants representing 16 million people in Southern California from April 2020 to August 2021. We sequenced SARS-CoV-2 with two methods: Illumina Respiratory Virus-Enriched metatranscriptomic sequencing (N = 269), and QIAseq SARS-CoV-2-tiled amplicon sequencing (N = 95). We classified SARS-CoV-2 reads into lineages and sublineages that approximated named variants and identified single nucleotide variants (SNVs), of which many are putatively novel SNVs and SNVs of unknown potential function and prevalence. Through our retrospective study, we also show that several SARS-CoV-2 sublineages were detected in wastewater before clinical detection, which may assist in the prediction of future variants of concern. Lastly, we show that sublineage diversity was similar across Southern California and that diversity changed over time, indicating that WBE is effective across megaregions. As the COVID-19 pandemic moves to new phases, and SARS-CoV-2 variants emerge, monitoring wastewater is important to understand local- and population-level dynamics of the virus. These results will aid in our ability to monitor the evolutionary potential of SARS-CoV-2 and help understand circulating SNVs to further combat COVID-19. [ABSTRACT FROM AUTHOR]

Background/Objectives: During the COVID-19 pandemic and the burden on hospital resources, the rapid categorization of high-risk COVID-19 patients became essential, and lung ultrasound (LUS) emerged as an alternative to chest computed tomography, offering speed, non-ionizing, repeatable, and bedside assessments. Various LUS score systems have been used, yet there is no consensus on an optimal severity cut-off. We assessed the performance of a 12-zone LUS score to identify adult COVID-19 patients with severe lung involvement using oxygen saturation (SpO2)/fractional inspired oxygen (FiO2) ratio as a reference standard to define the best cut-off for predicting adverse outcomes. Methods: We conducted a single-centre prospective study (August 2020–April 2021) at Hospital del Mar, Barcelona, Spain. Upon admission to the general ward or intensive care unit (ICU), clinicians performed LUS in adult patients with confirmed COVID-19 pneumonia. Severe lung involvement was defined as a SpO2/FiO2 ratio <315. The LUS score ranged from 0 to 36 based on the aeration patterns. Results: 248 patients were included. The admission LUS score showed moderate performance in identifying a SpO2/FiO2 ratio <315 (area under the ROC curve: 0.71; 95%CI 0.64–0.77). After adjustment for COVID-19 risk factors, an admission LUS score ≥17 was associated with an increased risk of in-hospital death (OR 5.31; 95%CI: 1.38–20.4), ICU admission (OR 3.50; 95%CI: 1.37–8.94) and need for IMV (OR 3.31; 95%CI: 1.19–9.13). Conclusions: Although the admission LUS score had limited performance in identifying severe lung involvement, a cut-off ≥17 score was associated with an increased risk of adverse outcomes. and could play a role in the rapid categorization of COVID-19 pneumonia patients, anticipating the need for advanced care. [ABSTRACT FROM AUTHOR]

The global urgency in response to the COVID-19 pandemic has catalyzed extensive research into discovering efficacious antiviral compounds against SARS-CoV-2. Among these, Nirmatrelvir (PF-07321332) has emerged as a promising candidate, exhibiting potent antiviral activity by targeting the main protease of SARS-CoV-2, and has been marketed in combination with ritonavir as the first oral treatment for COVID-19 with the name of PaxlovidTM. This review outlines the synthetic approaches to Nirmatrelvir, ranging from Pfizer's original method to newer, more sustainable strategies, such as flow chemistry strategies and multicomponent reactions. Each approach's novelty and contributions to yield and purification processes are highlighted. Additionally, the synthesis of key fragments comprising Nirmatrelvir and innovative optimization strategies are discussed. [ABSTRACT FROM AUTHOR]

Background and Objectives: Our aim was to perform a retrospective analysis of the volume of cervical screening tests, the number of patients treated with an excision method, and the incidence of invasive and non-invasive cervical during a pandemic and pre-pandemic period of 24 months. Materials and Methods: The study compared 404 patients who underwent cervical cone biopsy for cervical cancer. The study examined patients' specimens based on histopathological characteristics and categorized cervical lesions based on pap smear. Results: There was a statistically significant age difference between the two study periods. The mean difference was 32 years before the pandemic and 35 years during the pandemic (p-value > 0.05). The biggest patient loss ratio identified by age group was in the 50–59-year group, with a 14.53% loss in the pre-pandemic period and a 9.1% loss in the pandemic period. In the pandemic period, patients from rural areas presented in the clinical trial with a lower rate of 39.52% (83 patients) vs. 60.47% (127 patients) in urban areas. A higher percentage of patients experiencing cervicorrhagia as a clinical manifestation in the pandemic period vs. the pre-pandemic period, with an increase in more severe lesions in the pandemic period, had a statistical significance of 8% more newly diagnosed compared to the pre-pandemic period. Conclusions: The addressability of the patients during the COVID period was not affected in a drastic way in our study. We encountered a decrease in appointments in the age group of 50–59 years and a decrease in patients with rural residence. In our study, we found an increase in cervical bleeding as a reason for consultation in the pandemic period with a higher lesion degree, both on a pap smear and on a cervical biopsy. [ABSTRACT FROM AUTHOR]

Advantageous variants of the SARS-CoV-2 virus have arisen through mutations, particularly on a single amino acid basis. These point mutations can cause changes in the structure of SARS-CoV-2 and affect the efficiency of interaction with the ACE2 protein. N501Y and E484K mutations affecting binding by ACE2 have been widely observed. This study aimed to predict SARS-CoV-2 mutations that could be as effective as N501Y and E484K and pose a danger due to their high contagiousness. Experimental data on SARS-CoV-2 and ACE2 binding and stability were associated with different amino acid properties and integrated into machine learning and computational biology techniques. As a result of the analyses made in algorithms, N501M, Q414A, N354K, Q498H and N460K have been predicted to be likely to have a dangerous effect. The N501W mutations are most likely to have dangerous effects on the spread of the coronavirus. We suggest that attention should be paid to the position 501 mutation since this position is repeated in the lists of mutations that the algorithm detected as dangerous. G446, G447, Y505, T500, Q493, Y473, and G476 were determined as the positions where dangerous variants could be seen as a result of the analyses of the multiple interaction data created with the ACE2 and RBD interaction data. The 13 dangerous positions and mutations have been detected to accurately describe the position of the mutations caused by the Omicron variant and were among the known dangerous mutations similar to those occurring at Q498, G446, Y505 and Q493 positions. [ABSTRACT FROM AUTHOR]

