Development and Evaluation of Novel Real-Time Reverse Transcription-PCR Assays with Locked Nucleic Acid Probes Targeting Leader Sequences of Human-Pathogenic Coronaviruses

Nanotechnology-based diagnostic methods for coronavirus: From nucleic acid extraction to amplification

The recent emergence of human coronaviruses (CoVs) causing severe acute respiratory syndrome (SARS) is posing a great threat to global public health. Therefore, the rapid and accurate identification of pathogenic viruses plays a vital role in selecting appropriate treatments, saving people's lives and preventing epidemics. Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Applications of nucleic acid detection range from genotyping and genetic prognostics, to expression profiling and detection of infectious disease. The nucleic acid detection for infectious diseases is widely used, as evidenced by the widespread use of COVID-19 tests for the containment of the pandemic. Nanotechnology influences all medical disciplines and has been considered as an essential tool for novel diagnostics, nanotherapeutics, vaccines, medical imaging, and the utilization of biomaterials for regenerative medicine. In this review, the recent advances in the development of nanotechnology-based diagnostic methods for coronavirus, and their applications in nucleic acid detection are discussed in detail. The techniques for the amplification of nucleic acids are summarized, as well as the use of magnetic nanoparticles for nucleic acid extraction. Besides, current challenges and future prospects are proposed, along with the great potential of nanotechnology for the effective diagnosis of coronavirus.

Does a Low Score in the Respiratory Visual Triage Tool Predict a Negative COVID-19 Test in an Admitted Patient?

Background

Fast and accurate COVID-19 identification is important to population and epidemic monitoring in hospitals. Visual triage or respiratory triage should be efficient and utilized as visual clues to alert HCWs on the case definitions.

Objective

This study aims to evaluate the diagnostic value of the respiratory triage for COVID-19 infections and to evaluate the efficacy of the MOH triage tool in identifying low risk patients.

Methods

A single-center retrospective chart review that was conducted at King Fahd Hospital of the University (KFHU), Khober, KSA on all adult patients admitted to the hospital through the ED. The visual triage checklist comprises two main sections, with one focused on the risk of exposure and the other related to patient clinical signs and symptoms, each with a defined score where any score ≥ 4 will need to isolate and assessed by the physician while a score of less than 4 means that the patient can be admitted with other patients. The hospital swabbed all admitted patients regardless of their score. We compared their PCR result with their case definition score. The collected data was entered and analyzed using the Statistical Package for the Social Science (SPSS Inc. Chicago, IL, USA) version 23.

Results

The study included 7258 participants. 20% of participants aged between 21 to 30 years old, 52.2% of sample were females, and 78% were Saudi nationality. Visual triage score was less than 4 in n= 4745 participants (65.4%) and 4 or more in n= 2513 (34.6%). The test had sensitivity of 75% and specificity 21%.

Conclusion

Most studies shows that COVID 19 has an infectivity rate of 18 to 30%. Based on this low sensitivity result, using the screening tool alone puts patients and HCWs at risk of getting infected with COVID 19.

A low-cost, sensitive and specific PCR-based tool for rapid clinical detection of HLA-B*35 alleles associated with delayed drug hypersensitivity reactions

HLA (HLA) alleles are risk factors for CD8+ T-cell-mediated drug hypersensitivity reactions. However, as most HLA associations are incompletely predictive and/or involve risk alleles at low frequency, costly sequence-based typing can elude an economically productive cost: benefit ratio for clinical validation studies and diagnostic and/or preventative screening. Hence rapid and low-cost detection assays are now required, both for single alleles but also across risk loci associated with broader multi-disease risk; exemplified by associations with diverse alleles in HLA-B*35, including HLA-B*35:01 and green tea- or co-trimoxazole-induced liver injury. Here, we developed a cost-effective (<$10USD) qPCR assay for rapid (<2.5 h) clinical detection of HLA-B*35 alleles. The assay was validated using 430 DNA samples with previous American society for histocompatibility and immunogenetics-accredited sequence-based high-resolution HLA typing, positively detecting all HLA-B*35 allelic variants in our cohort, and as expected by primer design, the six samples that expressed low-frequency B*78:01. The assay did not result in positive detection for any negative control allele. With expected detection of B*35 and B*78, our assay sensitivity (95% CI, 95.07%-100.00%) and specificity (95% CI, 98.97%-100.00%) of 100% using as low as 10 ng of DNA provides a reliable HLA-B*35 screening tool for clinical validation and HLA-risk-based prevention and diagnostics.

Recent Advances in Understanding SARS-CoV-2 Infection and Updates on Potential Diagnostic and Therapeutics for COVID-19

Abstract:

A more focused approach is needed to understand the SARS-CoV-2 virulence, structure, and genomics to devise more effective diagnostic and treatment interventions as this virus can evade the immune attack and causes life-threatening complications such as cytokine storm. The spread of the virus is still amplifying and causing thousands of new cases worldwide. It is essential to review current diagnostics and treatment approaches to pave the way to correct or modify our current practices to make more effective interventions against COVID-19. COVID-19 vaccine development has moved at a breakneck pace since the outbreak began, utilizing practically all possible platforms or tactics to ensure the success of vaccines. A total of 42 vaccine candidates have already entered clinical trials, including promising results from numerous vaccine candidates in phase 1 or phase 2 trials. Further, many existing drugs are being explored on broad-spectrum antiviral medications for their use in clinical recovery against COVID- 19. The present review attempts to re-examine the SARS-CoV-2 structure, its viral life cycle, clinical symptoms and pathogenesis, mode of transmission, diagnostics, and treatment strategies that may be useful for resorting to more effective approaches for controlling COVID-19. Various antiviral drugs and vaccination strategies with their strengths and weaknesses are also discussed in the paper to augment our understanding of COVID-19 management.

COVID-19 immunotherapy: Treatment based on the immune cell-mediated approaches

Multiple efforts are currently underway to control and treat severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing coronavirus disease 2019 (COVID-19) worldwide. Despite all efforts, the virus that emerged in Wuhan city has rapidly spread globally and led to a public health emergency of international concern (PHEIC) due to the lack of approved antiviral therapy. Nevertheless, SARS-CoV-2 has had a significant influence on the evolution of cellular therapeutic approaches. Adoptive immune cell therapy is innovative and offers either promising prophylactic or therapy for patients with moderate-to-severe COVID-19. This approach is aimed at developing safety and providing secure and effective therapy in combination with standard therapy for all COVID-19 infected individuals. Based on the effective results of previous studies on both inflammatory and autoimmune diseases, various immune cell therapies against COVID-19 have been reviewed and discussed. It must be considered that the application of cell therapy for treatment and to eliminate infected respiratory cells could result in excessive inflammation, so this treatment must be used in combination with other treatments, despite its many beneficial efforts.

Current strategies in diagnostics and therapeutics against novel coronavirus disease (COVID-19)

The epidemic of COVID-19 spread quickly through China and engulfed all of the countries across the globe. Several advances have been made in understanding the novel coronavirus's pathophysiology and in the development of newer diagnostics with pinpoint accuracy. Several newer therapeutic methods have either been accepted or are awaiting acceptance. In many countries, vaccination programs have been rolled out. Despite all these efforts, coronavirus still exists, though with lesser propensity. Multiple new forms of the novel coronavirus unexpectedly appeared in various areas of the world, undermining previously existing diagnosis and care protocols. This article highlights our understanding of the novel coronavirus's symptoms in brief, pathogenesis, diagnostics, and therapeutic strategies to contain COVID-19. The clinical findings, including serological, radiological, and other advanced diagnostic strategies, contributed much to control the disease. To date, supportive interventions have been used in tandem with potent antiviral therapies such as remdesivir, lopinavir/ritonavir, or corticosteroids with a level of trust in the care of COVID-19 patients. However, in several areas of the world, vaccination initiatives took place; the vaccines' safety and efficacy to control the outbreak is yet to be identified. This review concludes that improvement in therapies and diagnostics for COVID-19 must continually be explored as new variants constantly emerge.

