COVID-19 Outbreak: An Overview

COVID-19 and Alzheimer's Disease: A Literature Review

There are a number of potential implications for the field of Alzheimer’s disease (AD) stemming from the global spread of “SARS-COV-2”. Many studies that were conducted by Cleveland Clinic researchers identified a link between COVID-19 infection and brain abnormalities seen in people with AD. This article explains the association between COVID-19 and AD and how people with AD are affected by COVID-19, whether directly or indirectly. First, this article begins by explaining AD and its types, then giving an overview about COVID-19, its symptoms and the associated complications. Then, direct and indirect consequences of COVID-19 on people experiencing AD are discussed briefly. Some management strategies are recommended at the end of this article in addition to a future perspective on this topic. This article concludes by summarizing the main points mentioned about the association between COVID-19 and AD.

Asunaprevir, a Potent Hepatitis C Virus Protease Inhibitor, Blocks SARS-CoV-2 Propagation

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has become a global health concern. Various SARS-CoV-2 vaccines have been developed and are being used for vaccination worldwide. However, no therapeutic agents against coronavirus disease 2019 (COVID-19) have been developed so far; therefore, new therapeutic agents are urgently needed. In the present study, we evaluated several hepatitis C virus direct-acting antivirals as potential candidates for drug repurposing against COVID-19. Theses include asunaprevir (a protease inhibitor), daclatasvir (an NS5A inhibitor), and sofosbuvir (an RNA polymerase inhibitor). We found that asunaprevir, but not sofosbuvir and daclatasvir, markedly inhibited SARS-CoV-2-induced cytopathic effects in Vero E6 cells. Both RNA and protein levels of SARS-CoV-2 were significantly decreased by treatment with asunaprevir. Moreover, asunaprevir profoundly decreased virion release from SARS-CoV-2-infected cells. A pseudoparticle entry assay revealed that asunaprevir blocked SARS-CoV-2 infection at the binding step of the viral life cycle. Furthermore, asunaprevir inhibited SARS-CoV-2 propagation in human lung Calu-3 cells. Collectively, we found that asunaprevir displays broad-spectrum antiviral activity and therefore might be worth developing as a new drug repurposing candidate for COVID-19.

Network neighbors of viral targets and differentially expressed genes in COVID-19 are drug target candidates

The COVID-19 pandemic is raging. It revealed the importance of rapid scientific advancement towards understanding and treating new diseases. To address this challenge, we adapt an explainable artificial intelligence algorithm for data fusion and utilize it on new omics data on viral-host interactions, human protein interactions, and drugs to better understand SARS-CoV-2 infection mechanisms and predict new drug-target interactions for COVID-19. We discover that in the human interactome, the human proteins targeted by SARS-CoV-2 proteins and the genes that are differentially expressed after the infection have common neighbors central in the interactome that may be key to the disease mechanisms. We uncover 185 new drug-target interactions targeting 49 of these key genes and suggest re-purposing of 149 FDA-approved drugs, including drugs targeting VEGF and nitric oxide signaling, whose pathways coincide with the observed COVID-19 symptoms. Our integrative methodology is universal and can enable insight into this and other serious diseases.

Comparison of Sexual Function Before and After COVID-19 Infection in Female Patients

Introduction Ample data regarding the impact of coronavirus disease-2019 (COVID-19) on the pulmonary, nervous, and gastrointestinal systems are available. However, its impact on sexual performance is understudied. In this study, we will determine the impact of COVID-19 on the sexual performance of females.  Methods This longitudinal study was conducted in the COVID-19 unit of a tertiary care hospital in Pakistan from June 2020 to March 2021. We enrolled 300 female patients admitted to the hospital due to severe COVID-19. Patients' female sexual function index (FSFI) scale was assessed at the time of discharge. Participants were asked to answer the question based on their sexual performance before they contracted COVID-19. They were asked to return after 60 days, where FSFI was assessed again. Results The mean FSFI score for participants before COVID-19 was significantly higher compared to the score 60 days after discharge (28.16 ± 1.9 vs. 24.43 ± 2.5; p-value: <0.0001). Participants who had FSFI score more than 26 were significantly higher before COVID-19 (72.5% vs. 51.0%; p-value: <0.0001). Conclusion There is a significant decline in sexual function of females, who had contracted COVID-19 infection. COVID-19 survivors should be counseled properly about the impact on the sexual function when discussing long-term complications of COVID-19.

Ways to Address Perinatal Mast Cell Activation and Focal Brain Inflammation, including Response to SARS-CoV-2, in Autism Spectrum Disorder

The prevalence of autism spectrum disorder (ASD) continues to increase, but no distinct pathogenesis or effective treatment are known yet. The presence of many comorbidities further complicates matters, making a personalized approach necessary. An increasing number of reports indicate that inflammation of the brain leads to neurodegenerative changes, especially during perinatal life, "short-circuiting the electrical system" in the amygdala that is essential for our ability to feel emotions, but also regulates fear. Inflammation of the brain can result from the stimulation of mast cells-found in all tissues including the brain-by neuropeptides, stress, toxins, and viruses such as SARS-CoV-2, leading to the activation of microglia. These resident brain defenders then release even more inflammatory molecules and stop "pruning" nerve connections, disrupting neuronal connectivity, lowering the fear threshold, and derailing the expression of emotions, as seen in ASD. Many epidemiological studies have reported a strong association between ASD and atopic dermatitis (eczema), asthma, and food allergies/intolerance, all of which involve activated mast cells. Mast cells can be triggered by allergens, neuropeptides, stress, and toxins, leading to disruption of the blood-brain barrier (BBB) and activation of microglia. Moreover, many epidemiological studies have reported a strong association between stress and atopic dermatitis (eczema) during gestation, which involves activated mast cells. Both mast cells and microglia can also be activated by SARS-CoV-2 in affected mothers during pregnancy. We showed increased expression of the proinflammatory cytokine IL-18 and its receptor, but decreased expression of the anti-inflammatory cytokine IL-38 and its receptor IL-36R, only in the amygdala of deceased children with ASD. We further showed that the natural flavonoid luteolin is a potent inhibitor of the activation of both mast cells and microglia, but also blocks SARS-CoV-2 binding to its receptor angiotensin-converting enzyme 2 (ACE2). A treatment approach should be tailored to each individual patient and should address hyperactivity/stress, allergies, or food intolerance, with the introduction of natural molecules or drugs to inhibit mast cells and microglia, such as liposomal luteolin.

COVID-19 Pandemic-Adapted Radiotherapy Guidelines: Are They Really Followed?

BACKGROUND

In our department, we provided guidelines to the radiation oncologists (ROs) regarding the omission, delay, or shortening of radiotherapy (RT). The purpose was to reduce the patients' exposure to the hospital environment and to minimize the departmental overcrowding. The aim was to evaluate the ROs' compliance to these guidelines.

METHODS

ROs were asked to fill out a data collection form during patients' first visits in May and June 2020. The collected data included the ROs' age and gender, patient age and residence, RT purpose, treated tumor, the dose and fractionation that would have been prescribed, and RT changes. The chi-square test and binomial logistic regression were used to analyze the correlation between the treatment prescription and the collected parameters.

RESULTS

One hundred and twenty-six out of 205 prescribed treatments were included in this analysis. Treatment was modified in 61.1% of cases. More specifically, the treatment was omitted, delayed, or shortened in 7.9, 15.9, and 37.3% of patients, respectively. The number of delivered fractions was reduced by 27.9%. A statistically significant correlation (p = 0.028) between younger patients' age and lower treatment modifications rate was recorded.

CONCLUSION

Our analysis showed a reasonably high compliance of ROs to the pandemic-adapted guidelines. The adopted strategy was effective in reducing the number of admissions to our department.

