Coronavirus pathogenesis

The Structure of the Porcine Deltacoronavirus Main Protease Reveals a Conserved Target for the Design of Antivirals

The existing zoonotic coronaviruses (CoVs) and viral genetic variants are important microbiological pathogens that cause severe disease in humans and animals. Currently, no effective broad-spectrum antiviral drugs against existing and emerging CoVs are available. The CoV main protease (M^pro) plays an essential role in viral replication, making it an ideal target for drug development. However, the structure of the Deltacoronavirus M^pro is still unavailable. Porcine deltacoronavirus (PDCoV) is a novel CoV that belongs to the genus Deltacoronavirus and causes atrophic enteritis, severe diarrhea, vomiting and dehydration in pigs. Here, we determined the structure of PDCoV M^pro complexed with a Michael acceptor inhibitor. Structural comparison showed that the backbone of PDCoV M^pro is similar to those of alpha-, beta- and gamma-CoV M^pros. The substrate-binding pocket of M^pro is well conserved in the subfamily Coronavirinae. In addition, we also observed that M^pros from the same genus adopted a similar conformation. Furthermore, the structure of PDCoV M^pro in complex with a Michael acceptor inhibitor revealed the mechanism of its inhibition of PDCoV M^pro. Our results provide a basis for the development of broad-spectrum antivirals against PDCoV and other CoVs.

Cannabidiol inhibits SARS-CoV-2 replication through induction of the host ER stress and innate immune responses

The spread of SARS-CoV-2 and ongoing COVID-19 pandemic underscores the need for new treatments. Here we report that cannabidiol (CBD) inhibits infection of SARS-CoV-2 in cells and mice. CBD and its metabolite 7-OH-CBD, but not THC or other congeneric cannabinoids tested, potently block SARS-CoV-2 replication in lung epithelial cells. CBD acts after viral entry, inhibiting viral gene expression and reversing many effects of SARS-CoV-2 on host gene transcription. CBD inhibits SARS-CoV-2 replication in part by up-regulating the host IRE1α RNase endoplasmic reticulum (ER) stress response and interferon signaling pathways. In matched groups of human patients from the National COVID Cohort Collaborative, CBD (100 mg/ml oral solution per medical records) had a significant negative association with positive SARS-CoV-2 tests. This study highlights CBD as a potential preventative agent for early-stage SARS-CoV-2 infection and merits future clinical trials. We caution against use of non-medical formulations including edibles, inhalants or topicals as a preventative or treatment therapy at the present time.

True or False: What are the factors that influence COVID-19 diagnosis by RT-qPCR?

Introduction

The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease has had a catastrophic impact on the world resulting in several deaths. Since World Health Organization declared the pandemic status of the disease, several molecular diagnostic kits have been developed to help the tracking of viruses spread.

Areas Covered

This review aims to describe and evaluate the currently reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) diagnosis kit. Several processes used in COVID-19 diagnostic procedures are detailed in further depth to demonstrate optimal practices. Therefore, we debate the main factors that influence the viral detection of SARS-COV-2 and how they can affect the diagnosis of patients.

Expert Opinion

Here is highlighted and discussed several factors that can interfere in the RT-PCR analysis, such as the viral load of the sample, collection site, collection methodology, sample storage, transport, primer, and probe mismatch/dimerization in different brand kits. This is a pioneer study to discuss the factor that could lead to the wrong interpretation of RT-qPCR diagnosis of SARS-CoV-2. This study aimed to help the readers to understand what very likely is behind a bad result of SARS-CoV-2 detection by RT-PCR and what could be done to reach a reliable diagnosis.

Evidence of Microglial Immune Response Following Coronavirus PHEV Infection of CNS

Porcine hemagglutinating encephalomyelitis virus (PHEV) is a highly neurotropic coronavirus that invades the host central nervous system (CNS) and causes neurological dysfunction. Microglia are key immune cells in the CNS, however, whether and how they response to PHEV infection remains unclear. Herein, microglial activation and proliferation were detected in the CNS of PHEV-infected mice, as along with the proinflammatory response. Moreover, the production of proinflammatory cytokines induced by moderately activated microglia limited viral replication in the early stage of infection. Microglial depletion assays showed that during late infection, excess activation of microglia aggravated neurological symptoms, BBB destruction, and peripheral monocyte/macrophage infiltration into the CNS. Using an in vitro brain slice model, PHEV was identified to specifically and moderately induce microglial activation in the absence of peripheral immune cells infiltration. Consistently, macrophage clearance from circulating blood indicated that peripheral monocytes/macrophages crossing the BBB of mice were responsible for excess activation of microglia and CNS damage in late PHEV infection. Overall, our findings provide evidence supporting a dual role for microglia in the host CNS in response to coronavirus PHEV invasion.

Assessment of myocardial performance index in patients with COVID-19: An echocardiographic follow-up study

Introduction and Objectives

Myocardial performance may be impaired in cytokine-mediated immune reactions. The myocardial performance index (MPI) is a practical parameter that reflects systolic and diastolic cardiac function. We aimed to assess the MPI in patients with COVID-19.

Methods

The study population consisted of 40 healthy controls and 40 patients diagnosed with COVID-19 who had mild pneumonia and did not need intensive care treatment. All participants underwent echocardiographic examination. First, the MPI and laboratory parameters were compared between healthy controls and patients in the acute period of infection. Second, the MPI and laboratory parameters were compared between the acute infection period and after clinical recovery.

Results

Compared with healthy controls, patients with COVID-19 had a significantly higher MPI (0.56±0.09 vs. 0.41±0.06, p<0.001), longer isovolumic relaxation time (IRT) (112.3±13.4 vs. 90.6±11.2 ms, p<0.001), longer deceleration time (DT) (182.1±30.6 vs. 160.8±42.7 ms, p=0.003), shorter ejection time (ET) (279.6±20.3 vs. 299.6±34.7 ms, p<0.001) and higher E/A ratio (1.53±0.7 vs. 1.21±0.3, p<0.001). Statistically significantly higher MPI (0.56±0.09 vs. 0.44±0.07, p<0.001), longer IRT (112.3±13.4 vs. 91.8±12.1 ms, p<0.001), longer DT (182.1±30.6 vs. 161.5±43.5 ms, p=0.003), shorter ET 279.6±20.3 vs. 298.8±36.8 ms, p<0.001) and higher E/A ratio (1.53±0.7 vs. 1.22±0.4, p<0.001) were observed during the acute infection period than after clinical recovery. Left ventricular ejection fraction was similar in the controls, during the acute infection period and after clinical recovery.

Conclusions

Subclinical diastolic impairment without systolic involvement may be observed in patients with COVID-19. This impairment may be reversible on clinical recovery.

SARS-CoV-2 infection triggers paracrine senescence and leads to a sustained senescence-associated inflammatory response

Reports of post-acute COVID-19 syndrome, in which the inflammatory response persists even after SARS-CoV-2 has disappeared, are increasing¹, but the underlying mechanisms of post-acute COVID-19 syndrome remain unknown. Here, we show that SARS-CoV-2-infected cells trigger senescence-like cell-cycle arrest^2,3 in neighboring uninfected cells in a paracrine manner via virus-induced cytokine production. In cultured human cells or bronchial organoids, these SASR-CoV-2 infection-induced senescent cells express high levels of a series of inflammatory factors known as senescence-associated secretory phenotypes (SASPs)⁴ in a sustained manner, even after SARS-CoV-2 is no longer detectable. We also show that the expression of the senescence marker CDKN2A (refs. ^5,6) and various SASP factor⁴ genes is increased in the pulmonary cells of patients with severe post-acute COVID-19 syndrome. Furthermore, we find that mice exposed to a mouse-adapted strain of SARS-CoV-2 exhibit prolonged signs of cellular senescence and SASP in the lung at 14 days after infection when the virus was undetectable, which could be substantially reduced by the administration of senolytic drugs⁷. The sustained infection-induced paracrine senescence described here may be involved in the long-term inflammation caused by SARS-CoV-2 infection.