Mass screening is a key component to fight against SARS-CoV-2 and return to normalcy

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had highly transmissible and pathogenic, which caused serious economic loss and hazard to public health. Different countries have developed strategies to deal with the COVID-19 pandemic that fit their epidemiological situations, capacities, and values. Mass screening combined with control measures rapidly reduced the transmission of the SARS-CoV-2 infection. The COVID-19 pandemic has dramatically highlighted the essential role of diagnostics capacity in the control of communicable diseases. Mass screening has been increasingly used to detect suspected COVID-19 cases and their close contacts, asymptomatic case, patients attending fever clinics, high-risk populations, employees, even all population to identify infectious individuals. Mass screening is a key component to fight against SARS-CoV-2 and return to normalcy. Here we describe the history of mass screening, define the scope of mass screening, describe its application scenarios, and discuss the impact and challenges of using this approach to control COVID-19. We conclude that through a comprehension screening program and strong testing capabilities, mass screening could help us return to normalcy more quickly.

Advanced Point-of-Care Testing Technologies for Human Acute Respiratory Virus Detection

The ever-growing global threats to human life caused by the human acute respiratory virus (RV) infections have cost billions of lives, created a significant economic burden, and shaped society for centuries. The timely response to emerging RVs could save human lives and reduce the medical care burden. The development of RV detection technologies is essential for potentially preventing RV pandemic and epidemics. However, commonly used detection technologies lack sensitivity, specificity, and speed, thus often failing to provide the rapid turnaround times. To address this problem, new technologies are devised to address the performance inadequacies of the traditional methods. These emerging technologies offer improvements in convenience, speed, flexibility, and portability of point-of-care test (POCT). Herein, recent developments in POCT are comprehensively reviewed for eight typical acute respiratory viruses. This review discusses the challenges and opportunities of various recognition and detection strategies and discusses these according to their detection principles, including nucleic acid amplification, optical POCT, electrochemistry, lateral flow assays, microfluidics, enzyme-linked immunosorbent assays, and microarrays. The importance of limits of detection, throughput, portability, and specificity when testing clinical samples in resource-limited settings is emphasized. Finally, the evaluation of commercial POCT kits for both essential RV diagnosis and clinical-oriented practices is included.

Mapping the footprints of COVID-19 pandemic

The new member of the coronavirus family created havoc in the world in few days of its discovery and was declared as a pandemic by March 2020. The enveloped, single-stranded RNA virus was first identified in a patient with dry cough, pain, and weakness for the past1 week with unknown etiology in Wuhan. The coronavirus soon spread across the globe in the next few weeks. To curb the spread of coronavirus, stringent measures such as lockdown and social distancing were enforced resulted in a declining of cases in various countries. However, unlocking, relaxation of preventive measures, and changing human behaviors led to a drastic increase in the number of COVID-19 cases resulting in the second wave of transmission. This resulted in reimposing of lockdown measures in countries such as Nepal, Italy, France, Netherland, and Germany. At present, the virus has affected over 110.7 million peoples and over 2.4 million deaths across the world, with India having the second-highest number of COVID-19 cases, following the United States of America. Furthermore, a cross-sectional view of the disease states several new strains being reported across the globe at one end and at another end there is rolling out of vaccine against COVID-19. There is still uncertainty related to curbing of the pandemic as effect of vaccine on new strains is undetermined. Thus, it is important to understand the transforming epidemiology of the virus as it helps in planning necessary steps for physicians and policymakers. The present review summarizes the updated information primarily about the epidemiology of COVID-19, from initiation to the present scenario.

Current diagnostic approaches to detect two important betacoronaviruses: Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are two common betacoronaviruses, which are still causing transmission among the human population worldwide. The major difference between the two coronaviruses is that MERS-CoV is now causing sporadic transmission worldwide, whereas SARS-CoV-2 is causing a pandemic outbreak globally. Currently, different guidelines and reports have highlighted several diagnostic methods and approaches which could be used to screen and confirm MERS-CoV and SARS-CoV-2 infections. These methods include clinical evaluation, laboratory diagnosis (nucleic acid-based test, protein-based test, or viral culture), and radiological diagnosis. With the presence of these different diagnostic approaches, it could cause a dilemma to the clinicians and diagnostic laboratories in selecting the best diagnostic strategies to confirm MERS-CoV and SARS-CoV-2 infections. Therefore, this review aims to provide an up-to-date comparison of the advantages and limitations of different diagnostic approaches in detecting MERS-CoV and SARS-CoV-2 infections. This review could provide insights for clinicians and scientists in detecting MERS-CoV and SARS-CoV-2 infections to help combat the transmission of these coronaviruses.

Updates of COVID-19

Causal Organism

COVID-19 is a disease caused by the novel coronavirus (SARS-CoV-2). Positive-sense ssRNA viruses are about 30 kb long. Coronaviruses have a broad spectrum of action and affect multiple organisms.

Origin of Disease

The disease outbreak has been initiated in Wuhan, China, in December 2019. The disease has been originated from the wet animal market of Wuhan City, where a large number of peoples have come in contact with animals. It is known to infect the neurological, respiratory, enteric, and hepatic systems. SARSCoV-2 is highly infectious, and its outbreak is worldwide (national and international level) and becomes pandemic.

Control

Presently, the number of cases continues to rise at a global level, and it is clear that these viruses pose a significant threat to public health. Consequently, extensive treatments, vaccines, and drugs have been developed by researchers to control the transmission of infection. This led to the isolation of patients that were administered a variety of treatments. Special attention and guidelines have been given by various government organizations to protect or reduce transmission between children, healthcare providers, and old-aged peoples.

Clofazimine broadly inhibits coronaviruses including SARS-CoV-2

The COVID-19 pandemic is the third outbreak this century of a zoonotic disease caused by a coronavirus, following the emergence of severe acute respiratory syndrome (SARS) in 2003¹ and Middle East respiratory syndrome (MERS) in 2012². Treatment options for coronaviruses are limited. Here we show that clofazimine-an anti-leprosy drug with a favourable safety profile³-possesses inhibitory activity against several coronaviruses, and can antagonize the replication of SARS-CoV-2 and MERS-CoV in a range of in vitro systems. We found that this molecule, which has been approved by the US Food and Drug Administration, inhibits cell fusion mediated by the viral spike glycoprotein, as well as activity of the viral helicase. Prophylactic or therapeutic administration of clofazimine in a hamster model of SARS-CoV-2 pathogenesis led to reduced viral loads in the lung and viral shedding in faeces, and also alleviated the inflammation associated with viral infection. Combinations of clofazimine and remdesivir exhibited antiviral synergy in vitro and in vivo, and restricted viral shedding from the upper respiratory tract. Clofazimine, which is orally bioavailable and comparatively cheap to manufacture, is an attractive clinical candidate for the treatment of outpatients and-when combined with remdesivir-in therapy for hospitalized patients with COVID-19, particularly in contexts in which costs are an important factor or specialized medical facilities are limited. Our data provide evidence that clofazimine may have a role in the control of the current pandemic of COVID-19 and-possibly more importantly-in dealing with coronavirus diseases that may emerge in the future.

COVID-19: Current understanding of its Pathophysiology, Clinical presentation and Treatment

BACKGROUND

The severe acute respiratory syndrome (SARS) coronavirus-2 is a novel coronavirus belonging to the family Coronaviridae and is now known to be responsible for the outbreak of a series of recent acute atypical respiratory infections originating in Wuhan, China. The disease caused by this virus, termed coronavirus disease 19 or simply COVID-19, has rapidly spread throughout the world at an alarming pace and has been declared a pandemic by the WHO on March 11, 2020. In this review, an update on the pathophysiology, clinical presentation and the most recent management strategies for COVID-19 has been described.

MATERIALS AND METHODS

A search was conducted for literature and various articles/case reports from 1997 to 2020 in PUBMED/MEDLINE for the keywords coronavirus, SARS, Middle East respiratory syndrome and mRNA virus.

