SARS-CoV-2 and dengue virus co-infection: Epidemiology, pathogenesis, diagnosis, treatment, and management.

SARS-CoV-2 and dengue virus co-infection cases have been on the rise in dengue-endemic regions as coronavirus disease 2019 (COVID-19) spreads over the world, posing a threat of a co-epidemic. The risk of comorbidity in co-infection cases is greater than that of a single viral infection, which is a cause of concern. Although the pathophysiologies of the two infections are different, the viruses have comparable effects within the body, resulting in identical clinical symptoms in the case of co-infection, which adds to the complexity. Overlapping symptoms and laboratory features make proper differentiation of the infections important. However, specific biomarkers provide precise results that can be utilised to diagnose and treat a co-infection, whether it is simply COVID-19, dengue, or a co-infection. Though their treatment is distinguished, it becomes more complicated in circumstances of co-infection. As a result, regardless of whatever infection the first symptom points to, confirmation diagnosis of both COVID-19 and dengue should be mandatory, particularly in dengue-endemic regions, to prevent health deterioration in individuals treated for a single infection. There is still a scarcity of concise literature on the epidemiology, pathophysiology, diagnosis, therapy, and management of SARS-CoV-2 and dengue virus co-infection. The epidemiology of SARS-CoV-2 and dengue virus co-infection, the mechanism of pathogenesis, and the potential impact on patients are summarised in this review. The possible diagnosis with biomarkers, treatment, and management of the SARS-CoV-2 and dengue viruses are also discussed. This review will shed light on the appropriate diagnosis, treatment, and management of the patients suffering from SARS-CoV-2 and dengue virus co-infection.

3D Bioprinting for Regenerating COVID-19-Mediated Irreversibly Damaged Lung Tissue.

While the tension of COVID-19 is still increasing, patients who recovered from the infection are facing life-threatening consequences such as multiple organ failure due to the presence of angiotensin-converting enzyme 2 receptor in different organs. Among all the complications, death caused by respiratory failure is the most common because severe acute respiratory syndrome coronavirus 2 infects lung's type II epithelial, mucociliary, and goblet cells that eventually cause pneumonia and acute respiratory distress syndrome, which are responsible for the irreversible lung damage. Risk factors, such as age, comorbidities, diet, and lifestyle, are associated with disease severity. This paper reviews the potential of three-dimensional bioprinting in printing an efficient organ for replacement by evaluating the patient's condition.

Differential gene expression profiling reveals potential biomarkers and pharmacological compounds against SARS-CoV-2: Insights from machine learning and bioinformatics approaches.

The COVID-19 pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has created an urgent global situation. Therefore, it is necessary to identify the differentially expressed genes (DEGs) in COVID-19 patients to understand disease pathogenesis and the genetic factor(s) responsible for inter-individual variability and disease comorbidities. The pandemic continues to spread worldwide, despite intense efforts to develop multiple vaccines and therapeutic options against COVID-19. However, the precise role of SARS-CoV-2 in the pathophysiology of the nasopharyngeal tract (NT) is still unfathomable. This study utilized machine learning approaches to analyze 22 RNA-seq data from COVID-19 patients (n = 8), recovered individuals (n = 7), and healthy individuals (n = 7) to find disease-related differentially expressed genes (DEGs). We compared dysregulated DEGs to detect critical pathways and gene ontology (GO) connected to COVID-19 comorbidities. We found 1960 and 153 DEG signatures in COVID-19 patients and recovered individuals compared to healthy controls. In COVID-19 patients, the DEG-miRNA, and DEG-transcription factors (TFs) interactions network analysis revealed that E2F1, MAX, EGR1, YY1, and SRF were the highly expressed TFs, whereas hsa-miR-19b, hsa-miR-495, hsa-miR-340, hsa-miR-101, and hsa-miR-19a were the overexpressed miRNAs. Three chemical agents (Valproic Acid, Alfatoxin B1, and Cyclosporine) were abundant in COVID-19 patients and recovered individuals. Mental retardation, mental deficit, intellectual disability, muscle hypotonia, micrognathism, and cleft palate were the significant diseases associated with COVID-19 by sharing DEGs. Finally, the detected DEGs mediated by TFs and miRNA expression indicated that SARS-CoV-2 infection might contribute to various comorbidities. Our results provide the common DEGs between COVID-19 patients and recovered humans, which suggests some crucial insights into the complex interplay between COVID-19 progression and the recovery stage, and offer some suggestions on therapeutic target identification in COVID-19 caused by the SARS-CoV-2.