COVID-19 mortality rate in children is U-shaped

Children are known to be better protected from COVID-19 than adults, but their susceptibility patterns and the risk relative to other diseases are insufficiently defined. Here, we found that the COVID-19 mortality rate is U-shaped in childhood: it initially decreases, reaching the minimum at the ages 3-10 years, and then increases throughout life. All-cause mortality and mortality from other diseases, such as pneumonia and influenza, show a similar pattern; however, childhood mortality rates from COVID-19 are considerably lower than from other diseases, with the best relative protection achieved at the youngest ages. Consistent with this, the fraction of COVID-19 deaths among all deaths increases as a function of age throughout childhood and the entire life. We discuss implications of the elevated postnatal COVID-19 risk and lower childhood COVID-19 mortality compared to other diseases.

The Exchange of Informational Support in Online Health Communities at the Onset of the COVID-19 Pandemic: Content Analysis

Background

Online health communities (OHCs) provide social support for ongoing health-related problems. COVID-19, the disease caused by SARS-CoV-2, has been an acute and substantial stressor worldwide. The disease and its impact, especially in the beginning phases, left many people with questions about the nature, treatment, and prevention of COVID-19. Unlike typical chronic ailments discussed on OHCs, which are more established, COVID-19, at least at the onset of the pandemic, is distinct in that it lacks a consensus of clinical diagnosis and an existing community foundation.

Objective

The study aims to investigate a newly formed OHC for COVID-19 to determine the topics and types of information exchange as well as the sources of information this community referenced during the early phases of the COVID-19 pandemic in the United States.

Methods

A total of 357 posts from a COVID-19 OHC on the MedHelp platform were annotated according to an open-coding process. Participants’ engagement patterns, topics of posts, and sources of information were quantified.

Results

Participants who offered informational support had a significantly higher percentage of responding more than once than those seeking information (P<.001). Among the information-seeking topics, symptoms and public health practice and psychological impacts were the most frequently discussed, with 26% (17/65) and 15% (10/65) of posts, respectively. Most informational support was expressed through feedback/opinion (181/220, 82.3%). Additionally, the most frequently referenced source of information was news outlets/websites, at 55% (11/20). Governmental websites were referenced less frequently.

Conclusions

The trends of this community could be useful in prioritizing public health responses to address the most common questions asked by the public during crisis communication and in identifying which venue of communication is most effective in reaching a public audience during such times.

HLA-dependent heterogeneity and macrophage immunoproteasome activation during lung COVID-19 disease

BACKGROUND

The worldwide pandemic caused by the SARS-CoV-2 virus is characterized by significant and unpredictable heterogeneity in symptoms that remains poorly understood.

METHODS

Transcriptome and single cell transcriptome of COVID19 lung were integrated with deeplearning analysis of MHC class I immunopeptidome against SARS-COV2 proteome.

RESULTS

An analysis of the transcriptomes of lung samples from COVID-19 patients revealed that activation of MHC class I antigen presentation in these tissues was correlated with the amount of SARS-CoV-2 RNA present. Similarly, a positive relationship was detected in these samples between the level of SARS-CoV-2 and the expression of a genomic cluster located in the 6p21.32 region (40 kb long, inside the MHC-II cluster) that encodes constituents of the immunoproteasome. An analysis of single-cell transcriptomes of bronchoalveolar cells highlighted the activation of the immunoproteasome in CD68 + M1 macrophages of COVID-19 patients in addition to a PSMB8-based trajectory in these cells that featured an activation of defense response during mild cases of the disease, and an impairment of alveolar clearance mechanisms during severe COVID-19. By examining the binding affinity of the SARS-CoV-2 immunopeptidome with the most common HLA-A, -B, and -C alleles worldwide, we found higher numbers of stronger presenters in type A alleles and in Asian populations, which could shed light on why this disease is now less widespread in this part of the world.

CONCLUSIONS

HLA-dependent heterogeneity in macrophage immunoproteasome activation during lung COVID-19 disease could have implications for efforts to predict the response to HLA-dependent SARS-CoV-2 vaccines in the global population.

X-ray and CT-scan-based automated detection and classification of covid-19 using convolutional neural networks (CNN)

Covid-19 (Coronavirus Disease-2019) is the most recent coronavirus-related disease that has been announced as a pandemic by the World Health Organization (WHO). Furthermore, it has brought the whole planet to a halt as a result of the worldwide introduction of lockdown and killed millions of people. While this virus has a low fatality rate, the problem is that it is highly infectious, and as a result, it has infected a large number of people, putting a strain on the healthcare system, hence, Covid-19 identification in patients has become critical. The goal of this research is to use X-rays images and computed tomography (CT) images to introduce a deep learning strategy based on the Convolutional Neural Network (CNN) to automatically detect and identify the Covid-19 disease. We have implemented two different classifications using CNN, i.e., binary and multiclass classification. A total of 3,877 images dataset of CT and X-ray images has been utilised to train the model in binary classification, out of which the 1,917 images are of Covid-19 infected individuals . An overall accuracy of 99.64%, recall (or sensitivity) of 99.58%, the precision of 99.56%, F1-score of 99.59%, and ROC of 100% has been observed for the binary classification. For multiple classifications, the model has been trained using a total of 6,077 images, out of which 1,917 images are of Covid-19 infected people, 1,960 images are of normal healthy people, and 2,200 images are of pneumonia infected people. An accuracy of 98.28%, recall (or sensitivity) of 98.25%, the precision of 98.22%, F1-score of 98.23%, and ROC of 99.87% has been achieved for the multiclass classification using the proposed method. On the currently available dataset, the our proposed model produced the desired results, and it can assist healthcare workers in quickly detecting Covid-19 positive patients.

SARS-CoV-2 Portrayed against HIV: Contrary Viral Strategies in Similar Disguise

SARS-CoV-2 and HIV are zoonotic viruses that rapidly reached pandemic scale, causing global losses and fear. The COVID-19 and AIDS pandemics ignited massive efforts worldwide to develop antiviral strategies and characterize viral architectures, biological and immunological properties, and clinical outcomes. Although both viruses have a comparable appearance as enveloped viruses with positive-stranded RNA and envelope spikes mediating cellular entry, the entry process, downstream biological and immunological pathways, clinical outcomes, and disease courses are strikingly different. This review provides a systemic comparison of both viruses' structural and functional characteristics, delineating their distinct strategies for efficient spread.

Comparative analysis of antibodies to SARS-CoV-2 between asymptomatic and convalescent patients

The SARS-CoV-2 viral pandemic has induced a global health crisis, which requires more in-depth investigation into immunological responses to develop effective treatments and vaccines. To understand protective immunity against COVID-19, we screened over 60,000 asymptomatic individuals in the Southeastern United States for IgG antibody positivity against the viral Spike protein, and approximately 3% were positive. Of these 3%, individuals with the highest anti-S or anti-RBD IgG level showed a strong correlation with inhibition of ACE2 binding and cross-reactivity against non-SARS-CoV-2 coronavirus S-proteins. We also analyzed samples from 94 SARS-CoV-2 patients and compared them with those of asymptomatic individuals. SARS-CoV-2 symptomatic patients had decreased antibody responses, ACE2 binding inhibition, and antibody cross-reactivity. Our study shows that healthy individuals can mount robust immune responses against SARS-CoV-2 without symptoms. Furthermore, IgG antibody responses against S and RBD may correlate with high inhibition of ACE2 binding in individuals tested for SARS-CoV-2 infection or post vaccination.

Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease

Coronaviruses are responsible for multiple pandemics and millions of deaths globally, including the current pandemic of coronavirus disease 2019 (COVID-19). Development of antivirals against coronaviruses, including the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) responsible for COVID-19, is essential for containing the current and future coronavirus outbreaks. SARS-CoV-2 proteases represent important targets for the development of antivirals because of their role in the processing of viral polyproteins. 3-Chymotrypsin-like protease (3CLpro) is one such protease. The cleavage of SARS-CoV-2 polyproteins by 3CLpro is facilitated by a Cys145–His41 catalytic dyad. We here characterized the catalytic roles of the cysteine–histidine pair for improved understanding of the 3CLpro reaction mechanism, to inform the development of more effective antivirals against Sars-CoV-2. The catalytic dyad residues were substituted by site-directed mutagenesis. All substitutions tested (H41A, H41D, H41E, C145A, and C145S) resulted in a complete inactivation of 3CLpro, even when amino acids with a similar catalytic function to that of the original residues were used. The integrity of the structural fold of enzyme variants was investigated by circular dichroism spectroscopy to test if the catalytic inactivation of 3CLpro was caused by gross changes in the enzyme secondary structure. C145A, but not the other substitutions, shifted the oligomeric state of the enzyme from dimeric to a higher oligomeric state. Finally, the thermodynamic stability of 3CLpro H41A, H41D, and C145S variants was reduced relative the wild-type enzyme, with a similar stability of the H41E and C145A variants. Collectively, the above observations confirm the roles of His41 and Cys145 in the catalytic activity and the overall conformational fold of 3CLpro SARS-CoV-2. We conclude that the cysteine–histidine pair should be targeted for inhibition of 3CLpro and development of antiviral against COVID-19 and coronaviruses.

Myricetin Inhibits SARS-CoV-2 Viral Replication by Targeting Mpro and Ameliorates Pulmonary Inflammation

The coronavirus disease 2019 (COVID-19) has spread widely around the world and has seriously affected the human health of tens of millions of people. In view of lacking anti-virus drugs target to SARS-CoV-2, there is an urgent need to develop effective new drugs. In this study, we reported our discovery of SARS-CoV-2 M^pro inhibitors. We selected 15 natural compounds, including 7 flavonoids, 3 coumarins, 2 terpenoids, one henolic, one aldehyde and one steroid compound for molecular docking and enzymatic screening. Myricetin were identified to have potent inhibit activity with IC₅₀ 3.684 ± 0.076 μM in the enzyme assay. The binding pose of Myricetin with SARS-CoV-2 M^pro was identified using molecular docking method. In the binding pocket of SARS-CoV-2 M^pro, the chromone ring of Myricetin interacts with His41 through π-π stacking, and the 3'-, 4'- and 7-hydroxyl of Myricetin interact with Phe140, Glu166and Asp187 through hydrogen bonds. Significantly, our results showed that Myricetin has potent effect on bleomycin-induced pulmonary inflammation by inhibiting the infiltration of inflammatory cells and the secretion of inflammatory cytokines IL-6, IL-1α, TNF-α and IFN-γ. Overall, Myricetin may be a potential drug for anti-virus and symptomatic treatment of COVID-19.

Rapid Isothermal Amplification for the Buccal Detection SARS-CoV-2 in the Context of Out-Patient COVID-19 Screening

A commercially available isothermal amplification of SARS-CoV-2 RNA was applied to self-collected saliva samples using dry dental cotton rolls, which were held in the mouth for two minutes. Of 212 tests, isothermal amplification yielded three (0.14%) invalid results, 120 (56.6%) positive results and 89 (42%) negative results. Compared to reference RT-PCR assays routinely performed simultaneously on nasopharyngeal swabs, excluding the three invalid isothermal amplification assays and one RT-PCR invalid assay, these figures indicated that 119/123 (96.7%) samples were positive in both methods and 85/85 samples were negative in both methods. Four positive buccal swabs which were missed by the isothermal amplification, exhibited Ct values of 26–34 in reference RT-PCR assays. Positive isothermal amplification detection was achieved in less than 10 min. Supervision of the self-sampling procedure was key to achieve these performances. These data support the proposal to use the protocol reported in this paper, including supervised buccal self-sampling, to screen people suspected of having COVID-19 at the point of care.

SARS-CoV-2 Variants in Lebanon: Evolution and Current Situation

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has seen a worldwide spread since its emergence in 2019, including to Lebanon, where 534,968 confirmed cases (8% of the population) and 7569 deaths have been reported as of 14 May 2021. With the genome sequencing of strains from various countries, several classification systems were established via genome comparison. For instance, the GISAID clades classification highlights key mutations in the encoded proteins that could potentially affect the virus' infectivity and transmission rates. In this study, 58 genomes of Lebanese SARS-CoV-2 strains were analyzed, 28 of which were sequenced for this study, and 30 retrieved from the GISAID and GenBank databases. We aimed to classify these strains, establish their phylogenetic relationships, and extract the mutations causing amino acid substitutions within, particularly, the structural proteins. The sequenced Lebanese SARS-COV-2 strains were classified into four GISAID clades and 11 Pango lineages. Moreover, 21 uncommon mutations in the structural proteins were found in the newly sequenced strains, underlining interesting combinations of mutations in the spike proteins. Hence, this study constitutes an observation and description of the current SARS-CoV-2 genetic and clade situation in Lebanon according to the available sequenced strains.

Nanobiocide Based-Silver Nanomaterials Upon Coronaviruses: Approaches for Preventing Viral Infections

The effectiveness of silver nanomaterials (AgNMs), as antiviral agents, has been confirmed in humans against many different types of viruses. Nanobiocides-based AgNMs can be effectively applied to eliminate coronaviruses (CoVs), as the cause of various diseases in animals and humans, particularly the fatal human respiratory infections. Mostly, these NMs act effectively against CoVs, thanks to the NMs' fundamental anti-viral structures like reactive oxygen species (ROS), and photo-dynamic and photo-thermal abilities. Particularly, the antiviral activity of AgNMs is clarified under three inhibitory mechanisms including viral entry limitation, attachment inhibition, and viral replication limitation. It is believed that nanobiocide with other possible materials such as TiO2, silica and, carbon NMs exclusively nano-graphene materials can emerge as a more effective disinfectant for long-term stability with low toxicity than common disinfectants. Nanobiocides also can be applied for the prevention and treatment of viral infections specifically against COVID-19.

Readability, content, and quality of COVID-19 patient education materials from academic medical centers in the United States

Background

SARS-CoV-2 has spread rapidly resulted in a global pandemic and public health crisis. The internet is a frequently used resource for providing patient education materials (PEMs). The aim of this study was to evaluate the readability, content, and quality of web-based PEMs on COVID-19 from US academic medical centers.

Methods

The names of US medical schools were obtained from the Association of American Medical Colleges website (n = 145). Institutional, hospital, and heath encyclopedia websites associated with each schools’ medical center were identified using Google. Readability of COVID-19 PEMs was calculated using three validated indices: (1) Flesh-Kincaid Grade Level, (2) Simple Measure of Gobbledygook, and (3) Gunning Frequency of Gobbledygook. Content was evaluated using a scoring matrix based on materials available on the Center for Disease Control website. The Patient Education Material Assessment Tool for Print (PEMAT-P) was used to assess usability and actionability.

Results

A total of 141 (97%) PEMs met inclusion criteria and were analyzed for readability, content, and quality. The mean readability was above the recommended sixth grade reading level (P < .001). Content was variable across PEMs. The PEMAT-P scores reflected good understandability with a median score of 83% (IQR 75%-87%), while actionability was poor with a median score of 41% (IQR 40%-60%).

Conclusions

Despite availability of web-based PEMs for COVID-19, the readability was significantly higher than the National Institute of Health and US Department of Health and Human Services recommended sixth grade reading level and actionability of PEMs was low. It is critical to provide readable PEMs on COVID-19 to effectively disseminate accurate information and facilitate patients’ understanding of the virus, how it spreads, and how to protect themselves.

ABO phenotype and SARS-CoV-2 infection: Is there any correlation?

