A novel human coronavirus: Middle East respiratory syndrome human coronavirus

Teicoplanin derivatives block spike protein mediated viral entry as pan-SARS-CoV-2 inhibitors

The rapid emergence of highly transmissible SARS-CoV-2 variants poses serious threat to the efficacy of vaccines and neutralizing antibodies. Thus, there is an urgent need to develop new and effective inhibitors against SARS-CoV-2 and future outbreaks. Here, we have identified a series of glycopeptide antibiotics teicoplanin derivatives that bind to the SARS-CoV-2 spike (S) protein, interrupt its interaction with ACE2 receptor and selectively inhibit viral entry mediated by S protein. Computation modeling predicts that these compounds interact with the residues in the receptor binding domain. More importantly, these teicoplanin derivatives inhibit the entry of both pseudotyped SARS-CoV-2 Delta and Omicron variants. Our study demonstrates the feasibility of developing small molecule entry inhibitors by targeting the interaction of viral S protein and ACE2. Together, considering the proven safety and pharmacokinetics of teicoplanin as a glycopeptide antibiotic, the teicoplanin derivatives hold great promise of being repurposed as pan-SARS-CoV-2 inhibitors.

Middle East Respiratory Syndrome (MERS) Virus-Pathophysiological Axis and the Current Treatment Strategies

Middle East respiratory syndrome (MERS) is a lethal respiratory disease with its first case reported back in 2012 (Jeddah, Saudi Arabia). It is a novel, single-stranded, positive-sense RNA beta coronavirus (MERS-CoV) that was isolated from a patient who died from a severe respiratory illness. Later, it was found that this patient was infected with MERS. MERS is endemic to countries in the Middle East regions, such as Saudi Arabia, Jordan, Qatar, Oman, Kuwait and the United Arab Emirates. It has been reported that the MERS virus originated from bats and dromedary camels, the natural hosts of MERS-CoV. The transmission of the virus to humans has been thought to be either direct or indirect. Few camel-to-human transmissions were reported earlier. However, the mode of transmission of how the virus affects humans remains unanswered. Moreover, outbreaks in either family-based or hospital-based settings were observed with high mortality rates, especially in individuals who did not receive proper management or those with underlying comorbidities, such as diabetes and renal failure. Since then, there have been numerous reports hypothesising complications in fatal cases of MERS. Over the years, various diagnostic methods, treatment strategies and preventive measures have been strategised in containing the MERS infection. Evidence from multiple sources implicated that no treatment options and vaccines have been developed in specific, for the direct management of MERS-CoV infection. Nevertheless, there are supportive measures outlined in response to symptom-related management. Health authorities should stress more on infection and prevention control measures, to ensure that MERS remains as a low-level threat to public health.

Monitoring Symptoms of Infectious Diseases: Perspectives for Printed Wearable Sensors

Infectious diseases possess a serious threat to the world's population, economies, and healthcare systems. In this review, we cover the infectious diseases that are most likely to cause a pandemic according to the WHO (World Health Organization). The list includes COVID-19, Crimean-Congo Hemorrhagic Fever (CCHF), Ebola Virus Disease (EBOV), Marburg Virus Disease (MARV), Lassa Hemorrhagic Fever (LHF), Middle East Respiratory Syndrome (MERS), Severe Acute Respiratory Syndrome (SARS), Nipah Virus diseases (NiV), and Rift Valley fever (RVF). This review also investigates research trends in infectious diseases by analyzing published research history on each disease from 2000-2020 in PubMed. A comprehensive review of sensor printing methods including flexographic printing, gravure printing, inkjet printing, and screen printing is conducted to provide guidelines for the best method depending on the printing scale, resolution, design modification ability, and other requirements. Printed sensors for respiratory rate, heart rate, oxygen saturation, body temperature, and blood pressure are reviewed for the possibility of being used for disease symptom monitoring. Printed wearable sensors are of great potential for continuous monitoring of vital signs in patients and the quarantined as tools for epidemiological screening.

A computational tool for trend analysis and forecast of the COVID-19 pandemic

Purpose:

This paper proposes a methodology and a computational tool to study the COVID-19 pandemic throughout the world and to perform a trend analysis to assess its local dynamics.