RESULTS AND CONCLUSIONS

COVID-19 has now spread globally with increasing morbidity and mortality among all populations. In the absence of a proper and effective antibody test, the diagnosis is presently based on a reverse-transcription PCR of nasopharyngeal and oropharyngeal swab samples. The clinical spectrum of the disease presents in the form of a mild, moderate or severe illness. Most patients are either asymptomatic carriers who despite being without symptoms have the potential to be infectious to others coming in close contact, or have a mild influenza-like illness which cannot be differentiated from a simple upper respiratory tract infection. Moderate and severe cases require hospitalisation as well as intensive therapy which includes non-invasive as well as invasive ventilation, along with antipyretics, antivirals, antibiotics and steroids. Complicated cases may require treatment by immunomodulatory drugs and plasma exchange therapy. The search for an effective vaccine for COVID-19 is presently in full swing, with pharmaceutical corporations having started human trials in many countries.

Current diagnostic and therapeutic strategies for COVID-19

The outbreak and spread of novel coronavirus disease 2019 (COVID-19) with pandemic features, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), have greatly threatened global public health. Given the perniciousness of COVID-19 pandemic, acquiring a deeper understanding of this viral illness is critical for the development of new vaccines and therapeutic options. In this review, we introduce the systematic evolution of coronaviruses and the structural characteristics of SARS-CoV-2. We also summarize the current diagnostic tools and therapeutic strategies for COVID-19.

Laboratory detection methods for the human coronaviruses

Coronaviruses are a group of envelop viruses which lead to diseases in birds and mammals as well as human. Seven coronaviruses have been discovered in humans that can cause mild to lethal respiratory tract infections. HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1 are the low-risk members of this family and the reason for some common colds. Besides, SARS-CoV, MERS-CoV, and newly identified SARS-CoV-2, which is also known as 2019-nCoV, are the more dangerous viruses. Due to the rapid spread of this novel coronavirus and its related disease, COVID-19, a reliable, simple, fast, and low-cost detection method is necessary for patient diagnosis and tracking worldwide. Human coronaviruses detection methods were classified and presented in this article. The laboratory detection techniques include RT-PCR, RT-LAMP, electrochemical and optical biosensors for RNA detection, and whole virus or viral proteins detection assays.

Ravaging SARS-CoV-2: rudimentary diagnosis and puzzling immunological responses

INTRODUCTION

In December 2019, the first COVID-19 case, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was reported in Wuhan, China. The SARS-CoV-2 rapidly disseminated throughout the world via community spread, acquiring pandemic status with significant fatality.

OBSERVATIONS

Rapid SARS-CoV-2 diagnosis was soon perceived critical for arresting community spread and effective therapy development. Human SARS-CoV-2 infection can be diagnosed either by nucleic acid identification or specific antibody detection. Contrary to nucleic acid identification confirmed active SARS-CoV-2 infection; antibody detection confirms a past infection, even in asymptomatic subjects. SARS-CoV-2 specific antibodies augment the ability to effectively counter the virus. A crucial hurdle limiting the steadfast implementation of antibody detection is the time required for threshold B lymphocyte population generation. This process is dependent on precise antigen recognition and MHC class I molecules presentation.

CONCLUSIONS

Thus, nucleic acid and antibody dependent tests complement each other in identifying human SARS-CoV-2 infection and shaping up subsequent immunological responses. This article discusses the complimentary association of nucleic acid identification (corresponding to an active infection) and antibody testing (the yester CoV-2 infection vulnerability) as the diagnostic and screening measures of SARS-CoV-2 infection. Highlights Nucleic acid (RNA) identification and specific antibody detection against SARS-CoV-2 are the noted diagnostic mechanisms for screening human SARS-CoV-2 infection. While nucleic acid identification screens prevailing SARS-CoV-2 infection, detection of SARS-CoV-2 specific antibodies signifies a past infection, even in asymptomatic subjects. Antibodies against SARS-CoV-2 provide a potential therapeutic option via transfer from antibody rich plasma of a recovered subject to an infected individual. Nucleic acid identification may not absolutely confirm the infection because of frequent SARS-CoV-2 genome mutations and possible technical errors, while specific antibody detection also needs at least (8-14) days for detectable screening of B-cell generated antibodies. Nucleic acid and antibody tests are complementary to each other as an early stage diagnostic assay for SARS-CoV-2 infection and possible therapy (antibodies). Sufferers with a high clinical suspicion but negative RT-PCR screening could be examined via combined imaging and repeated swab test.

MERS-CoV: epidemiology, molecular dynamics, therapeutics, and future challenges

The Severe Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has gained research attention worldwide, given the current pandemic. Nevertheless, a previous zoonotic and highly pathogenic coronavirus, the Middle East Respiratory Syndrome coronavirus (MERS-CoV), is still causing concern, especially in Saudi Arabia and neighbour countries. The MERS-CoV has been reported from respiratory samples in more than 27 countries, and around 2500 cases have been reported with an approximate fatality rate of 35%. After its emergence in 2012 intermittent, sporadic cases, nosocomial infections and many community clusters of MERS continued to occur in many countries. Human-to-human transmission resulted in the large outbreaks in Saudi Arabia. The inherent genetic variability among various clads of the MERS-CoV might have probably paved the events of cross-species transmission along with changes in the inter-species and intra-species tropism. The current review is drafted using an extensive review of literature on various databases, selecting of publications irrespective of favouring or opposing, assessing the merit of study, the abstraction of data and analysing data. The genome of MERS-CoV contains around thirty thousand nucleotides having seven predicted open reading frames. Spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins are the four main structural proteins. The surface located spike protein (S) of betacoronaviruses has been established to be one of the significant factors in their zoonotic transmission through virus-receptor recognition mediation and subsequent initiation of viral infection. Three regions in Saudi Arabia (KSA), Eastern Province, Riyadh and Makkah were affected severely. The epidemic progression had been the highest in 2014 in Makkah and Riyadh and Eastern Province in 2013. With a lurking epidemic scare, there is a crucial need for effective therapeutic and immunological remedies constructed on sound molecular investigations.

Age Distribution of Clinical Symptoms, Isolation, Co-morbidities and Case Fatality Rate of COVID-19 Cases in Najaf City, Iraq

Introduction:

The first case of coronavirus disease 2019 (COVID-19) in holy Najaf city in February 22, 2020. The outbreak then rose up all over Iraq from 519 cases and 20 deaths in June 2, 2020 to 3484 cases and 72 deaths per day in August 10, 2020 per 24 hours.

Aim:

The aim of the study is to describe the distribution of confirmed cases by age, demographic factors, isolation, comorbidities and case fatality rate.

Methods:

Prospectively collected and analyzed data on patients with laboratory-confirmed 2019-nCoV infection by real-time RT-PCR and next-generation sequencing. The demographic and clinical outcomes data of 1153 diagnosed patients were collected from consecutive patients, analyzed, and described. About two third of cases 789 (68.4%) acquired infection through contact with positive patients.

Results:

The reported cases were 743 (64.4%) males and 410 (35.6%) females with large number among age range 21 to 50 years. The most frequent presenting symptoms were fever, sore throat and dyspnea or cough, most of patients; 868 (75%) patients were isolated at home versus 285 (24.72) patients required hospitalization which represented the intermediate and sever cases. The overall case fatality rate was 2.4%.

Conclusion:

Most of COVID-19 cases in this locality were male from urban areas. The common onset symptoms were the fever, sore throat and dyspnea or cough. Majority of cases were isolated and treated at home. The estimated case fatality rate was within the global range (2.4%).

Recent insights for the emerging COVID-19: Drug discovery, therapeutic options and vaccine development

SARS-CoV-2 has been marked as a highly pathogenic coronavirus of COVID-19 disease into the human population, causing over 5.5 million confirmed cases worldwide. As COVID-19 has posed a global threat with significant human casualties and severe economic losses, there is a pressing demand to further understand the current situation and develop rational strategies to contain the drastic spread of the virus. Although there are no specific antiviral therapies that have proven effective in randomized clinical trials, currently, the rapid detection technology along with several promising therapeutics for COVID-19 have mitigated its drastic transmission. Besides, global institutions and corporations have commenced to parse out effective vaccines for the prevention of COVID-19. Herein, the present review will give exhaustive details of extensive researches concerning the drug discovery and therapeutic options for COVID-19 as well as some insightful discussions of the status of COVID-19.