COVID-19 is the currently evolving viral disease worldwide. It mainly targets the respiratory organs, tissues and causes illness. A plethora of studies has been performing to bring proper treatment and prevent people from the infection. Likewise, susceptibility to some infectious diseases has been associated with blood group phenotypes. The co-relationship of blood group with the occurrence of SARS-CoV-2 infection and death has been examined in numerous studies. This review explained the described studies regarding the correlation of blood group and the other essential factors with COVID-19.

Application of reinforcement learning for effective vaccination strategies of coronavirus disease 2019 (COVID-19)

Since December 2019, the new coronavirus has raged in China and subsequently all over the world. From the first days, researchers have tried to discover vaccines to combat the epidemic. Several vaccines are now available as a result of the contributions of those researchers. As a matter of fact, the available vaccines should be used in effective and efficient manners to put the pandemic to an end. Hence, a major problem now is how to efficiently distribute these available vaccines among various components of the population. Using mathematical modeling and reinforcement learning control approaches, the present article aims to address this issue. To this end, a deterministic Susceptible-Exposed-Infectious-Recovered-type model with additional vaccine components is proposed. The proposed mathematical model can be used to simulate the consequences of vaccination policies. Then, the suppression of the outbreak is taken to account. The main objective is to reduce the effects of Covid-19 and its domino effects which stem from its spreading and progression. Therefore, to reach optimal policies, reinforcement learning optimal control is implemented, and four different optimal strategies are extracted. Demonstrating the efficacy of the proposed methods, finally, numerical simulations are presented.

A simple and rapid approach for human herpesvirus type 8 subtype characterization using single base extension

Sequence analysis of the ORFK1 of human herpesvirus type 8 (HHV-8) allows the identification of six major subtypes (A-F), which are related to human migrations and the clinical progression of Kaposi's sarcoma. Sequencing and subsequent phylogenetic analysis of ORFK1 is considered to be the most reliable method for HHV-8 genotyping. However, it exhibits challenges and limitations. Herein, we designed and validated a single base extension (SBE) protocol for characterization of HHV-8 ORFK1 subtypes. A nested polymerase chain reaction (PCR) protocol was carried out to amplify a small 294-bp PCR product encompassing four single nucleotide polymorphisms at positions 360, 406, 465 and 527 of the HHV-8 genome. Finally, a multiplex SBE technique was developed and validated in 20 samples previously genotyped by phylogenetic analysis. The patterns obtained in this reaction could successfully discriminate between ORFK1 subtypes. The typing results obtained completely matched with those of the 'gold standard' method in all analysed samples. This method can reliably identify HHV-8 subtypes A, B and C, which are the most prevalent ones worldwide, and the remaining subtypes (D, E and F). SBE can be useful as an efficient, rapid and low-cost screening method for viral genotyping in a single tube, particularly samples with low-quality DNA, and with easy data interpretation.

COVID-19 in normal, diseased and transplanted liver

Starting from December 2019 the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has extended in the entire world giving origin to a pandemic. Although the respiratory system is the main apparatus involved by the infection, several other organs may suffer coronavirus disease 2019 (COVID-19)-related injuries. The human tissues expressing angiotensin-converting enzyme 2 (ACE2) are all possible targets of viral damage. In fact myocarditis, meningo-encephalitis, acute kidney injury and other complications have been described with regard to SARS-CoV-2 infection. The liver has a central role in the body homeostasis contributing to detoxification, catabolism and also synthesis of important factor such as plasma proteins. ACE2 is significantly expressed just by cholangiocytes within the liver, however transaminases are increased in more than one third of COVID-19 patients, at hospital admission. The reasons for liver impairment in the course of this infection are not completely clear at present and multiple factors such as: Direct viral effect, release of cytokines, ischemic damage, use of hepatotoxic drugs, sepsis, and others, may contribute to damage. While COVID-19 seems to elicit just a transient alteration of liver function tests in subjects with normal hepatic function, of concern, more severe sequelae are frequently observed in patients with a reduced hepatic reserve. In this review we report data regarding SARS-CoV-2 infection in subjects with normal or diseased liver. In addition the risks of COVID-19 in immunosuppressed patients (either transplanted or suffering for autoimmune liver diseases) are also described.

Segmenting lung lesions of COVID-19 from CT images via pyramid pooling improved Unet

Segmenting lesion regions of Coronavirus Disease 2019 (COVID-19) from computed tomography (CT) images is a challenge owing to COVID-19 lesions characterized by high variation, low contrast between infection lesions and around normal tissues, and blurred boundaries of infections. Moreover, a shortage of available CT dataset hinders deep learning techniques applying to tackling COVID-19. To address these issues, we propose a deep learning-based approach known as PPM-Unet to segmenting COVID-19 lesions from CT images. Our method improves an Unet by adopting pyramid pooling modules instead of the conventional skip connection and then enhances the representation of the neural network by aiding the global attention mechanism. We first pre-train PPM-Unet on COVID-19 dataset of pseudo labels containing1600 samples producing a coarse model. Then we fine-tune the coarse PPM-Unet on the standard COVID-19 dataset consisting of 100 pairs of samples to achieve a fine PPM-Unet. Qualitative and quantitative results demonstrate that our method can accurately segment COVID-19 infection regions from CT images, and achieve higher performance than other state-of-the-art segmentation models in this study. It offers a promising tool to lay a foundation for quantitatively detecting COVID-19 lesions.

Simple hemogram to support the decision-making of COVID-19 diagnosis using clusters analysis with self-organizing maps neural network

The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which is related to new coronavirus disease (COVID-19) has mobilized several scientifics to explore clinical data using soft-computing approaches. In the context of machine learning, previous studies have explored supervised algorithms to predict and support diagnosis based on several clinical parameters from patients diagnosed with and without COVID-19. However, in most of them the decision is based on a "black-box" method, making it impossible to discover the variable relevance in decision making. Hence, in this study, we introduce a non-supervised clustering analysis with neural network self-organizing maps (SOM) as a strategy of decision-making. We propose to identify potential variables in routine blood tests that can support clinician decision-making during COVID-19 diagnosis at hospital admission, facilitating rapid medical intervention. Based on SOM features (visual relationships between clusters and identification of patterns and behaviors), and using linear discriminant analysis , it was possible to detect a group of units of the map with a discrimination power around 83% to SARS-CoV-2-positive patients. In addition, we identified some variables in admission blood tests (Leukocytes, Basophils, Eosinophils, and Red cell Distribution Width) that, in combination had strong influence in the clustering performance, which could assist a possible clinical decision. Thus, although with limitations, we believe that SOM can be used as a soft-computing approach to support clinician decision-making in the context of COVID-19.

Demographic and socioeconomic determinants of COVID-19 across Oman - A geospatial modelling approach

Local, bivariate relationships between coronavirus 2019 (COVID-19) infection rates and a set of demographic and socioeconomic variables were explored at the district level in Oman. To limit multicollinearity a principal component analysis was conducted, the results of which showed that three components together could explain 65% of the total variance that were therefore subjected to further study. Comparison of a generalized linear model (GLM) and geographically weighted regression (GWR) indicated an improvement in model performance using GWR (goodness of fit=93%) compared to GLM (goodness of fit=86%). The local coefficient of determination (R2) showed a significant influence of specific demographic and socioeconomic factors on COVID-19, including percentages of Omani and non-Omani population at various age levels; spatial interaction; population density; number of hospital beds; total number of households; purchasing power; and purchasing power per km2. No direct correlation between COVID- 19 rates and health facilities distribution or tobacco usage. This study suggests that Poisson regression using GWR and GLM can address unobserved spatial non-stationary relationships. Findings of this study can promote current understanding of the demographic and socioeconomic variables impacting the spatial patterns of COVID-19 in Oman, allowing local and national authorities to adopt more appropriate strategies to cope with this pandemic in the future and also to allocate more effective prevention resources.