Investigating the Transmission Dynamics of SARS-CoV-2 in Nigeria: A SEIR Modelling Approach

This study was designed to investigate the transmission dynamics of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to inform policy advisory vital for managing the spread of the virus in Nigeria. We applied the Susceptible-Exposed-Infectious-Recovered (SEIR)-type predictive model to discern the transmission dynamics of SARS-CoV-2 at different stages of the pandemic; incidence, during and after the lockdown from 27th March 2020 to 22nd September 2020 in Nigeria. Our model was calibrated with the COVID-19 data (obtained from the Nigeria Centre for Disease Control) using the “lsqcurvefit” package in MATLAB to fit the “cumulative active cases” and “cumulative death” data. We adopted the Latin hypercube sampling with a partial rank correlation coefficient index to determine the measure of uncertainty in our parameter estimation at a 99% confidence interval (CI). At the incidence of SARS-CoV-2 in Nigeria, the basic reproduction number (R₀) was 6.860; 99%CI [6.003, 7.882]. R₀ decreased by half (3.566; 99%CI [3.503, 3.613]) during the lockdown, and R₀ was 1.238; 99%CI [1.215, 1.262] after easing the lockdown. If all parameters are maintained (as in after easing the lockdown), our model forecasted a gradual and perpetual surge through the next 12 months or more. In the light of our results and available data, evidence of human-to-human transmission at higher rates is still very likely. A timely, proactive, and well-articulated effort should help mitigate the transmission of SARS-CoV-2 in Nigeria.

Host E3 ligase HUWE1 attenuates the proapoptotic activity of the MERS-CoV accessory protein ORF3 by promoting its ubiquitin-dependent degradation

With the outbreak of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), coronaviruses have begun to attract great attention across the world. Of the known human coronaviruses, however, Middle East respiratory syndrome coronavirus (MERS-CoV) is the most lethal. Coronavirus proteins can be divided into three groups: nonstructural proteins, structural proteins, and accessory proteins. While the number of each of these proteins varies greatly among different coronaviruses, accessory proteins are most closely related to the pathogenicity of the virus. We found for the first time that the ORF3 accessory protein of MERS-CoV, which closely resembles the ORF3a proteins of severe acute respiratory syndrome coronavirus and SARS-CoV-2, has the ability to induce apoptosis in cells in a dose-dependent manner. Through bioinformatics analysis and validation, we revealed that ORF3 is an unstable protein and has a shorter half-life in cells compared to that of severe acute respiratory syndrome coronavirus and SARS-CoV-2 ORF3a proteins. After screening, we identified a host E3 ligase, HUWE1, that specifically induces MERS-CoV ORF3 protein ubiquitination and degradation through the ubiquitin-proteasome system. This results in the diminished ability of ORF3 to induce apoptosis, which might partially explain the lower spread of MERS-CoV compared to other coronaviruses. In summary, this study reveals a pathological function of MERS-CoV ORF3 protein and identifies a potential host antiviral protein, HUWE1, with an ability to antagonize MERS-CoV pathogenesis by inducing ORF3 degradation, thus enriching our knowledge of the pathogenesis of MERS-CoV and suggesting new targets and strategies for clinical development of drugs for MERS-CoV treatment.

Basic reproduction numbers of three strains of mouse hepatitis viruses in mice

Mouse hepatitis virus (MHV) is a murine coronavirus and one of the most important pathogens in laboratory mice. Although various strains of MHV have been isolated, they are generally excreted in the feces and transmitted oronasally via aerosols and contaminated bedding. In this study, we attempted to determine the basic reproduction numbers (R₀) of three strains of MHV to improve our understanding of MHV infections in mice. Five‐week‐old female C57BL/6J mice were inoculated intranasally with either the Y, NuU, or JHM variant strain of MHV and housed with two naïve mice. After 4 weeks, the presence or absence of anti‐MHV antibody in the mice was determined by ELISA. We also examined the distribution of MHV in the organs of Y, NuU, or JHM variant‐infected mice. Our data suggest that the transmissibility of MHV is correlated with viral growth in the gastrointestinal tract of infected mice. To the best of our knowledge, this is the first report to address the basic reproduction numbers among pathogens in laboratory animals.

COVIDXception-Net: A Bayesian Optimization-Based Deep Learning Approach to Diagnose COVID-19 from X-Ray Images

COVID-19 is spreading around the world like wildfire. Chest X-rays are used as one of the primary tools for diagnosing COVID-19. However, about two-thirds of the world population do not have access to sufficient radiological services. In this work, we propose a deep learning-driven automated system, COVIDXception-Net, for diagnosing COVID-19 from chest X-rays. A primary challenge in any data-driven COVID-19 detection is the scarcity of COVID-19 data, which heavily deteriorates a deep learning model’s performance. To address this issue, we incorporate a weighted-loss function that ensures the COVID-19 cases are given more importance during the training process. We also propose using Bayesian Optimization to find the best architecture for detecting COVID-19. Extensive experimentation on four publicly available COVID-19 datasets shows that our proposed model achieves an accuracy of 0.94, precision 0.95, recall 0.94, specificity 0.997, F1-score 0.94, and Matthews correlation coefficient 0.992 outperforming three widely used architectures—VGG16, MobileNetV2, and InceptionV3. It also surpasses the performance of several state-of-the-art COVID-19 detection methods. We also performed two ablation studies that show our model’s accuracy degrades from 0.994 to 0.950 when a random search is used and to 0.983 when a regular loss function is employed instead of the Bayesian and weighted loss, respectively.

Molecular Characterization of Infectious Bronchitis Virus Strain HH06 Isolated in a Poultry Farm in Northeastern China

Spike (S) glycoprotein is an important virulent factor for coronaviruses (CoVs), and variants of CoVs have been characterized based on S gene analysis. We present phylogenetic relationship of an isolated infectious bronchitis virus (IBV) strain with reference to the available genome and protein sequences based on network, multiple sequence, selection pressure, and evolutionary fingerprinting analysis in People's Republic of China. One hundred and elven strains of CoVs i.e., Alphacoronaviruses (Alpha-CoVs; n = 12), Betacoronaviruses (Beta-CoVs; n = 37), Gammacoronaviruses (Gamma-CoVs; n = 46), and Deltacoronaviruses (Delta-CoVs; n = 16) were selected for this purpose. Phylogenetically, SARS-CoV-2 and SARS-CoVs clustered together with Bat-CoVs and MERS-CoV of Beta-CoVs (C). The IBV HH06 of Avian-CoVs was closely related to Duck-CoV and partridge S14, LDT3 (teal and chicken host). Beluga whale-CoV (SW1) and Bottlenose dolphin-CoVs of mammalian origin branched distantly from other animal origin viruses, however, making group with Avian-CoVs altogether into Gamma-CoVs. The motif analysis indicated well-conserved domains on S protein, which were similar within the same phylogenetic class and but variable at different domains of different origins. Recombination network tree indicated SARS-CoV-2, SARS-CoV, and Bat-CoVs, although branched differently, shared common clades. The MERS-CoVs of camel and human origin spread branched into a different clade, however, was closely associated closely with SARS-CoV-2, SARS-CoV, and Bat-CoVs. Whereas, HCoV-OC43 has human origin and branched together with bovine CoVs with but significant distant from other CoVs like SARS CoV-2 and SARS-CoV of human origin. These findings explain that CoVs' constant genetic recombination and evolutionary process that might maintain them as a potential veterinary and human epidemic threat.

Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study

The spike protein of SARS-CoV-2 and the host ACE2 receptor plays a vital role in the entry to the cell. Among which the hotspot residue 501 is continuously subjected to positive selection pressure and induces unusual virulence. Keeping in view the importance of the hot spot residue 501, we predicted the potentially emerging structural variants of 501 residue. We analyzed the binding pattern of wild type and mutants (Spike RBD) to the ACE2 receptor by deciphering variations in the amino acids’ interaction networks by graph kernels along with evolutionary, network metrics, and energetic information. Our analysis revealed that N501I, N501T, and N501V increase the binding affinity and alter the intra and inter-residue bonding networks. The N501T has shown strong positive selection and fitness in other animals. Docking results and repeated simulations (three times) confirmed the structural stability and tighter binding of these three variants, correlated with the previous results following the global stability trend. Consequently, we reported three variants N501I, N501T, and N501V could worsen the situation further if they emerged. The relations between the viral fitness and binding affinity is a complicated game thus the emergence of high affinity mutations in the SARS-CoV-2 RBD brings up the question of whether or not positive selection favours these mutations or not?

COVID-19 classification in X-ray chest images using a new convolutional neural network: CNN-COVID

Purpose

COVID-19 causes lung inflammation and lesions, and chest X-ray and computed tomography images are remarkably suitable for differentiating the new disease from patients with other lung diseases. In this paper, we propose a computer model to classify X-ray images of patients diagnosed with COVID-19. Chest X-ray exams were chosen over computed tomography scans because they are low cost, results are quickly obtained, and X-ray equipment is readily available.

Methods

A new CNN network, called CNN-COVID, has been developed to classify X-ray patient’s images. Images from two different datasets were used. The images of Dataset I is originated from the COVID-19 image data collection and the ChestXray14 repository, and the images of Dataset II belong to the BIMCV COVID-19+ repository. To assess the accuracy of the network, 10 training and testing sessions were performed in both datasets. A confusion matrix was generated to evaluate the model’s performance and calculate the following metrics: accuracy (ACC), sensitivity (SE), and specificity (SP). In addition, Receiver Operating Characteristic (ROC) curves and Areas Under the Curve (AUCs) were also considered.

Results

After running 10 tests, the average accuracy for Dataset I and Dataset II was 0.9787 and 0.9839, respectively. Since the weights of the best test results were applied in the validation, it was obtained the accuracy of 0.9722 for Dataset I and 0.9884 for Dataset II.

Conclusions

The results showed that the CNN-COVID is a promising tool to help physicians classify chest images with pneumonia, considering pneumonia caused by COVID-19 and pneumonia due to other causes.

Aseptic Meningitis Following Second Dose of an mRNA Coronavirus Disease 2019 Vaccine in a Healthy Male: Case Report and Literature Review

Vaccines are one of the most important strategies against pandemics or epidemics involving infectious diseases. With the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there have been global efforts for rapid development of coronavirus disease 2019 (COVID-19) vaccine and vaccination is being performed globally on a massive scale. With rapid increase in vaccination, rare adverse events have been reported. Well-known neurological adverse events associated with COVID-19 vaccination include Guillain–Barré syndrome, myelitis, and encephalitis. However, COVID-19 vaccine-related aseptic meningitis has rarely been reported. A 32-year-old healthy man visited our hospital with a complaint of headache for 1 week. He had received the second dose of the BNT162b2 mRNA COVID-19 vaccine 2 weeks before the onset of headache. Since the initial cerebrospinal fluid (CSF) profile suggested viral meningitis, we started treatment with an antiviral agent. However, the symptoms and follow-up CSF profile on day 7 of hospitalization showed no improvement and SARS-CoV-2 IgG antibodies were detected in the CSF. We suspected aseptic meningitis associated with the vaccination and intravenous methylprednisolone (500 mg/day) was administered for 3 days. The symptoms improved and the patient was discharged on day 12 of hospitalization.

Implications of testicular ACE2 and the renin-angiotensin system for SARS-CoV-2 on testis function

Although many studies have focused on SARS-CoV-2 infection in the lungs, comparatively little is known about the potential effects of the virus on male fertility. SARS-CoV-2 infection of target cells requires the presence of furin, angiotensin-converting enzyme 2 (ACE2) receptors, and transmembrane protease serine 2 (TMPRSS2). Thus, cells in the body that express these proteins might be highly susceptible to viral entry and downstream effects. Currently, reports regarding the expression of the viral entry proteins in the testes are conflicting; however, other members of the SARS-CoV family of viruses - such as SARS-CoV - have been suspected to cause testicular dysfunction and/or orchitis. SARS-CoV-2, which displays many similarities to SARS-CoV, could potentially cause similar adverse effects. Commonalities between SARS family members, taken in combination with sparse reports of testicular discomfort and altered hormone levels in patients with SARS-CoV-2, might indicate possible testicular dysfunction. Thus, SARS-CoV-2 infection has the potential for effects on testis somatic and germline cells and experimental approaches might be required to help identify potential short-term and long-term effects of SARS-CoV-2 on male fertility.

Gut-lung cross talk in COVID-19 pathology and fatality rate

Coronavirus disease 2019 (COVID-19) is the leading pandemic facing the world in 2019/2020; it is caused by a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, which necessitates clear understanding of the infectious agent. The virus manifests aggressive behavior with severe clinical presentation and high mortality rate, especially among the elderly and patients living with chronic diseases. In the recent years, the role of gut microbiota, in health and disease, has been progressively studied and highlighted. It is through gut microbiota-organ bidirectional pathways, such as gut-brain axis, gut-liver axis, and gut-lung axis, that the role of gut microbiota in prompting lung disease, among other diseases, has been proposed and accepted. It is also known that respiratory viral infections, such as COVID-19, induce alterations in the gut microbiota, which can influence immunity. Based on the fact that gut microbiota diversity is decreased in old age and in patients with certain chronic diseases, which constitute two of the primary fatality groups in COVID-19 infections, it can be assumed that the gut microbiota may play a role in COVID-19 pathology and fatality rate. Improving gut microbiota diversity through personalized nutrition and supplementation with prebiotics/probiotics will mend the immunity of the body and hence could be one of the prophylactic strategies by which the impact of COVID-19 can be minimized in the elderly and immunocompromised patients. In this chapter, the role of dysbiosis in COVID-19 will be clarified and the possibility of using co-supplementation of personalized prebiotics/probiotics with current therapies will be discussed.

The COVID-19 pandemic: Workplace safety management practices, job insecurity, and employees' organizational citizenship behavior

How do organizations and employees react to the COVID-19 pandemic? Can workplace safety management practices (WSPs) maintain employees' organizational citizenship behavior (OCB) in this time of global health crisis? Can employees' perceptions of the risk associated with COVID-19 and job insecurity mediate the WSPs-OCB relationship? Drawing upon social exchange and protection motivation theories, this research aims to answer such questions. Analyzing the survey data from 501 Vietnamese employees using SmartPLS software, we find that WSPs positively influence the OCB and negatively influence the perceived job insecurity. Furthermore, the perceived risk associated with COVID-19 positively affects perceived job insecurity and OCB. Unexpectedly, in the context of Vietnam, a developing country with a collectivist culture, WSPs increase the employees' perceived risk associated with COVID-19 instead of reducing their fear. Also, employees' perceptions of job insecurity are not statistically correlated with OCB. In addition, we reveal a partial mediating role of the perceived risk associated with COVID-19 in the WSPs-OCB relationship. This research highlights the power of WSPs as well as measures to psychologically reassure employees during the pandemics.