Bronchial asthma (BA) continues to be a difficult disease to diagnose. Various factors have been described in the development of BA, but to date, there is no clear evidence for the etiology of this chronic disease. The emergence of COVID-19 has contributed to the pandemic course of asthma and immunologic features. However, there are no unambiguous data on asthma on the background and after COVID-19. There is correlation between various trigger factors that provoke the development of bronchial asthma. It is now obvious that the SARS-CoV-2 virus is one of the provoking factors. COVID-19 has affected the course of asthma. Currently, there is no clear understanding of whether asthma progresses during or after COVID-19 infection. According to the results of some studies, a significant difference was identified between the development of asthma in people after COVID-19. Mild asthma and moderate asthma do not increase the severity of COVID-19 infection. Nevertheless, oral steroid treatment and hospitalization for severe BA were associated with higher COVID-19 severity. The influence of SARS-CoV-2 infection is one of the protective factors. It causes the development of severe bronchial asthma. The accumulated experience with omalizumab in patients with severe asthma during COVID-19, who received omalizumab during the pandemic, has strongly suggested that continued treatment with omalizumab is safe and may help prevent the severe course of COVID-19. Targeted therapy for asthma with the use of omalizumab may also help to reduce severe asthma associated with COVID-19. However, further studies are needed to prove the effect of omalizumab. Data analysis should persist, based on the results of the course of asthma after COVID-19 with varying degrees of severity. [ABSTRACT FROM AUTHOR]

Despite evidence demonstrating the risks of developing diabetes mellitus because of SARS-CoV-2, there is, however, insufficient scientific data available to elucidate the relationship between diabetes mellitus and COVID-19. Research indicates that SARS-CoV-2 infection is associated with persistent damage to organ systems due to the systemic inflammatory response. Since COVID-19 is known to induce these conditions, further investigation is necessary to fully understand its long-term effects on human health. Consequently, it is essential to consider the effect of the COVID-19 pandemic when predicting the prevalence of diabetes mellitus in the future, especially since the incidence of diabetes mellitus was already on the rise before the pandemic. Additional research is required to fully comprehend the impact of SARS-CoV-2 infection on glucose tolerance and insulin sensitivity. Therefore, this article delves deeper into the current literature and links the perceived relationship between SARS-CoV-2 and diabetes. In addition, the article highlights the necessity for further research to fully grasp the mechanisms that SARS-CoV-2 utilises to induce new-onset diabetes. Where understanding and consensus are reached, therapeutic interventions to prevent the onset of diabetes could be proposed. Lastly, we propose advocating for the regular screening of diabetes and pre-diabetes, particularly for the high-risk population with a history of COVID-19 infection. [ABSTRACT FROM AUTHOR]

Patients with chronic obstructive pulmonary disease (COPD) infected with SARS-CoV-2 indicate a higher risk of severe COVID-19 course, which is defined as the need for hospitalization in the intensive care unit, mechanical ventilation, or death. However, simple tools to stratify the risk in patients with COPD suffering from COVID-19 are lacking. The current study aimed to evaluate the predictive value of the C2HEST score in patients with COPD. A retrospective analysis of medical records from 2184 patients hospitalized with COVID-19 at the University Hospital in Wroclaw from February 2020 to June 2021, which was previously used in earlier studies, assessed outcomes such as mortality during hospitalization, all-cause mortality at 3 and 6 months, non-fatal discharge, as well as adverse clinical incidents. This re-analysis specifically examines the outcomes using a COPD split. In the COPD group, 42 deaths were recorded, including 18 in-hospital deaths. In-hospital mortality rates at 3 and 6 months did not significantly differ among C2HEST strata, nor did their impact on subsequent treatment. However, a notable association between the C2HEST score and prognosis was observed in the non-COPD cohort comprising 2109 patients. The C2HEST score's predictive ability is notably lower in COPD patients compared to non-COPD subjects, with COPD itself indicating a high mortality risk. However, C2HEST effectively identifies patients at high risk of cardiac complications during COVID-19, especially in non-COPD cases. [ABSTRACT FROM AUTHOR]

Background: The long-term survival of patients hospitalized with COVID-19 and the factors associated with poorer survival months after infection are not well understood. The aims of the present study were to analyze the overall mortality 10 months after admission. Methods: 762 patients with COVID-19 disease were included. Patients underwent a complete clinical evaluation, routine laboratory analysis and chest X-ray. Data collected included demographic and clinical data, such as vascular risk factors, tobacco or alcohol use, comorbidity, and institutionalization. Results: Ten-month mortality was 25.6%: 108 deaths occurred in-hospital, while 87 patients died after discharge. In-hospital mortality was independently related to NT-proBNP values > 503.5 pg/mL [OR = 4.67 (2.38–9.20)], urea > 37 mg/dL [3.21 (1.86–7.31)] and age older than 71 years [OR = 1.93 (1.05–3.54)]. NT-proBNP values > 503.5 pg/mL [OR = 5.00 (3.06–8.19)], urea > 37 mg/dL [3.51 (1.97–6.27)], cognitive impairment [OR = 1.96 (1.30–2.95), cancer [OR = 2.23 (1.36–3.68), and leukocytes > 6330/mm3 [OR = 1.64 (1.08–2.50)], were independently associated with long-term mortality. Conclusions: the risk of death remains high even months after COVID-19 infection. Overall mortality of COVID-19 patients during 10 months after hospital discharge is nearly as high as that observed during hospital admission. Comorbidities such as cancer or cognitive impairment, organ dysfunction and inflammatory reaction are independent prognostic markers of long-term mortality. [ABSTRACT FROM AUTHOR]

Infection with the novel coronavirus SARS-CoV-2, the cause of coronavirus disease (COVID-19), has emerged as a global pandemic, with a high toll on casualties, economic impact, and human lifestyle. Despite the recent approval of various vaccines against the virus, challenges remain, including the limited availability of these vaccines, the prevalent rejection of vaccination by a large proportion of the population, and the recurrent appearance of new variants of the virus due to mutations. This context raises the alarm for scientists and clinicians to seek alternative and complementary therapies. In this context, natural products and their derivatives serve as reservoirs for potential therapeutic compounds that can be exploited in the research and production of antiviral drugs against COVID-19. Among these substances, lectin and polysaccharides isolated from fauna and flora emerge as complementary strategies for treating coronavirus infection. The review objective is to cover and analyze the specific role of polysaccharides and lectins and their synergy in the fight against this deadly SARS-CoV-2 virus. For this purpose, a primary literature search was conducted on Google Scholar, PubMed, and Web of Sciences using relevant keywords like "SARS-CoV-2 Variants"; "Antiviral Strategies"; "Antiviral Polysaccharides"; "Antiviral Lectins"; and "Synergistic effect". The results demonstrate that lectins and polysaccharides exhibit antiviral activities against SARS-CoV-2 via mechanisms related to binding and steric blocking, the binding of glycan-based decoys, chemical reactions, virus particle disruption strategies, and steric blocking for competitive inhibition to block SARS-CoV-2 and its variants' entry. In addition, this review analyzes the rationale behind combining polysaccharides and lectins, emphasizing complementary mechanisms of action. By simultaneously targeting multiple stages of the viral life cycle, this dual strategy aims to comprehensively inhibit viral propagation and enhance the durability of antiviral strategies over time. [ABSTRACT FROM AUTHOR]