Methods:

Mathematical functions are employed to describe the number of cases and demises in each region and to predict their final numbers, as well as the dates of maximum daily occurrences and the local stabilization date. The model parameters are calibrated using a computational methodology for numerical optimization. Trend analyses are run, allowing to assess the effects of public policies. Easy to interpret metrics over the quality of the fitted curves are provided. Country-wise data from the European Centre for Disease Prevention and Control (ECDC) concerning the daily number of cases and demises around the world are used, as well as detailed data from Johns Hopkins University and from the Brasil.io project describing individually the occurrences in United States counties and in Brazilian states and cities, respectively. U. S. and Brazil were chosen for a more detailed analysis because they are the current focus of the pandemic.

Results:

Illustrative results for different countries, U. S. counties and Brazilian states and cities are presented and discussed.

Conclusion:

The main contributions of this work lie in (i) a straightforward model of the curves to represent the data, which allows automation of the process without requiring interventions from experts; (ii) an innovative approach for trend analysis, whose results provide important information to support authorities in their decision-making process; and (iii) the developed computational tool, which is freely available and allows the user to quickly update the COVID-19 analyses and forecasts for any country, United States county or Brazilian state or city present in the periodic reports from the authorities.

An Intelligent and Energy-Efficient Wireless Body Area Network to Control Coronavirus Outbreak

The coronaviruses are a deadly family of epidemic viruses that can spread from one individual to another very quickly, infecting masses. The literature on epidemics indicates that the early diagnosis of a coronavirus infection can lead to a reduction in mortality rates. To prevent coronavirus disease 2019 (COVID-19) from spreading, the regular identification and monitoring of infected patients are needed. In this regard, wireless body area networks (WBANs) can be used in conjunction with machine learning and the Internet of Things (IoT) to identify and monitor the human body for health-related information, which in turn can aid in the early diagnosis of diseases. This paper proposes a novel coronavirus-body area network (CoV-BAN) model based on IoT technology as a real-time health monitoring system for the detection of the early stages of coronavirus infection using a number of wearable biosensors to examine the health status of the patient. The proposed CoV-BAN model is tested with five machine learning-based classification methods, including random forest, logistic regression, Naive Bayes, support vector machine and multi-layer perceptron classifiers, to optimize the accuracy of the diagnosis of COVID-19. For the long-term sustainability of the sensor devices, the development of energy-efficient WBAN is critical. To address this issue, a long-range (LoRa)-based IoT program is used to receive biosensor signals from the patient and transmit them to the cloud directly for monitoring. The experimental results indicate that the proposed model using the random forest classifier outperforms models using the other classifiers, with an average accuracy of 88.6%. In addition, power consumption is reduced when LoRa technology is used as a relay node.

An Efficient Method for Coronavirus Detection Through X-rays using deep Neural Network

BACKGROUND

Coronavirus (COVID-19) is a group of infectious diseases caused by related viruses called coronaviruses. In humans, the seriousness of infection caused by a coronavirus in the respiratory tract can vary from mild to lethal. A serious illness can be developed in old people and those with underlying medical problems like diabetes, cardiovascular disease, cancer, and chronic respiratory disease. For the diagnosis of the coronavirus disease, due to the growing number of cases, a limited number of test kits for COVID-19 are available in the hospitals. Hence, it is important to implement an automated system as an immediate alternative diagnostic option to pause the spread of COVID-19 in the population.

OBJECTIVE

This paper proposes a deep learning model for classification of coronavirus infected patient detection using chest X-ray radiographs.

METHODS

A fully connected convolutional neural network model is developed to classify healthy and diseased X-ray radiographs. The proposed neural network model consists of seven convolutional layers with rectified linear unit, softmax (last layer) activation functions and max pooling layers which were trained using the publicly available COVID-19 dataset.

RESULTS AND CONCLUSION

For validation of the proposed model, the publicly available chest X-ray radiograph dataset consisting COVID-19 and normal patient's images were used. Considering the performance of the results that are evaluated based on various evaluation metrics such as precision, recall, MSE, RMSE & accuracy, it is seen that the accuracy of the proposed CNN model is 98.07%.