Diagnosis of COVID-19 in symptomatic patients: An updated review

A group of pneumonia patients was detected in Hubei Province, in China in December 2019. The etiology of the disease was unknown. Later, the researchers diagnosed the novel Coronavirus as the causal agent of this respiratory disease. On February 12th 2020, the World Health Organization (WHO) officially named this disease Coronavirus disease 2019 (COVID-19). Consequently, the disease spread globally and became a pandemic. As there is no specific treatment for the symptomatic patients and several vaccines are approved by WHO, the efficacy and effectiveness of these vaccines are not fully understood yet and the availability of these vaccines are very limited. In addition, new variants and mutants of SARS-CoV-2 are thought to be able to evade the immune system of the host. So, diagnosis and isolation of infected individuals is advised. Currently, real-time reverse transcription-polymerase chain reaction (RT-PCR) is considered the gold standard method to detect novel Coronavirus, however, there are few limitations associated with RT-PCR such as false-negative results. This demanded another diagnostic tool to detect and isolate COVID-19 early and accurately. Chest computed tomography (CT) became another option to diagnose COVID-19 patients accurately (about 98% sensitivity). However, it did not apply to the asymptomatic carriers and sometimes the results were misinterpreted as from other groups of Coronavirus infection. The combination of RT-PCR and chest CT might be the best option in detecting novel Coronavirus infection early and accurately thereby allowing adaptation of measures for the prevention and control of the COVID-19.

Mini-Review on SARS-CoV-2 Infection and Neurological Manifestations: A Perspective

The coronavirus, also known as SARS-CoV-2 (Severe Acute Respiratory Syndrome Corona Virus-19), with its rapid rate of transmission, has progressed with a great impact on respiratory function and mortality worldwide. The nasal cavity is the promising gateway of SARS-CoV-2 to reach the brain via systemic circulatory distribution. Recent reports have revealed that the loss of involuntary process of breathing control into the brainstem that results in death is a signal of neurological involvement. Early neurological symptoms, like loss of smell, convulsions, and ataxia, are the clues of the involvement of the central nervous system that makes the entry of SARS-CoV-2 further fatal and life-threatening, requiring artificial respiration and emergency admission in hospitals. Studies performed on patients infected with SARS-CoV-2 has revealed three-stage involvement of the Central Nervous System (CNS) in the progression of SARS-CoV-2 infection: Direct involvement of CNS with headache, ataxia, dizziness, altered or impaired consciousness, acute stroke or seizures as major symptoms, peripheral involvement with impaired taste, smell, vision, and altered nociception, and skeletal muscle impairment that includes skeletal muscle disorders leading to acute paralysis in a particular area of the body. In the previous era, most studied and researched viruses were beta coronavirus and mouse hepatitis virus, which were studied for acute and chronic encephalitis and Multiple Sclerosis (MS). Although the early symptoms of SARS-CoV are respiratory pathogenesis, the differential diagnosis should always be considered for neurological perspective to stop the mortalities.

Animal Models of COVID-19. I. Comparative Virology and Disease Pathogenesis

The Coronavirus Disease 2019 (COVID-19) pandemic has fueled unprecedented development of animal models to understand disease pathogenesis, test therapeutics, and support vaccine development. Models previously developed to study severe acute respiratory syndrome coronavirus (SARS-CoV) have been rapidly deployed to study SARS-CoV-2. However, it has become clear that despite the common use of ACE2 as a receptor for both viruses, the host range of the 2 viruses does not entirely overlap. Distinct ACE2-interacting residues within the receptor binding domain of SARS-CoV and SARS-CoV-2, as well as species differences in additional proteases needed for activation and internalization of the virus, are likely sources of host differences between the 2 viruses. Spontaneous models include rhesus and cynomolgus macaques, African Green monkeys, hamsters, and ferrets. Viral shedding and transmission studies are more frequently reported in spontaneous models. Mice can be infected with SARS-CoV; however, mouse and rat ACE2 does not support SARS-CoV-2 infection. Murine models for COVID-19 are induced through genetic adaptation of SARS-CoV-2, creation of chimeric SARS-CoV and SARS-CoV-2 viruses, use of human ACE2 knock-in and transgenic mice, and viral transfection of wild-type mice with human ACE2. Core aspects of COVID-19 are faithfully reproduced across species and model. These include the acute nature and predominantly respiratory source of viral shedding, acute transient and nonfatal disease with a largely pulmonary phenotype, similar short-term immune responses, and age-enhanced disease. Severity of disease and tissue involvement (particularly brain) in transgenic mice varies by promoter. To date, these models have provided a remarkably consistent template on which to test therapeutics, understand immune responses, and test vaccine approaches. The role of comorbidity in disease severity and the range of severe organ-specific pathology in humans remains to be accurately modeled.

SARS-CoV-2 and Variant Diagnostic Testing Approaches in the United States

Purpose of Review Given the rapid development of diagnostic approaches to test for and diagnose infection with SARS-CoV-2 and its associated variants including Omicron (B.1.1.529), many options are available to diagnose infection. Multiple established diagnostic companies are now providing testing platforms whereas initially, testing was being performed with simple PCR-based tests using standard laboratory reagents. Recent Findings Additional testing platforms continue to be developed, including those to detect specific variants, but challenges with testing, including obtaining testing reagents and other related supplies, are frequently encountered. With time, the testing supply chain has improved, and more established companies are providing materials to support these testing efforts. In the United States (U.S.), the need for rapid assay development and subsequent approval through the attainment of emergency use authorization (EUA) has superseded the traditional arduous diagnostic testing approval workflow mandated by the FDA. Through these efforts, the U.S. has been able to continue to significantly increase its testing capabilities to address this pandemic; however, challenges still remain due to the diversity of the performance characteristics of tests being utilized and newly discovered viral variants. Summary This review provides an overview of the current diagnostic testing landscape, with pertinent information related to SARS-CoV-2 virology, variants and antibody responses that are available to diagnose infection in the U.S.

Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches

Recently, a new variant, B.1620, with mutations (S477N-E484K) in the spike protein's receptor-binding domain (RBD) has been reported in Europe. In order to design therapeutic strategies suitable for B.1.620, further studies are required. A detailed investigation of the structural features and variations caused by these substitutions, that is, a molecular level investigation, is essential to uncover the role of these changes. To determine whether and how the binding affinity of ACE2-RBD is affected, we used protein-protein docking and all-atom simulation approaches. Our analysis revealed that B.1.620 binds more strongly than the wild type and alters the hydrogen bonding network. The docking score for the wild type was reported to be -122.6 +/- 0.7 kcal/mol, while for B.1.620, the docking score was -124.9 +/- 3.8 kcal/mol. A comparative binding investigation showed that the wild-type complex has 11 hydrogen bonds and one salt bridge, while the B.1.620 complex has 14 hydrogen bonds and one salt bridge, among which most of the interactions are preserved between the wild type and B.1.620. A dynamic analysis of the two complexes revealed stable dynamics, which corroborated the global stability trend, compactness, and flexibility of the three essential loops, providing a better conformational optimization opportunity and binding. Furthermore, binding free energy revealed that the wild type had a total binding energy of -51.14 kcal/mol, while for B.1.628, the total binding energy was -68.25 kcal/mol. The current findings based on protein complex modeling and bio-simulation methods revealed the atomic features of the B.1.620 variant harboring S477N and E484K mutations in the RBD and the basis for infectivity. In conclusion, the current study presents distinguishing features of B.1.620, which can be used to design structure-based drugs against the B.1.620 variant.

Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure

The Coronavirus Disease 2019 (COVID-19) was declared a pandemic in March 2020 by the World Health Organization (WHO). As of May 25th, 2021 there were 2.059.941 SARS-COV2 genome sequences that have been submitted to the GISAID database, with numerous variations. Here, we aim to analyze the SARS-CoV-2 genome data submitted to the GISAID database from Turkey and to determine the variant and clade distributions by the end of May 2021, in accordance with their appearance timeline. We compared these findings to USA, Europe, and Asia data as well. We have also evaluated the effects of spike protein variations, detected in a group of genome sequences of 13 patients who applied to our clinic, by using 3D modeling algorithms. For this purpose, we analyzed 4607 SARS-CoV-2 genome sequences submitted by different lab centers from Turkey to the GISAID database between March 2020 and May 2021. Described mutations were also introduced in silico to the spike protein structure to analyze their isolated impacts on the protein structure. The most abundant clade was GR followed by G, GH, and GRY and we did not detect any V clade. The most common variant was B.1, followed by B.1.1, and the UK variant, B.1.1.7. Our results clearly show a concordance between the variant distributions, the number of cases, and the timelines of different variant accumulations in Turkey. The 3D simulations indicate an increase in the surface hydrophilicity of the reference spike protein and the detected mutations. There was less surface hydrophilicity increase in the Asp614Gly mutation, which exhibits a more compact conformation around the ACE-2 receptor binding domain region, rendering the structure in a “down” conformation. Our genomic findings can help to model vaccination programs and protein modeling may lead to different approaches for COVID-19 treatment strategies.