The emergence of the novel coronavirus in Wuhan, China since 2019, has put the world in an exotic state of emergency and affected millions of lives. It is five times more deadly than Influenza and causes significant morbidity and mortality. COVID-19 mainly affects the pulmonary system leading to respiratory disorders. However, earlier studies indicated that COVID-19 infection may cause cardiovascular diseases, which can be detected using an electrocardiogram (ECG). This work introduces an advanced deep learning architecture for the automatic detection of COVID-19 and heart diseases from ECG images. In particular, a hybrid combination of the EfficientNet-B0 CNN model and Vision Transformer is adopted in the proposed architecture. To our knowledge, this study is the first research endeavor to investigate the potential of the vision transformer model to identify COVID-19 in ECG data. We carry out two classification schemes, a binary classification to identify COVID-19 cases, and a multi-class classification, to differentiate COVID-19 cases from normal cases and other cardiovascular diseases. The proposed method surpasses existing state-of-the-art approaches, demonstrating an accuracy of 100% and 95.10% for binary and multiclass levels, respectively. These results prove that artificial intelligence can potentially be used to detect cardiovascular anomalies caused by COVID-19, which may help clinicians overcome the limitations of traditional diagnosis. [ABSTRACT FROM AUTHOR]

Essential in halting the COVID-19 pandemic caused by SARS-CoV-2, it is crucial to have stable, effective, and easy-to-manufacture vaccines. We developed a potential vaccine using a tobacco mosaic virus (TMV) epitope display model presenting peptides derived from the SARS-CoV-2 spike protein. The TMV-epitope fusions in laboratory tests demonstrated binding to the SARS-CoV-2 polyclonal antibodies. The fusion constructs maintained critical epitopes of the SARS-CoV-2 spike protein, and two in particular spanned regions of the receptor-binding domain that have mutated in the more recent SARS-CoV-2 variants. This would allow for the rapid modification of vaccines in response to changes in circulating variants. The TMV-peptide fusion constructs also remained stable for over 28 days when stored at temperatures between −20 and 37 °C, an ideal property when targeting developing countries. Immunogenicity studies conducted on BALB/c mice elicited robust antibody responses against SARS-CoV-2. A strong IFNγ response was also observed in immunized mice. Three of the six TMV-peptide fusion constructs produced virus-neutralizing titers, as measured with a pseudovirus neutralization assay. These TMV-peptide fusion constructs can be combined to make a multivalent vaccine that could be adapted to meet changing virus variants. These findings demonstrate the development of a stable COVID-19 vaccine candidate by combining SARS-CoV-2 spike protein-derived peptides presented on the surface of a TMV nanoparticle. [ABSTRACT FROM AUTHOR]

Amid the global challenges posed by the COVID-19 pandemic, unraveling the genomic intricacies of SARS-CoV-2 became crucial. This study explores viral evolution using an innovative high-throughput next-generation sequencing (NGS) approach. By taking advantage of nasal swab and mouthwash samples from patients who tested positive for COVID-19 across different geographical regions during sequential infection waves, our study applied a targeted enrichment protocol and pooling strategy to increase detection sensitivity. The approach was extremely efficient, yielding a large number of reads and mutations distributed across 10 distinct viral gene regions. Notably, the genes Envelope, Nucleocapsid, and Open Reading Frame 8 had the highest number of unique mutations per 1000 nucleotides, with both spike and Nucleocapsid genes showing evidence for positive selection. Focusing on the spike protein gene, crucial in virus replication and immunogenicity, our findings show a dynamic SARS-CoV-2 evolution, emphasizing the virus–host interplay. Moreover, the pooling strategy facilitated subtle sequence variability detection. Our findings painted a dynamic portrait of SARS-CoV-2 evolution, emphasizing the intricate interplay between the virus and its host populations and accentuating the importance of continuous genomic surveillance to understand viral dynamics. As SARS-CoV-2 continues to evolve, this approach proves to be a powerful, versatile, fast, and cost-efficient screening tool for unraveling emerging variants, fostering understanding of the virus's genetic landscape. [ABSTRACT FROM AUTHOR]

Wastewater-based epidemiology has garnered considerable research interest, concerning the COVID-19 pandemic. Restrictive public health interventions and mobility limitations are measures to avert a rising case prevalence. The current study integrates WBE monitoring strategies, Google mobility data, and restriction information to assess the epidemiological development of COVID-19. Various SARIMAX models were employed to predict SARS-CoV-2 cases in Liechtenstein and two Austrian regions. This study analyzes four primary strategies for examining the progression of the pandemic waves, described as follows: 1—a univariate model based on active cases; 2—a multivariate model incorporating active cases and WBE data; 3—a multivariate model considering active cases and mobility data; and 4—a sensitivity analysis of WBE and mobility data incorporating restriction policies. Our key discovery reveals that, while WBE for SARS-CoV-2 holds immense potential for monitoring COVID-19 on a societal level, incorporating the analysis of mobility data and restriction policies enhances the precision of the trained models in predicting the state of public health during the pandemic. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has significantly impacted global healthcare, underscoring the importance of exploring the virus's effects on infected individuals beyond treatments and vaccines. Notably, recent findings suggest that SARS-CoV-2 can infect the gut, thereby altering the gut microbiota. This study aimed to analyze the gut microbiota composition differences between COVID-19 patients experiencing mild and severe symptoms. We conducted 16S rRNA metagenomic sequencing on fecal samples from 49 mild and 43 severe COVID-19 cases upon hospital admission. Our analysis identified a differential abundance of specific bacterial species associated with the severity of the disease. Severely affected patients showed an association with Enterococcus faecium, Akkermansia muciniphila, and others, while milder cases were linked to Faecalibacterium prausnitzii, Alistipes putredinis, Blautia faecis, and additional species. Furthermore, a network analysis using SPIEC-EASI indicated keystone taxa and highlighted structural differences in bacterial connectivity, with a notable disruption in the severe group. Our study highlights the diverse impacts of SARS-CoV-2 on the gut microbiome among both mild and severe COVID-19 patients, showcasing a spectrum of microbial responses to the virus. Importantly, these findings align, to some extent, with observations from other studies on COVID-19 gut microbiomes, despite variations in methodologies. The findings from this study, based on retrospective data, establish a foundation for future prospective research to confirm the role of the gut microbiome as a predictive biomarker for the severity of COVID-19. [ABSTRACT FROM AUTHOR]

