SARS-CoV-2 and COVID-19: The most important research questions

Impact of COVID-19 on child tuberculosis hospitalization

INTRODUCTION

Morocco has made remarkable progress in the fight against tuberculosis, but the Covid-19 pandemic has affected tuberculosis control worldwide, with notable fluctuations in tuberculosis epidemiology during and after the pandemic.

AIM

To describe the impact of the Covid-19 pandemic on the rate of hospitalization for tuberculosis and its different localizations in children.

METHODS

We conducted a retrospective study based on the analysis of medical records of TB patients hospitalized within the Children's Hospital in Casablanca, during the periods before (2018-2019), during (2020) and after (2021-2022) Covid-19 quarantine.

RESULTS

Throughout the study period (2018-2022), the total number of patients hospitalized in our department was 7390, including 283 children were hospitalized for tuberculosis, with a mean age of 6 years. Before the Covid-19 pandemic, the average number of tuberculosis cases was 49 per year, of which the percentage of pulmonary tuberculosis was 32% and extra-pulmonary tuberculosis 68%. The number of cases was 23 per year during the quarantine period, with a percentage of pulmonary tuberculosis of 26% and extra-pulmonary tuberculosis of 74%. After the quarantine period, this number rose to 81 cases per year, of which 21% were pulmonary tuberculosis and 79% extrapulmonary tuberculosis (pleural tuberculosis was predominant in 44.1% of cases).

CONCLUSION

These results are consistent with data published by the World Health Organization, and with the findings of another study we carried out on the impact of COVID-19 on hospital admissions for acute lower respiratory tract infections. It is very likely that the reduction in the number of tuberculosis cases during the quarantine period is due to social distancing, which leads to a reduction in the transmission of tuberculosis between people as well as to the disruption of the national tuberculosis control program in Morocco, when positive cases are identified.

Immunization against Medically Important Human Coronaviruses of Public Health Concern

SARS-CoV-2 is a virus that affects the human immune system. It was observed to be on the rise since the beginning of 2020 and turned into a life-threatening pandemic. Scientists have tried to develop a possible preventive and therapeutic drug against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and other related coronaviruses by assessing COVID-19-recovered persons' immunity. This study aims to review immunization against SARS-CoV-2, along with exploring the interventions that have been developed for the prevention of SARS-CoV-2. This study also highlighted the role of phototherapy in treating SARS-CoV infection. The study adopted a review approach to gathering the information available and the progress that has been made in the treatment and prevention of COVID-19. Various vaccinations, including nucleotide, subunit, and vector-based vaccines, as well as attenuated and inactivated forms that have already been shown to have prophylactic efficacy against the Middle East respiratory syndrome coronavirus (MERS-CoV) and SARS-CoV, have been summarized. Neutralizing and non-neutralizing antibodies are all associated with viral infections. Because there is no specific antiviral vaccine or therapies for coronaviruses, the main treatment strategy is supportive care, which is reinforced by combining broad-spectrum antivirals, convalescent plasma, and corticosteroids. COVID-19 has been a challenge to keep reconsidering the usual approaches to regulatory evaluation as a result of getting mixed and complicated findings on the vaccines, as well as licensing procedures. However, it is observed that medicinal herbs also play an important role in treating infection of the upper respiratory tract, the principal symptom of SARS-CoV due to their natural bioactive composite. However, some Traditional Chinese Medicines contain mutagens and nephrotoxins and the toxicological properties of the majority of Chinese herbal remedies are unknown. Therefore, to treat the COVID-19 infection along with conventional treatment, it is recommended that herb-drug interaction be examined thoroughly.

Diagnostic performance of a point-of-care molecular system for the detection of SARS-CoV-2 in Peru

The present study assessed the diagnostic performance of the Xpert®Xpress SARS-CoV-2 test in comparison with the Charité protocol real-time RT PCR for the detection of SARS-CoV-2 in Peruvian patients. This was a diagnostic test study that included 100 nasal and pharyngeal swab samples. We obtained an overall concordance of 98.70% (95%CI: 92.98-99.97), with a kappa coefficient of 0.97 (95%CI: 0.86-1.00) and sensitivity and relative specificity rates of 100% and 96.15%, respectively. Additionally, the percentage of the area under the ROC curve was 98.08% in both cases, and an analytical specificity rate of 100% was obtained for the different respiratory viruses evaluated. In conclusion, the Xpert®Xpress SARS-CoV-2 test, by using nasal and pharyngeal swab samples, was highly sensitive and specific, and the kappa coefficient showed an excellent correlation when compared to the reference test. Motivation for the study. To describe and evaluate a closed molecular platform, easy to use and of importance in Peru for the management of diseases of public health priority, now implemented for the detection of SARS-CoV-2. Main findings. Highly sensitive and specific molecular test, with excellent correlation compared to the reference test for detecting SARS-CoV-2. Implications. Can be used in point-of-care laboratories for rapid molecular detection of different infectious agents, including SARS-CoV-2. Little expertise and minimal infrastructure are required to implement it.

The Development of Aptamer-Based Gold Nanoparticle Lateral Flow Test Strips for the Detection of SARS-CoV-2 S Proteins on the Surface of Cold-Chain Food Packaging

The COVID-19 pandemic over recent years has shown a great need for the rapid, low-cost, and on-site detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this study, an aptamer-based colloidal gold nanoparticle lateral flow test strip was well developed to realize the visual detection of wild-type SARS-CoV-2 spike proteins (SPs) and multiple variants. Under the optimal reaction conditions, a low detection limit of SARS-CoV-2 S proteins of 0.68 nM was acquired, and the actual detection recovery was 83.3% to 108.8% for real-world samples. This suggests a potential tool for the prompt detection of SARS-CoV-2 with good sensitivity and accuracy, and a new method for the development of alternative antibody test strips for the detection of other viral targets.

Identification of a druggable site on GRP78 at the GRP78-SARS-CoV-2 interface and virtual screening of compounds to disrupt that interface

SARS-CoV-2, the virus that causes COVID-19, led to a global health emergency that claimed the lives of millions. Despite the widespread availability of vaccines, the virus continues to exist in the population in an endemic state which allows for the continued emergence of new variants. Most of the current vaccines target the spike glycoprotein interface of SARS-CoV-2, creating a selection pressure favoring viral immune evasion. Antivirals targeting other molecular interactions of SARS-CoV-2 can help slow viral evolution by providing orthogonal selection pressures on the virus. GRP78 is a host auxiliary factor that mediates binding of the SARS-CoV-2 spike protein to human cellular ACE2, the primary pathway of cell infection. As GRP78 forms a ternary complex with SARS-CoV-2 spike protein and ACE2, disrupting the formation of this complex is expected to hinder viral entry into host cells. Here, we developed a model of the GRP78-Spike RBD-ACE2 complex. We then used that model together with hot spot mapping of the GRP78 structure to identify the putative binding site for spike protein on GRP78. Next, we performed structure-based virtual screening of known drug/candidate drug libraries to identify binders to GRP78 that are expected to disrupt spike protein binding to the GRP78, and thereby preventing viral entry to the host cell. A subset of these compounds has previously been shown to have some activity against SARS-CoV-2. The identified hits are starting points for the further development of novel SARS-CoV-2 therapeutics, potentially serving as proof-of-concept for GRP78 as a potential drug target for other viruses.

Environmental monitoring of SARS-CoV-2 in the metropolitan area of Porto Alegre, Rio Grande do Sul (RS), Brazil

Since starts the coronavirus disease 2019 (COVID-19) pandemic identified the presence of genomic fragments of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in various environmental matrices: domestic sewage, surface waters, and contaminated freshwater. Environmental monitoring of SARS-CoV-2 is a tool for evaluating trend curves over the months, compared to several clinical cases of the disease. The objective of this study was to monitor the SARS-CoV-2 in environmental samples collected in different sites in a metropolitan area of Porto Alegre, Southern Brazil. During 10 months from 2020 to 2021, 300 samples were collected weekly and biweekly from nine points located in 3 cities: one point from a wastewater treatment plant (WWTP) in São Leopoldo (fortnightly collection), two points in Dilúvio Stream in Porto Alegre (fortnightly collection), two points in Pampa and Luiz Rau Streams (weekly collection), and two points in public fountains (fortnightly collection) in Novo Hamburgo. After collection, samples were concentrated by ultracentrifugation, and viral nucleic acids were extracted using MagMax® Core Nucleic Acid Purifications kits and submitted to RT-qPCR, using E, N1, and N2 gene targets of SARS-CoV-2. Only 7% (3/41) samples from public fountains were positive, with a mean viral load (VL) of SARS-CoV-2 RNA of 5.02 × 101 gc/l (2.41~8.59 × 101 gc/l), while the streams had average VL of 7.43 × 105 gc/l (Pampa), 7.06 × 105 gc/l (Luiz Rau), 2.01 × 105 gc/l (Dilúvio), and 4.46 × 105 cg/l (WWTP). The results showed varying levels of viral presence in different sample types, with a demonstrated correlation between environmental viral load and clinical COVID-19 cases. These findings contribute to understanding virus persistence and transmission pathways in the environment. Continuous monitoring, especially in less developed regions, is crucial for early detection of vaccine resistance, new variants, and potential COVID-19 resurgence.