Analysis of natural compounds against the activity of SARS-CoV-2 NSP15 protein towards an effective treatment against COVID-19: a theoretical and computational biology approach

Coronavirus infectious disease 2019 (COVID-19), a viral infection caused by a novel coronavirus (nCoV), continues to emerge as a serious threat to public health. This pandemic caused by SARS-CoV-2 (severe acute respiratory syndrome-coronavirus-2) has infected globally with 1,550,000 plus deaths to date, representing a high risk to public health. No effective drug or vaccine is available to curb down this deadly virus. The expedition for searching for a potential drug or vaccine against COVID-19 is of massive potential and favour to the community. This study is focused on finding an effective natural compound that can be processed further into a potential inhibitor to check the activity of SARS-CoV-2 with minimal side effects targeting NSP15 protein, which belongs to the EndoU enzyme family. The natural screening suggested two efficient compounds (PubChem ID: 95372568 and 1776037) with dihydroxyphenyl region of the compound, found to be important in the interaction with the viral protein showing promising activity which may act as a potent lead inhibitory molecule against the virus. In combination with virtual screening, modelling, drug likeliness, molecular docking, and 500 ns cumulative molecular dynamics simulations (100 ns for each complex) along with the decomposition analysis to calculate and confirm the stability and fold, we propose 95372568 and 1776037 as novel compounds of natural origin capable of getting developed into potent lead molecules against SARS-CoV-2 target protein NSP15.

Mental Health of Medical Staff During the Coronavirus Disease 2019 Pandemic: A Systematic Review and Meta-Analysis

OBJECTIVE

This study aimed to quantify the prevalence of the adverse mental health outcomes in medical staff working in the hospital settings during the coronavirus disease 2019 (COVID-19) pandemic and explore the relative distribution of anxiety and depressive symptoms.

METHODS

PubMed, EMBASE, China National Knowledge Infrastructure, WANFANG DATA, and VIP Database for Chinese Technical Periodicals were searched for articles published from January 1, 2019, to April 19, 2020. The prevalence estimates of adverse mental health symptoms in medical staff were pooled using the random-effects model.

RESULTS

A total of 35 articles and data of 25,343 medical staff were used in the final analysis. The pooled prevalence estimates in medical staff during the COVID-19 pandemic were as follows (ordered from high to low): fear-related symptoms, 67% (95% confidence interval [CI] = 61%-73%); high levels of perceived stress, 56% (95% CI = 32%-79%), anxiety symptoms, 41% (95% CI = 35%-47%); insomnia, 41% (95% CI = 33%-50%); posttraumatic stress disorder symptoms, 38% (95% CI = 34%-43%); depressive symptoms, 27% (95% CI = 20%-34%); and somatic symptoms, 16% (95% CI = 3%-36%). The subgroup analysis revealed that the prevalence estimates of fear-related symptoms were consistently high.

CONCLUSIONS

Medical staff during the COVID-19 epidemic have a high prevalence of adverse mental health symptoms. Data-based strategies are needed to optimize mental health of medical staff and other health care professionals during times of high demand such as the COVID-19 and other epidemics.PROSPERO Registration: CRD42020182433.

Amachawadi R, Dash AP, Yadav MP, Prasad KS, P S, Jain AS, Shivamallu C. COVID-19 PANDEMIC: A SYSTEMATIC REVIEW ON THE CORONAVIRUSES OF ANIMALS AND SARS-CoV-2

Coronaviruses (CoVs), classified into four genera, viz., alpha-, beta-, gamma-, and Delta- CoV, represent an important group of diverse transboundary pathogens that can infect a variety of mammalian and avian species including humans, animals, poultry, and non-poultry birds. CoVs primarily infect lung and gut epithelial cells, besides monocytes and macrophages. CoVs have high mutation rates causing changes in host specificity, tissue tropism, and mode of virus excretion and transmissions. The recent CoV zoonoses are SARS, MERS, and COVID-19 that are caused by the transmission of beta-CoVs of bats to humans. Recently, reverse zoonoses of the COVID-19 virus have been detected in dogs, tigers, and minks. Beta-CoV strains also infect bovine (BCoV) and canine species (CRCoV); both these beta-CoVs might have originated from a common ancestor. Despite the high genetic similarity between BCoV, CRCoV, and HCoV-OC43, these differ in species specificity. Alpha-CoV strains infect canine (CCoV), feline (FIPV), swine (TGEV and PEDV), and humans (HCoV229E and NL63). Six coronavirus species are known to infect and cause disease in pigs, seven in human beings, and two in dogs. The high mutation rate in CoVs is attributed to error-prone 3′-5′ exoribonuclease (NSP 14), and genetic recombination to template shift by the polymerase. The present compilation describes the important features of the CoVs and diseases caused in humans, animals, and birds that are essential in surveillance of diverse pool of CoVs circulating in nature, and monitoring interspecies transmission, zoonoses, and reverse zoonoses.

Diffusion modeling of COVID-19 under lockdown

Viral immune evasion by sequence variation is a significant barrier to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine design and coronavirus disease-2019 diffusion under lockdown are unpredictable with subsequent waves. Our group has developed a computational model rooted in physics to address this challenge, aiming to predict the fitness landscape of SARS-CoV-2 diffusion using a variant of the bidimensional Ising model (2DIMV) connected seasonally. The 2DIMV works in a closed system composed of limited interaction subjects and conditioned by only temperature changes. Markov chain Monte Carlo method shows that an increase in temperature implicates reduced virus diffusion and increased mobility, leading to increased virus diffusion.

Landscape of humoral immune responses against SARS-CoV-2 in patients with COVID-19 disease and the value of antibody testing

A new pandemic is ongoing in several parts of the world. The agent responsible is the newly emerged severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The symptoms associated with this virus are known as the coronavirus disease-2019 (COVID-19). In this review, we summarize the published data on virus specific antibodies in hospitalized patients with COVID-19 disease, patients recovered from the disease and the individuals who are asymptomatic with SARS-CoV-2 infections. The review highlights the following: i) an adjunct role of antibody tests in the diagnosis of COVID-19 in combination with RT-PCR; ii) status of antibodies from COVID-19 convalescent patients to select donors for plasma therapy; iii) the potential confounding effects of other coronaviruses, measles, mumps and rubella in antibody testing due to homology of certain viral genes; and iv) the role of antibody testing for conducting surveillance in populations, incidence estimation, contact tracing and epidemiologic studies.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seroconversion in hematology-oncology patients

Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) in China at the end of 2019, the virus has spread rapidly across the globe leading to millions of infections and subsequent deaths. Although the virus infects those exposed indiscriminately, there are groups in society at an increased risk of severe infection, leading to increased morbidity. Patients suffering from hematological cancers, particularly leukemia, lymphoma, and myeloma, may be one such group and previous studies have suggested that they may be at a three to four times greater risk of severe COVID‐19 after SARS‐CoV‐2 infection, leading to admissions to ICU, mechanical ventilation, and death compared to those without such malignancies. Serological testing for IgG seroconversion has been extensively studied in the immunocompetent, but fewer publications have characterized this process in large series of immunocompromised patients. This study described 20 patients with hematological cancers who tested positive for SARS‐CoV‐2 via PCR with 12 of the patients receiving further serological testing. We found that of the 12 patients screened for SARS‐CoV‐2 IgG antibodies, only 2 (16.6%) were able to generate an immune response to the infection. Yet despite this low seroconversion rate in this cohort, none of these patients died or became particularly unwell with COVID‐19 or its related complications.

Investigation into the immune response of haematology patients to SARS‐CoV‐2.

Although haematology patients are at a greater risk of infection they appear to be less susceptible to severe SARS‐CoV‐2 infections.

Suppression of the immune response could potentially confer some protection from severe COVID‐19.