Coinfection of COVID-19 and Dengue: A Case Report

While the COVID-19 pandemic takes the world by storm, dengue-endemic regions risk developing a co-epidemic in COVID-19/dengue coinfection. With both infections as causes of high morbidity rates, the potentially fatal outcomes of coinfection are even greater, and several cases are emerging, severe and moderate, showing how common it may become in certain regions. The case reported here shows a 38-year-old male patient with high-grade fever, with complaints of nausea, joint, and muscle aches, all characteristic symptoms of COVID-19 and dengue. Initially suspected of being infected with COVID-19 only, the RT-PCR test of the nasopharyngeal swab confirmed COVID-19 infection, while the positive reactivity to IgG and IgM in the Dengue Duo test revealed a dengue coinfection. Except for the persistent high fever, the Patient's symptoms were not severe, although the tests confirmed the infections to be “moderate to severe” and showed steady and rapid recovery. The tests showed some interesting results, which provided additional research opportunities. Overall, this case report illustrates the existence of coinfections in the Philippines, demonstrating the difficulty in distinguishing the two infections and the need for proper diagnosis, prevention, and management measures.

The Deltacron conundrum: Its origin and potential health risks.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), since its outbreak in December 2019, has been capable of continuing the pandemic by mutating itself into different variants. Mass vaccinations, antibiotic treatment therapy, herd immunity, and preventive measures have reduced the disease's severity from the emerging variants. However, the virus is undergoing recombination among the current two variants: Delta and Omicron, resulting in a new variant, informally known as "Deltacron," which was controversial as it might be a product of lab contamination between Omicron and Delta samples. However, the proclamation was proved wrong, and the experts are putting more effort into better understanding the variant's epidemiological characteristics to control potential outbreaks. This review has discussed the potential mutations in the novel variant and prospective risk factors and therapeutic options in the context of this new variant. This study could be used as a guide for implementing appropriate controls in a sudden outbreak of this new variant.

Immunoinformatic Design of a Multivalent Peptide Vaccine Against Mucormycosis: Targeting FTR1 Protein of Major Causative Fungi.

Mucormycosis is a potentially fatal illness that arises in immunocompromised people due to diabetic ketoacidosis, neutropenia, organ transplantation, and elevated serum levels of accessible iron. The sudden spread of mucormycosis in COVID-19 patients engendered massive concern worldwide. Comorbidities including diabetes, cancer, steroid-based medications, long-term ventilation, and increased ferritin serum concentration in COVID-19 patients trigger favorable fungi growth that in turn effectuate mucormycosis. The necessity of FTR1 gene-encoded ferrous permease for host iron acquisition by fungi has been found in different studies recently. Thus, targeting the transit component could be a potential solution. Unfortunately, no appropriate antifungal vaccine has been constructed as of yet. To date, mucormycosis has been treated with antiviral therapy and surgical treatment only. Thus, in this study, the FTR1 protein has been targeted to design a convenient and novel epitope-based vaccine with the help of immunoinformatics against four different virulent fungal species. Furthermore, the vaccine was constructed using 8 CTL, 2 HTL, and 1 LBL epitopes that were found to be highly antigenic, non-allergenic, non-toxic, and fully conserved among the fungi under consideration. The vaccine has very reassuring stability due to its high pI value of 9.97, conclusive of a basic range. The vaccine was then subjected to molecular docking, molecular dynamics, and immune simulation studies to confirm the biological environment's safety, efficacy, and stability. The vaccine constructs were found to be safe in addition to being effective. Finally, we used in-silico cloning to develop an effective strategy for vaccine mass production. The designed vaccine will be a potential therapeutic not only to control mucormycosis in COVID-19 patients but also be effective in general mucormycosis events. However, further in vitro, and in vivo testing is needed to confirm the vaccine's safety and efficacy in controlling fungal infections. If successful, this vaccine could provide a low-cost and effective method of preventing the spread of mucormycosis worldwide.