Alterations in microbiome of COVID-19 patients and its impact on forensic investigations

The human microbiome is vital for maintaining human health and has garnered substantial attention in recent years, particularly in the context of the coronavirus disease 2019 (COVID-19) outbreak. Studies have underscored significant alterations in the microbiome of COVID-19 patients across various body niches, including the gut, respiratory tract, oral cavity, skin, and vagina. These changes manifest as shifts in microbiota composition, characterized by an increase in opportunistic pathogens and a decrease in beneficial commensal bacteria. Such microbiome transformations may play a pivotal role in influencing the course and severity of COVID-19, potentially contributing to the inflammatory response. This ongoing relationship between COVID-19 and the human microbiome serves as a compelling subject of research, underscoring the necessity for further investigations into the underlying mechanisms and their implications for patient health. Additionally, these alterations in the microbiome may have significant ramifications for forensic investigations, given the microbiome's potential in establishing individual characteristics. Consequently, changes in the microbiome could introduce a level of complexity into forensic determinations. As research progresses, a more profound understanding of the human microbiome within the context of COVID-19 may offer valuable insights into disease prevention, treatment strategies, and its potential applications in forensic science. Consequently, this paper aims to provide an overarching review of microbiome alterations due to COVID-19 and the associated impact on forensic applications, bridging the gap between the altered microbiome of COVID-19 patients and the challenges forensic investigations may encounter when analyzing this microbiome as a forensic biomarker.

Novel Mutations in the Non-Structure Protein 2 of SARS-CoV-2

Introduction

Mutation in the genome of SARS-CoV-2 may play a role in immune evasion, pathogenicity, and speed of its transmission. Our investigation aimed to evaluate the mutations that exist in the NSP2.

Materials and Method

RNA was extracted from nasopharyngeal swabs from 100 COVID-19 patients. RT-PCR was performed on all samples using NSP2-specific primers. Following gel electrophoresis, the bands were cut, purified, and sequenced using the Sanger method. After sequencing, 90 sequences could be used for further analysis. Bioinformatics analysis was conducted to investigate the effect of mutations on protein structure, stability, prediction of homology models, and phylogeny tree.

Results

The patients' mean age was 51.08. The results revealed that 8 of the 17 NSP2 mutations (R207C, T224I, G262V, T265I, K337D, N348S, G392D, and I431M) were missense. One deletion was also found in NSP2. Among NSP2 missense mutations studied, K337D and G392D increased structural stability while the others decreased it. The homology-designed models demonstrated that the homologies were comparable to the sequences of the Wuhan-HU-1 virus.

Conclusion

Our study suggested that the mutations K337D and G392D modulate the stability of NSP2, and tracking viral evolution should be implemented and vaccine development updated.

Comparison of Maternal and Neonatal Outcomes between SARS-CoV-2 Variants: A Retrospective, Monocentric Study

The impact of SARS-CoV-2 variants on maternal and neonatal outcomes during pregnancy is still poorly understood, and the emergence of different variants has further complicated our understanding of the virus's effects. This retrospective, monocentric study aimed to fill this knowledge gap by analyzing the outcomes of pregnant women with acute SARS-CoV-2 infection caused by the Alpha, Delta, and Omicron variants. The study, conducted between December 2020 and March 2022 at San Marco Hospital, included 313 pregnant women with confirmed SARS-CoV-2 infection. The results showed that the Delta variant was associated with a significantly higher incidence of adverse outcomes, such as premature births, maternal intensive care unit admission, intrauterine growth restriction, and small for gestational age infants. Additionally, the Delta variant was linked to lower Apgar scores, higher maternal and fetal mortality rates, and increased levels of various biomarkers indicating more severe illness. Finally, the Delta variant also presented a greater possibility of vertical transmission. These findings underscore the complexity of understanding the impact of SARS-CoV-2 on pregnancy outcomes, especially considering the distinctive characteristics of different variants. By better understanding the specific impacts of each variant, appropriate preventive measures and management strategies can be implemented to optimize maternal and neonatal outcomes.

Remote monitoring as a surveillance method in patients on automated peritoneal dialysis for preventing complications and COVID-19 contagion

BACKGROUND

Due to the health emergency of COVID-19, telemedicine has become more relevant. Remote monitoring conspicuous as a valuable tool for the clinical follow-up of kidney patients, in this case, who are treated with automated peritoneal dialysis. This study aims to describe the use of remote monitoring as a surveillance method in a cohort of patients on automated peritoneal dialysis prevent complications and COVID-19 contagion.

METHODS

Study of a cohort of patients who initially participated in a randomized block clinical trial in which the use of Automated Peritoneal Dialysis with Remote Monitoring (APD-RM) was compared with conventional treatment. A descriptive analysis was performed of the rates of infection by COVID-19, the time of incidence until this, mortality, and rates of transfer to hemodialysis. In addition, survival was measured by survival curves.

RESULTS

Of the 509 patients, 19 were positive for COVID-19 (incidence rate of 7.0 episodes/100 patient-year), and only six patients recovered from the infection; the death rate was 2.6 % compared to all-cause death of 9.8 %. The most affected group of patients were those over 50 years old, with 71.4 % mortality, in contrast to younger patients infected, with a mortality of 60 %. During the follow-up period, 21 patients were transferred to HD: six due to peritonitis, five due to UF failure, seven due to catheter dysfunction, one due to uremic syndrome, one due to COVID-19, and one by surgical intervention.

CONCLUSION

APD-RM patients have a significant advantage over other dialysis therapies because the use of telemedicine not only provides continuity in the patient's clinical treatment but also favors the prevention of COVID-19 infection, the management and prevention of complications inherent to therapy and the preservation of the life of Peritoneal Dialysis patients.

The 21st century disaster: The COVID-19 epidemiology, risk factors and control

The 21st century will be indelible in the world as ruin of the outbreak of COVID-19 was arose in Wuhan, China has now spread all over the world, up to August 2020. This study was based on the factors affecting the epidemiology of this virus in human societies of global concern. We studied the articles published in journals on various aspects of nCoVID19. The Wikipedia and WHO situation reports have also been searched out for related information. Outcomes were followed up until 2020. The COVID-19 is a virus with pandemic potential which may continue to cause regular infection in human. The pandemic outbreak of COVID-19 threatened public health across the globe in form of system as reflected in the shape of emergency. Approximately 21 million humans are infected and 759,400 have lost their lives till 2020 in all over the world. We have described epidemiological features, reservoirs, transmission, incubation period, rate of fatality, management including recent clinical chemotherapeutic approach and preventive measurements and masses which are at risk of COVID19. This virus causes viral pneumonia when it attacks on respiratory system and multiple failure which can leads to life threatening complications. It is believed to be zoonotic importance although it is not clear from which animal and how it is transmitted. Zoonotic transmission of COVID-19 has not yet known by science. The current study will help to establish a baseline for early effective control of this rapidly spreading severe viral illness. The available data on COVID-19 indicates that older males with comorbidities would have been more infected, which can result in severe respiratory complications. Implementation of preventive measurements, investigation of proper chemotherapeutics and detection of cross species transmission agents must be ensured.