The long-term sequelae of SARS-CoV-2 infection are still under research, since extensive studies showed plenty of systemic effects of the viral infection, extending even after the acute phase of the infection. This study evaluated kidney function tests six months after SARS-CoV-2 infection in patients clinically diagnosed with Post-COVID Syndrome, hypothesizing persistent renal dysfunction evidenced by altered kidney function tests compared to baseline levels. Continuous eGFR decrease <30 at six months post-infection was considered the main study outcome. Conducted at the "Victor Babes" Hospital, this retrospective observational study involved adults with laboratory-confirmed SARS-CoV-2 infection and clinically-diagnosed Post-COVID Syndrome, excluding those with prior chronic kidney disease or significant renal impairment. Kidney function tests, including serum creatinine, blood urea nitrogen (BUN), estimated glomerular filtration rate (eGFR), alongside markers of kidney damage such as proteinuria and hematuria, were analyzed. Among 206 participants, significant differences were observed between the control (n = 114) and the Post-COVID group (n = 92). The Post-COVID group exhibited higher serum creatinine (109.7 μmol/L vs. 84.5 μmol/L, p < 0.001), lower eGFR (65.3mL/min/1.73 m2 vs. 91.2 mL/min/1.73 m2, p < 0.001), and elevated BUN levels (23.7 mg/dL vs. 15.2 mg/dL, p < 0.001) compared to the control group. Regression analysis highlighted significant predictors of continuous eGFR decrease <30 at six months post-infection. The development of acute kidney injury (AKI) during the initial COVID-19 illness emerged as a strong predictor of reduced eGFR (β = 3.47, p < 0.001). Additional factors, including a creatinine increase (23 μmol/L above the normal range) and an elevated Albumin to Creatinine Ratio (ACR) (>11 mg/g above the normal range), were significantly associated with eGFR reduction. Patients with Post-COVID Syndrome demonstrate significant renal impairment six months post-SARS-CoV-2 infection. The study's findings stress the need for ongoing monitoring and intervention strategies for renal health in affected individuals, underscoring the persistent impact of COVID-19 on renal function. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic has underscored the critical need for the advancement of diagnostic and therapeutic platforms. These platforms rely on the rapid development of molecular binders that should facilitate surveillance and swift intervention against viral infections. In this study, we have evaluated by three independent research groups the binding characteristics of various published RNA and DNA aptamers targeting the spike protein of the SARS-CoV-2 virus. For this comparative analysis, we have employed different techniques such as biolayer interferometry (BLI), enzyme-linked oligonucleotide assay (ELONA), and flow cytometry. Our data show discrepancies in the reported specificity and affinity among several of the published aptamers and underline the importance of standardized methods, the impact of biophysical techniques, and the controls used for aptamer characterization. We expect our results to contribute to the selection and application of suitable aptamers for the detection of SARS-CoV-2. [ABSTRACT FROM AUTHOR]

During the COVID-19 pandemic, wastewater-based epidemiology has been extensively used as a helpful tool for evaluation of the epidemic situation in catchments of wastewater treatment plants. In this context, knowledge about the rate of virus inactivation in wastewater is important for characterization of the influence of retention times in sewers on virus concentrations, of the storage periods before analysis in the laboratory, on virus elimination during treatment and for modeling approaches. In the present study, we genotyped SARS-CoV-2 in the respiratory tract specimens of infected patients and spiked the raw wastewater of five treatment plants with aliquots of these samples. The test preparations were incubated under practically relevant temperature conditions (14 °C) over 31 days. The linear decay rates resulted in comparable T90 values (30.5 d) for the Delta and the Omicron BA1 variants of SARS-CoV-2 without differences in using the E or S gene of the virus as the target for amplification. In contrast, the origin of wastewater influenced the inactivation rate of both variants significantly, with the mean T90 values varying between 24.3 and 53.1 days in the wastewater from the five plants. The data suggest that the inactivation rate of SARS-CoV-2 in wastewater is more strongly determined by the composition of the water than by the virus variant. [ABSTRACT FROM AUTHOR]

Background/Objectives: Upper-limb function of chronic stroke patients declined when outpatient rehabilitation was interrupted and outings restricted, owing to the novel coronavirus infection (COVID-19) pandemic. We investigated whether these patients recovered upper-limb function post-resumption of outpatient rehabilitation. Methods: In this observational study, 43 chronic stroke hemiparesis patients with impaired upper extremity function were scored for limb function via the Fugl-Meyer assessment of the upper extremity (FMA-UE) and the Action Research Arm Test (ARAT) after a structured interview, evaluation, and intervention. Scores at 6 and 3 months pre- and 3 months post-rehabilitation interruption were examined retrospectively; scores immediately and at 3 and 6 months post-resumption of care were examined prospectively. The amount of change for each time period and an analysis of covariance were performed with time as a factor, changes in the FMA-UE and the ARAT scores as dependent variables, and statistical significance at 5%. Results: The time of evaluation significantly impacted the total score, as well as part C and part D of FMA-UE and total, pinch, and gross movement of the ARAT. Post-hoc tests showed that the magnitude of change in limb-function scores from immediately to 3 months post-resumption was significantly higher than the change from 3 months pre- to immediately post-interruption for the total score and part D of the FMA-UE, as well as grip and gross movement of the ARAT (p < 0.05). Conclusions: Upper-limb functional decline in chronic stroke patients, caused by the COVID-19 pandemic-related therapy interruption and outing restrictions, was resolved approximately 3 months post-resumption of rehabilitation therapy. Our data can serve as reference standards for planning and evaluating treatment for chronic stroke patients with inactivity-related impaired upper-limb function. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic prompted rapid research on SARS-CoV-2 pathogenicity. Consequently, new data can be used to advance the molecular understanding of SARS-CoV-2 infection. The present bioinformatics study discusses the "spikeopathy" at the molecular level and focuses on the possible post-transcriptional regulation of the SARS-CoV-2 spike protein S1 subunit in the host cell/tissue. A theoretical protein–RNA recognition code was used to check the compatibility of the SARS-CoV-2 spike protein S1 subunit with mRNAs in the human transcriptome (1-L transcription). The principle for this method is elucidated on the defined RNA binding protein GEMIN5 (gem nuclear organelle-associated protein 5) and RNU2-1 (U2 spliceosomal RNA). Using the method described here, it was shown that 45% of the genes/proteins identified by 1-L transcription of the SARS-CoV-2 spike protein S1 subunit are directly linked to COVID-19, 39% are indirectly linked to COVID-19, and 16% cannot currently be associated with COVID-19. The identified genes/proteins are associated with stroke, diabetes, and cardiac injury. [ABSTRACT FROM AUTHOR]