Insights from a computational analysis of the SARS-CoV-2 Omicron variant: Host-pathogen interaction, pathogenicity, and possible drug therapeutics.

INTRODUCTION: Prominently accountable for the upsurge of COVID-19 cases as the world attempts to recover from the previous two waves, Omicron has further threatened the conventional therapeutic approaches. The lack of extensive research regarding Omicron has raised the need to establish correlations to understand this variant by structural comparisons. Here, we evaluate, correlate, and compare its genomic sequences through an immunoinformatic approach to understand its epidemiological characteristics and responses to existing drugs. METHODS: We reconstructed the phylogenetic tree and compared the mutational spectrum. We analyzed the mutations that occurred in the Omicron variant and correlated how these mutations affect infectivity and pathogenicity. Then, we studied how mutations in the receptor-binding domain affect its interaction with host factors through molecular docking. Finally, we evaluated the drug efficacy against the main protease of the Omicron through molecular docking and validated the docking results with molecular dynamics simulation. RESULTS: Phylogenetic and mutational analysis revealed the Omicron variant is similar to the highly infectious B.1.620 variant, while mutations within the prominent proteins are hypothesized to alter its pathogenicity. Moreover, docking evaluations revealed significant differences in binding affinity with human receptors, angiotensin-converting enzyme 2 and NRP1. Surprisingly, most of the tested drugs were proven to be effective. Nirmatrelvir, 13b, and Lopinavir displayed increased effectiveness against Omicron. CONCLUSION: Omicron variant may be originated from the highly infectious B.1.620 variant, while it was less pathogenic due to the mutations in the prominent proteins. Nirmatrelvir, 13b, and Lopinavir would be the most effective, compared to other promising drugs that were proven effective.

Omicron variant of SARS-CoV-2: Genomics, transmissibility, and responses to current COVID-19 vaccines.

Currently, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide as an Omicron variant. This variant is a heavily mutated virus and designated as a variant of concern by the World Health Organization (WHO). WHO cautioned that the Omicron variant of SARS-CoV-2 held a very high risk of infection, reigniting anxieties about the economy's recovery from the 2-year pandemic. The extensively mutated Omicron variant is likely to spread internationally, posing a high risk of infection surges with serious repercussions in some areas. According to preliminary data, the Omicron variant of SARS-CoV-2 has a higher risk of reinfection. On the other hand, whether the current COVID-19 vaccines could effectively resist the new strain is still under investigation. However, there is very limited information on the current situation of the Omicron variant, such as genomics, transmissibility, efficacy of vaccines, treatment, and management. This review focused on the genomics, transmission, and effectiveness of vaccines against the Omicron variant, which will be helpful for further investigation of a new variant of SARS-CoV-2.

COVID-19-Associated Candidiasis: Possible Patho-Mechanism, Predisposing Factors, and Prevention Strategies.

The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is threatening public health. A large number of affected people need to be hospitalized. Immunocompromised patients and ICU-admitted patients are predisposed to further bacterial and fungal infections, making patient outcomes more critical. Among them, COVID-19-associated candidiasis is becoming more widely recognized as a part of severe COVID-19 sequelae. While the molecular pathophysiology is not fully understood, some factors, including a compromised immune system, iron and zinc deficiencies, and nosocomial and iatrogenic transmissions, predispose COVID-19 patients to candidiasis. In this review, we discuss the existing knowledge of the virulence characteristics of Candida spp. and summarize the key concepts in the possible molecular pathogenesis. We analyze the predisposing factors that make COVID-19 patients more susceptible to candidiasis and the preventive measures which will provide valuable insights to guide the effective prevention of candidiasis in COVID-19 patients.