How SARS-CoV-2 Alters the Regulation of Gene Expression in Infected Cells

Nonstructural accessory proteins in viruses play a key role in hijacking the basic cellular mechanisms, which is essential to promote the virus survival and evasion of the immune system. The immonuglobulin-like open reading frame 8 (ORF8) protein expressed by SARS-CoV-2 accumulates in the nucleus and may influence the regulation of the gene expression in infected cells. In this contribution, by using microsecond time-scale all-atom molecular dynamics simulations, we unravel the structural bases behind the epigenetic action of ORF8. In particular, we highlight how the protein is able to form stable aggregates with DNA through a histone tail-like motif, and how this interaction is influenced by post-translational modifications, such as acetylation and methylation, which are known epigenetic markers in histones. Our work not only clarifies the molecular mechanisms behind the perturbation of the epigenetic regulation caused by the viral infection but also offers an unusual perspective which may foster the development of original antivirals.

Interleukin-6 in COVID-19 Severity Stratification

Background

The increase in the number of patients with COVID-19 on a global scale made the early recognition of severe forms of the disease essential. Considering that IL-6 acts as a pro-inflammatory mediator, mediating acute phase responses, the objective of this study was to assess its value in the early severity stratification of SARS-CoV2 infection.

Materials and Methods

It was a prospective study included IL-6 measurement in patients with SARS-CoV2 infection upon admission to the emergency department. Two groups were considered (Group I: patients without hospitalization criteria; Group II: patients with hospitalization criteria). Analyzed variables were serum levels of IL-6, C-reactive protein, ferritin, d-dimers, sociodemographics, ventilator support, ICU admission, mortality, dates of diagnosis, hospitalization, and discharge. For the statistical analyses, Mann-Whitney test, Pearson's chi-square test, area under the receiver operating characteristic curve, Youden index, and Spearman correlation were applied.

Results

A total number of 117 patients were included. Mean age was significantly higher for group II (72,35±15,39 years; p<0,001). No statistically significant difference was seen between the groups regarding gender (p=0,111). The IL-6 values showed an excellent power of discrimination for the need for hospitalization (AUC=0,888; p<0,001) and the need for ICU admission (AUC=0,897; p=7.9 × 10-5). Also, its cut-off value of 12,4pg/mL for the need for hospitalization and 42,95 pg/mL for the need for ICU admission was determined. Positive correlation was seen between IL-6 value and length of stay [r(35)=0,380; p=0,020]. Three deaths were observed among patients with hospitalization criteria (8,1%).

Conclusion

The value of IL-6 at admission seems to independently influence the probability of hospitalization (general ward or ICU) and its duration.

Endothelial dysfunction in COVID-19: an overview of evidence, biomarkers, mechanisms and potential therapies

The fight against coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 infection is still raging. However, the pathophysiology of acute and post-acute manifestations of COVID-19 (long COVID-19) is understudied. Endothelial cells are sentinels lining the innermost layer of blood vessel that gatekeep micro- and macro-vascular health by sensing pathogen/danger signals and secreting vasoactive molecules. SARS-CoV-2 infection primarily affects the pulmonary system, but accumulating evidence suggests that it also affects the pan-vasculature in the extrapulmonary systems by directly (via virus infection) or indirectly (via cytokine storm), causing endothelial dysfunction (endotheliitis, endothelialitis and endotheliopathy) and multi-organ injury. Mounting evidence suggests that SARS-CoV-2 infection leads to multiple instances of endothelial dysfunction, including reduced nitric oxide (NO) bioavailability, oxidative stress, endothelial injury, glycocalyx/barrier disruption, hyperpermeability, inflammation/leukocyte adhesion, senescence, endothelial-to-mesenchymal transition (EndoMT), hypercoagulability, thrombosis and many others. Thus, COVID-19 is deemed as a (micro)vascular and endothelial disease. Of translational relevance, several candidate drugs which are endothelial protective have been shown to improve clinical manifestations of COVID-19 patients. The purpose of this review is to provide a latest summary of biomarkers associated with endothelial cell activation in COVID-19 and offer mechanistic insights into the molecular basis of endothelial activation/dysfunction in macro- and micro-vasculature of COVID-19 patients. We envisage further development of cellular models and suitable animal models mimicking endothelial dysfunction aspect of COVID-19 being able to accelerate the discovery of new drugs targeting endothelial dysfunction in pan-vasculature from COVID-19 patients.

SARS-CoV-2 ORF8: A Rapidly Evolving Immune and Viral Modulator in COVID-19

The COVID-19 pandemic has resulted in upwards of 6.8 million deaths over the past three years, and the frequent emergence of variants continues to strain global health. Although vaccines have greatly helped mitigate disease severity, SARS-CoV-2 is likely to remain endemic, making it critical to understand its viral mechanisms contributing to pathogenesis and discover new antiviral therapeutics. To efficiently infect, this virus uses a diverse set of strategies to evade host immunity, accounting for its high pathogenicity and rapid spread throughout the COVID-19 pandemic. Behind some of these critical host evasion strategies is the accessory protein Open Reading Frame 8 (ORF8), which has gained recognition in SARS-CoV-2 pathogenesis due to its hypervariability, secretory property, and unique structure. This review discusses the current knowledge on SARS-CoV-2 ORF8 and proposes actualized functional models describing its pivotal roles in both viral replication and immune evasion. A better understanding of ORF8's interactions with host and viral factors is expected to reveal essential pathogenic strategies utilized by SARS-CoV-2 and inspire the development of novel therapeutics to improve COVID-19 disease outcomes.

Evaluation of quality of life and physical activity in patients with type 1 diabetes mellitus during the COVID-19 pandemic

Objective

The aim of the study is to compare the quality of life, physical activity, anxiety, depression, fear of hypoglycemia, loneliness perception in patients with type 1 diabetes mellitus and controls.

Subjects and methods

Forty-four patients and 63 controls were included in this cross-sectional study. Quality of life (Short Form 36-SF-36), physical activity level (International Physical Activity Questionnaire-short form), anxiety and depression (Hospital Anxiety and Depression Scale), fear of hypoglycemia (Hypoglycemia Fear Survey), loneliness perception (UCLA Loneliness Scale) were evaluated.

Results

Physical role limitations and general health perception subscale scores of SF-36 questionnaire in patients were significantly higher than the controls (p < 0.05).

Conclusion

Role limitations due to physical problems and fear of hypoglycemia are increased, and general health perception is impaired in patients with type 1 diabetes mellitus. Physical inactivity is an important symptom in individuals in the pandemic period. In this regard, telerehabilitation approaches will be beneficial for all individuals in increasing physical activity, improving quality of life, and decreasing anxiety, depression and loneliness perception during the pandemic period for all individuals. The importance of a multidisciplinary approach in diabetes management and dealing with problems should be considered in pandemic.

Protein Arginylation Is Regulated during SARS-CoV-2 Infection

BACKGROUND

In 2019, the world witnessed the onset of an unprecedented pandemic. By February 2022, the infection by SARS-CoV-2 has already been responsible for the death of more than 5 million people worldwide. Recently, we and other groups discovered that SARS-CoV-2 infection induces ER stress and activation of the unfolded protein response (UPR) pathway. Degradation of misfolded/unfolded proteins is an essential element of proteostasis and occurs mainly in lysosomes or proteasomes. The N-terminal arginylation of proteins is characterized as an inducer of ubiquitination and proteasomal degradation by the N-degron pathway.

RESULTS

The role of protein arginylation during SARS-CoV-2 infection was elucidated. Protein arginylation was studied in Vero CCL-81, macrophage-like THP1, and Calu-3 cells infected at different times. A reanalysis of in vivo and in vitro public omics data combined with immunoblotting was performed to measure levels of arginyl-tRNA-protein transferase (ATE1) and its substrates. Dysregulation of the N-degron pathway was specifically identified during coronavirus infections compared to other respiratory viruses. We demonstrated that during SARS-CoV-2 infection, there is an increase in ATE1 expression in Calu-3 and Vero CCL-81 cells. On the other hand, infected macrophages showed no enzyme regulation. ATE1 and protein arginylation was variant-dependent, as shown using P1 and P2 viral variants and HEK 293T cells transfection with the spike protein and receptor-binding domains (RBD). In addition, we report that ATE1 inhibitors, tannic acid and merbromine (MER) reduce viral load. This finding was confirmed in ATE1-silenced cells.

CONCLUSIONS

We demonstrate that ATE1 is increased during SARS-CoV-2 infection and its inhibition has potential therapeutic value.