Background: Neutrophil gelatinase-associated lipocalin (NGAL) is part of the innate immune system and acute-phase protein. Current data state that acute COVID-19 patients have higher levels of serum NGAL (sNGAL), but it is not known if higher protein levels are maintained in the convalescents. As post-COVID complications are currently the most important aspect of the disease, further research into metabolic and immunological consequences of the disease is needed. Methods: We aimed to determine the levels of sNGAL in a patient population 3 months after the acute phase of the disease and to identify the factors that may be related to the elevation of sNGAL levels in the mentioned cohort. The study included 146 patients diagnosed with COVID-19 in different stages of the disease. Three months after COVID-19 diagnosis, patients' sera were sampled and tested. Results: We demonstrate an association between the severity of the disease in the acute phase and elevated sNGAL levels three months after recovery, with the exception of the most severe hospitalized patients, who received early treatment. Moreover, we establish that sNGAL levels could be associated with prolonged dyspnea and the regulation of hunger and satiety in COVID-19 convalescents. Conclusions: These observations support the view that the introduction of antiviral treatment, steroids, and intense oxygen therapy reduces post-COVID immune-associated complications. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic has brought about diverse impacts on the global population. Individuals with comorbidities were more susceptible to the severe symptoms caused by the virus. Within the crisis scenario, metabolomics represents a potential area of science capable of providing relevant information for understanding the metabolic pathways associated with the intricate interaction between the viral disease and previous comorbidities. This work aims to provide a comprehensive description of the scientific production pertaining to metabolomics within the specific context of COVID-19 and comorbidities, while highlighting promising areas for exploration by those interested in the subject. In this review, we highlighted the studies of metabolomics that indicated a variety of metabolites associated with comorbidities and COVID-19. Furthermore, we observed that the understanding of the metabolic processes involved between comorbidities and COVID-19 is limited due to the urgent need to report disease outcomes in individuals with comorbidities. The overlap of two or more comorbidities associated with the severity of COVID-19 hinders the comprehension of the significance of each condition. Most identified studies are observational, with a restricted number of patients, due to challenges in sample collection amidst the emergent situation. [ABSTRACT FROM AUTHOR]

Measuring fecal nucleic acid indicators for data normalization can increase costs during wastewater-based epidemiology (WBE). The efficacy of routinely assayed water quality parameters was assessed as an alternative or complement to fecal nucleic acid viral indicator data for their utility in adjusting measured SARS-CoV-2 gene concentrations to improve the relationship between wastewater molecular data and clinical COVID-19 case data. This research covers two study designs: grab samples collected from sewers serving The Ohio State University campus and composite influent samples collected at five wastewater treatment plants (WWTPs) across the state of Ohio. Weekly mandatory clinical testing was used to monitor infections in the student population, and statewide cases were reported through voluntary clinical testing. Statewide WWTP results showed significant strong correlation between SARS-CoV-2 concentrations in the wastewater and confirmed COVID-19 cases, and correlation increased when normalized by flow and additionally increased when normalized by pH, total suspended solids, and temperature, but correlation decreased when normalized by a nucleic acid fecal viral indicator (PMMoV). On campus, correlations were generally not significant unless normalized by PMMoV and/or UV absorbance parameters. Because water quality parameters are routinely assayed at wastewater treatment plants and some may be collected by autosamplers, incorporating wastewater quality data may improve WBE models and could minimize molecular and cellular testing for fecal indicators to decrease costs. [ABSTRACT FROM AUTHOR]

In the context of the global COVID-19 pandemic, understanding the intricate mechanisms of the body's response to infection and inflammation has become a priority for the medical and research communities. It has been proven that during COVID-19 infection, molecules are secreted—namely organokines, which may directly or indirectly play a role in the pathophysiology of COVID-19. The objective of this study was to scrutinize the potential correlation between the levels of selected myokines (myostatin, agrin, irisin, and myonectin) and the duration of rehabilitation in post-COVID-19 patients. Additionally, the study aimed to investigate whether there is a correlation between the levels of these myokines and the length of hospitalization during COVID-19 treatment. The study was conducted at the Rehabilitation Hospital in Szczecin (Poland). Patients in the study participated in a comprehensive rehabilitation program following COVID-19 treatment. In order to assess the effectiveness of rehabilitation, the following tests were performed: a 6 min walk test with an assessment of exercise tolerance (Borg scale), an assessment of dyspnea severity (mMRC scale), a spirometric assessment of respiratory function, a measurement of arm strength, and an assessment of fatigue using the Fatigue Assessment Scale (FAS). Myokine levels were measured using commercially available enzyme-linked immunosorbent assays (ELISA) according to the manufacturer's instructions. Statistical analysis was performed using Statistica 13.1 software. Lower concentrations of irisin and myonectin and higher concentrations of myostatin correlated with longer rehabilitation time. Baseline levels of specific myokines in post-COVID-19 patients could play a crucial role in anticipating the duration of rehabilitation. The duration of hospitalization for the infection may influence myokine levels in patients recovering from COVID-19. [ABSTRACT FROM AUTHOR]

Background: As the global battle against the COVID-19 pandemic endures, the spread of the Delta variant has introduced nuanced challenges, prompting a nuanced examination. Materials and Methods: We performed a multilevel logistic regression analysis encompassing 197 patients, comprising 44 vaccinated individuals (V group) and 153 unvaccinated counterparts (UV). These patients, afflicted with the Delta variant of SARS-CoV-2, were hospitalized between October 2021 and February 2022 at the COVID-19 department of a University Centre in Cluj-Napoca, Romania. We compared patient characteristics, CT lung involvement, Padua score, oxygen saturation (O2 saturation), ventilation requirements, dynamics of arterial blood gas (ABG) parameters, ICU admission rates, and mortality rates between the two groups. Results: The UV group exhibited a statistically significant (p < 0.05) proclivity toward developing a more severe form of infection, marked by elevated rates of lung involvement, oxygen requirement, ICU admission, and mortality. Conclusion: Our findings underscore the substantial efficacy of the vaccine in diminishing the incidence of severe disease, lowering the rates of ICU admissions, and mitigating mortality among hospitalized patients. [ABSTRACT FROM AUTHOR]