Additive manufacturing for COVID-19: Devices, materials, prospects, and challenges

The current COVID-19 pandemic has caused the shortage of personal protective equipment (PPE) where improvised manufacturing in particular 3D printing has addressed many needs. This prospective discusses the current global crisis, then follows the wide interest in addressing the shortage of medical devices and PPEs used for treatment and protection against pathogens. An overview of the 3D printing process with polymer materials is given followed by the different 3D printing projects of PPEs and medical devices that emerged for the pandemic (including validation/testing). The potential for rapid prototyping with different polymer materials and eventual high-throughput production is emphasized.

Liver Function Tests Profile in COVID-19 Patients at the Admission Time: A Systematic Review of Literature and Conducted Researches

BACKGROUND

Since the start of coronavirus epidemic in Wuhan, China, in early December 2019, many literatures addressed its epidemiology, virology, and clinical presentation. In this review, we systematically reviewed the published literature in the field of liver function tests profile in COVID-19 patients at the admission time.

MATERIALS AND METHODS

systematic literature search were performed in EMBASE, PubMed, Science Direct, and Scopus using "severe acute respiratory syndrome 2 coronavirus (SARS-CoV-2)", "SARS," "SARS-CoV," "coronavirus," "novel coronavirus," "liver," "hepatitis," "Liver function" keywords. The search was limited to range from 2019 to May 19, 2020.

RESULTS

From a total 7298 articles, 145 were screened and 18 were eligible for further analysis. The highest rate of liver associated comorbidities was reported 11%. The aspartate aminotransferase (AST) and alanine aminotransferase (ALT) were the most frequent assessed enzymes. Increase in AST level was seen in 10%-53% of patients while The ALT increase was seen in 5%-28% of COVID-19 patients at the admission time. The prothrombin time was increase in 7%-12% of patients and the D-dimer was reports increase in 14%-36% of COVID-19 patients at the admission time. Furthermore, albumin decrease was seen in 6%-98% of COVID-19 patients at the admission time.

CONCLUSION

In conclusion, by using the results of study, it could be suggested that the liver function tests assessment is critical assessment in COVID-19 patients at the admission time. This liver function test could be used as potential prognostic factor in COVID-19 severity in future.

Laboratory diagnosis of emerging human coronavirus infections - the state of the art

The three unprecedented outbreaks of emerging human coronavirus (HCoV) infections at the beginning of the twenty-first century have highlighted the necessity for readily available, accurate and fast diagnostic testing methods. The laboratory diagnostic methods for human coronavirus infections have evolved substantially, with the development of novel assays as well as the availability of updated tests for emerging ones. Newer laboratory methods are fast, highly sensitive and specific, and are gradually replacing the conventional gold standards. This presentation reviews the current laboratory methods available for testing coronaviruses by focusing on the coronavirus disease 2019 (COVID-19) outbreak going on in Wuhan. Viral pneumonias typically do not result in the production of purulent sputum. Thus, a nasopharyngeal swab is usually the collection method used to obtain a specimen for testing. Nasopharyngeal specimens may miss some infections; a deeper specimen may need to be obtained by bronchoscopy. Alternatively, repeated testing can be used because over time, the likelihood of the SARS-CoV-2 being present in the nasopharynx increases. Several integrated, random-access, point-of-care molecular devices are currently under development for fast and accurate diagnosis of SARS-CoV-2 infections. These assays are simple, fast and safe and can be used in the local hospitals and clinics bearing the burden of identifying and treating patients.

Mesenchymal Stem Cells (MSCs) as a Potential Therapeutic Strategy in COVID-19 Patients: Literature Research

In 2019, an outbreak of an unknown coronavirus - SARS-CoV-2 - responsible for COVID-19 disease, was first reported in China, and evolved into a pandemic of huge dimensions and raised serious concerns for global health. The number of critical cases continues to increase dramatically, while vaccines and specific treatments are not yet available. There are several strategies currently being studied for the treatment of adverse symptoms of COVID-19, that encompass Acute Lung Injury (ALI)/Acute Respiratory Distress Syndrome (ARDS), extensive pulmonary inflammation, cytokine storm, and pulmonary edema, due to virus-induced pneumonia. Mesenchymal stem cells (MSCs) are at the origin of new revolutionary treatments, which may come to be applied in such as Regenerative Medicine, Immunotherapy, Tissue Engineering, and Cell and Molecular Biology due to immunomodulation and anti-inflammatory activity. MSCs have already been studied with positive outcomes for other lung pathologies, thus representing and being identified as an important opportunity for the treatment of COVID-19. It has recently been shown that these cells allow hopeful and effective therapies for serious or critical COVID-19, minimizing its adverse symptoms. In this study we will analyze the MSCs, their origin, differentiation, and therapeutic potential, making a bridge with the COVID-19 disease and its characteristics, as a potential therapeutic strategy but also reporting recent studies where these cell-based therapies were used for the treatment of COVID-19 patients.

Recommendations for the Diagnosis, Prevention, and Control of Coronavirus Disease-19 in Children-The Chinese Perspectives

Ever since SARS-CoV-2 began infecting people by the end of 2019, of whom some developed severe pneumonia (about 5%), which could be fatal (case fatality ~3.5%), the extent and speed of the COVID-19 outbreak has been phenomenal. Within 2.5 months (by March 18, 2020) over 191,127 COVID-19 patients have been identified in 161 countries. By then, over 700 pediatric patients were confirmed to have COVID-19 in China, with only about 58 diagnosed elsewhere. By now, there are thousands of children and adolescents infected. Chinese pediatricians would like to share their experience on how these patients were managed in China and the key recommendations that had guided them in meeting the evolving challenges. A group of experts were summoned by the Chinese Pediatric Society and Editorial Board of Chinese Journal of Pediatrics to extract informative data from a survey on confirmed COVID-19 pediatric patients in China. Consensus on diagnosis, management, and prevention of pediatric COVID-19 were drawn up based on the analysis of such data plus insights gained from the past SARS and MERS coronavirus outbreaks. Relevant cumulating experiences from physicians managing adult patients, expedited reports on clinical and scientific COVID-19 and SARS-CoV-2 data, and the National Health Committee guidelines on COVID-19 management were integrated into this proposal.

Update of the current knowledge on genetics, evolution, immunopathogenesis, and transmission for coronavirus disease 19 (COVID-19)

In December 2019, an acute respiratory disease caused by novel species of coronavirus (SARS-CoV-2), emerged in China and has spread throughout the world. On 11th March 2020, the World Health Organization (WHO) officially declared coronavirus disease 19 (COVID-19) a pandemic, severe coronavirus-mediated human disease. Based on genomic and phylogenetic studies, SARS-CoV-2 might originate from bat coronaviruses and infects humans directly or through intermediate zoonotic hosts. However, the exact origin or the host intermediate remains unknown. Genetically, SARS-CoV-2 is similar to several existing coronaviruses, particularly SARS-CoV, but differs by silent and non-silent mutations. The virus uses different transmission routes and targets cells and tissues with angiotensin-converting enzyme 2 (ACE2) protein, which makes it contagious. COVID-19 shares both the main clinical features and excessive/dysregulated cell responses with the two previous Middle East respiratory syndrome coronavirus (MERS) and severe acute respiratory syndrome coronavirus (SARS) epidemics. In this review, we provide an update of the current knowledge on the COVID-19 pandemic. Gaining a deeper understanding of SARS-CoV-2 structure, transmission routes, and molecular responses, will assist in the prevention and control of COVID-19 outbreaks in the future.