Mapping the output of the global literature on the links between gut microbiota and COVID-19

BACKGROUND

The term "human microbiota" refers to populations of microorganisms that live harmoniously in co-existence with humans. They contribute significantly to the host's immunological response when confronted with a respiratory viral infection. However, little is known about the relationship between the human microbiome and COVID-19. Therefore, our objective is to perform a bibliometric analysis to explore the overall structure and hotspots of research activity on the links between microbiota and COVID-19 at the global level.

METHODS

The research literature on the microbiota and COVID-19 published between 2020 and 2022 was obtained from the Scopus database. Bibliometric analysis and network visualization were performed with VOSviewer.

RESULTS

Of the 701 publications selected, the USA contributed the most (n = 157, 22.40%), followed by China (n = 118, 16.83%) and Italy (n = 82, 11.70%). Hotspots in this field were "COVID-19 is associated with an altered upper respiratory tract microbiome," "the effect of antibiotics on the gut microbiome," as well as "patient nutrition and probiotic therapy in COVID-19."

CONCLUSIONS

The links between microbiota and COVID-19 remain an urgent concern at present, and the use of probiotics or/and antibiotics during the pandemic needs to be further improved. This landscape analysis of the links between the microbiota and COVID-19 will provide a basis for future research.

Rhino-orbito-cerebral invasive fungal sinusitis associated with COVID-19 infection in a malnurished child

Background

Corona virus disease has been associated with a wide variety of fungal and bacterial co-infections. These secondary infections could be due to the irrational use of antibiotics, immunosuppressive therapy, pre-existing co morbidities, and immune modulator effects of the virus. But here, we report a very rare occurring of rhino-orbito-cerebral invasive fungal sinusitis in a malnourished child and no other co morbidities.

Case presentation

This is a case of a 6-year-old boy with severe thinness and no other co-morbidities, with mild COVID-19 infection, during the course of illness developed rhino-orbito-cerebral invasive fungal sinusitis. The child’s mother had COVID-19 1 week prior to child’s illness. The child then developed fever followed by headache. The child reported to hospital on seventh day of illness and RTPCR for COVID-19, turned positive. The child’s vitals were stable and maintaining saturation. Child was being treated with supplements and symptomatic treatment for fever. On his second day of stay at hospital, he started to develop gradually progressive left-sided peri-orbital swelling. Due to the association of COVID-19 with fungal infection, child was started on AMPHOTERICIN-B and given for 4 days and referred to a higher center for further management. Radiological imaging was suggestive of rhino-sinusitis with orbital cellulitis with meningeal enhancement suggestive of fungal etiology. Debridement was done, child was adequately treated with anti-fungal, and the child showed significant improvement along with radiological clearing.

Conclusion

Invasive fungal infection can occur in association with COVID-19 among malnourished pediatric age groups with no other comorbidities.

Recent advances of nanotechnology in COVID 19: A critical review and future perspective

The global anxiety and economic crisis causes the deadly pandemic coronavirus disease of 2019 (COVID 19) affect millions of people right now. Subsequently, this life threatened viral disease is caused due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, morbidity and mortality of infected patients are due to cytokines storm syndrome associated with lung injury and multiorgan failure caused by COVID 19. Thereafter, several methodological advances have been approved by WHO and US-FDA for the detection, diagnosis and control of this wide spreadable communicable disease but still facing multi-challenges to control. Herein, we majorly emphasize the current trends and future perspectives of nano-medicinal based approaches for the delivery of anti-COVID 19 therapeutic moieties. Interestingly, Nanoparticles (NPs) loaded with drug molecules or vaccines resemble morphological features of SARS-CoV-2 in their size (60–140 nm) and shape (circular or spherical) that particularly mimics the virus facilitating strong interaction between them. Indeed, the delivery of anti-COVID 19 cargos via a nanoparticle such as Lipidic nanoparticles, Polymeric nanoparticles, Metallic nanoparticles, and Multi-functionalized nanoparticles to overcome the drawbacks of conventional approaches, specifying the site-specific targeting with reduced drug loading and toxicities, exhibit their immense potential. Additionally, nano-technological based drug delivery with their peculiar characteristics of having low immunogenicity, tunable drug release, multidrug delivery, higher selectivity and specificity, higher efficacy and tolerability switch on the novel pathway for the prevention and treatment of COVID 19.

Comparison of COVID-19 Outcomes With Alpha-1 Antitrypsin Deficiency Prevalence in Europe: A Cross-Sectional Study

Introduction We hypothesized that the geographic distributions of COVID-19 and alpha-1 antitrypsin alleles prevalence are similar. We investigate whether there is a relationship between the geographical density of the COVID-19 pandemic and the distributions of alpha-1 antitrypsin alleles. Methods This research is a cross-sectional study. Alpha-1 antitrypsin PI*MS, PI*MZ, PI*SS, PI*SZ, and PI*ZZ genotypes frequencies of European countries were compared with the case and death data related to the COVID-19 pandemic as of March 1, 2022.  Results A significant relationship was found between the rates of COVID-19 cases and the rates of individuals with alpha-1 antitrypsin PI*MS, PI*MZ, PI*SS, PI*SZ, and PI*ZZ genotypes allele in European countries. Conclusions The findings showed that the prevalence distribution of the alleles of the gene defect that causes alpha-1 antitrypsin insufficiency is related to the prevalence of COVID-19 pandemic data.

Nursing Students’ Applications, Knowledge Needs, Self-Efficacy During COVID-19: A Descriptive Study

Aim: Nursing students are also a health educator. During the COVID-19 process, nursing students both provided health education to individuals in need in their environment and implemented protective measures themselves. The aim of this study was to determine nursing students' self-efficacy, basic knowledge, and protective measures they applied during the COVID-19 outbreak.Method: This was a descriptive study. Ethics committee approval was obtained for the study. Data were collected interactively. The sample consisted of 672 voluntary nursing students 18 years of age from the universities in Turkey. Data were made using Statistical Package for Social Sciences (SPSS, v 21.0); Kruskal-Wallis and Mann Whitney-U tests, and Spearman’s correlation were used. "STROBE" checklist has been followed.Results: Gender had an effect on self-efficacy. Income level, place of residence, and self-efficacy had an effect on the number of in-house preventive measures. Regarding COVID-19 protection measures; girls, those living in rural areas and those with low income were found to be disadvantaged.Conclusion: Nursing students may need to be supported to feel competent. It may be recommended to educate disadvantaged groups as a priority in preventing the spread of the epidemic. In addition, nursing students can take part in the health education of the community. The findings of this study emphasize the importance of improving nursing education. Nursing students can guide society in public education.

Investigating Derivatives of Tanshinone IIA Sulfonate Sodium and Chloroxine for Their Inhibition Activities against the SARS-CoV-2 Papain-like Protease

SARS-CoV-2 has caused a global pandemic of COVID-19, posing a huge threat to public health. The SARS-CoV-2 papain-like cysteine protease (PLpro) plays a significant role in virus replication and host immune regulation, which is a promising antiviral drug target. Several potential inhibitors have been identified in vitro. However, the detailed mechanism of action and structure-activity relationship require further studies. Here, we investigated the structure-activity relationships of the series of derivatives of tanshinone IIA sulfonate sodium (TSS) and chloroxine based on biochemical analysis and molecular dynamics simulation. We found that compound 7, a derivative of chloroxine, can disrupt PLpro-ISG15 interaction and exhibits an antiviral effect for SARS-CoV-2 variants (wild type, delta, and omicron) at the low micromolar level. These studies confirmed that inhibiting PLpro-ISG15 interaction and, thus, restoring the host's innate immunity are effective methods for fighting against viral infection.

Gastrointestinal microbiota: A predictor of COVID-19 severity?

Coronavirus disease 2019 (COVID-19), caused by a severe acute respiratory syndrome coronavirus 2 infection, has raised serious concerns worldwide over the past 3 years. The severity and clinical course of COVID-19 depends on many factors (e.g., associated comorbidities, age, etc) and may have various clinical and imaging findings, which raises management concerns. Gut microbiota composition is known to influence respiratory disease, and respiratory viral infection can also influence gut microbiota. Gut and lung microbiota and their relationship (gut-lung axis) can act as modulators of inflammation. Modulating the intestinal microbiota, by improving its composition and diversity through nutraceutical agents, can have a positive impact in the prophylaxis/treatment of COVID-19.