This research analyzes immunological response patterns to SARS-CoV-2 infection in blood and urine in individuals with serum cotinine-confirmed exposure to nicotine. Samples of blood and urine were obtained from a total of 80 patients admitted to hospital within 24 h of admission (tadm), 48 h later (t48h), and 7 days later (t7d) if patients remained hospitalized or at discharge. Serum cotinine above 3.75 ng/mL was deemed as biologically significant exposure to nicotine. Viral load was measured with serum SARS-CoV-2 S-spike protein. Titer of IgG, IgA, and IgM against S- and N-protein assessed specific antiviral responses. Cellular destruction was measured by high mobility group box protein-1 (HMGB-1) serum levels and heat shock protein 60 (Hsp-60). Serum interleukin 6 (IL-6), and ferritin gauged non-specific inflammation. The immunological profile was assessed with O-link. Serum titers of IgA were lower at tadm in smokers vs. nonsmokers (p = 0.0397). IgM at t48h was lower in cotinine-positive individuals (p = 0.0188). IgG did not differ between cotinine-positive and negative individuals. HMGB-1 at admission was elevated in cotinine positive individuals. Patients with positive cotinine did not exhibit increased markers of non-specific inflammation and tissue destruction. The blood immunological profile had distinctive differences at admission (MIC A/B↓), 48 h (CCL19↓, MCP-3↓, CD28↑, CD8↓, IFNγ↓, IL-12↓, GZNB↓, MIC A/B↓) or 7 days (CD28↓) in the cotinine-positive group. The urine immunological profile showed a profile with minimal overlap with blood as the following markers being affected at tadm (CCL20↑, CXCL5↑, CD8↑, IL-12↑, MIC A/B↑, GZNH↑, TNFRS14↑), t48h (CCL20↓, TRAIL↓) and t7d (EGF↑, ADA↑) in patients with a cotinine-positive test. Here, we showed a distinctive immunological profile in hospitalized COVID-19 patients with confirmed exposure to nicotine. [ABSTRACT FROM AUTHOR]

To date, the SARS-CoV-2 pandemic still represents a great clinical challenge worldwide, and effective anti-COVID-19 drugs are limited. For this reason, nutritional supplements have been investigated as adjuvant therapeutic approaches in disease management. Among such supplements, vitamin D has gained great interest, due to its immunomodulatory and anti-inflammatory actions both in adult and pediatric populations. Even if there is conflicting evidence about its prevention and/or mitigation effectiveness in SARS-CoV-2 infection, several studies demonstrated a strict correlation between hypovitaminosis D and disease severity in acute COVID-19 and MIS-C (multisystem inflammatory syndrome in children). This narrative review offers a resume of the state of the art about vitamin D's role in immunity and its clinical use in the context of the current pandemic, specially focusing on pediatric manifestations and MIS-C. It seems biologically reasonable that interventions aimed at normalizing circulating vitamin D levels could be beneficial. To help clinicians in establishing the correct prophylaxis and/or supportive therapy with vitamin D, well-designed and adequately statistically powered clinical trials involving both adult and pediatric populations are needed. Moreover, this review will also discuss the few other nutraceuticals evaluated in this context. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic has sparked a surge in research on microbiology and virology, shedding light on overlooked aspects such as the infection of bacteria by RNA virions in the animal microbiome. Studies reveal a decrease in beneficial gut bacteria during COVID-19, indicating a significant interaction between SARS-CoV-2 and the human microbiome. However, determining the origins of the virus remains complex, with observed phenomena such as species jumps adding layers to the narrative. Prokaryotic cells play a crucial role in the disease's pathogenesis and transmission. Analyzing previous studies highlights intricate interactions from clinical manifestations to the use of the nitrogen isotope test. Drawing parallels with the history of the Poliovirus underscores the need to prioritize investigations into prokaryotic cells hosting RNA viruses. [ABSTRACT FROM AUTHOR]

Since the inception of the SARS-CoV-2 pandemic, healthcare systems around the world observed an increased rate of Acute Limb Ischemia (ALI) in patients with a COVID-19 infection. Despite several pieces of evidence suggesting that COVID-19 infection may also worsen the prognosis associated with ALI, only a small number of published studies include a direct comparison regarding the outcomes of both COVID-19 and non-COVID-19 ALI patients. Based on the above, a systematic review and a meta-analysis of the literature were conducted, evaluating differences in the incidence of two major outcomes (amputation and mortality rate) between patients concurrently affected by COVID-19 and negative ALI subjects. PubMed (MEDLINE), Web of Science, and Embase (OVID) databases were scrutinized from January 2020 up to 31 December 2023, and 7906 total articles were recovered. In total, 11 studies (n: 15,803 subjects) were included in the systematic review, and 10 of them (15,305 patients) were also included in the meta-analysis. Across all the studies, COVID-19-positive ALI patients experienced worse outcomes (mortality rates ranging from 6.7% to 47.2%; amputation rates ranging from 7.0% to 39.1%) compared to non-infected ALI patients (mortality rates ranging from 3.1% to 16.7%; amputation rates ranging from 2.7% to 18%). Similarly, our meta-analysis shows that both the amputation rate (OR: 2.31; 95% CI: 1.68–3.17; p < 0.00001) and mortality (OR: 3.64; 95% CI: 3.02–4.39; p < 0.00001) is significantly higher in COVID-19 ALI patients compared to ALI patients. [ABSTRACT FROM AUTHOR]

Purpose: We conducted a retrospective case series of seven male COVID-19 patients with respiratory failure and suspected OSA based on clinical features to evaluate the effects of undiagnosed obstructive sleep apnea (OSA) on COVID-19 outcomes and the response to a continuous positive airway pressure (CPAP) treatment. Cardiorespiratory polygraphy (CRP) and a continuous positive airway pressure treatment were used for diagnosis and management. They confirmed severe obstructive sleep apnea in all patients (apnea/hypopnea index > 30) and improved overnight oxygenation and symptoms at the 1-month follow-up. Conclusions: Undiagnosed obstructive sleep apnea may negatively impact COVID-19 outcomes by exacerbating respiratory failure. Recognition and treatment with continuous positive airway pressure can optimize the management of such patients. [ABSTRACT FROM AUTHOR]