SARS-CoV-2 molecular identification and clinical data analysis of associated risk factors from a COVID-19 testing laboratory of a coastal region in Bangladesh

Background and aim

Outbreak of COVID-19 seems to have exacerbated across the globe, including Bangladesh. Scientific literature on the clinical data record of COVID-19 patients in Bangladesh is inadequate. Our study analyzes the clinical data of COVID-19 positive patients based on molecular identification and risk factor correlated with three variables (age, sex, residence) and COVID-19 prevalence in the four districts of Chattogram Division (Noakhali, Feni, Lakshmipur and Chandpur) with an aim to understand the trajectory of this pandemic in Chattogram, Southern Bangladesh.

Methods

A cross-sectional study is conducted in the context of RT-PCR-based COVID-19 positive 5,589 individuals diagnosed with SARS-CoV-2 infection from the COVID-19 testing laboratory, Abdul Malek Ukil Medical College, Noakhali-3800, Bangladesh. For molecular confirmation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), standard diagnostic protocols through real-time reverse transcriptase-polymerase chain reaction (RT-qPCR) were conducted. Different patient demographics were analyzed using SPSS version 22 for exploring the relationship of three factors – age, sex, and residence with a cumulative number of COVID-19 positive cases and prevalence of COVID-19 in four districts in Chattogram division. The data was recorded between May to July, 2020.

Results

Among the three parameters, the present study revealed that 20–40 cohort had the highest incidence of infection rate (51.80%, n = 2895) among the different age groups. Among the infected individuals, 56.8% (n = 3177) were male and 43.2% (n = 2412) were female, denoting males being the most susceptible to this disease. Urban residents (52.7%, n = 2948) were more vulnerable to SARS-CoV-2 infection than those residing in rural areas (47.3%, n = 2641). The prevalence of COVID-19 positive cases among the four districts was recorded highest in the Noakhali district with 36.8% (n = 2057), followed by the Feni, Lakshmipur and Chandpur districts with 25.9% (n = 1448), 20.8% (n = 1163) and 16.5% (n = 921), respectively.

Conclusions

This study presents a statistical correlation of certain factors linked to Bangladesh with confirmed COVID-19 patients, which will enable health practitioners and policy makers to take proactive steps to control and mitigate disease transmission.

Computationally approached inhibition potential of Tinospora cordifolia towards COVID-19 targets

The recent emergence of novel coronavirus (SARS-CoV-2) has been a major threat to human society, as the challenge of finding suitable drug or vaccine is not met till date. With increasing morbidity and mortality, the need for novel drug candidates is under great demand. The investigations are progressing towards COVID-19 therapeutics. Among the various strategies employed, the use of repurposed drugs is competing along with novel drug inventions. Based on the therapeutic significance, the chemical constituents from the extract of Tinospora cordifolia belonging to various classes like alkaloids, lignans, steroids and terpenoids are investigated as potential drug candidates for COVID-19. The inhibition potential of the proposed compounds against viral spike protein and human receptor ACE2 were evaluated by computational molecular modeling (Auto dock), along with their ADME/T properties. Prior to docking, the initial geometry of the compounds were optimized by Density functional theory (DFT) method employing B3LYP hybrid functional and 6-311 +  + G (d,p) basis set. The results of molecular docking and ADME/T studies have revealed 6 constituents as potential drug candidates that can inhibit the binding of SARS-CoV-2 spike protein with the human receptor ACE2 protein. The narrowed down list of constituents from Tinospora cordifolia paved way for further tuning their ability to inhibit COVID-19 by modifying the chemical structures and by employing computational geometry optimization and docking methods.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13337-021-00666-7.

Generation and Characterization of recombinant SARS-CoV-2 expressing reporter genes

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen responsible of coronavirus disease 2019 (COVID-19), has devastated public health services and economies worldwide. Despite global efforts to contain the COVID-19 pandemic, SARS-CoV-2 is now found in over 200 countries and has caused an upward death toll of over 1 million human lives as of November 2020. To date, only one Food and Drug Administration (FDA)-approved therapeutic drug (Remdesivir) and a monoclonal antibody, MAb (Bamlanivimab) are available for the treatment of SARS-CoV-2. As with other viruses, studying SARS-CoV-2 requires the use of secondary approaches to detect the presence of the virus in infected cells. To overcome this limitation, we have generated replication-competent recombinant (r)SARS-CoV-2 expressing fluorescent (Venus or mCherry) or bioluminescent (Nluc) reporter genes. Vero E6 cells infected with reporter-expressing rSARS-CoV-2 can be easily detected via fluorescence or luciferase expression and display a good correlation between reporter gene expression and viral replication. Moreover, rSARS-CoV-2 expressing reporter genes have comparable plaque sizes and growth kinetics to those of wild-type virus, rSARS-CoV-2/WT. We used these reporter-expressing rSARS-CoV-2 to demonstrate their feasibility to identify neutralizing antibodies (NAbs) or antiviral drugs. Our results demonstrate that reporter-expressing rSARS-CoV-2 represent an excellent option to identify therapeutics for the treatment of SARS-CoV-2, where reporter gene expression can be used as valid surrogates to track viral infection. Moreover, the ability to manipulate the viral genome opens the feasibility of generating viruses expressing foreign genes for their use as vaccines for the treatment of SARS-CoV-2 infection.IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen that causes coronavirus disease 2019 (COVID-19), has significantly impacted the human health and economic status worldwide. There is an urgent need to identify effective prophylactics and therapeutics for the treatment of SARS-CoV-2 infection and associated COVID-19 disease. The use of fluorescent- or luciferase-expressing reporter expressing viruses has significantly advanced viral research. Here, we generated recombinant (r)SARS-CoV-2 expressing fluorescent (Venus and mCherry) or luciferase (Nluc) reporter genes and demonstrate that they represent an excellent option to track viral infections in vitro. Importantly, reporter-expressing rSARS-CoV-2 display similar growth kinetics and plaque phenotype that their wild-type counterpart (rSARS-CoV-2/WT), demonstrating their feasibility to identify drugs and/or neutralizing antibodies (NAbs) for the therapeutic treatment of SARS-CoV-2. Henceforth, these reporter-expressing rSARS-CoV-2 can be used to interrogate large libraries of compounds and/or monoclonal antibodies (MAb), in high-throughput screening settings, to identify those with therapeutic potential against SARS-CoV-2.

SARS-CoV-2 infection affects the lower urinary tract and male genital system: A systematic review

PubMed, Scopus, and ISI Web of Knowledge databases were searched to identify studies published up to December 2020 on the involvement of urinary and male genital systems in COVID‐19. Sixteen studies involving a total of 575 patients (538 males and 37 females) were included in this systematic review. The COVID‐19 phase was available for 479 patients: 426 in the acute and 53 in the recovery phase. De novo lower urinary tract symptoms (LUTS) were observed in 43 patients and deterioration of pre‐existing LUTS in 7. Bladder hemorrhage was observed in three patients and acute urinary retention in one. Regarding the male genital system, scrotal discomfort was observed in 8 patients, swelling in 14, pain in 16, and erythema in 1; low flow priapism was observed in 2 patients. Ultrasound examination identified acute orchitis in 10 patients, acute epididymitis in 7, and acute epididymo‐orchitis in 16. A case–control study reported that patients with moderate COVID‐19 show a significant reduction in sperm concertation, the total number of sperms per ejaculate, progressive motility, and complete motility. In contrast to what is known from the first studies on the subject, this review also includes subsequent studies that give evidence of the involvement of the lower urinary tract and male genital system in COVID‐19.