Non-uniform aspects of the SARS-CoV-2 intraspecies evolution reopen question of its origin

Several hypotheses have been presented on the origin of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) from its identification as the agent causing the current coronavirus disease 19 (COVID-19) pandemic. So far, no solid evidence has been found to support any hypothesis on the origin of this virus, and the issue continue to resurface over and over again. Here we have unfolded a pattern of distribution of several mutations in the SARS-CoV-2 proteins in 24 geo-locations across different continents. The results showed an evenly uneven distribution of the unique protein variants, distinct mutations, unique frequency of common conserved residues, and mutational residues across these 24 geo-locations. Furthermore, ample mutations were identified in the evolutionarily conserved invariant regions in the SARS-CoV-2 proteins across almost all geo-locations studied. This pattern of mutations potentially breaches the law of evolutionary conserved functional units of the beta-coronavirus genus. These mutations may lead to several novel SARS-CoV-2 variants with a high degree of transmissibility and virulence. A thorough investigation on the origin and characteristics of SARS-CoV-2 needs to be conducted in the interest of science and for the preparation of meeting the challenges of potential future pandemics.

Clinical and laboratory factors associated with mortality among hospitalized patients with COVID-19 infection in Lebanon: A multicenter study

BACKGROUND

With the dire economic situation in Lebanon, many of the basic resources of the hospitals needed to help fight COVID-19 infections are not available. In this paper, we studied the possible factors associated with increased mortality in a sample of Lebanese adults enrolled in three hospitals.

METHOD

In this retrospective cohort study, we analyzed data from 416 adults hospitalized in three institutions for a COVID-19 infection, from the opening of the COVID unit until their closure (period extending from March 2020 to June 2021). We used multivariate analyses to assess potential factors associated with COVID-19 mortality: gender, age, the presence of underlying medical conditions, and some medication taken during hospitalization.

RESULTS

Using variables related to baseline characteristics entered as independent variables, acute kidney injury (aOR = 4.057) and older age (aOR = 1.053) were associated with a higher probability of death. After adjusting baseline characteristics and factors related to admission entered as independent variables, enoxaparin intake (aOR = 0.435) was significantly associated with a lower probability of death, whereas old age (aOR = 1.049) and ventilation (aOR = 1.2) were significantly associated with higher odds of death. When all variables that showed significance in bivariate analysis were entered, old age (aOR = 1.243) and highest PaCO2 during hospitalization (aOR = 1.192) were significantly associated with higher mortality. With a weak effect, atrial fibrillation, COPD, and higher leucocyte counts on admission were significantly associated with higher odds of death.

CONCLUSION

These findings could help us prevent severe diseases in patients with several comorbidities and adjust therapeutic care to improve future outcomes. More studies should compare the outcome of different COVID-19 strains as well as the impact of vaccination on those with multiple comorbidities, especially on the mortality rate culminating from disease complications.

A survival analysis approach for identifying the risk factors in time to recovery of COVID-19 patients using Cox proportional hazard model

The coronavirus pandemic was a global health crisis taking away millions of lives worldwide. People diseased by the virus, differ in the extent of severity of the infection. While it turns out to be fatal for some, for several others the extent of severity is as ordinary as common cold. These people are reported to have recovered from the disease without hospitalization and consuming some relevant medicine and home remedies. But people who have comorbidity like geriatric, high blood pressure, heart and lung problems, diabetes, cancer etc. are at high risk of developing serious illness from the infection. This study is an application of the Cox proportional hazard model with an aim to identify the risk factors that affect the recovery time of the COVID-19 patients. The model is an advanced regression technique that can be utilized to evaluate simultaneously the effect of several factors on the possibility of instantaneous failure in patients. The paper also uses the Mantel-Haenszel test (Log-Rank test) to compare if the probability of survival of different treatment procedures or different groups of patients differ significantly. The information is collected from 129 respondents of Assam, India. The study identifies that the significant risk factors that prolong the recovery time from COVID-19 are pre-disease, location, and food habits.

Cloud-based COVID-19 disease prediction system from X-Ray images using convolutional neural network on smartphone

COVID-19 has engulfed over 200 nations through human-to-human transmission, either directly or indirectly. Reverse Transcription-polymerase Chain Reaction (RT-PCR) has been endorsed as a standard COVID-19 diagnostic procedure but has caveats such as low sensitivity, the need for a skilled workforce, and is time-consuming. Coronaviruses show significant manifestation in Chest X-Ray (CX-Ray) images and, thus, can be a viable option for an alternate COVID-19 diagnostic strategy. An automatic COVID-19 detection system can be developed to detect the disease, thus reducing strain on the healthcare system. This paper discusses a real-time Convolutional Neural Network (CNN) based system for COVID-19 illness prediction from CX-Ray images on the cloud. The implemented CNN model displays exemplary results, with training accuracy being 99.94% and validation accuracy reaching 98.81%. The confusion matrix was utilized to assess the models' outcome and achieved 99% precision, 98% recall, 99% F1 score, 100% training area under the curve (AUC) and 98.3% validation AUC. The same CX-Ray dataset was also employed to predict the COVID-19 disease with deep Convolution Neural Networks (DCNN), such as ResNet50, VGG19, InceptonV3, and Xception. The prediction outcome demonstrated that the present CNN was more capable than the DCNN models. The efficient CNN model was deployed to the Platform as a Service (PaaS) cloud.

Plasma Metabolome Alterations Discriminate between COVID-19 and Non-COVID-19 Pneumonia

Pneumonia is a common cause of morbidity and mortality and is most often caused by bacterial pathogens. COVID-19 is characterized by lung infection with potential progressive organ failure. The systemic consequences of both disease on the systemic blood metabolome are not fully understood. The aim of this study was to compare the blood metabolome of both diseases and we hypothesize that plasma metabolomics may help to identify the systemic effects of these diseases. Therefore, we profiled the plasma metabolome of 43 cases of COVID-19 pneumonia, 23 cases of non-COVID-19 pneumonia, and 26 controls using a non-targeted approach. Metabolic alterations differentiating the three groups were detected, with specific metabolic changes distinguishing the two types of pneumonia groups. A comparison of venous and arterial blood plasma samples from the same subjects revealed the distinct metabolic effects of pulmonary pneumonia. In addition, a machine learning signature of four metabolites was predictive of the disease outcome of COVID-19 subjects with an area under the curve (AUC) of 86 ± 10 %. Overall, the results of this study uncover systemic metabolic changes that could be linked to the etiology of COVID-19 pneumonia and non-COVID-19 pneumonia.

A Review of the Rational and Current Evidence on Colchicine for COVID-19

The current coronavirus disease (COVID-19) pandemic has affected millions of individuals worldwide. Despite extensive research efforts, few therapeutic options currently offer direct clinical benefits for COVID-19 patients. Despite the advances in our understanding of COVID-19, the mortality rates remain significantly high owing to the high viral transmission rates in several countries and the rise of various mutations in the SARS-CoV-2. One currently available and widely used drug that combines both anti-inflammatory and immunomodulatory actions is colchicine, which has been proposed as a possible treatment option for COVID-19. Colchicine still did not get much attention from the medical and scientific communities despite its antiinflammatory and immunomodulatory mechanisms of action and positive preliminary data from early trials. This literature review article provides the scientific rationale for repurposing colchicine as a potential therapy for COVID-19. Further, we summarize colchicine's mechanisms of action and possible roles in COVID-19 patients. Finally, we supplement this review with a summary of the doses, side effects, and early efficacy data from clinical trials to date. Despite the promising early findings from multiple observational and clinical trials about the potential of colchicine in COVID-19, the data from the RECOVERY trial, the largest COVID-19 randomized controlled trial (RCT) in the world, showed no evidence of clinical benefits in mortality, hospital stays, or disease progression (n = 11340 patients). However, multiple other smaller clinical trials showed significant clinical benefits. We conclude that while current evidence does not support the use of colchicine for treating COVID-19, the present body of evidence is heterogeneous and inconclusive. The drug cannot be used in clinical practice or abandoned from clinical research without additional large RCTs providing more robust evidence. At present, the drug should not be used except for investigational purposes.