Development and Evaluation of Novel and Highly Sensitive Single-Tube Nested Real-Time RT-PCR Assays for SARS-CoV-2 Detection

Sensitive molecular assays are critical for coronavirus disease 2019 (COVID-19) diagnosis. Here, we designed and evaluated two single-tube nested (STN) real-time RT-PCR assays, targeting SARS-CoV-2 RdRp/Hel and N genes. Both STN assays had a low limit of detection and did not cross react with other human coronaviruses and respiratory viruses. Using 213 initial respiratory specimens from suspected COVID-19 patients, the sensitivity of both the STN COVID-19-RdRp/Hel and the STN COVID-19-N assays was 100% (99/99), while that of the comparator non-nested N assay was 95% (94/99). Among 108 follow-up specimens from confirmed COVID-19 patients who tested negative by the non-nested COVID-19-RdRp/Hel assay, 28 (25.9%) were positive for SARS-CoV-2 by the STN COVID-19-RdRp/Hel or the STN COVID-19-N assay. To evaluate the performance of our novel STN assays in pooled specimens, we created four sample pools, with each pool consisting of one low positive specimen and 49 negative specimens. While the non-nested COVID-19-RdRp/Hel assay was positive in only one of four sample pools (25%), both of the STN assays were positive in two of four samples pools (50%). In conclusion, the STN assays are highly sensitive and specific for SARS-CoV-2 detection. Their boosted sensitivity offers advantages in non-traditional COVID-19 testing algorithms such as saliva screening and pooled sample screening during massive screening.

Understanding the epidemiology, pathophysiology, diagnosis and management of SARS-CoV-2

The emergence of coronavirus disease 2019 (COVID-19) in December 2019 has resulted in over 20 million cases and 741,808 deaths globally, affecting more than 200 countries. COVID-19 was declared a pandemic on 11 March 2020 by the World Health Organization. The disease is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). There is limited information on COVID-19, and treatment has so far focused on supportive care and use of repurposed drugs. COVID-19 can be transmitted via person-to-person contact through droplet spread. Some of the recommended precautionary measures to reduce the rate of disease spread include social distancing, good hygiene practices, and avoidance of crowded areas. These measures are effective because the droplets are heavy and can only travel approximately 1 meter in the air, settling quickly on fixed surfaces. Promising strategies to combat SARS-CoV-2 include discovery of therapeutic targets/drugs and vaccines. In this review, we summarize the epidemiology, pathophysiology, and diagnosis of COVID-19. We also address the mechanisms of action of approved repurposed drugs for therapeutic management of the disease.

A Review on Currently Available Potential Therapeutic Options for COVID-19

A series of unexplained pneumonia cases currently were first reported in December 2019 in Wuhan, China. Official names have been announced for the virus responsible, previously known as "2019 novel coronavirus" and the diseases it causes are, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease (COVID-19), respectively. Despite great efforts worldwide to control SARS-CoV-2, the spread of the virus has reached a pandemic. Infection prevention and control of this virus is the primary concern of public health officials and professionals. Currently, several therapeutic options for COVID-19 are proposed and vaccine development has been initiated for prevention purposes. In this review, we will discuss the most recent evidence about the current potential treatment options including anti-inflammatory drugs, angiotensin-converting enzyme inhibitors/angiotensin receptor blockers, nucleoside analogs, protease inhibitors, monoclonal antibodies, and convalescent plasma therapy. Some other agents such as vitamin D and melatonin, which were recommended as potential adjuvant treatments for COVID-19 infection are also presented. Moreover, the potential use of convalescent plasma for treatment of COVID-19 infection was described. Furthermore, in the next part of the current review, various vaccination approaches against COVID-19 including whole virus vaccines, recombinant subunit vaccine, DNA vaccines, and mRNA vaccines are discussed.

A one-step, one-tube real-time RT-PCR based assay with an automated analysis for detection of SARS-CoV-2

Early diagnosis of SARS-CoV-2 infected patients is essential to control the dynamics of the COVID-19 pandemic. We develop a rapid and accurate one-step multiplex TaqMan probe-based real-time RT-PCR assay, along with a computational tool to systematically analyse the data. Our assay could detect to a limit of 15 copies of SARS-CoV-2 transcripts-based on experiments performed by spiking total human RNA with in vitro synthesized viral transcripts. The assay was evaluated by performing 184 validations for the SARS-CoV-2 Nucleocapsid gene and human RNase P as an internal control reference gene with dilutions ranging from 1-100 ng for human RNA on a cohort of 26 clinical samples. 5 of 26 patients were confirmed to be infected with SARS-CoV-2, while 21 tested negative, consistent with the standards. The accuracy of the assay was found to be 100% sensitive and 100% specific based on the 26 clinical samples that need to be further verified using a large number of clinical samples. In summary, we present a rapid, easy to implement real-time PCR based assay with automated analysis using a novel COVID qPCR Analyzer tool with graphical user interface (GUI) to analyze the raw qRT-PCR data in an unbiased manner at a cost of under $3 per reaction and turnaround time of less than 2h, to enable in-house SARS-CoV-2 testing across laboratories.

CRISPR-cas systems based molecular diagnostic tool for infectious diseases and emerging 2019 novel coronavirus (COVID-19) pneumonia

Emerging infectious diseases, the persistent potential for destabilising pandemics, remain a global threat leading to excessive morbidity and mortality. The current outbreak of pneumonia caused by 2019 novel coronavirus (COVID-19) illustrated difficulties in lack of effective drugs for treatment. Accurate and rapid diagnostic tools are essential for early recognition and treatment of infectious diseases, allowing timely implementation of infection control, improved clinical care and other public health measures to stop the spread of the disease. CRISPR-Cas technology speed up the development of infectious disease diagnostics with high rapid and accurate. In this review, we summarise current advance regarding diverse CRISPR-Cas systems, including CRISPR-Cas9, CRISPR-Cas12 and CRISPR-Cas13, in the development of fast, accurate and portable diagnostic tests and highlight the potential of CRISPR-Cas13 in COVID-19 Pneumonia and other emerging infectious diseases diagnosis.

α-Ketoamides as Broad-Spectrum Inhibitors of Coronavirus and Enterovirus Replication: Structure-Based Design, Synthesis, and Activity Assessment

The main protease of coronaviruses and the 3C protease of enteroviruses share a similar active-site architecture and a unique requirement for glutamine in the P1 position of the substrate. Because of their unique specificity and essential role in viral polyprotein processing, these proteases are suitable targets for the development of antiviral drugs. In order to obtain near-equipotent, broad-spectrum antivirals against alphacoronaviruses, betacoronaviruses, and enteroviruses, we pursued a structure-based design of peptidomimetic α-ketoamides as inhibitors of main and 3C proteases. Six crystal structures of protease-inhibitor complexes were determined as part of this study. Compounds synthesized were tested against the recombinant proteases as well as in viral replicons and virus-infected cell cultures; most of them were not cell-toxic. Optimization of the P2 substituent of the α-ketoamides proved crucial for achieving near-equipotency against the three virus genera. The best near-equipotent inhibitors, 11u (P2 = cyclopentylmethyl) and 11r (P2 = cyclohexylmethyl), display low-micromolar EC50 values against enteroviruses, alphacoronaviruses, and betacoronaviruses in cell cultures. In Huh7 cells, 11r exhibits three-digit picomolar activity against the Middle East Respiratory Syndrome coronavirus.

The epidemiology, diagnosis and treatment of COVID-19

In December 2019, the outbreak of the novel coronavirus disease (COVID-19) in China spread worldwide, becoming an emergency of major international concern. SARS-CoV-2 infection causes clusters of severe respiratory illness similar to severe acute respiratory syndrome coronavirus. Human-to-human transmission via droplets, contaminated hands or surfaces has been described, with incubation times of 2-14 days. Early diagnosis, quarantine, and supportive treatments are essential to cure patients. This paper reviews the literature on all available information about the epidemiology, diagnosis, isolation and treatments of COVID-19. Treatments, including antiviral agents, chloroquine and hydroxychloroquine, corticosteroids, antibodies, convalescent plasma transfusion and vaccines, are discussed in this article. In addition, registered trials investigating treatment options for COVID-19 infection are listed.