Background and aim: Antimicrobial resistance (AMR) is a chronic issue of our Westernized society, mainly because of the uncontrolled and improper use of antimicrobials. The coronavirus disease 2019 (COVID-19) pandemic has triggered and expanded AMR diffusion all over the world, and its clinical and therapeutic features have changed. Thus, we aimed to review evidence from the literature on the definition and causative agents of AMR in the frame of the COVID-19 post-pandemic era. Methods: We conducted a search on PubMed and Medline for original articles, reviews, meta-analyses, and case series using the following keywords, their acronyms, and their associations: antibiotics, antimicrobial resistance, severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), COVID-19 pandemic, personal protective equipment. Results: AMR had a significant rise in incidence both in in-hospital and outpatient populations (ranging from 5 up to 50%) worldwide, but with a variegated profile according to the germ and microorganism considered. Not only bacteria but also fungi have developed more frequent and diffuse AMR. These findings are explained by the increased use and misuse of antibiotics and preventive measures during the first waves of the SARS-CoV2 pandemic, especially in hospitalized patients. Subsequently, the reduction in and end of the lockdown and the use of personal protective equipment have allowed for the indiscriminate circulation of resistant microorganisms from low-income countries to the rest of the world with the emergence of new multi- and polyresistant organisms. However, there is not a clear association between COVID-19 and AMR changes in the post-pandemic period. Conclusions: AMR in some microorganisms has significantly increased and changed its characteristics during and after the end of the pandemic phase of COVID-19. An integrated supranational monitoring approach to this challenge is warranted in the years to come. In detail, a rational, personalized, and regulated use of antibiotics and antimicrobials is needed. [ABSTRACT FROM AUTHOR]

Wastewater-based epidemiology (WBE) is currently used to monitor not only the spread of the viral SARS-CoV-2 pandemic but also that of other viruses in endemic conditions, particularly in the absence of syndromic surveillance. The continuous monitoring of sewage requires high expenditure and significant time investments, highlighting the need for standardized methods and structured monitoring strategies. In this context, we conducted weekly wastewater monitoring in northwestern Tuscany (Italy) and targeted human adenovirus (HAdV), norovirus genogroup II (NoVggII), enterovirus (EV), and SARS-CoV-2. Samples were collected at the entrances of treatment plants and concentrated using PEG/NaCl precipitation, and viral nucleic acids were extracted and detected through real-time reverse transcription qPCR. NoVggII was the most identified target (84.4%), followed by HAdV, SARS-CoV-2, and EV. Only HAdV and EV exhibited seasonal peaks in spring and summer. Compared with data that were previously collected in the same study area (from February 2021 to September 2021), the results for SARS-CoV-2 revealed a shift from an epidemic to an endemic pattern, at least in the region under investigation, which was likely due to viral mutations that led to the spreading of new variants with increased resistance to summer environmental conditions. In conclusion, using standardized methods and an efficient monitoring strategy, WBE proves valuable for viral surveillance in pandemic and epidemic scenarios, enabling the identification of temporal–local distribution patterns that are useful for making informed public health decisions. [ABSTRACT FROM AUTHOR]

During the COVID-19 pandemic, immunosuppressed patients showed prolonged SARS-CoV-2 infections, with several studies reporting the accumulation of mutations in the viral genome. The weakened immune system present in these individuals, along with the effect of antiviral therapies, are thought to create a favourable environment for intra-host viral evolution and have been linked to the emergence of new viral variants which strongly challenged containment measures and some therapeutic treatments. To assess whether impaired immunity could lead to the increased instability of viral genomes, longitudinal nasopharyngeal swabs were collected from eight immunocompromised patients and fourteen non-immunocompromised subjects, all undergoing SARS-CoV-2 infection. Intra-host viral evolution was compared between the two groups through deep sequencing, exploiting a probe-based enrichment method to minimise the possibility of artefactual mutations commonly generated in amplicon-based methods, which heavily rely on PCR amplification. Although, as expected, immunocompromised patients experienced significantly longer infections, the acquisition of novel intra-host viral mutations was similar between the two groups. Moreover, a thorough analysis of viral quasispecies showed that the variability of viral populations in the two groups is comparable not only at the consensus level, but also when considering low-frequency mutations. This study suggests that a compromised immune system alone does not affect SARS-CoV-2 within-host genomic variability. [ABSTRACT FROM AUTHOR]

Genomic sequencing of clinical samples to identify emerging variants of SARS-CoV-2 has been a key public health tool for curbing the spread of the virus. As a result, an unprecedented number of SARS-CoV-2 genomes were sequenced during the COVID-19 pandemic, which allowed for rapid identification of genetic variants, enabling the timely design and testing of therapies and deployment of new vaccine formulations to combat the new variants. However, despite the technological advances of deep sequencing, the analysis of the raw sequence data generated globally is neither standardized nor consistent, leading to vastly disparate sequences that may impact identification of variants. Here, we show that for both Illumina and Oxford Nanopore sequencing platforms, downstream bioinformatic protocols used by industry, government, and academic groups resulted in different virus sequences from same sample. These bioinformatic workflows produced consensus genomes with differences in single nucleotide polymorphisms, inclusion and exclusion of insertions, and/or deletions, despite using the same raw sequence as input datasets. Here, we compared and characterized such discrepancies and propose a specific suite of parameters and protocols that should be adopted across the field. Consistent results from bioinformatic workflows are fundamental to SARS-CoV-2 and future pathogen surveillance efforts, including pandemic preparation, to allow for a data-driven and timely public health response. [ABSTRACT FROM AUTHOR]

Throughout the SARS-CoV-2 pandemic, several variants of concern (VOCs) have been identified, many of which share recurrent mutations in the spike glycoprotein's receptor-binding domain (RBD). This region coincides with known epitopes and can therefore have an impact on immune escape. Protracted infections in immunosuppressed patients have been hypothesized to lead to an enrichment of such mutations and therefore drive evolution towards VOCs. Here, we present the case of an immunosuppressed patient that developed distinct populations with immune escape mutations throughout the course of their infection. Notably, by investigating the co-occurrence of substitutions on individual sequencing reads in the RBD, we found quasispecies harboring mutations that confer resistance to known monoclonal antibodies (mAbs) such as S:E484K and S:E484A. These mutations were acquired without the patient being treated with mAbs nor convalescent sera and without them developing a detectable immune response to the virus. We also provide additional evidence for a viral reservoir based on intra-host phylogenetics, which led to a viral substrain that evolved elsewhere in the patient's body, colonizing their upper respiratory tract (URT). The presence of SARS-CoV-2 viral reservoirs can shed light on protracted infections interspersed with periods where the virus is undetectable, and potential explanations for long-COVID cases. [ABSTRACT FROM AUTHOR]