SARS-CoV-2 disrupts host epigenetic regulation via histone mimicry

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged at the end of 2019 and caused the devastating global pandemic of coronavirus disease 2019 (COVID-19), in part because of its ability to effectively suppress host cell responses1-3. In rare cases, viral proteins dampen antiviral responses by mimicking critical regions of human histone proteins4-8, particularly those containing post-translational modifications required for transcriptional regulation9-11. Recent work has demonstrated that SARS-CoV-2 markedly disrupts host cell epigenetic regulation12-14. However, how SARS-CoV-2 controls the host cell epigenome and whether it uses histone mimicry to do so remain unclear. Here we show that the SARS-CoV-2 protein encoded by ORF8 (ORF8) functions as a histone mimic of the ARKS motifs in histone H3 to disrupt host cell epigenetic regulation. ORF8 is associated with chromatin, disrupts regulation of critical histone post-translational modifications and promotes chromatin compaction. Deletion of either the ORF8 gene or the histone mimic site attenuates the ability of SARS-CoV-2 to disrupt host cell chromatin, affects the transcriptional response to infection and attenuates viral genome copy number. These findings demonstrate a new function of ORF8 and a mechanism through which SARS-CoV-2 disrupts host cell epigenetic regulation. Further, this work provides a molecular basis for the finding that SARS-CoV-2 lacking ORF8 is associated with decreased severity of COVID-19.

An Internet-of-Disease System for COVID-19 Testing Using Saliva by an AI-Controlled Microfluidic ELISA Device

Throughout coronavirus disease (COVID-19) outbreaks, the centers for disease control and prevention (CDCP) of a country require monitoring of particular territories to provide public health guidance. In this work, the Internet of Diseases (IoD) is suggested for continuous real-time monitoring of infectious diseases for public health. Because converging information and communication technologies (ICTs) with point-of-care (POC) devices to enable the IoD for continuous real-time health monitoring and processing of clinical records are crucial, an IoD platform associating a lab-on-a-chip (LOC) device to diagnose severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) from oropharyngeal saliva samples have been developed and uploaded the resulted diagnostic data into a cloud-based system to be connected with CDCP. Moreover, a choropleth IoD map to visualize provincial infection rate is proposed along with the IoD platform. The developed platform is applied for the quantification of SARS-CoV-2 N-protein antigen with a LOD as low as 0.013 ng mL-1 and the infection rate of various provinces is projected with the IoD map successfully. Thus, the proposed IoD system has the potential to become an imperative tool for the disease control and prevention centers to restrain COVID-19 outbreaks by identifying the severity of particular regions.

Review of Method and a New Tool for Decline and Inactive SARS-CoV-2 in Wastewater Treatment

Following the recent outbreak of the COVID-19 pandemic caused by the SARS-CoV-2 virus, monitoring sewage has become crucial, according to reports that the virus was detected in sewage. Currently, various methods are discussed for understanding the SARS-CoV-2 using wastewater surveillance. This paper first introduces the fundamental knowledge of primary, secondary, and tertiary water treatment on SARS-CoV-2. Next, a thorough overview is presented to summarize the recent developments and breakthroughs in removing SARS-CoV-2 using solar water disinfection (SODIS) and UV (UVA (315–400 nm), UVB (280-315 nm), and UVC (100–280 nm)) process. In addition, Due to the fact that the distilled water can be exposed to sunlight if there is no heating source, it can be disinfected using solar water disinfection (SODIS). SODIS, on the other hand, is a well-known method of reducing pathogens in contaminated water; moreover, UVC can inactivate SARS-CoV-2 when the wavelength is between 100 to 280 nanometers. High temperatures (more than 56°C) and UVC are essential for eliminating SARS-CoV-2; however, the SODIS systems use UVA and work at lower temperatures (less than45°C). Therefore, using SODIS methods for wastewater treatment (or providing drinking water) is not appropriate during a situation like the ongoing pandemic. Finally, a wastewater-based epidemiology (WBE) tracking tool for SARS-CoV-2 can be used to detect its presence in wastewater.

Investigating the Potential Effects of COVID-19 Pandemic on Intestinal Coccidian Infections

New infectious agents pose a global threat to the healthcare system, and studies are conducted to estimate their health and epidemiological outcomes in the long run. The SARS-CoV-2 virus, which has caused the COVID-19 disease, was formerly assumed to be a respiratory virus; however, it can have serious systemic effects, affecting organs such as the gastrointestinal tract (GIT). Viral RNA was reported in the stool in a subset of patients, indicating another mode of transmission and diagnosis. In COVID-19, prolonged GIT symptoms, especially diarrhea, were associated with reduced diversity and richness of gut microbiota, immunological dysregulation, and delayed viral clearance. Intestinal coccidian parasites are intracellular protozoa that are most typically transmitted to humans by oocysts found in fecally contaminated food and water. Their epidemiological relevance is coupled to opportunistic infections, which cause high morbidity and mortality among immunocompromised individuals. Among immunocompetent people, intestinal coccidia is also involved in acute diarrhea, which is usually self-limiting. Evaluating the available evidence provided an opportunity to carefully consider that; the COVID-19 virus and coccidian protozoan parasites: namely, Cryptosporidium spp., Cyclospora cayetanensis, and Isospora belli, could mutually influence each other from the microbiological, clinical, diagnostic, and elimination aspects. We further systemically highlighted the possible shared pathogenesis mechanisms, transmission routes, clinical manifestations, parasite-driven immune regulation, and intestinal microbiota alteration. Finally, we showed how this might impact developing and developed countries prevention and vaccination strategies. To the best of our knowledge, there is no review that has discussed the reciprocal effect between coccidian parasites and COVID-19 coinfection.

Biomarker based biosensors: An opportunity for diagnosis of COVID-19

Early diagnosis and treatment of diseases are crucial research areas of human health. For early diagnosis, one method that has proven efficient is the detection of biomarkers which can provide real-time and accurate biological information. Most biomarker detection is currently carried out at localised dedicated laboratories using large and automated analysers, increasing waiting time and costs. Smaller, faster, and cheaper devices could potentially replace these time-consuming laboratory analyses and make analytical results available as point-of-care diagnostics. Innovative biosensor-based strategies could allow biomarkers to be tested reliably in a decentralised setting. Early diagnosis of COVID-19 patients has a key role in order to use quarantine and treatment strategies in a timely manner. Raised levels of several biomarkers in COVID-19 patients are associated with respiratory infections or dysfunction of various organs. Through clinical studies of COVID-19 patient biomarkers such as ferritin, Interleukins, albumin and …are found to reveals significant differences in their excretion ranges from healthy patients and patients with SARS-CoV-2, in addition to the development of biomarkers based biosensor such as stated biomarkers can be used and to investigate more specific biomarkers further proteomic analysis can be performed. This review presents several biomarker alterations in COVID-19 patients such as salivary, circulatory, coagulation, cardiovascular, renal, liver, C-reactive protein (CRP), immunological and inflammatory biomarkers. Also, biomarker sensors based on electrochemical, optical, and lateral flow characteristics which have potential applications for SARS-COV-2 in the recent COVID-19 pandemic, will be discussed.

Gomes AB, Matheus VA, Antunes ASLM, Crunfli F, Antunes KH, de Souza APD, Consonni SR, Leiria LO, Alves-Filho JC, Cunha TM, Moraes-Vieira PMM, Proença-Módena JL, R. Vinolo MA. Impact of Microbiota Depletion by Antibiotics on SARS-CoV-2 Infection of K18-hACE2 Mice

Clinical and experimental data indicate that severe acute respiratory syndrome coronavirus (SARS-CoV)-2 infection is associated with significant changes in the composition and function of intestinal microbiota. However, the relevance of these effects for SARS-CoV-2 pathophysiology is unknown. In this study, we analyzed the impact of microbiota depletion after antibiotic treatment on the clinical and immunological responses of K18-hACE2 mice to SARS-CoV-2 infection. Mice were treated with a combination of antibiotics (kanamycin, gentamicin, metronidazole, vancomycin, and colistin, Abx) for 3 days, and 24 h later, they were infected with SARS-CoV-2 B lineage. Here, we show that more than 80% of mice succumbed to infection by day 11 post-infection. Treatment with Abx had no impact on mortality. However, Abx-treated mice presented better clinical symptoms, with similar weight loss between infected-treated and non-treated groups. We observed no differences in lung and colon histopathological scores or lung, colon, heart, brain and kidney viral load between groups on day 5 of infection. Despite some minor differences in the expression of antiviral and inflammatory markers in the lungs and colon, no robust change was observed in Abx-treated mice. Together, these findings indicate that microbiota depletion has no impact on SARS-CoV-2 infection in mice.