Genome-scale CRISPR screen identifies TMEM41B as a multi-function host factor required for coronavirus replication

Emerging coronaviruses (CoVs) pose a severe threat to human and animal health worldwide. To identify host factors required for CoV infection, we used α-CoV transmissible gastroenteritis virus (TGEV) as a model for genome-scale CRISPR knockout (KO) screening. Transmembrane protein 41B (TMEM41B) was found to be a bona fide host factor involved in infection by CoV and three additional virus families. We found that TMEM41B is critical for the internalization and early-stage replication of TGEV. Notably, our results also showed that cells lacking TMEM41B are unable to form the double-membrane vesicles necessary for TGEV replication, indicating that TMEM41B contributes to the formation of CoV replication organelles. Lastly, our data from a mouse infection model showed that the KO of this factor can strongly inhibit viral infection and delay the progression of a CoV disease. Our study revealed that targeting TMEM41B is a highly promising approach for the development of broad-spectrum anti-viral therapeutics.

The mediterranean diet: Healthy and sustainable dietary pattern in the time of Sars-Cov-2

COVID-19, first reported in Wuhan, China in December 2019 quickly spread worldwide leading to serious health, social and economic consequences. A crucial role in the pathogenesis of severe disease has been attributed to the inflammatory status, that in more severe cases may evolve in an overproduction of pro-inflammatory cytokines (“cytokine storm)” and fatal outcome. Non-communicable diseases, nutritional disorders and advanced age, conditions associated with a low-grade systemic inflammation and immune function alterations, have been identified as major risks for severe COVID-19. General recommendations for fighting COVID-19 highlighted the paramount importance of adopting a healthy plant-based dietary pattern and healthy lifestyle. The Mediterranean dietary pattern is considered as one of the healthiest dietary patterns, and its benefits are supported by a large body of evidence. Furthermore, it is considered as a sustainable lifestyle model. The aim of this research was to update the multiple benefits of the Mediterranean dietary pattern on physical and mental health, focusing on the effects that it may have in combating COVID-19. The potential effects and mechanisms of action of the main bioactive components of Mediterranean diet were also analyzed. Considering its effects in modulating inflammation and oxidative stress and supporting the immune system, the Mediterranean dietary pattern may be considered the most promising dietary approach to combat COVID-19.

SARS-CoV-2 spike protein: Site-specific breakpoints for the development of COVID-19 vaccines

SARS-CoV2 is a member of human coronaviruses and is the causative agent of the present pandemic COVID-19 virus. In order to control COVID-19, studies on viral structure and mechanism of infectivity and pathogenicity are sorely needed. The spike (S) protein is comprised of S1 & S2 subunits. These spike protein subunits enable viral attachment by binding to the host cell via ACE-2 (angiotensin converting enzyme-2) receptor, thus facilitating the infection. During viral entry, one of the key steps is the cleavage of the S1-S2 spike protein subunits via surface TMPRSS2 (transmembrane protease serine 2) and results in viral infection. Hence, the S-protein is critical for the viral attachment and penetration into the host. The rapid advancement of our knowledge on the structural and functional aspects of the spike protein could lead to development of numerous candidate vaccines against SARS-CoV2. Here the authors discuss about the structure of spike protein and explore its related functions. Our aim is to provide a better understanding that may aid in fighting against CoVID-19 and its treatment.

Immunity-Boosting Natural Herbs to Combat COVID-19 Pandemic: A Narrative Review

Coronaviruses cause some severe forms of respiratory infections such as Severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and Coronavirus disease 2019 (Covid-19). These viruses cause diarrhea in pigs and cows and upper respiratory disease in chickens, while other symptoms may differ. In humans, a total of six coronaviruses have been identified HCoVs-NL63, HCoVs-OC43, HCoVs-229E, HCoVs-HKU1, MERS-CoV, and SARS-CoV. The world health organization (WHO) has done a great deal of hard work regarding combating the monstrous effects of this virus. So far, no specific antiviral drugs have been developed for the treatment of Covid-19. Therefore, the medicinal plants used for the previous epidemic outbreaks are getting attention for their potential treatment against the virus. It has been reported that 70 to 80% of people in developing countries depend on medicinal plants or phytomedicine compared to allopathic drugs for their primary healthcare. The south Asian subcontinents have used almost up to 25,000 formulations and extracts obtained from medicinal plants for treatment in folk medicine. The present review discusses an overview of the coronavirus, its immune responses, and some immunity-boosting herbs to combat Covid-19.

A current novel perspective approach for coronavirus disease-2019 pandemic outbreak

Coronavirus disease-2019 is a serious health threat around the globe. Across the world, approximately 142 million people were infected, and three million deaths happened. The fast propagation is also associated with constant anxiety, mental stress, and discomfort in public and health-care professionals. Lack of approved drugs regimen to combat the pandemic challenge concretely is a challenging project for all who are committed to developing remedial assistance. However, the successful development of three vaccines gives a solid roadmap to combat this disease. In this review, we highlighted the current development and challenges of this pandemic.

Visualizing in deceased COVID-19 patients how SARS-CoV-2 attacks the respiratory and olfactory mucosae but spares the olfactory bulb

Anosmia, the loss of smell, is a common and often the sole symptom of COVID-19. The onset of the sequence of pathobiological events leading to olfactory dysfunction remains obscure. Here, we have developed a postmortem bedside surgical procedure to harvest endoscopically samples of respiratory and olfactory mucosae and whole olfactory bulbs. Our cohort of 85 cases included COVID-19 patients who died a few days after infection with SARS-CoV-2, enabling us to catch the virus while it was still replicating. We found that sustentacular cells are the major target cell type in the olfactory mucosa. We failed to find evidence for infection of olfactory sensory neurons, and the parenchyma of the olfactory bulb is spared as well. Thus, SARS-CoV-2 does not appear to be a neurotropic virus. We postulate that transient insufficient support from sustentacular cells triggers transient olfactory dysfunction in COVID-19. Olfactory sensory neurons would become affected without getting infected.

Antiviral and antibacterial activity of hand sanitizer and surface disinfectant formulations

Emergent diseases caused by viral and bacterial infections have proven to be a current and future challenge. The occurrence of these diseases is usually accompanied by the lack of vaccines and dedicated therapies leaving prevention as the best strategy to adopt. In that context, and apart from confinement and physical distancing measures, an increase in hygiene actions, namely hand and surface cleaning and disinfection can reduce the infection spread originated from our day-to-day routines. However, during crisis situations the high disinfectants demand can very likely lead to having them running out of stock. This impels many individuals and companies to produce their own disinfectants. Here, we explore the main components of a disinfection formulation, both for hand-rub and surface cleaning. Alcohol and non-alcohol based formulations are described, including the possibility to fine tune the properties of the final product in order to increase public acceptance while maintaining product efficacy. The action mechanisms of the main active principles are also described conjugating information from experimental and theoretical data. Overall, the main aspects to develop a disinfectant formulation are addressed, as well as their function, helping formulation developers to better understand the impact of their choices.