Improved Molecular Diagnosis of COVID-19 by the Novel, Highly Sensitive and Specific COVID-19-RdRp/Hel Real-Time Reverse Transcription-PCR Assay Validated In Vitro and with Clinical Specimens

On 31 December 2019, the World Health Organization was informed of a cluster of cases of pneumonia of unknown etiology in Wuhan, China. Subsequent investigations identified a novel coronavirus, now named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), from the affected patients. Highly sensitive and specific laboratory diagnostics are important for controlling the rapidly evolving SARS-CoV-2-associated coronavirus disease 2019 (COVID-19) epidemic. In this study, we developed and compared the performance of three novel real-time reverse transcription-PCR (RT-PCR) assays targeting the RNA-dependent RNA polymerase (RdRp)/helicase (Hel), spike (S), and nucleocapsid (N) genes of SARS-CoV-2 with that of the reported RdRp-P2 assay, which is used in >30 European laboratories.

On 31 December 2019, the World Health Organization was informed of a cluster of cases of pneumonia of unknown etiology in Wuhan, China. Subsequent investigations identified a novel coronavirus, now named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), from the affected patients. Highly sensitive and specific laboratory diagnostics are important for controlling the rapidly evolving SARS-CoV-2-associated coronavirus disease 2019 (COVID-19) epidemic. In this study, we developed and compared the performance of three novel real-time reverse transcription-PCR (RT-PCR) assays targeting the RNA-dependent RNA polymerase (RdRp)/helicase (Hel), spike (S), and nucleocapsid (N) genes of SARS-CoV-2 with that of the reported RdRp-P2 assay, which is used in >30 European laboratories. Among the three novel assays, the COVID-19-RdRp/Hel assay had the lowest limit of detection in vitro (1.8 50% tissue culture infective doses [TCID₅₀]/ml with genomic RNA and 11.2 RNA copies/reaction with in vitro RNA transcripts). Among 273 specimens from 15 patients with laboratory-confirmed COVID-19 in Hong Kong, 77 (28.2%) were positive by both the COVID-19-RdRp/Hel and RdRp-P2 assays. The COVID-19-RdRp/Hel assay was positive for an additional 42 RdRp-P2-negative specimens (119/273 [43.6%] versus 77/273 [28.2%]; P < 0.001), including 29/120 (24.2%) respiratory tract specimens and 13/153 (8.5%) non-respiratory tract specimens. The mean viral load of these specimens was 3.21 × 10⁴ RNA copies/ml (range, 2.21 × 10² to 4.71 × 10⁵ RNA copies/ml). The COVID-19-RdRp/Hel assay did not cross-react with other human-pathogenic coronaviruses and respiratory pathogens in cell culture and clinical specimens, whereas the RdRp-P2 assay cross-reacted with SARS-CoV in cell culture. The highly sensitive and specific COVID-19-RdRp/Hel assay may help to improve the laboratory diagnosis of COVID-19.

Origin, Potential Therapeutic Targets and Treatment for Coronavirus Disease (COVID-19)

The ongoing episode of coronavirus disease 19 (COVID-19) has imposed a serious threat to global health and the world economy. The disease has rapidly acquired a pandemic status affecting almost all populated areas of the planet. The causative agent of COVID-19 is a novel coronavirus known as SARS-CoV-2. The virus has an approximate 30 kb single-stranded positive-sense RNA genome, which is 74.5% to 99% identical to that of SARS-CoV, CoV-pangolin, and the coronavirus the from horseshoe bat. According to available information, SARS-CoV-2 is inferred to be a recombinant virus that originated from bats and was transmitted to humans, possibly using the pangolin as the intermediate host. The interaction of the SARS-CoV-2 spike protein with the human ACE2 (angiotensin-converting enzyme 2) receptor, and its subsequent cleavage by serine protease and fusion, are the main events in the pathophysiology. The serine protease inhibitors, spike protein-based vaccines, or ACE2 blockers may have therapeutic potential in the near future. At present, no vaccine is available against COVID-19. The disease is being treated with antiviral, antimalarial, anti-inflammatory, herbal medicines, and active plasma antibodies. In this context, the present review article provides a cumulative account of the recent information regarding the viral characteristics, potential therapeutic targets, treatment options, and prospective research questions.

Development of a Novel, Genome Subtraction-Derived, SARS-CoV-2-Specific COVID-19-nsp2 Real-Time RT-PCR Assay and Its Evaluation Using Clinical Specimens

The pandemic novel coronavirus infection, Coronavirus Disease 2019 (COVID-19), has affected at least 190 countries or territories, with 465,915 confirmed cases and 21,031 deaths. In a containment-based strategy, rapid, sensitive and specific testing is important in epidemiological control and clinical management. Using 96 SARS-CoV-2 and 104 non-SARS-CoV-2 coronavirus genomes and our in-house program, GolayMetaMiner, four specific regions longer than 50 nucleotides in the SARS-CoV-2 genome were identified. Primers were designed to target the longest and previously untargeted nsp2 region and optimized as a probe-free real-time reverse transcription-polymerase chain reaction (RT-PCR) assay. The new COVID-19-nsp2 assay had a limit of detection (LOD) of 1.8 TCID50/mL and did not amplify other human-pathogenic coronaviruses and respiratory viruses. Assay reproducibility in terms of cycle threshold (Cp) values was satisfactory, with the total imprecision (% CV) values well below 5%. Evaluation of the new assay using 59 clinical specimens from 14 confirmed cases showed 100% concordance with our previously developed COVID-19-RdRp/Hel reference assay. A rapid, sensitive, SARS-CoV-2-specific real-time RT-PCR assay, COVID-19-nsp2, was developed.

Recent advances in the detection of respiratory virus infection in humans

Respiratory tract viral infection caused by viruses or bacteria is one of the most common diseases in human worldwide, while those caused by emerging viruses, such as the novel coronavirus, 2019-nCoV that caused the pneumonia outbreak in Wuhan, China most recently, have posed great threats to global public health. Identification of the causative viral pathogens of respiratory tract viral infections is important to select an appropriate treatment, save people's lives, stop the epidemics, and avoid unnecessary use of antibiotics. Conventional diagnostic tests, such as the assays for rapid detection of antiviral antibodies or viral antigens, are widely used in many clinical laboratories. With the development of modern technologies, new diagnostic strategies, including multiplex nucleic acid amplification and microarray-based assays, are emerging. This review summarizes currently available and novel emerging diagnostic methods for the detection of common respiratory viruses, such as influenza virus, human respiratory syncytial virus, coronavirus, human adenovirus, and human rhinovirus. Multiplex assays for simultaneous detection of multiple respiratory viruses are also described. It is anticipated that such data will assist researchers and clinicians to develop appropriate diagnostic strategies for timely and effective detection of respiratory virus infections.

Systematic Comparison of Two Animal-to-Human Transmitted Human Coronaviruses: SARS-CoV-2 and SARS-CoV

After the outbreak of the severe acute respiratory syndrome (SARS) in the world in 2003, human coronaviruses (HCoVs) have been reported as pathogens that cause severe symptoms in respiratory tract infections. Recently, a new emerged HCoV isolated from the respiratory epithelium of unexplained pneumonia patients in the Wuhan seafood market caused a major disease outbreak and has been named the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This virus causes acute lung symptoms, leading to a condition that has been named as "coronavirus disease 2019" (COVID-19). The emergence of SARS-CoV-2 and of SARS-CoV caused widespread fear and concern and has threatened global health security. There are some similarities and differences in the epidemiology and clinical features between these two viruses and diseases that are caused by these viruses. The goal of this work is to systematically review and compare between SARS-CoV and SARS-CoV-2 in the context of their virus incubation, originations, diagnosis and treatment methods, genomic and proteomic sequences, and pathogenic mechanisms.