The Urban Development in Relation to the Occurrence of Diseases in the Casa-Settat Region of Morocco during the Emergence of SARS-CoV-2

The Casa-Settat region is experiencing very worrying environmental and epidemiological problems and challenges, namely, population growth, the significant development of unsupervised industrial activities, road traffic, the significant weight of the spread of diseases with high epidemiological potential such as SARS-CoV-2, the increase in hospital activities, and the significant discharge of hospital effluents highly contaminated and untreated. To understand and analyze the factors influencing the high prevalence of deaths and the occurrence of diseases under surveillance, among others SARS-CoV-2, on the quantitative data recorded relating to ten regions of Morocco, and informing, on the one hand, on intrinsic data linked to the urban development, and on the other hand, on the evolution of diseases under epidemiological surveillance, a multidimensional analysis was made. The results reveal the typological framework highlighted by the factorial map F1 × F2 which showed the individualization of the region of Casablanca explained by a large number of variables and diseases that affect it. Finally, these results call for a diagnosis that will make it possible to model new approaches and implement new actions promoting the dynamics of environmental and epidemiological change in one of the most polluted and infected regions of Morocco.

Measuring the Intention in Favour and Against Getting Vaccinated from COVID-19 Using the Health Belief Model: Cross-Sectional Study of Pakistan

Vaccination is without a doubt one of the most efficient ways to stop the COVID-19 pandemic from spreading. The goal of this study was to look into the acceptance and resistance to COVID-19 vaccination and its associated components using the Health Belief Model, which is a framework for changing health behaviours (HBM). The current study is quantitative; hence data was collected from attendants of patients admitted to hospitals in Pakistan's top-tier cities using a survey-based self-administered questionnaire. Nonprobability convenient sampling was utilised to approach the respondents. The model was tested in two stages using partial least squares (variance-based structural equation modelling). The measurement model's reliability and validity imply that the data is reliable and valid. Except for the impact of benefits on accepting behaviour, all of the study postulated relationships are supported by the results. The study agenda adds to our understanding of health care, immunisation, consumer behaviour, and behavioural research. It adds to the body of knowledge in the fields of immunisation and behavioural research by examining people's behaviours and changes during the worldwide mass vaccination period.

Rapid Assessment of Biological Activity of Ag-Based Antiviral Coatings for the Treatment of Textile Fabrics Used in Protective Equipment Against Coronavirus

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants have rapidly spread worldwide, causing coronavirus disease (COVID-19) with numerous infected cases and millions of deaths. Therefore, developing approaches to fight against COVID-19 is currently the most priority goal of the scientific community. As a sustainable solution to stop the spread of the virus, a green dip-coating method is utilized in the current work to prepare antiviral Ag-based coatings to treat cotton and synthetic fabrics, which are the base materials used in personal protective equipment such as gloves and gowns. Characterization results indicate the successful deposition of silver (Ag) and stabilizers on the cotton and polypropylene fiber surface, forming Ag coatings. The deposition of Ag and stabilizers on cotton and etched polypropylene (EPP) fabrics is dissimilar due to fiber surface behavior. The obtained results of biological tests reveal the excellent antibacterial property of treated fabrics with large zones of bacterial inhibition. Importantly, these treated fabrics exhibit an exceptional antiviral activity toward human coronavirus OC43 (hCoV-OC43), whose infection could be eliminated up to 99.8% when it was brought in contact with these fabrics after only a few tens of minutes. Moreover, the biological activity of treated fabrics is well maintained after a long period of up to 40 days of post-treatment.

A First Assessment of SARS-CoV-2 Circulation in Bats of Central-Southern Italy

One serious concern associated with the SARS-CoV-2 pandemic is that the virus might spill back from humans to wildlife, which would render some animal species reservoirs of the human virus. We assessed the potential circulation of SARS-CoV-2 caused by reverse infection from humans to bats, by performing bat surveillance from different sites in Central-Southern Italy. We restricted our survey to sampling techniques that are minimally invasive and can therefore be broadly applied by non-medical operators such as bat workers. We collected 240 droppings or saliva from 129 bats and tested them using specific and general primers for SARS-CoV-2 and coronaviruses, respectively. All samples (127 nasal swabs and 113 faecal droppings) were negative for SARS-CoV-2, and these results were confirmed by testing the samples with the Droplet Digital PCR. Additionally, pancoronavirus end-point RT-PCR was performed, and no sample showed specific bands. This outcome is a first step towards a better understanding of the reverse transmission of this virus to bats. Although the occurrence of a reverse zoonotic pattern can only be fully established by serological testing, the latter might represent an in-depth follow-up to a broad-scale preliminary assessment performed with our approach. We encourage the systematic surveillance of bats to help prevent reverse zoonotic episodes that would jeopardize human health, as well as biodiversity conservation and management.

Hijacking of Cellular Functions by Severe Acute Respiratory Syndrome Coronavirus-2. Permeabilization and Polarization of the Host Lipid Membrane by Viroporins

Like all viral infections, SARS-CoV-2 acts at multiple levels, hijacking fundamental cellular functions and assuring its replication and immune system evasion. In particular, the viral 3' Open Reading Frame (ORF3a) codes for a hydrophobic protein, which embeds in the cellular membrane, where it acts as an ion viroporin and is related to strong inflammatory response. Here we report equilibrium and enhanced sampling molecular dynamic simulation of the SARS-CoV-2 ORF3a in a model lipid bilayer, showing how the protein permeabilizes the lipid membrane, via the formation of a water channel, which in turn assures ion transport. We report the free energy profile for both K+ and Cl- transfer from the cytosol to the extracellular domain. The important role of ORF3a in the viral cycle and its high conservation among coronaviruses may also make it a target of choice for future antiviral development, further justifying the elucidation of its mechanism at the atomistic level.

COVID-19: Rapid prototyping and production of face shields via flat, laser-cut, and 3D-printed models

The use of personal protective equipment (PPE) has become essential to reduce the transmission of coronavirus disease 2019 (COVID-19) as it prevents the direct contact of body fluid aerosols expelled from carriers. However, many countries have reported critical supply shortages due to the spike in demand during the outbreak in 2020. One potential solution to ease pressure on conventional supply chains is the local fabrication of PPE, particularly face shields, due to their simplistic design. The purpose of this paper is to provide a research protocol and cost implications for the rapid development and manufacturing of face shields by individuals or companies with minimal equipment and materials. This article describes a best practice case study in which the establishment of a local manufacturing hub resulted in the swift production of 12,000 face shields over a seven-week period to meet PPE shortages in the North-West region of Ireland. Protocols and processes for the design, materials sourcing, prototyping, manufacturing, and distribution of face shields are described. Three types of face shields were designed and manufactured, including Flat, Laser-cut, and 3D-printed models. Of the models tested, the Flat model proved the most cost-effective (€0.51/unit), while the Laser-cut model was the most productive (245 units/day). The insights obtained from this study demonstrate the capacity for local voluntary workforces to be quickly mobilised in response to a healthcare emergency, such as the COVID-19 pandemic.

Increased Risk of COVID-19 in Patients with Diabetes Mellitus-Current Challenges in Pathophysiology, Treatment and Prevention

Coronavirus disease-COVID-19 (coronavirus disease 2019) has become the cause of the global pandemic in the last three years. Its etiological factor is SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus type 2). Patients with diabetes (DM-diabetes mellitus), in contrast to healthy people not suffering from chronic diseases, are characterised by higher morbidity and mortality due to COVID-19. Patients who test positive for SARCoV-2 are at higher risk of developing hyperglycaemia. In this paper, we present, analyse and summarize the data on possible mechanisms underlying the increased susceptibility and mortality of patients with diabetes mellitus in the case of SARS-CoV-2 infection. However, further research is required to determine the optimal therapeutic management of patients with diabetes and COVID-19.