The Pandemic of Coronavirus Disease 2019 (COVID-19)

Currently, the world is facing the emergence of a virus that causes pneumonia in humans, which has a higher probability of causing complications that include respiratory distress syndrome and death. The new coronavirus 2019 (2019-nCoV), which is currently known as SARS-CoV-2, is the cause of the Coronavirus disease 2019 (COVID-19) . This virus was first detected in Wuhan, Hubei Province of China, and appears to have been a zoonotic infection that has now adapted to humans. On March 11 2020, COVID-19 was announced as a pandemic by the World Health Organisation (WHO), causing widespread panic worldwide. SARS-CoV-2 is genetically similar to the 2003 Severe Acute Respiratory Syndrome-related (SARS) and shares many similarities with the disease features of influenza virus infection. Scientists around the world are racing towards the development of vaccines and antiviral for COVID-19. This review will provide an update of COVID-19, a brief review of the symptoms and route of transmission, SARS-CoV-2 virus, and why it is highly infectious as well as the currently available treatments and comorbidities.

Underlying selection for the diversity of spike protein sequences of SARS-CoV-2

The global spread of SARS-CoV-2 is fast moving and has caused a worldwide public health crisis. In the present article, we analyzed spike protein sequences of SARS-CoV-2 genomes to assess the impact of mutational diversity. We observed from amino acid usage patterns that spike proteins are associated with a diversity of mutational changes and most important underlying cause of variation of amino acid usage is the changes in hydrophobicity of spike proteins. The changing patterns of hydrophobicity of spike proteins over time and its influence on the receptor binding affinity provides crucial information on the SARS-CoV-2 interaction with human receptor. Our results also show that spike proteins have evolved to prefer more hydrophobic residues over time. The present study provides a comprehensive analysis of molecular sequence data to consider that mutational variants might play a crucial role in modulating the virulence and spread of the virus and has immediate implications for therapeutic strategies.

Public perception towards medical waste generated in the environment during the COVID-19 pandemic in Eastern Province, Saudi Arabia

Airborne droplets and contaminated surfaces are the main routes for the epidemic virus outbreak that causes the novel coronavirus. To reduce virus spread, people wear face masks and gloves daily, which massively increases the amount of waste generated in the environment. Also, the inappropriate disposal of used masks and gloves in communities may boost the spread of the novel coronavirus. However, no studies have been conducted to evaluate a public perception regarding the management of generated masks and gloves during the global health threat. Therefore, this paper proposes a study of public awareness, attitudes, and practices towards gloves and masks generated during the novel coronavirus pandemic in Saudi Arabia. The study showed that most of the participants (74%) have adequate awareness regarding the proper way to dispose of used masks and gloves, with 76% showing positive attitudes toward waste management. Gender shows a significant correlation with the regulations of medical waste collection and disposal (r = 0.169, p = 0.0001), and the consideration of the effective disposal of COVID-19 waste management as a collective responsibility of the community (r = 0.158, p = 0.0001). Also, the study shows that the majority of participants were aware on the availability of regulations for the collection and disposal of biomedical waste. Moreover, it demonstrates that public awareness regarding the attitude and measures taken by regional municipalities to reduce the spread of coronavirus has a significant positive correlation (r = 0.279, p = 0.0001). The study further recognized that the effective management of contagious wastes significantly protects the public against the improper practices of wastes disposal generated during the novel coronavirus pandemic.

Superiority of lymphocyte ratio over total leukocyte count in detecting the severity of COVID- 19 pneumonia

BACKGROUND

Coronavirus disease (COVID-19) is an infectious disease caused by a recently discovered coronavirus. Blood test including complete blood count is crucial in diagnosing of several viral and bacterial infection.

AIMS

This study aimed to assess the association between lymphocyte ratio and other WBC types and severity of COVID-19 pneumonia.

METHODS

The design of this study was a cross-sectional study. A complete blood count and erythrocyte sedimentation rate (ESR) was done for one hundred twenty-six COVID-19 patients (76 males and 50 females; aged 20-70 years). Patients were randomly recruited from multicenter in Al-Najaf Governorate, Iraq.

RESULTS

The study had revealed an inverse correlation between severity of COVID-19 infection and both lymphocytes and monocytes ratio even in patients with normal WBC count. Additionally, there was a direct correlation between platelets and leukocyte count. The relation between leukocyte count and ESR level was significant in a patient with elevated WBC only.

CONCLUSION

Lymphocytes and monocyte ratios inpatient with COVID-19 infection can be used as predictors for the severity of infection. Increased leukocyte count resulted in increases in platelets inpatient with COVID-19.

Neurobiology of COVID-19: how can the virus affect the brain?

Severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) causes the coronavirus disease 2019 (COVID-19), which has been declared a public health emergency of international interest, with confirmed cases in most countries. COVID-19 presents manifestations that can range from asymptomatic or mild infections up to severe manifestations that lead to hospitalization and death. A growing amount of evidence indicates that the virus may cause neuroinvasion. Postmortem brain study findings have included edema, hemorrhage, hydrocephalus, atrophy, encephalitis, infarcts, swollen axons, myelin loss, gliosis, neuronal satellitosis, hypoxic-ischemic damage, arteriolosclerosis, leptomeningeal inflammation, neuronal loss, and axon degeneration. In addition, the COVID-19 pandemic is causing dangerous effects on the mental health of the world population, some of which can be attributed to its social impact (social distancing, financial issues, and quarantine). There is also a concern that environmental stressors, enhanced by psychological factors, are contributing to the emergence of psychiatric outcomes during the pandemic. Although clinical studies and diagnosing SARS-CoV-2-related neurological disease can be challenging, they are necessary to help define the manifestations and burden of COVID-19 in neurological and psychiatric symptoms during and after the pandemic. This review aims to present the neurobiology of coronavirus and postmortem neuropathological hallmarks.

COVID-19 and Its Repercussions on Oral Health: A Review

In 2019, a new type of coronavirus, SARS-CoV-2, the causing agent of COVID-19, was first detected in Wuhan, China. On 11 March 2020, the World Health Organization declared a pandemic. The manifestations of COVID-19 are mostly age-dependent and potentially more severe in cases with involved co-morbidities. The gravity of the symptoms depends on the clinical stage of the infection. The most common symptoms include runny nose and nasal congestion, anosmia, dysgeusia or hypogeusia, diarrhea, nausea/vomiting, respiratory distress, fatigue, ocular symptoms, diarrhea, vomiting, and abdominal pain. These systemic conditions are often accompanied by skin and mucosal lesions. Oral lesions reported in patients with COVID-19 include: herpex simplex, candidiasis, geographic tongue, aphthous-like ulcers, hemorrhagic ulcerations, necrotic ulcerations, white hairy tongue, reddish macules, erythematous surfaces, petechiae, and pustular enanthema. It is still unclear if these manifestations are a direct result of the viral infection, a consequence of systemic deterioration, or adverse reactions to treatments. Poor oral hygiene in hospitalized or quarantined COVID-19 patients should also be considered as an aggravating condition. This narrative review is focused on presenting the most relevant data from the literature regarding oral manifestations related to SARS-CoV-2, as well as the challenges faced by the dental system during this pandemic. A routine intraoral examination is recommended in COVID-19 patients, either suspected or confirmed, as, in certain cases, oral manifestations represent a sign of severe infection or even of a life-threatening condition. It is our belief that extensive knowledge of all possible manifestations, including oral lesions, in cases of COVID-19 is of great importance in the present uncertain context, including new, currently emerging viral variants with unknown future impact.