Recent advances in materials science: a reinforced approach toward challenges against COVID-19

With the recent COVID-19 pandemic, medical professionals and scientists have encountered an unprecedented trouble to make the latest technological solutions to work. Despite of abundant tools available as well as initiated for diagnosis and treatment, researchers in the healthcare systems were in backfoot to provide concrete answers to the demanding challenge of SARS-CoV-2. It has incited global collaborative efforts in every field from economic, social, and political to dedicated science to confront the growing demand toward solution to this outbreak. Field of materials science has been in the frontline to the current scenario to provide major diagnostic tools, antiviral materials, safety materials, and various therapeutic means such as, antiviral drug design, drug delivery, and vaccination. In the present article, we emphasized the role of materials science to the development of PPE kits such as protecting suits, gloves, and masks as well as disinfection of the surfaces/surroundings. In addition, contribution of materials science towards manufacturing diagnostic devices such as microfluidics, immunosensors as well as biomaterials with a point of care analysis has also been discussed. Further, the efficacy of nanoparticles and scaffolds for antiviral drug delivery and micro-physiological systems as well as materials derived from human tissues for extracorporeal membrane oxygenation (ECMO) devices have been elaborated towards therapeutic applications.

The Synthesis of a Two-Photon Fluorescence Labelling Probe and its Immunochromatographic Strip for Rapid Diagnosis of COVID-19

A two-photon fluorescence labelling probe (LP) was synthesised, and LP-Ag was obtained by LP labelling the N-protein antigen (Ag) of COVID-19. LP-Ag was made into an immunochromatographic strip. When a blood sample was added to the sample hole of the test card, it would move forward along the nitrocellulose (NC) film. If the sample contained IgM, the IgM bound to LP-Ag and formed an M line with the coated mouse anti-human IgM antibody, giving a positive response to the presence of IgM of COVID-19. The sensitivity, specificity, and accuracy of the immunochromatographic strip based on the LP was compared with those of the nucleic acid detection method and the colloidal gold method, proving it to be much simpler than the nucleic acid detection method, which can greatly shorten the detection period, and to be much more stable than the colloidal gold method, which can overcome uncertainty. LP-Ag can be used to image lung tissue with COVID-19 by two-photon fluorescence microscopy (TFM).

Rapid Detection of Respiratory Pathogens for Community-Acquired Pneumonia by Capillary Electrophoresis-Based Multiplex PCR

Community-acquired pneumonia (CAP) is a common infectious disease linked to high rates of morbidity and mortality. Fast and accurate identification of the pathogens responsible for CAP will aid in diagnosis. We established a capillary electrophoresis-based multiplex PCR (CEMP) panel to enable the detection of viral and bacterial pathogens associated with CAP. The assay simultaneously detects and identifies the 13 common unculturable CAP viral and bacterial pathogens within 4 h. We evaluated the performance of a commercially available panel with 314 samples collected from CAP patients. We compared the results to those obtained with the liquid chip-based Luminex xTAG Respiratory Viral Panel (RVP) Fast Kit (for viruses) and the agarose gel-based Seegene PneumoBacter ACE Detection Kit (for atypical bacteria). All positive samples were further verified by the Sanger sequencing method. The sensitivity, specificity, positive predictive value, and negative predictive value of CEMP were 97.31%, 100%, 100%, and 99.85%, respectively. CEMP provides a rapid and accurate method for the high-throughput detection of pathogens in patients with CAP.

Protective T Cell Responses Featured by Concordant Recognition of Middle East Respiratory Syndrome Coronavirus-Derived CD8+ T Cell Epitopes and Host MHC