Analysis of the Protective Efficacy of Approved COVID-19 Vaccines Against Various Mutants

The outbreak of COVID-19 (caused by SARS-CoV-2) has posed a significant threat to global public health security because of its high pathogenicity and infectivity. To date, the pathogenic mechanism of this novel coronavirus (SARS-CoV-2) is still unclear, and there is no effective treatment. As one of the most effective strategies to prevent viral infection, vaccines have become a research hotspot. Based on the current understanding of SARS-CoV-2, the research and development of its vaccines cover almost all forms of current vaccine research, including inactivated vaccines, recombinant protein vaccines, viral vector vaccines, and nucleic acid vaccines. Moreover, with the spread of the new mutant virus, it is necessary to evaluate the protection rate of previous administered vaccines. This article reviews the candidate targets, vaccine types, research and development status, progress of SARS-CoV-2 vaccines, and the effectiveness of neutralizing antibodies against SARS-CoV-2 mutants (B.1.1.7, B.1.351, P.1, B.1.617.2, and B.1.1.529) induced by these vaccines, to provide a reference for follow-up research and prevention.

Evolutionary Traits and Genomic Surveillance of SARS-CoV-2 in South America

Since the zoonotic event from which SARS-CoV-2 started infecting humans late in 2019, the virus has caused more than 5 million deaths and has infected over 500 million people around the world. The pandemic has had a severe impact on social and economic activities, with greater repercussions in low-income countries. South America, with almost 5% of the world's population, has reckoned with almost a fifth of the total people infected and more than 26% (>1/4) of the deceased. Fortunately, the full genome structure and sequence of SARS-CoV-2 have been rapidly obtained and studied thanks to all the scientific efforts and data sharing around the world. Such molecular analysis of SARS-CoV-2 dynamics showed that rates of mutation, similar to other members of the Coronaviridae family, along with natural selection forces, could result in the emergence of new variants; few of them might be of high consequence. However, this is a serious threat to controlling the pandemic and, of course, enduring the process of returning to normalization with the implicit monetary cost of such a contingency. The lack of updated knowledge in South America justifies the need to develop a structured genomic surveillance program of current and emerging SARS-CoV-2 variants. The modeling of the molecular events and microevolution of the virus will contribute to making better decisions on public health management of the pandemic and developing accurate treatments and more efficient vaccines.

Promising antivirals for PLpro of SARS-CoV-2 using virtual screening, molecular docking, dynamics, and MMPBSA

The recent pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (COVID-19) is a viral respiratory disease that has been spread all over the globe. Therefore, it is an urgent requirement to identify and develop drugs for this contagious infection. The papain-like protease (PLpro) of SARS-CoV-2 performs critical functions in virus replication and immune evasion, making it an enticing therapeutic target. SARS-CoV-2 and SARS-CoV PLpro proteases have significant similarities, and an inhibitor discovered for SARS-CoV PLpro is an exciting first step toward therapeutic development. Here, a set of antiviral molecules were screened at the catalytic and S-binding allosteric sites of papain-like protease (PLpro). Molecular docking results suggested that five molecules (44560613, 136277567, S5652, SC75741, and S3833) had good binding affinities at both sites of PLpro. Molecular dynamics analysis like root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), and hydrogen bond results showed that identified molecules with PLpro tend to form stable PLpro-inhibitor(s) complexes. Molecular Mechanics/Position-Boltzmann Surface Area (MMPBSA) analysis confirmed that antiviral molecules bound PLpro complex had lower energy (-184.72 ± 7.81 to -215.67 ± 6.73 kJ/mol) complexes. Noticeably, computational approaches revealed promising antivirals candidates for PLpro, which may be further tested by biochemical and cell-based assays to assess their potential for SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

mRNA vaccines for COVID-19 and diverse diseases

Since its outbreak in late 2019, the novel coronavirus disease 2019 (COVID-19) has spread to every continent on the planet. The global pandemic has affected human health and socioeconomic status around the world. At first, the global response to the pandemic was to isolate afflicted individuals to prevent the virus from spreading, while vaccine development was ongoing. The genome sequence was first presented in early January 2020, and the phase I clinical trial of the vaccine started in March 2020 in the United States using novel lipid-based nanoparticle (LNP), encapsulated with mRNA termed as mRNA-1273. Till now, various mRNA-based vaccines are in development, while one mRNA-based vaccine got market approval from US-FDA for the prevention of COVID-19. Previously, mRNA-based vaccines were thought to be difficult to develop, but the current development is a significant accomplishment. However, widespread production and global availability of mRNA-based vaccinations to combat the COVID-19 pandemic remains a major challenge, especially when the mutations continually occur on the virus (e.g., the recent outbreaks of Omicron variant). This review elaborately discusses the COVID-19 pandemic, the biology of SARS-CoV-2 and the progress of mRNA-based vaccines. Moreover, the review also highlighted a detailed description of mRNA delivery technologies and the application potential in controlling other life-threatening diseases. Therefore, it provides a comprehensive view and multidisciplinary insights into mRNA therapy for broader audiences.

Plant Polysaccharides Modulate Immune Function via the Gut Microbiome and May Have Potential in COVID-19 Therapy

Plant polysaccharides can increase the number and variety of beneficial bacteria in the gut and produce a variety of active substances, including short-chain fatty acids (SCFAs). Gut microbes and their specific metabolites have the effects of promoting anti-inflammatory activity, enhancing the intestinal barrier, and activating and regulating immune cells, which are beneficial for improving immunity. A strong immune system reduces inflammation caused by external viruses and other pathogens. Coronavirus disease 2019 (COVID-19) is still spreading globally, and patients with COVID-19 often have intestinal disease and weakened immune systems. This article mainly evaluates how polysaccharides in plants can improve the immune system barrier by improving the intestinal microecological balance, which may have potential in the prevention and treatment of COVID-19.

Comparison of Allplex™ 2019-nCoV and TaqPath™ COVID-19 Assays

The clinical presentation of COVID-19 is non-specific, and to improve and limit the spread of the SARS-CoV-2 virus, an accurate diagnosis with a robust method is needed. A total of 500 nasopharyngeal swab specimens were tested for SARS-CoV-2. Of these, 184 samples were found to be positive with Allplex™ 2019-nCoV Assay, which is fully automated. All the positive samples were retested with TaqPath™ COVID-19 CE-IVD RT-PCR Kit (after this, referred to as TaqPath™ COVID-19), semi-automated. The comparison of RT-qPCR for SARS-CoV-2 genes target points shows only one target point in common, the N gene. Therefore, the N gene was used to compare both assays. We noticed different Ct values between the tests. Therefore, samples were divided into four groups depending to the Ct value results: (1) Ct < 25, (2) Ct 25–30, (3) Ct 30–35, (4) Ct > 35. TaqPath™ COVID-19 Kit reconfirmed the results obtained from Allplex™ 2019-nCoV Assay. In conclusion, both the Allplex™ 2019-nCoV assay and TaqPath™ COVID-19 tests accurately confirm the diagnosis of SARS-CoV-2 infection. Even if TaqPath™ COVID-19 has a semi-automated workflow, it does not introduce bias in the diagnostic screening of SARS-CoV-2, and it supports the indirect identification of variants of concern to undergo sequencing.

Water-sanitation-health nexus in the Indus-Ganga-Brahmaputra River Basin: need for wastewater surveillance of SARS-CoV-2 for preparedness during the future waves of pandemic

The Indus-Ganga-Brahmaputra River Basin (IGBRB) is a trans-boundary river basin flowing through four major countries in South Asia viz., India, Pakistan, Bangladesh, and Nepal. Contamination of surface water by untreated or inadequately treated wastewater has been a huge problem for pathogenic microorganisms in economies in transition. Recent studies have reported that sewage surveillance can provide prior information of the outbreak data, because faeces can contain the novel coronavirus (SARS-CoV-2) shed by infected humans. Hence, in this study we geo-spatially mapped the COVID-19 hotspots during the peak time in the first and second wave of pandemic to demonstrate the need and usefulness of wastewater surveillance strategy in IGBRB during ongoing pandemic. Further we discussed the status of sanitation, health and hand-hygiene in the IGBRB along with characterization of the challenges posed by the pandemic in achieving the United Nations Sustainable Development Goals (UN-SDGs). Monthly Geographical Information System (GIS) mapping of COVID-19 hotspots in the IGBRB showed an increase in the spread along the direct sewage discharge points. The social inequalities expose the vulnerabilities of the urban poor in terms of the burden, risks and access to Water, Sanitation, and Hygiene (WASH) needs. Such an evidence-based image of the actual SARS-CoV-2 viral load in the community along the IGBRB can provide valuable insights and recommendations to deal with the future waves of COVID-19 pandemic in this region that can go a long way in achieving the UN-SDGs.