Recent advances in the detection of respiratory virus infection in humans

Respiratory tract viral infection caused by viruses or bacteria is one of the most common diseases in human worldwide, while those caused by emerging viruses, such as the novel coronavirus, 2019‐nCoV that caused the pneumonia outbreak in Wuhan, China most recently, have posed great threats to global public health. Identification of the causative viral pathogens of respiratory tract viral infections is important to select an appropriate treatment, save people's lives, stop the epidemics, and avoid unnecessary use of antibiotics. Conventional diagnostic tests, such as the assays for rapid detection of antiviral antibodies or viral antigens, are widely used in many clinical laboratories. With the development of modern technologies, new diagnostic strategies, including multiplex nucleic acid amplification and microarray‐based assays, are emerging. This review summarizes currently available and novel emerging diagnostic methods for the detection of common respiratory viruses, such as influenza virus, human respiratory syncytial virus, coronavirus, human adenovirus, and human rhinovirus. Multiplex assays for simultaneous detection of multiple respiratory viruses are also described. It is anticipated that such data will assist researchers and clinicians to develop appropriate diagnostic strategies for timely and effective detection of respiratory virus infections.

Respiratory tract viral infection including 2019‐nCoV poses great threats worldwide. Currently available and novel emerging diagnostic methods are summarized for several common respiratory viruses, including influenza virus, human respiratory syncytial virus, coronavirus, human adenovirus and human rhinovirus. Multiplex assays for simultaneous detection of multiple respiratory viruses are also described. This review is aimed to assist researchers and clinicians to develop timely and effective diagnostic strategies to detect respiratory virus infections.

Generation of a Nebulizable CDR-Modified MERS-CoV Neutralizing Human Antibody

Middle East respiratory syndrome coronavirus (MERS-CoV) induces severe aggravating respiratory failure in infected patients, frequently resulting in mechanical ventilation. As limited therapeutic antibody is accumulated in lung tissue following systemic administration, inhalation is newly recognized as an alternative, possibly better, route of therapeutic antibody for pulmonary diseases. The nebulization process, however, generates diverse physiological stresses, and thus, the therapeutic antibody must be resistant to these stresses, remain stable, and form minimal aggregates. We first isolated a MERS-CoV neutralizing antibody that is reactive to the receptor-binding domain (RBD) of spike (S) glycoprotein. To increase stability, we introduced mutations into the complementarity-determining regions (CDRs) of the antibody. In the HCDRs (excluding HCDR3) in this clone, two hydrophobic residues were replaced with Glu, two residues were replaced with Asp, and four residues were replaced with positively charged amino acids. In LCDRs, only two Leu residues were replaced with Val. These modifications successfully generated a clone with significantly greater stability and equivalent reactivity and neutralizing activity following nebulization compared to the original clone. In summary, we generated a MERS-CoV neutralizing human antibody that is reactive to recombinant MERS-CoV S RBD protein for delivery via a pulmonary route by introducing stabilizing mutations into five CDRs.

Emerging role of nanomedicine in the treatment of neuropathic pain

Neuropathic pain (NeP) is a complex chronic pain condition associated with nerve injury. Approximately, 7-10% of the general population across the globe is suffering from this traumatic condition, but the existing treatment strategies are inadequate to deliver pain relief and are associated with severe adverse effects. To overcome these limitations, lot of research is focussed on developing new molecules with high potency and fewer side effects, novel cell and gene-based therapies and modification of the previously approved drugs by different formulation aspects. Nanomedicine has attracted a lot of attention in the treatment of many diverse pathological conditions because of their unique physiochemical and biological properties. In this manuscript, we highlighted the emerging role of nanomedicine in different therapies (drug, cell and gene), also we emphasised on the challenges associated with nanomedicine such as development of well-characterised nanoformulation, scaling of batches with reproducible results and toxicity along with this we discussed about the future of nanomedicine in the treatment of neuropathic pain.

Middle East respiratory syndrome coronavirus (MERS-CoV): A review

As a novel coronavirus first reported by Saudi Arabia in 2012, the Middle East respiratory syndrome coronavirus (MERS-CoV) is responsible for an acute human respiratory syndrome. The virus, of 2C beta-CoV lineage, expresses the dipeptidyl peptidase 4 (DPP4) receptor and is densely endemic in dromedary camels of East Africa and the Arabian Peninsula. MERS-CoV is zoonotic but human-to-human transmission is also possible. Surveillance and phylogenetic researches indicate MERS-CoV to be closely associated with bats' coronaviruses, suggesting bats as reservoirs, although unconfirmed. With no vaccine currently available for MERS-CoV nor approved prophylactics, its global spread to over 25 countries with high fatalities highlights its role as ongoing public health threat. An articulated action plan ought to be taken, preferably from a One Health perspective, for appropriately advanced countermeasures against MERS-CoV.

Characterization of the Lipidomic Profile of Human Coronavirus-Infected Cells: Implications for Lipid Metabolism Remodeling upon Coronavirus Replication

Lipids play numerous indispensable cellular functions and are involved in multiple steps in the replication cycle of viruses. Infections by human-pathogenic coronaviruses result in diverse clinical outcomes, ranging from self-limiting flu-like symptoms to severe pneumonia with extrapulmonary manifestations. Understanding how cellular lipids may modulate the pathogenicity of human-pathogenic coronaviruses remains poor. To this end, we utilized the human coronavirus 229E (HCoV-229E) as a model coronavirus to comprehensively characterize the host cell lipid response upon coronavirus infection with an ultra-high performance liquid chromatography-mass spectrometry (UPLC–MS)-based lipidomics approach. Our results revealed that glycerophospholipids and fatty acids (FAs) were significantly elevated in the HCoV-229E-infected cells and the linoleic acid (LA) to arachidonic acid (AA) metabolism axis was markedly perturbed upon HCoV-229E infection. Interestingly, exogenous supplement of LA or AA in HCoV-229E-infected cells significantly suppressed HCoV-229E virus replication. Importantly, the inhibitory effect of LA and AA on virus replication was also conserved for the highly pathogenic Middle East respiratory syndrome coronavirus (MERS-CoV). Taken together, our study demonstrated that host lipid metabolic remodeling was significantly associated with human-pathogenic coronavirus propagation. Our data further suggested that lipid metabolism regulation would be a common and druggable target for coronavirus infections.

MERS coronavirus outbreak: Implications for emerging viral infections

In September 2012, a novel coronavirus was isolated from a patient who died in Saudi Arabia after presenting with acute respiratory distress and acute kidney injury. Analysis revealed the disease to be due to a novel virus which was named Middle East Respiratory Coronavirus (MERS-CoV). There have been several MERS-CoV hospital outbreaks in KSA, continuing to the present day, and the disease has a mortality rate in excess of 35%. Since 2012, the World Health Organization has been informed of 2220 laboratory-confirmed cases resulting in at least 790 deaths. Cases have since arisen in 27 countries, including an outbreak in the Republic of Korea in 2015 in which 36 people died, but more than 80% of cases have occurred in Saudi Arabia.. Human-to-human transmission of MERS-CoV, particularly in healthcare settings, initially caused a ‘media panic’, however human-to-human transmission appears to require close contact and thus far the virus has not achieved epidemic potential. Zoonotic transmission is of significant importance and evidence is growing implicating the dromedary camel as the major animal host in spread of disease to humans. MERS-CoV is now included on the WHO list of priority blueprint diseases for which there which is an urgent need for accelerated research and development as they have the potential to cause a public health emergency while there is an absence of efficacious drugs and/or vaccines. In this review we highlight epidemiological, clinical, and infection control aspects of MERS-CoV as informed by the Saudi experience. Attention is given to recommended treatments and progress towards vaccine development.

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2220 laboratory-confirmed cases of MERS-CoV resulting in at least 790 deaths since 2012

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MERS-CoV is on the WHO list of priority blueprint diseases

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Zoonotic and human-to-human transmission modes need further clarification.

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No specific therapy has yet been approved.

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There is a need for well-controlled clinical trials on potential direct therapies.