The coordinated recognition of virus-derived T cell epitopes and MHC molecules by T cells plays a pivotal role in cellular immunity-mediated virus clearance. It has been demonstrated that the conformation of MHC class I (MHC I) molecules can be adjusted by the presented peptide, which impacts T cell activation. However, it is still largely unknown whether the conformational shift of MHC I influences the protective effect of virus-specific T cells. In this study, utilizing the Middle East respiratory syndrome coronavirus-infected mouse model, we observed that through the unusual secondary anchor Ile5, a CD8⁺ T cell epitope drove the conformational fit of Trp⁷³ on the α1 helix of murine MHC I H-2K^d In vitro renaturation and circular dichroism assays indicated that this shift of the structure did not influence the peptide/MHC I binding affinity. Nevertheless, the T cell recognition and the protective effect of the peptide diminished when we made an Ile to Ala mutation at position 5 of the original peptide. The molecular bases of the concordant recognition of T cell epitopes and host MHC-dependent protection were demonstrated through both crystal structure determination and tetramer staining using the peptide-MHC complex. Our results indicate a coordinated MHC I/peptide interaction mechanism and provide a beneficial reference for T cell-oriented vaccine development against emerging viruses such as Middle East respiratory syndrome coronavirus.

High diversity of picornaviruses in rats from different continents revealed by deep sequencing

Outbreaks of zoonotic diseases in humans and livestock are not uncommon, and an important component in containment of such emerging viral diseases is rapid and reliable diagnostics. Such methods are often PCR-based and hence require the availability of sequence data from the pathogen. Rattus norvegicus (R. norvegicus) is a known reservoir for important zoonotic pathogens. Transmission may be direct via contact with the animal, for example, through exposure to its faecal matter, or indirectly mediated by arthropod vectors. Here we investigated the viral content in rat faecal matter (n=29) collected from two continents by analyzing 2.2 billion next-generation sequencing reads derived from both DNA and RNA. Among other virus families, we found sequences from members of the Picornaviridae to be abundant in the microbiome of all the samples. Here we describe the diversity of the picornavirus-like contigs including near-full-length genomes closely related to the Boone cardiovirus and Theiler's encephalomyelitis virus. From this study, we conclude that picornaviruses within R. norvegicus are more diverse than previously recognized. The virome of R. norvegicus should be investigated further to assess the full potential for zoonotic virus transmission.

Macro Domain from Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Is an Efficient ADP-ribose Binding Module: CRYSTAL STRUCTURE AND BIOCHEMICAL STUDIES

The newly emerging Middle East respiratory syndrome coronavirus (MERS-CoV) encodes the conserved macro domain within non-structural protein 3. However, the precise biochemical function and structure of the macro domain is unclear. Using differential scanning fluorimetry and isothermal titration calorimetry, we characterized the MERS-CoV macro domain as a more efficient adenosine diphosphate (ADP)-ribose binding module than macro domains from other CoVs. Furthermore, the crystal structure of the MERS-CoV macro domain was determined at 1.43-Å resolution in complex with ADP-ribose. Comparison of macro domains from MERS-CoV and other human CoVs revealed structural differences in the α1 helix alters how the conserved Asp-20 interacts with ADP-ribose and may explain the efficient binding of the MERS-CoV macro domain to ADP-ribose. This study provides structural and biophysical bases to further evaluate the role of the MERS-CoV macro domain in the host response via ADP-ribose binding but also as a potential target for drug design.

Detecting respiratory viral RNA using expanded genetic alphabets and self-avoiding DNA

Nucleic acid (NA)-targeted tests detect and quantify viral DNA and RNA (collectively xNA) to support epidemiological surveillance and, in individual patients, to guide therapy. They commonly use polymerase chain reaction (PCR) and reverse transcription PCR. Although these all have rapid turnaround, they are expensive to run. Multiplexing would allow their cost to be spread over multiple targets, but often only with lower sensitivity and accuracy, noise, false positives, and false negatives; these arise by interactions between the multiple nucleic acid primers and probes in a multiplexed kit. Here we offer a multiplexed assay for a panel of respiratory viruses that mitigates these problems by combining several nucleic acid analogs from the emerging field of synthetic biology: (i) self-avoiding molecular recognition systems (SAMRSs), which facilitate multiplexing, and (ii) artificially expanded genetic information systems (AEGISs), which enable low-noise PCR. These are supplemented by “transliteration” technology, which converts standard nucleotides in a target to AEGIS nucleotides in a product, improving hybridization. The combination supports a multiplexed Luminex-based respiratory panel that potentially differentiates influenza viruses A and B, respiratory syncytial virus, severe acute respiratory syndrome coronavirus (SARS), and Middle East respiratory syndrome (MERS) coronavirus, detecting as few as 10 MERS virions in a 20-μl sample.