Functional food: complementary to fight against COVID-19

Background The novel coronavirus has embarked on a global pandemic and severe mortality with limited access for its treatments and medications. For the lack of time, research, and enough efficacy, most vaccines are underdeveloped or unreachable to society. However, many recent studies suggest various alternative, complementary remedies for COVID-19, which are functional foods. This review provides an overview of how functional foods can play a great role through modulating the host immune system, generating antiviral activities, and synthesizing biologically active agents effective against the coronavirus. Main body This review article summarizes the natural defense mechanisms in tackling SARS-CoV-2 alongside conventional therapeutic options and their corresponding harmful side effects. By analyzing bioactive components of functional foods, we have outlined its different contributions to human health and its potential immunomodulatory and antiviral properties that can enhance resistivity to viral infection. Moreover, we have provided a myriad of accessible and cost-effective functional foods that could be further investigated to target specific key symptoms of COVID-19 infections. Finally, we have found various functional foods with potent bioactive compounds that can inhibit or prevent COVID-19 infections and disease progression. Short conclusion Numerous functional foods can help the body fight COVID-19 through several mechanisms such as the reduced release of pro-inflammatory cytokines, reduced expression of ACE2 receptors in cells, and inhibiting essential enzymes in SARS-CoV-2.

Management of asthma patients during the COVID-19 pandemic: pathophysiological considerations to address the challenges.

BACKGROUND: The coronavirus disease 2019 (COVID-19) has become a serious global health issue, especially for people with pre-existing health conditions. Patients dealing with asthma are presumed to be at higher risk as COVID-19 may cause severe respiratory distress. MAIN BODY: From the initial stage of the pandemic, several clinical trials and studies have assessed the association between COVID-19 and asthma; however, no significant association was reported. This may be due to the fact that most of the asthma cases remained undiagnosed and overlapping respiratory features make it difficult to differentiate between these two diseases. The pathomechanism of the conditions and the immune response generated in response to the conditions suggest that the presence of any of the conditions is very likely to influence the presence or severity of the other condition. So far, no specific treatments are known for COVID-19; however, the use of plasma therapy and broad-spectrum antiviral drugs during the initial phase of the pandemic and widespread vaccination during the latter phase has given positive outcomes in reducing COVID-19 cases as well as disease severity. SHORT CONCLUSION: Taking asthma as an increased risk factor for COVID-19 morbidity, this article aims to provide comprehensive insights into the risk and proper management of asthma patients during this COVID-19 pandemic. The common medications of asthma patients suppress their respiratory immune response that might facilitate cytokine storm in COVID-19 patients. Similarly, there are risks of viral-induced asthma exacerbations. Besides, different social issues such as shortage of medicines, SDOH, and delayed clinical trials put asthma patients through inconvenience. The primary focus at this point should be to reduce probable asthma attacks and severity to prevent hospitalization of asthma patients. Moreover, for better management of asthma patients maintaining an asthma action plan and healthy lifestyle, ensuring a nutritious diet, and developing self-management interventions can play a crucial role.

Influence on attitudes and lifestyle due to lockdown amidst COVID-19 pandemic: a perception-based analysis among Bangladeshi residents.