SARS-CoV-2: what it is, how it acts, and how it manifests in imaging studies

COVID-19 is a disease with many clinical, biochemical, and radiological signs that has a predilection for the lungs, probably because of the high number of ACE-2 receptors in this organ. The infection of cells activates proinflammatory substances, causing diffuse alveolar damage, which is the histopathological basis of ARDS. The exudative phase would manifest as ground-glass opacities and consolidation, and the proliferative phase would manifest as a tendency toward a more linear morphology. Both CT and PET/CT findings support the inflammatory character of the lung lesions in the initial phase of the disease and in patients with mild-moderate disease. Severe cases have pulmonary hypoperfusion that is likely due to abnormal alveolar ventilation and perfusion. On the other hand, a prothrombotic state increases the risk of thromboembolic disease through the activation of coagulation and platelet pathways with the production of fibrin degradation products (D-dimer) and consumption of platelets.

SARS-CoV-2: what it is, how it acts, and how it manifests in imaging studies

COVID-19 is a disease with many clinical, biochemical, and radiological signs that has a predilection for the lungs, probably because of the high number of ACE-2 receptors in this organ. The infection of cells activates proinflammatory substances, causing diffuse alveolar damage, which is the histopathological basis of ARDS. The exudative phase would manifest as ground-glass opacities and consolidation, and the proliferative phase would manifest as a tendency toward a more linear morphology. Both CT and PET/CT findings support the inflammatory character of the lung lesions in the initial phase of the disease and in patients with mild-moderate disease.

Severe cases have pulmonary hypoperfusion that is likely due to abnormal alveolar ventilation and perfusion. On the other hand, a prothrombotic state increases the risk of thromboembolic disease through the activation of coagulation and platelet pathways with the production of fibrin degradation products (D-dimer) and consumption of platelets.

COVID-19: A methyl-group assault?

The socio-economic implications of COVID-19 are devastating. Considerable morbidity is attributed to ‘long-COVID’ – an increasingly recognized complication of infection. Its diverse symptoms are reminiscent of vitamin B₁₂ deficiency, a condition in which methylation status is compromised.

We suggest why SARS-CoV-2 infection likely leads to increased methyl-group requirements and other disturbances of one-carbon metabolism. We propose these might explain the varied symptoms of long-COVID. Our suggested mechanism might also apply to similar conditions such as myalgic encephalomyelitis/chronic fatigue syndrome.

The hypothesis is evaluable by detailed determination of vitamin B₁₂ and folate status, including serum formate as well as homocysteine and methylmalonic acid, and correlation with viral and host RNA methylation and symptomatology. If confirmed, methyl-group support should prove beneficial in such individuals.

Screened antipsychotic drugs inhibit SARS-CoV-2 binding with ACE2 in vitro

AIM

The coronavirus disease 2019 (COVID-19) pandemic has swept the globe and no specific effective drug has been identified. Drug repurposing is a well-known method to address the crisis in a time-critical fashion. Antipsychotic drugs (APDs) have been reported to inhibit DNA replication of hepatitis B virus, measles virus germination, and HIV infection, along with replication of SARS-CoV and MERS-CoV, both of which interact with host cells as SARS-CoV-2.

METHODS

Nineteen APDs were screened using ACE2-HEK293T cell membrane chromatography (ACE2-HEK293T/CMC). Cytotoxicity assay, coronavirus spike pseudotype virus entry assay, surface plasmon resonance, and virtual molecular docking were applied to detect affinity between ACE2 protein and drugs and a potential antiviral property of the screened compounds.

KEY FINDINGS

After the CMC screening, 8 of the 19 APDs were well-retained on ACE2-HEK293T/CMC column and showed significant antiviral activities in vitro. Three quarters of them belong to phenothiazine and could significantly inhibit the entrance of coronavirus into ACE2-HEK293T cells. Aother two drugs, aripiprazole and tiapride, exhibited weaker inhibition. We selected five of the drugs for subsequent evaluation. All five showed similar affinity to ACE2 and virtual molecular docking demonstrated they bound with different amino acids respectively on ACE2 which SARS-CoV-2 binds to.

SIGNIFICANCE

Eight APDs were screened for binding with ACE2, five of which demonstrated potential protective effects against SARS-CoV-2 through acting on ACE2. Although the five drugs have a weak ability to block SARS-CoV-2 with a single binding site, they may provide a synergistic effect in adjuvant therapy of COVID-19 infection.

Occurrence, fate and removal of SARS-CoV-2 in wastewater: Current knowledge and future perspectives

The coronavirus disease 2019 (COVID-19), a pandemic of global concern, is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recently, many studies have documented the detection of SARS-CoV-2 in human excreta and wastewater. The presence of SARS-CoV-2 in human excreta and wastewater poses serious implications for wastewater treatment. Thus, this review aims to understand the fate of SARS-CoV-2 in the urban water cycle and its inactivation in different stages of treatment in wastewater treatment plants (WWTPs) for effective control to prevent any recurrence of the outbreak. The viral load of SARS-CoV-2 in feces of individuals tested positive has been reported to be in the range of 104-108 copies/L depending on the infection stages. In the wastewater, dilution of feces results in the decrease of the viral load in the range of 102-106.5 copies/L. Monitoring of SARS-CoV-2 in WWTP samples following the wastewater-based epidemiology (WBE) can complement real epidemiological data from clinical testing to help to monitor disease outbreaks in a community. Though promising, high uncertainty involved with the WBE technique warrants further research for reliable and quantitative information. Inactivation of SARS-CoV-2 in WWTPs depends on the operational parameters and is generally enhanced by the tertiary treatment and disinfection techniques with a higher dosage. However, the risk of SARS-CoV-2 dissemination by the treated effluent intended to be disposed of or reused in the urban water cycle needs to be assessed with respect to the extent of viral infectivity.

Nucleic Acid-Sensing Pathways During SARS-CoV-2 Infection: Expectations versus Reality

The coronavirus disease 2019 (COVID-19) pandemic has affected millions of people and crippled economies worldwide. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for this pandemic has triggered avid research on its pathobiology to better understand the pathophysiology of COVID-19. In the absence of approved antiviral therapeutic strategies or vaccine platforms capable of effectively targeting this global threat, the hunt for effective therapeutics has led to many candidates being actively evaluated for their efficacy in controlling or preventing COVID-19. In this review, we gathered current evidence on the innate nucleic acid-sensing pathways expected to be elicited by SARS-CoV-2 and the immune evasion mechanisms they have developed to promote viral replication and infection. Within the nucleic acid-sensing pathways, SARS-CoV-2 infection and evasion mechanisms trigger the activation of NOD-signaling and NLRP3 pathways leading to the production of inflammatory cytokines, IL-1β and IL-6, while muting or blocking cGAS-STING and interferon type I and III pathways, resulting in decreased production of antiviral interferons and delayed innate response. Therefore, blocking the inflammatory arm and boosting the interferon production arm of nucleic acid-sensing pathways could facilitate early control of viral replication and dissemination, prevent disease progression, and cytokine storm development. We also discuss the rationale behind therapeutic modalities targeting these sensing pathways and their implications in the treatment of COVID-19.

The Prognostic Value of Eosinophil Recovery in COVID-19: A Multicentre, Retrospective Cohort Study on Patients Hospitalised in Spanish Hospitals

OBJECTIVES

A decrease in blood cell counts, especially lymphocytes and eosinophils, has been described in patients with serious Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), but there is no knowledge of their potential role of the recovery in these patients' prognosis. This article aims to analyse the effect of blood cell depletion and blood cell recovery on mortality due to COVID-19.

DESIGN

This work was a retrospective, multicentre cohort study of 9644 hospitalised patients with confirmed COVID-19 from the Spanish Society of Internal Medicine's SEMI-COVID-19 Registry.

SETTING

This study examined patients hospitalised in 147 hospitals throughout Spain.

PARTICIPANTS

This work analysed 9644 patients (57.12% male) out of a cohort of 12,826 patients ≥18 years of age hospitalised with COVID-19 in Spain included in the SEMI-COVID-19 Registry as of 29 May 2020.