Middle East respiratory syndrome coronavirus "MERS-CoV": current knowledge gaps

The Middle East respiratory syndrome coronavirus (MERS-CoV) that causes a severe lower respiratory tract infection in humans is now considered a pandemic threat to the Gulf region. Since its discovery in 2012, MERS-CoV has reached 23 countries affecting about 1100 people, including a dozen children, and claiming over 400 lives. Compared to SARS (severe acute respiratory syndrome), MERS-CoV appears to kill more people (40% versus 10%), more quickly, and is especially more severe in those with pre-existing medical conditions. Most MERS-CoV cases (>85%) reported thus far have a history of residence in, or travel to the Middle East. The current epidemiology is characterised by slow and sustained transmission with occasional sparks. The dromedary camel is the intermediate host of MERS-CoV, but the transmission cycle is not fully understood. In this current review, we have briefly summarised the latest information on the epidemiology, clinical features, diagnosis, treatment and prevention of MERS-CoV especially highlighting the knowledge gaps in its transmission dynamics, diagnosis and preventive strategy.

Target-dependent enrichment of virions determines the reduction of high-throughput sequencing in virus discovery

Viral infections cause many different diseases stemming both from well-characterized viral pathogens but also from emerging viruses, and the search for novel viruses continues to be of great importance. High-throughput sequencing is an important technology for this purpose. However, viral nucleic acids often constitute a minute proportion of the total genetic material in a sample from infected tissue. Techniques to enrich viral targets in high-throughput sequencing have been reported, but the sensitivity of such methods is not well established. This study compares different library preparation techniques targeting both DNA and RNA with and without virion enrichment. By optimizing the selection of intact virus particles, both by physical and enzymatic approaches, we assessed the effectiveness of the specific enrichment of viral sequences as compared to non-enriched sample preparations by selectively looking for and counting read sequences obtained from shotgun sequencing. Using shotgun sequencing of total DNA or RNA, viral targets were detected at concentrations corresponding to the predicted level, providing a foundation for estimating the effectiveness of virion enrichment. Virion enrichment typically produced a 1000-fold increase in the proportion of DNA virus sequences. For RNA virions the gain was less pronounced with a maximum 13-fold increase. This enrichment varied between the different sample concentrations, with no clear trend. Despite that less sequencing was required to identify target sequences, it was not evident from our data that a lower detection level was achieved by virion enrichment compared to shotgun sequencing.

Antiviral potential of ERK/MAPK and PI3K/AKT/mTOR signaling modulation for Middle East respiratory syndrome coronavirus infection as identified by temporal kinome analysis

Middle East respiratory syndrome coronavirus (MERS-CoV) is a lineage C betacoronavirus, and infections with this virus can result in acute respiratory syndrome with renal failure. Globally, MERS-CoV has been responsible for 877 laboratory-confirmed infections, including 317 deaths, since September 2012. As there is a paucity of information regarding the molecular pathogenesis associated with this virus or the identities of novel antiviral drug targets, we performed temporal kinome analysis on human hepatocytes infected with the Erasmus isolate of MERS-CoV with peptide kinome arrays. bioinformatics analysis of our kinome data, including pathway overrepresentation analysis (ORA) and functional network analysis, suggested that extracellular signal-regulated kinase (ERK)/mitogen-activated protein kinase (MAPK) and phosphoinositol 3-kinase (PI3K)/serine-threonine kinase (AKT)/mammalian target of rapamycin (mTOR) signaling responses were specifically modulated in response to MERS-CoV infection in vitro throughout the course of infection. The overrepresentation of specific intermediates within these pathways determined by pathway and functional network analysis of our kinome data correlated with similar patterns of phosphorylation determined through Western blot array analysis. In addition, analysis of the effects of specific kinase inhibitors on MERS-CoV infection in tissue culture models confirmed these cellular response observations. Further, we have demonstrated that a subset of licensed kinase inhibitors targeting the ERK/MAPK and PI3K/AKT/mTOR pathways significantly inhibited MERS-CoV replication in vitro whether they were added before or after viral infection. Taken together, our data suggest that ERK/MAPK and PI3K/AKT/mTOR signaling responses play important roles in MERS-CoV infection and may represent novel drug targets for therapeutic intervention strategies.