PABPC4 Broadly Inhibits Coronavirus Replication by Degrading Nucleocapsid Protein through Selective Autophagy

Emerging coronaviruses (CoVs) can cause severe diseases in humans and animals, and, as of yet, none of the currently available broad-spectrum drugs or vaccines can effectively control these diseases. Host antiviral proteins play an important role in inhibiting viral proliferation. One of the isoforms of cytoplasmic poly(A)-binding protein (PABP), PABPC4, is an RNA-processing protein, which plays an important role in promoting gene expression by enhancing translation and mRNA stability. However, its function in viruses remains poorly understood. Here, we report that the host protein, PABPC4, could be regulated by transcription factor SP1 and broadly inhibits the replication of CoVs, covering four genera (Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus) of the Coronaviridae family by targeting the nucleocapsid (N) protein through the autophagosomes for degradation. PABPC4 recruited the E3 ubiquitin ligase MARCH8/MARCHF8 to the N protein for ubiquitination. Ubiquitinated N protein was recognized by the cargo receptor NDP52/CALCOCO2, which delivered it to the autolysosomes for degradation, resulting in impaired viral proliferation. In addition to regulating gene expression, these data demonstrate a novel antiviral function of PABPC4, which broadly suppresses CoVs by degrading the N protein via the selective autophagy pathway. This study will shed light on the development of broad anticoronaviral therapies. IMPORTANCE Emerging coronaviruses (CoVs) can cause severe diseases in humans and animals, but none of the currently available drugs or vaccines can effectively control these diseases. During viral infection, the host will activate the interferon (IFN) signaling pathways and host restriction factors in maintaining the innate antiviral responses and suppressing viral replication. This study demonstrated that the host protein, PABPC4, interacts with the nucleocapsid (N) proteins from eight CoVs covering four genera (Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus) of the Coronaviridae family. PABPC4 could be regulated by SP1 and broadly inhibits the replication of CoVs by targeting the nucleocapsid (N) protein through the autophagosomes for degradation. This study significantly increases our understanding of the novel host restriction factor PABPC4 against CoV replication and will help develop novel antiviral strategies.

Elevation of Serum Transaminase Levels Due to Favipiravir Use in the Treatment of COVID-19

Background and aims: Favipiravir is a ribonucleic acid (RNA)-dependent RNA polymerase (RdRP) inhibitor antiviral agent used in the treatment of coronavirus disease-2019 (COVID-19). In this study, we investigated the changes in serum transaminase levels of patients and the relationship between serum transaminase elevation with mortality in patients who were hospitalized with the diagnosis of COVID-19 and received favipiravir treatment.

Materials and methods: 454 patients who received favipiravir and 113 patients who did not receive favipiravir were evaluated. Serum transaminase levels of the patients were compared at baseline and after five days of treatment, and the relationship between serum transaminase elevation and mortality was investigated.

Results: No significant aspartate aminotransferase (AST) or alanine aminotransferase (ALT) elevation was detected due to favipiravir treatment. AST elevation was found, respectively, as 133 (29.3%), 32 (28.3%) (p=0.100), ALT elevation as 112 (24.7%), 35 (29.3%) (p=0.100) in the groups receiving and not receiving favipiravir. High AST level was found as a risk factor for mortality in all patient groups (p=0.008).

Conclusions: There was no statistically significant elevation in serum transaminase levels due to favipiravir use in patients hospitalized for COVID-19. A high level of AST is a significant risk factor to show mortality and intensive care unit (ICU) admission in patients with COVID-19.

Diagnostic Testing for SARS-CoV-2 Infection

PURPOSE OF REVIEW

Given the rapid development of diagnostic approaches to test for and diagnose infection with SARS-CoV-2, many options are available to assess infection. Multiple established diagnostic companies are now providing testing platforms whereas initially, testing was being performed with simple PCR-based tests using standard laboratory reagents.

RECENT FINDINGS

Additional testing platforms continue to be developed but challenges with testing, including obtaining testing reagents and other related supplies, are frequently encountered. With time, the testing supply chain will improve and more companies will be providing materials to support these testing efforts. In the USA, the need for rapid assay development and subsequent approval through attainment of emergency use authorization (EUA) has superseded the traditional arduous diagnostic testing approval workflow mandated by the FDA. It is anticipated that the USA will be able to continue to significantly increase its testing capabilities to address this pandemic; however, challenges remain due to the diversity of the performance characteristics of tests being utilized.

SUMMARY

This review provides an overview of the current diagnostic testing landscape, with pertinent information related to SARS-CoV-2 virology and antibody responses, that is available to diagnose infection.

Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure

The novel coronavirus SARS-CoV-2, which emerged in late 2019, has since spread around the world and infected hundreds of millions of people with coronavirus disease 2019 (COVID-19). While this viral species was unknown prior to January 2020, its similarity to other coronaviruses that infect humans has allowed for rapid insight into the mechanisms that it uses to infect human hosts, as well as the ways in which the human immune system can respond. Here, we contextualize SARS-CoV-2 among other coronaviruses and identify what is known and what can be inferred about its behavior once inside a human host. Because the genomic content of coronaviruses, which specifies the virus's structure, is highly conserved, early genomic analysis provided a significant head start in predicting viral pathogenesis and in understanding potential differences among variants. The pathogenesis of the virus offers insights into symptomatology, transmission, and individual susceptibility. Additionally, prior research into interactions between the human immune system and coronaviruses has identified how these viruses can evade the immune system's protective mechanisms. We also explore systems-level research into the regulatory and proteomic effects of SARS-CoV-2 infection and the immune response. Understanding the structure and behavior of the virus serves to contextualize the many facets of the COVID-19 pandemic and can influence efforts to control the virus and treat the disease. IMPORTANCE COVID-19 involves a number of organ systems and can present with a wide range of symptoms. From how the virus infects cells to how it spreads between people, the available research suggests that these patterns are very similar to those seen in the closely related viruses SARS-CoV-1 and possibly Middle East respiratory syndrome-related CoV (MERS-CoV). Understanding the pathogenesis of the SARS-CoV-2 virus also contextualizes how the different biological systems affected by COVID-19 connect. Exploring the structure, phylogeny, and pathogenesis of the virus therefore helps to guide interpretation of the broader impacts of the virus on the human body and on human populations. For this reason, an in-depth exploration of viral mechanisms is critical to a robust understanding of SARS-CoV-2 and, potentially, future emergent human CoVs (HCoVs).

The emergence of Covid-19: evolution from endemic to pandemic

Human race has survived several outbreak of pandemics in the past and their impact was long lasting. Some of the recent pandemics have been caused by a viruses known as Coronaviruses (CoVs) which are diverse, complex, adaptable viruses that have a significant impact on human health and animal productivity. The novel coronavirus that emerged in Wuhan, China (SARS-CoV-2) in 2019 has quickly spread throughout the world. Human coronaviruses (HCoVs), including severe acute respiratory syndrome coronavirus (SARS-CoV) and 2019 novel coronavirus (2019-nCoV, also known as SARS-CoV-2), have led to a global epidemic with high morbidity and mortality. Human pathogenic coronaviruses, SARS-CoV and SARS-CoV-2, bind to their target cells through angiotensin-converting enzyme 2 (ACE2), which is expressed by epithelial cells of the lung, intestine, kidneys, and blood vessels. The efforts to contain the virus are undergoing throughout the world, given the many uncertainties regarding pathogen transmissibility and virulence. Thus, the ongoing studies to promote the understanding of HCoVs will help to avoid or/and minimize the impact of anticipated pandemics in future.

UVC-based photoinactivation as an efficient tool to control the transmission of coronaviruses

The ongoing COVID-19 pandemic made us re-realize the importance of environmental disinfection and sanitation in indoor areas, hospitals, and clinical rooms. UVC irradiation of high energy and short wavelengths, especially in the 200-290-nm range possesses the great potential for germicidal disinfection. These properties of UVC allow to damage or destruct the nucleic acids (DNA/RNA) in diverse microbes (e.g., bacteria, fungi, and viruses). UVC light can hence be used as a promising tool for prevention and control of their infection or transmission. The present review offers insights into the historical perspective, mode of action, and recent advancements in the application of UVC-based antiviral therapy against coronaviruses (including SARS CoV-2). Moreover, the application of UVC lights in the sanitization of healthcare units, public places, medical instruments, respirators, and personal protective equipment (PPE) is also discussed. This article, therefore, is expected to deliver a new path for the developments of UVC-based viricidal approach.