BACKGROUND: Countrywide lockdown or stay-at-home order has been implemented to slow down the transmission of emergent coronavirus. However, the influence on attitudes and lifestyle due to lockdown amidst the coronavirus disease 2019 (COVID-19) pandemic has been poorly understood. The present study aimed to investigate the influence on attitudes and lifestyle due to lockdown amidst the COVID-19 pandemic among Bangladeshi residents. METHODS: A cross-sectional survey carried out involving 1635 community dwellers across eight divisions in Bangladesh conducted from April 15, 2020 to May 10, 2020. A structured questionnaire incorporating socio-demographic, attitudes towards lockdown and adverse lifestyle amidst lockdown measures was employed to collect data using the Google Forms. Multiple regression analyses were executed to determine the associated factors of positive attitudes towards lockdown and adverse lifestyle. RESULTS: The mean scores of attitudes towards lockdown were 67.9 (SD = 8.4) out of 85 with an overall correct rate (positive attitudes) of 79.9%; whereas the mean scores of adverse lifestyle amidst lockdown were 16.1 (SD = 4.8) out of 34 with an overall rate of 47.4%. The factors associated with more positive attitudes towards lockdown included being female, divorced, higher educated, and students. Conversely, being male, having no formal education, and rural residence were associated factors of adverse lifestyle amidst the COVID-19 pandemic. CONCLUSIONS: The findings reflect how the COVID-19 lockdown has preciously impacted the attitudes, and lifestyle of Bangladeshi citizens, which will contribute to promoting appropriate measures during a subsequent zonal or complete lockdown.

COVID-19-associated-mucormycosis: possible role of free iron uptake and immunosuppression.

COVID-19-associated-mucormycosis, commonly referred to as the "Black Fungus," is a rare secondary fungal infection in COVID-19 patients prompted by a group of mucor molds. Association of this rare fungal infection with SARS-CoV-2 infection has been declared as an endemic in India, with minor cases in several other countries around the globe. Although the fungal infection is not contagious like the viral infection, the causative fungal agent is omnipresent. Infection displays an overall mortality rate of around 50%, with many other secondary side effects posing a potential threat in exacerbating COVID-19 mortality rates. In this review, we have accessed the role of free iron availability in COVID-19 patients that might correlate to the pathogenesis of the causative fungal agent. Besides, we have analyzed the negative consequences of using immunosuppressive drugs in encouraging this opportunistic fungal infection.

Corticosteroids for COVID-19: worth it or not?

Pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induced COVID-19 implied the presence of excessive proinflammatory cytokines and chemokines in patients causing significant morbidity and mortality. To diminish systemic hyper inflammation, a few physicians and researchers have utilized corticosteroids. Corticosteroid implementation has increased after the publication of interim guidelines regarding corticosteroid use in COVID-19 patients by WHO, despite the remaining controversies regarding long-term side effects and disease progression capability of corticosteroids. In different studies, the implementation of corticosteroids on COVID-19 patients revealed controversial results, which require further intensive research. This review will present the current outcomes and possibilities of using corticosteroids to treat COVID-19 patients.

Prospect of 3D bioprinting over cardiac cell therapy and conventional tissue engineering in the treatment of COVID-19 patients with myocardial injury.

Due to multiple mutations of SARS-CoV-2, the mystery of defeating the virus is still unknown. Cardiovascular complications are one of the most concerning effects of COVID-19 recently, originating from direct and indirect mechanisms. These complications are associated with long-term Cardio-vascular diseases and can induce sudden cardiac death in both infected and recovered COVID-19 patients. The purpose of this research is to do a competitive analysis between conventional techniques with the upgraded alternative 3D bioprinting to replace the damaged portion of the myocardium. Additionally, this study focuses on the potential of 3D bioprinting to be a novel alternative. Finally, current challenges and future perspective of 3D bioprinting technique is briefly discussed.

Prospective selected biomarkers in COVID-19 diagnosis and treatment.

COVID-19 has become a global health concern, due to the high transmissible nature of its causal agent and lack of proper treatment. Early diagnosis and nonspecific medical supports of the patients appeared to be effective strategy so far to combat the pandemic caused by COVID-19 outbreak. Biomarkers can play pivotal roles in timely and proper diagnosis of COVID-19 patients, as well as for distinguishing them from other pulmonary infections. Besides, biomarkers can help in reducing the rate of mortality and evaluating viral pathogenesis with disease prognosis. This article intends to provide a broader overview of the roles and uses of different biomarkers in the early diagnosis of COVID-19, as well as in the classification of COVID-19 patients into multiple risk groups.

Genome Sequences of Two Novel Coronavirus (SARS-CoV-2) Isolates from Dhaka, Bangladesh.