A Rapid and Specific Assay for the Detection of MERS-CoV

Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel human coronavirus that can cause human respiratory disease. The development of a detection method for this virus that can lead to rapid and accurate diagnosis would be significant. In this study, we established a nucleic acid visualization technique that combines the reverse transcription loop-mediated isothermal amplification technique and a vertical flow visualization strip (RT-LAMP-VF) to detect the N gene of MERS-CoV. The RT-LAMP-VF assay was performed in a constant temperature water bath for 30 min, and the result was visible by the naked eye within 5 min. The RT-LAMP-VF assay was capable of detecting 2 × 10¹ copies/μl of synthesized RNA transcript and 1 × 10¹ copies/μl of MERS-CoV RNA. The method exhibits no cross-reactivities with multiple CoVs including SARS-related (SARSr)-CoV, HKU4, HKU1, OC43 and 229E, and thus exhibits high specificity. Compared to the real-time RT-PCR (rRT-PCR) method recommended by the World Health Organization (WHO), the RT-LAMP-VF assay is easy to handle, does not require expensive equipment and can rapidly complete detection within 35 min.

Performance Evaluation of the PowerChek MERS (upE & ORF1a) Real-Time PCR Kit for the Detection of Middle East Respiratory Syndrome Coronavirus RNA

Background

Molecular detection of Middle East respiratory syndrome coronavirus (MERS-CoV) using real-time reverse transcription (rRT)-PCR assays is the method of choice for diagnosis of MERS. We evaluated the performance of the PowerChek MERS (upE & ORF1a) real-time PCR Kit (PowerChek MERS assay; Kogene Biotech, Korea) a one-step rRT-PCR assay for the qualitative detection of MERS-CoV.

Methods

We evaluated PowerChek MERS assay performance in comparison with nested RT-PCR and sequencing of the RNA-dependent RNA polymerase (RdRp) and N genes. To evaluate diagnostic sensitivity and specificity, 100 clinical specimens (50 positive and 50 negative for MERS-CoV) were simultaneously tested by using the PowerChek MERS and sequencing assays. Assay performance, including limit of detection and precision, was evaluated in vitro by using MERS-CoV RNA transcripts. Analytical specificity was evaluated with a diverse collection of 16 respiratory virus–positive clinical specimens and 14 respiratory bacterial isolates.

Results

The 95% limits of detection of the PowerChek MERS assay for the upE and the open rading frame (ORF)1a were 16.2 copies/µL and 8.2 copies/µL, respectively. No cross-reactivity was observed. The diagnostic sensitivity and specificity of the PowerChek MERS assay were both 100% (95% confidence interval, 91.1–100%).

Conclusions

The PowerChek MERS assay is a straightforward and accurate assay for detecting MERS-CoV RNA. The assay will be a useful tool for the rapid diagnosis of MERS and could prove especially important for MERS outbreak control.

Development of Middle East Respiratory Syndrome Coronavirus vaccines - advances and challenges

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is an emerging pathogen with the potential to pose a threat to global public health. Sporadic cases and outbreaks continue to be reported in the Middle East, and case fatality rates remain high at approximately 36% globally. No specific preventive or therapeutic countermeasures currently exist. A safe and effective vaccine could play an important role in protecting against the threat from MERS-CoV. This review discusses human vaccine candidates currently under development, and explores viral characteristics, molecular epidemiology and immunology relevant to MERS-CoV vaccine development. At present, a DNA vaccine candidate has begun a human clinical trial, while two vector-based candidates will very soon begin human trials. Protein-based vaccines are still at pre-clinical stage. Challenges to successful development include incomplete understanding of viral transmission, pathogenesis and immune response (in particular at the mucosal level), no optimal animal challenge models, lack of standardized immunological assays, and insufficient sustainable funding.

Large-scale machine learning of media outlets for understanding public reactions to nation-wide viral infection outbreaks

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The emotional public responses to a nation-wide outbreak of Middle East respiratory syndrome (MERS) in Korea was analyzed.

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Massive media outlet data was collected during the outbreak.

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An intriguing loop of information transfers between the media and the public was discovered.

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This method would be helpful for alleviating the unnecessary fear and overreaction of the public regarding infectious diseases.

From May to July 2015, there was a nation-wide outbreak of Middle East respiratory syndrome (MERS) in Korea. MERS is caused by MERS-CoV, an enveloped, positive-sense, single-stranded RNA virus belonging to the family Coronaviridae. Despite expert opinions that the danger of MERS might be exaggerated, there was an overreaction by the public according to the Korean mass media, which led to a noticeable reduction in social and economic activities during the outbreak. To explain this phenomenon, we presumed that machine learning-based analysis of media outlets would be helpful and collected a number of Korean mass media articles and short-text comments produced during the 10-week outbreak. To process and analyze the collected data (over 86 million words in total) effectively, we created a methodology composed of machine-learning and information-theoretic approaches. Our proposal included techniques for extracting emotions from emoticons and Internet slang, which allowed us to significantly (approximately 73%) increase the number of emotion-bearing texts needed for robust sentiment analysis of social media. As a result, we discovered a plausible explanation for the public overreaction to MERS in terms of the interplay between the disease, mass media, and public emotions.

Additional molecular testing of saliva specimens improves the detection of respiratory viruses

Emerging infectious diseases in humans are often caused by respiratory viruses such as pandemic or avian influenza viruses and novel coronaviruses. Microbiological testing for respiratory viruses is important for patient management, infection control and epidemiological studies. Nasopharyngeal specimens are frequently tested, but their sensitivity is suboptimal. This study evaluated the incremental benefit of testing respiratory viruses in expectorated saliva using molecular assays. A total of 258 hospitalized adult patients with suspected respiratory infections were included. Their expectorated saliva was collected without the use of any special devices. In the first cohort of 159 patients whose nasopharyngeal aspirates (NPAs) tested positive for respiratory viruses during routine testing, the viral load was measured using quantitative reverse transcription PCR. Seventeen percent of the patients (27/159) had higher viral loads in the saliva than in the NPA. The second cohort consisted of 99 patients whose NPAs tested negative for respiratory viruses using a direct immunofluorescence assay. Their NPA and saliva specimens were additionally tested using multiplex PCR. In these patients, the concordance rate by multiplex PCR between NPA and saliva was 83.8%. Multiplex PCR detected viruses in saliva samples from 16 patients, of which nine (56.3%) had at least one virus that was not detected in the NPA. Decisions on antiviral or isolation precautions would be affected by salivary testing in six patients. Although NPAs have high viral loads and remain the specimen of choice for most patients with respiratory virus infections, supplementary molecular testing of saliva can improve the clinical management of these patients.

Improved detection of Zika virus RNA in human and animal specimens by a novel, highly sensitive and specific real-time RT-PCR assay targeting the 5'-untranslated region of Zika virus

OBJECTIVE AND METHOD

We developed and evaluated five novel real-time RT-PCR assays targeting conserved regions in the 5'-untranslated region (5'-UTR), envelope (E'), non-structural protein 2A (NS2A), NS5 and 3'-UTR of the ZIKV genome.

RESULTS

The ZIKV-5'-UTR assay exhibited the lowest in vitro limit of detection (5-10 RNA copies/reaction and 3.0 × 10^-1 plaque-forming units/ml). Compared to the modified version of a widely adopted RT-PCR assay targeting the ZIKV-E gene, the ZIKV-5'-UTR assay showed better sensitivity in human clinical specimens, and representative mouse specimens, including many organs which are known to be involved in human ZIKV infection but difficult to obtain in clinical settings. The ZIKV-5'-UTR assay detected ZIKV RNA in 84/84 (100.0%) ZIKV-E'-positive and an additional 30/296 (10.1%, P < 0.01) ZIKV-E'-negative mouse specimens. The higher sensitivity of the ZIKV-5'-UTR assay was most significant in kidney and testis/epididymis specimens (P < 0.01). No in vitro or in vivo cross-reactivity was found between the ZIKV-5'-UTR assay and dengue virus, yellow fever virus, Japanese encephalitis virus, West Nile virus, hepatitis C virus and Chikungunya virus.

CONCLUSIONS

The highly sensitive and specific ZIKV-5'-UTR assay may help to improve the laboratory diagnosis of ZIKV infection.