The continuous emergence of SARS-CoV-2 variants caused the persistence of the COVID-19 epidemic and challenged the effectiveness of the existing vaccines. The viral proteases are the most attractive targets for developing antiviral drugs. In this scenario, our study explores the use of HIV-1 protease inhibitors against SARS-CoV-2. An in silico screening of a library of HIV-1 proteases identified four anti-HIV compounds able to interact with the 3CLpro of SARS-CoV-2. Thus, in vitro studies were designed to evaluate their potential antiviral effectiveness against SARS-CoV-2. We employed pseudovirus technology to simulate, in a highly safe manner, the adsorption of the alpha (α-SARS-CoV-2) and omicron (ο-SARS-CoV-2) variants of SARS-CoV-2 and study the inhibitory mechanism of the selected compounds for cell–virus interaction. The results reported a mild activity against the viral proteases 3CLpro and PLpro, but efficient inhibitory effects on the internalization of both variants mediated by cathepsin B/L. Our findings provide insights into the feasibility of using drugs exhibiting antiviral effects for other viruses against the viral and host SARS-CoV-2 proteases required for entry. [ABSTRACT FROM AUTHOR]

Between 7 December 2022 and 28 February 2023, China experienced a new wave of COVID-19 that swept across the entire country and resulted in an increasing amount of respiratory infections and hospitalizations. The purpose of this study is to reveal the intensity and composition of coinfecting microbial agents. In total, 196 inpatients were recruited from The Third People's Hospital of Shenzhen, and 169 respiratory and 73 blood samples were collected for metagenomic next-generation sequencing. The total "Infectome" was characterized and compared across different groups defined by the SARS-CoV-2 detection status, age groups, and severity of disease. Our results revealed a total of 22 species of pathogenic microbes (4 viruses, 13 bacteria, and 5 fungi), and more were discovered in the respiratory tract than in blood. The diversity of the total infectome was highly distinguished between respiratory and blood samples, and it was generally higher in patients that were SARS-CoV-2-positive, older in age, and with more severe disease. At the individual pathogen level, HSV-1 seemed to be the major contributor to these differences observed in the overall comparisons. Collectively, this study reveals the highly complex respiratory infectome and high-intensity coinfection in patients admitted to the hospital during the period of the 2023 COVID-19 pandemic in China. [ABSTRACT FROM AUTHOR]

Background: Seroepidemiology studies are useful for quantifying the magnitude of past infections and estimating the extent of population-based immunity to inform risk mitigation strategies for the future. We report on the only national population-based survey of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) immunoglobulin G (IgG) seroprevalence in Eswatini. Methods: The survey was undertaken from 31 August to 30 September 2021, following three earlier waves of coronavirus disease (COVID-19), and preceded the onset of the fourth wave, which was dominated by the Omicron variant of concern. We also report on epidemiological trends of recorded COVID-19 cases and hospitalizations before and after the fourth COVID-19 wave through to March 2022. We evaluated the immunoglobulin G (IgG) seropositivity based on either anti-nucleocapsid (N) or anti-spike (S) antigens. Results: Of 4564 individuals, 58.5% were female, 36.0% were aged 18–50 years, and 863 (18.9%) of adults who were older than 18 years had received at least a single dose of COVID-19 vaccine. Overall, 2769 (60.7%) were seropositive with heterogeneity across sub-regions (53.7%; 95% CI:49.2–58.1 to 68.6%; 95% CI:64.5–72.4), with the highest rates occurring in sub-regions of the Manzini region. Seropositivity was higher in vaccinated individuals (84.5%; 95% CI: 81.9–86.7) compared to unvaccinated individuals (55.1%; 95% CI:53.5–56.7). Amongst unvaccinated individuals, seropositivity was highest in 18–50-year-olds (59.5%;95% CI: 56.9–62.1). Seropositivity was associated with female gender, previous positive SARS-CoV-2 NAAT status and being vaccinated, non-smoking, and being formally employed. We estimated as of 15 September 2021 that there had been 639,475 SARS-CoV-2 infections (95% CI; 620,824–658,003) in Eswatini, which was 25.5-fold greater than the 25,048 COVID-19 cases that had been recorded by then. The national case fatality rate (CFR) based on recorded cases was 4.8%, being 25-fold greater than the infection fatality rate (0.19; 95% CI: 0.18–0.19) based on recorded deaths and extrapolating the force of infection from seroprevalence. Nationally and across all four regions, we report the decoupling of COVID-19 cases from hospitalisations and deaths, observed as early as during the third wave, which was dominated by the Delta variant compared with earlier waves. Conclusions: We identified that 60.7% of people in Eswatini had been infected by SARS-CoV-2 at least once and before the onset of the Omicron wave in mid-November 2021. Despite a modest uptake of COVID-19 vaccines, the evolution of population immunity from infection has likely contributed to the decoupling of infection and severe COVID-19 in Eswatini. [ABSTRACT FROM AUTHOR]

Worldwide, the COVID-19 pandemic, caused by the brand-new coronavirus SARS-CoV-2, has claimed a sizable number of lives. The virus' rapid spread and impact on every facet of human existence necessitate a continuous and dynamic examination of its biology and management. Despite this urgency, COVID-19 does not currently have any particular antiviral treatments. As a result, scientists are concentrating on repurposing existing antiviral medications or creating brand-new ones. This comprehensive review seeks to provide an in-depth exploration of our current understanding of SARS-CoV-2, starting with an analysis of its prevalence, pathology, and evolutionary trends. In doing so, the review aims to clarify the complex network of factors that have contributed to the varying case fatality rates observed in different geographic areas. In this work, we explore the complex world of SARS-CoV-2 mutations and their implications for vaccine efficacy and therapeutic interventions. The dynamic viral landscape of the pandemic poses a significant challenge, leading scientists to investigate the genetic foundations of the virus and the mechanisms underlying these genetic alterations. Numerous hypotheses have been proposed as the pandemic has developed, covering various subjects like the selection pressures driving mutation, the possibility of vaccine escape, and the consequences for clinical therapy. Furthermore, this review will shed light on current clinical trials investigating novel medicines and vaccine development, including the promising field of drug repurposing, providing a window into the changing field of treatment approaches. This study provides a comprehensive understanding of the virus by compiling the huge and evolving body of knowledge on SARS-CoV-2, highlighting its complexities and implications for public health, and igniting additional investigation into the control of this unprecedented global health disaster. [ABSTRACT FROM AUTHOR]