This study reports the genome sequences of two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains detected in the nasopharyngeal swab specimens of two coronavirus disease 2019 (COVID-19) patients from Dhaka, Bangladesh.

Silent hypoxia in COVID-19: pathomechanism and possible management strategy.

The novel coronavirus disease 2019 (COVID-19) has become a severe health issue, especially to the patients who develop silent hypoxia condition after SARS-CoV-2 infection. Due to the lack of dyspnoea and extremely low oxygen saturation level, these patients are at exceptionally higher risk. Although the prevalence of silent hypoxia in COVID-19 patients has been evident in several cases, the underlying pathomechanism behind this condition is still unclear. Silent hypoxia in SARS-CoV-2 infected patients can be diagnosed with the help of a pulse oximeter, blood gas levels, and a 6-min walking test. While the clinicians and researchers figure out the exact reason for this phenomenon, the patients must be under strict day-to-day monitoring. In this article, we aim to provide comprehensive insights into the underlying symptoms, mechanism, and possible factors behind the occurrence of silent hypoxia among COVID-19 patients.

Choice of assemblers has a critical impact on de novo assembly of SARS-CoV-2 genome and characterizing variants.

BACKGROUND: Coronavirus Disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a global pandemic following its initial emergence in China. SARS-CoV-2 has a positive-sense single-stranded RNA virus genome of around 30Kb. Using next-generation sequencing technologies, a large number of SARS-CoV-2 genomes are being sequenced at an unprecedented rate and being deposited in public repositories. For the de novo assembly of the SARS-CoV-2 genomes, a myriad of assemblers is being used, although their impact on the assembly quality has not been characterized for this virus. In this study, we aim to understand the variabilities on assembly qualities due to the choice of the assemblers. RESULTS: We performed 6648 de novo assemblies of 416 SARS-CoV-2 samples using eight different assemblers with different k-mer lengths. We used Illumina paired-end sequencing reads and compared the assembly quality of those assemblers. We showed that the choice of assembler plays a significant role in reconstructing the SARS-CoV-2 genome. Two metagenomic assemblers, e.g. MEGAHIT and metaSPAdes, performed better compared with others in most of the assembly quality metrics including, recovery of a larger fraction of the genome, constructing larger contigs and higher N50, NA50 values, etc. We showed that at least 09% (259/2873) of the variants present in the assemblies between MEGAHIT and metaSPAdes are unique to one of the assembly methods. CONCLUSION: Our analyses indicate the critical role of assembly methods for assembling SARS-CoV-2 genome using short reads and their impact on variant characterization. This study could help guide future studies to determine the best-suited assembler for the de novo assembly of virus genomes.

Immunoinformatics-guided designing and in silico analysis of epitope-based polyvalent vaccines against multiple strains of human coronavirus (HCoV).

OBJECTIVES: The group of human coronaviruses (HCoVs) consists of some highly pathogenic viruses that have caused several outbreaks in the past. The newly emerged strain of HCoV, the SARS-CoV-2 is responsible for the recent global pandemic that has already caused the death of hundreds of thousands of people due to the lack of effective therapeutic options. METHODS: In this study, immunoinformatics methods were used to design epitope-based polyvalent vaccines which are expected to be effective against four different pathogenic strains of HCoV i.e., HCoV-OC43, HCoV-SARS, HCoV-MERS, and SARS-CoV-2. RESULTS: The constructed vaccines consist of highly antigenic, non-allergenic, nontoxic, conserved, and non-homologous T-cell and B-cell epitopes from all the four viral strains. Therefore, they should be able to provide strong protection against all these strains. Protein-protein docking was performed to predict the best vaccine construct. Later, the MD simulation and immune simulation of the best vaccine construct also predicted satisfactory results. Finally, in silico cloning was performed to develop a mass production strategy of the vaccine. CONCLUSION: If satisfactory results are achieved in further in vivo and in vitro studies, then the vaccines designed in this study might be effective as preventative measures against the selected HCoV strains.