A Bioinformatics Approach for the Prediction of Immunogenic Properties and Structure of the SARS-COV-2 B.1.617.1 Variant Spike Protein

Background

B.1.617.1, a variant of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causing respiratory illness is responsible for the second wave of COVID-19 and associated with a high incidence of infectivity and mortality. To mitigate the B.1.617.1 variant of SARS-CoV-2, deciphering the protein structure and immunological responses by employing bioinformatics tools for data mining and analysis is pivotal.

Objectives

Here, an in silico approach was employed for deciphering the structure and immune function of the subunit of spike (S) protein of SARS-CoV-2 B.1.617.1 variant.

Methods

The partial amino acid sequence of SARS-CoV-2 B.1.617.1 variant S protein was analyzed, and its putative secondary and tertiary structure was predicted. Immunogenic analyses including B- and T-cell epitopes, interferon-gamma (IFN-γ) response, chemokine, and protective antigens for SARS-CoV 2 S proteins were predicted using appropriate tools.

Results

B.1.617.1 variant S protein sequence was found to be highly stable and amphipathic. ABCpred and CTLpred analyses led to the identification of two potential antigenic B cell and T cell epitopes with starting amino acid positions at 60 and 82 (for B cell epitopes) and 54 and 98 (for T cell epitopes) having prediction scores > 0.8. Further, RAMPAGE tool was used for determining the allowed and disallowed regions of the three-dimensional predicted structure of SARS-CoV-2 B.1.617.1 variant S protein.

Conclusion

Together, the in silico analysis revealed the predicted structure of partial S protein, immunogenic properties, and possible regions for S protein of SARS-CoV-2 and provides a valuable prelude for engineering the targeted vaccine or drug against B.1.617.1 variant of SARS-CoV-2.

An updated review on potential therapeutic drug candidates, vaccines and an insight on patents filed for COVID-19

The outbreak of COVID-19 was recognized in December 2019 in China and as of October5th, the pandemic was swept through 216 countries and infected around 34,824,108 individuals, thus posing an unprecedented threat to world's health and economy. Several researchers reported that, a significant mutation in membrane proteins and receptor binding sites of preceding severe acute respiratory syndrome coronavirus (SARS-CoV) to turned as novel SARS-CoV-2 virus and disease was named as COVID-19 (Coronavirus disease 2019). Unfortunately, there is no specific treatment available for COVID-19 patients. The lessons learned from the past management of SARS-CoV and other pandemics, have provided some insights to treat COVID-19. Currently, therapies like anti-viral treatment, immunomodulatory agents, plasma transfusion and supportive intervention etc., are using to treat the COVID-19. Few of these were proven to provide significant therapeutic benefits in treating the COVID-19, however no drug is approved by the regulatory agencies. As the fatality rate is high in patients with comorbid conditions, we have also enlightened the current in-line treatment therapies and specific treatment strategies in comorbid conditions to combat the emergence of COVID-19. In addition, pharmaceutical, biological companies and research institutions across the globe have begun to develop thesafe and effective vaccine for COVID-19. Globally around 170 teams of researchers are racing to develop the COVID-19 vaccine and here we have discussed about their current status of development. Furthermore, recent patents filed in association with COVID-19 was elaborated. This can help many individuals, researchers or health workers, in applying these principles for diagnosis/prevention/management/treatment of the current pandemic.

Clinical Treatment Experience in Severe and Critical COVID-19

Compared with other deadly diseases, the coronavirus disease 2019 (COVID-19) is highly infectious with a relatively low mortality rate. Although critical cases account for only 5% of cases, the mortality rate for the same is nearly 50%. Therefore, the key to the COVID-19 treatment is to effectively treat severe patients and reduce the transition from severe to critical cases. A retrospective study was carried out to evaluate outcomes of treatment in patients with severe and critical COVID-19 admitted to a COVID-19 special hospital in Wuhan, China. A total of 75 severe and critical COVID-19 patients were admitted and treated with immunomodulation as the main strategy combined with anti-inflammatory therapy and appropriate anticoagulation. Leukocyte levels in patients with 7-14 days of onset to diagnosis were significantly lower than in those with >14 days. Higher levels of globulin and D-dimer and lower lymphocyte levels were found in the older age group (>65 years) than in the middle-aged group (50-64 years). Patients with comorbidity had higher levels of inflammatory indicators. After treatment, 65 (86.67%) patients were cured, 7 (9.33%) had improved, and 3 (4.00%) had died. Median hospitalization duration was 23 days. Fatal cases showed continuously increased levels of globulin, dehydrogenase (LDH), hypersensitive C-reactive protein (hs-CRP), D-dimer, and cytokines during treatment. Time from onset to diagnosis, age, and comorbidity are important influencing factors on treatment effects. The occurrence of immunosuppression, “cytokine storm,” and thrombosis may be an important cause of death in severely infected cases. In conclusion, high cure rate and low mortality suggested that immunomodulation combined with anti-inflammatory therapy and appropriate anticoagulant therapy is a good strategy for treatment of patients with severe and critical COVID-19.

SDAV, the Rat Coronavirus-How Much Do We Know about It in the Light of Potential Zoonoses

Sialodacryoadenitis virus (SDAV) is known to be an etiological agent, causing infections in laboratory rats. Until now, its role has only been considered in studies on respiratory and salivary gland infections. The scant literature data, consisting mainly of papers from the last century, do not sufficiently address the topic of SDAV infections. The ongoing pandemic has demonstrated, once again, the role of the Coronaviridae family as extremely dangerous etiological agents of human zoonoses. The ability of coronaviruses to cross the species barrier and change to hosts commonly found in close proximity to humans highlights the need to characterize SDAV infections. The main host of the infection is the rat, as mentioned above. Rats inhabit large urban agglomerations, carrying a vast epidemic threat. Of the 2277 existing rodent species, 217 are reservoirs for 66 zoonotic diseases caused by viruses, bacteria, fungi, and protozoa. This review provides insight into the current state of knowledge of SDAV characteristics and its likely zoonotic potential.

Overview of Coronaviruses in Veterinary Medicine

Coronaviruses infect humans and a wide range of animals, causing predominantly respiratory and intestinal infections. This review provides background on the taxonomy of coronaviruses, the functions of viral proteins, and the life cycle of coronaviruses. In addition, the review focuses on coronaviral diseases in several agriculturally important, companion, and laboratory animal species (cats, cattle, chickens, dogs, mice, rats and swine) and briefly reviews human coronaviruses and their origins.

A comprehensive review of COVID-19 biology, diagnostics, therapeutics, and disease impacting the central nervous system

The ongoing COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a highly transmissible disease. SARS-CoV-2 is estimated to have infected over 153 million people and to have caused over 3.2 million global deaths since its emergence in December 2019. SARS-CoV-2 is the seventh coronavirus known to infect humans, and like other coronaviruses, SARS-CoV-2 infection is characterized by a variety of symptoms including general flu-like symptoms such as a fever, sore throat, fatigue, and shortness of breath. Severe cases often display signs of pneumonia, lymphopenia, acute kidney injury, cardiac injury, cytokine storms, lung damage, acute respiratory distress syndrome (ARDS), multiple organ failure, sepsis, and death. There is evidence that around 30% of COVID-19 cases have central nervous system (CNS) or peripheral nervous system (PNS) symptoms along with or in the absence of the previously mentioned symptoms. In cases of CNS/PNS impairments, patients display dizziness, ataxia, seizure, nerve pain, and loss of taste and/or smell. This review highlights the neurological implications of SARS-CoV-2 and provides a comprehensive summary of the research done on SARS-CoV-2 pathology, diagnosis, therapeutics, and vaccines up to May 5.