Isolation and characterization of dengue virus serotype 2 from the large dengue outbreak in Guangdong, China in 2014

Dengue has been well recognized as a global public health threat, but only sporadic epidemics and imported cases were reported in recent decades in China. Since July 2014, an unexpected large dengue outbreak has occurred in Guangdong province, China, resulting in more than 40000 patients including six deaths. To clarify and characterize the causative agent of this outbreak, the acute phase serum from a patient diagnosed with severe dengue was subjected to virus isolation and high-throughput sequencing (HTS). Traditional real-time RT-PCR and HTS with Ion Torrent PGM detected the presence of dengue virus serotype 2 (DENV-2). A clinical DENV-2 isolate GZ05/2014 was obtained by culturing the patient serum in mosquito C6/36 cells. The complete genome of GZ05/2014 was determined and deposited in GenBank under the access number KP012546. Phylogenetic analysis based on the complete envelope gene showed that the newly DENV-2 isolate belonged to Cosmopolitan genotype and clustered closely with other Guangdong strains isolated in the past decade. No amino acid mutations that are obviously known to increase virulence or replication were identified throughout the genome of GZ05/2014. The high homology of Guangdong DENV-2 strains indicated the possibility of establishment of local DENV-2 circulation in Guangdong, China. These results help clarify the origin of this epidemic and predict the future status of dengue in China.

Unmet needs in respiratory diseases : "You can't know where you are going until you know where you have been"--Anonymous

The care of patients with respiratory diseases has improved vastly in the past 50 years. In spite of that, there are still massive challenges that have not been resolved. Although the incidence of tuberculosis has decreased in the developed world, it is still a significant public health problem in the rest of the world. There are still over 2 million deaths annually from tuberculosis, with most of these occurring in the developing world. Even with the development of new pharmaceuticals to treat tuberculosis, there is no indication that the disease will be eradicated. Respiratory syncytial virus, severe acute respiratory syndrome, and pertussis are other respiratory infectious diseases with special problems of their own, from vaccine development to vaccine coverage. Asthma, one of the most common chronic diseases in children, still accounts for significant mortality and morbidity, as well as high health care costs worldwide. Even in developed countries such as the USA, there are over 4,000 deaths per year. Severe asthma presents a special problem, but the question is whether there can be one treatment pathway for all patients with severe asthma. Severe asthma is a heterogeneous disease with many phenotypes and endotypes. The gene for cystic fibrosis was discovered over 24 years ago. The promise of gene therapy as a cure for the disease has fizzled out, and while new antimicrobials and other pharmaceuticals promise improved longevity and better quality of life, the average life span of a patient with cystic fibrosis is still at about 35 years. What are the prospects for gene therapy in the twenty-first century? Autoimmune diseases of the lung pose a different set of challenges, including the development of biomarkers to diagnose and monitor the disease and biological modulators to treat the disease.

MERS-CoV: Ein aktueller Überblick

Der folgende Artikel gibt eine aktuelle Übersicht zu dem neu aufgetretenen Middle East Respiratory Syndrome Coronavirus (MERS-CoV). Erstmals im Sommer 2012 kam es in Ländern der arabischen Halbinsel zu schweren Infektionen der Atemwege durch ein neues Coronavirus (MERS-CoV). Dabei wurden die meisten Erkrankungsfälle aus Saudi-Arabien gemeldet, in Deutschland wurden bisher mehrere importierte Krankheitsfälle berichtet.

Nach Beginn mit grippeähnlichen Symptomen folgt meist die Entwicklung einer Pneumonie mit Übergang in ein akutes Atemnotsyndrom. Die Letalitätsrate wird auf 55% geschätzt. Über die Erkrankung sollte im Rahmen der reisemedizinischen Beratung ausführlich aufgeklärt werden und sie ist insofern auch für die Arbeitsmedizin von groβer Bedeutung.