MAIN OUTCOME MEASURES

The main outcome measure of this work is the effect of blood cell depletion and blood cell recovery on mortality due to COVID-19. Univariate analysis was performed to determine possible predictors of death, and then multivariate analysis was carried out to control for potential confounders.

RESULTS

An increase in the eosinophil count on the seventh day of hospitalisation was associated with a better prognosis, including lower mortality rates (5.2% vs. 22.6% in non-recoverers, OR 0.234; 95% CI, 0.154 to 0.354) and lower complication rates, especially regarding the development of acute respiratory distress syndrome (8% vs. 20.1%, p = 0.000) and ICU admission (5.4% vs. 10.8%, p = 0.000). Lymphocyte recovery was found to have no effect on prognosis. Treatment with inhaled or systemic glucocorticoids was not found to be a confounding factor.

CONCLUSION

Eosinophil recovery in patients with COVID-19 who required hospitalisation had an independent prognostic value for all-cause mortality and a milder course.

Development of Plant-Produced Recombinant ACE2-Fc Fusion Protein as a Potential Therapeutic Agent Against SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease (COVID-19) which has recently emerged as a potential threat to global public health. SARS-CoV-2 is the third known human coronavirus that has huge impact on the human population after SARS-CoV and MERS-CoV. Although some vaccines and therapeutic drugs are currently in clinical trials, none of them are approved for commercial use yet. As with SARS-CoV, SARS-CoV-2 utilizes angiotensin-converting enzyme 2 (ACE2) as the cell entry receptor to enter into the host cell. In this study, we have transiently produced human ACE2 fused with the Fc region of human IgG1 in Nicotiana benthamiana and the in vitro neutralization efficacy of the plant-produced ACE2-Fc fusion protein was assessed. The recombinant ACE2-Fc fusion protein was expressed in N. benthamiana at 100 μg/g leaf fresh weight on day 6 post-infiltration. The recombinant fusion protein showed potent binding to receptor binding domain (RBD) of SARS-CoV-2. Importantly, the plant-produced fusion protein exhibited potent anti-SARS-CoV-2 activity in vitro. Treatment with ACE2-Fc fusion protein after viral infection dramatically inhibit SARS-CoV-2 infectivity in Vero cells with an IC50 value of 0.84 μg/ml. Moreover, treatment with ACE2-Fc fusion protein at the pre-entry stage suppressed SARS-CoV-2 infection with an IC50 of 94.66 μg/ml. These findings put a spotlight on the plant-produced ACE2-Fc fusion protein as a potential therapeutic candidate against SARS-CoV-2.

COVID-19 and Dementia

The World Health Organization has declared the COVID-19 outbreak a pandemic. The causative agent for COVID-19 is an RNA virus of the Coronaviridae family. In addition to the respiratory and other complications, a significant proportion of COVID-19 patients show neurological manifestations. Dementia is a neurocognitive disorder, the prevalence of which is projected to increase in the coming decades. This review provides an overview of the effects of COVID-19 on dementia patients.

Do Animals Play a Role in the Transmission of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2)? A Commentary

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) belongs to the Beta-coronavirus genus. It is 96.2% homologous to bat CoV RaTG13 and 88% homologous to two bat SARS-like coronaviruses. SARS-CoV-2 is the infectious agent responsible for the coronavirus disease (COVID-19), which was first reported in the Hubei province of Wuhan, China, at the beginning of December 2019. Human transmission from COVID-19 patients or incubation carriers occurs via coughing, sneezing, speaking, discharge from the nose, or fecal contamination. Various strains of the virus have been reported around the world, with different virulence and behavior. In addition, SARS-CoV-2 shares certain epitopes with some taxonomically related viruses, with tropism for the most common synanthropic animals. By elucidating the immunological properties of the circulating SARS-CoV-2, a partial protection due to human-animal interactions could be supposed in some situations. In addition, differential epitopes could be used for the differential diagnosis of SARS-CoV-2 infection. There have been cases of transmission from people with COVID-19 to pets such as cats and dogs. In addition, wild felines were infected. All These animals were either asymptomatic or mildly symptomatic and recovered spontaneously. Experimental studies showed cats and ferrets to be more susceptible to COVID-19. COVID-19 positive dogs and felines do not transmit the infection to humans. In contrast, minks at farms were severely infected from people with COVID-19. A SARS-Cov-2 variant in the Danish farmed mink that had been previously infected by COVID-19 positive workers, spread to mink workers causing the first case of animal-to-human infection transmission that causes a moderate decreased sensitivity to neutralizing antibodies. Thus, more investigations are necessary. It remains important to understand the risk that people with COVID-19 pose to their pets, as well as wild or farm animals so effective recommendations and risk management measures against COVID-19 can be made. A One Health unit that facilitates collaboration between public health and veterinary services is recommended.

Consequences of COVID-19 Outbreak in Italy: Medical Responsibilities and Governmental Measures

The COVID-19 pandemic has shocked the world causing more victims than the latest global epidemics such as Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) in 2003, and the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in 2012. Italy has been one of the most affected countries, and it had to deal with an already weak economic condition and cuts to public health services due to budgetary requirements from the last decade—something that made the situation even more dramatic. Deaths have exceeded 600.000 worldwide. During the emergency, regulatory measures were taken to counter the situation. This study highlights the main anti-COVID-19 government measures to support doctors and healthcare professionals, and it analyzes how to respond to the many requests complaining about neglectful healthcare professionals during the spread of the infection. For all those healthcare workers who died on duty, a compensation plan is assumed through a solidarity fund. The same solution cannot be granted to all patients, given the difficulty in assessing the responsibility of the doctor not only during an emergency but with insufficient instruments to cope with it as well.

The importance of cycle threshold values in interpreting molecular tests for SARS-CoV-2

Using the Allplex™ 2019-nCoV assay (Seegene, South Korea), 285 samples were tested; 49 (17%) were positive for 3 genes, 4 (1.4%) samples were positive for 2 genes (all N gene and RdRP gene), 8 (3%) samples were positive for 1 gene (all N gene only), and 224 (78.5%) samples were negative.

A systematic review of etiology, epidemiology, clinical manifestations, image findings, and medication of 2019 Corona Virus Disease-19 in Wuhan, China

BACKGROUND

Unknown origin pneumonia has been furiously spreading since the late of December 2019, subsequently spread to approximately all provinces and areas in China and many countries, which was announced as a Public Health Emergency of International Concern by World Health Organization (WHO). The studies on 2019 Corona Virus Disease-19 (COVID-19) conducted from various fields around the world. Herein, the objective of the present study is to summarize the etiology, epidemiology, clinical manifestations, image findings, traceability analysis, and drug development of COVID-19.

METHODS

The following electronic databases were searched: Cochrane Central Register of Controlled Trials (CENTRAL), PubMed, EMBASE, Cochrane Library, China National Knowledge Infrastructure (CNKI), Chinese Biomedical Literature Database, VIP Chinese Science and Technology Periodical Database, and Wanfang Data. Other relevant literature will be manually searched as a compliment. We have reviewed etiology, epidemiology, clinical manifestations, image findings, and medication from case reports and retrospective clinical studies relating to COVID-19 published since the outbreak.

RESULTS

The coronavirus is closely related to bat coronavirus and pangolin coronavirus. Besides, the infection pathway is confirmed to be the respiratory and digestive systems. The virus indicates person-to-person transmission and some patients present asymptomatic. The elderly have a higher mortality rate. Rapid and sensitive nucleic acid testing is usually used as a basis for diagnosis. Currently, there is no specific vaccine and antiviral drug. Intervention actions such as travel bans and quarantine adopted have effectively reduced the spread of the epidemic.

CONCLUSION

This systemic review will provide high-quality evidence to summarize etiology, epidemiology, clinical manifestations, image findings, traceability analysis, drug development in patients with COVID-19.