Severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection. Clin Microbiol Rev. 2007;20:660-694. [PMID: 17934078 DOI: 10.1128/cmr.00023-07]

5G-enabled ultra-sensitive fluorescence sensor for proactive prognosis of COVID-19

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is spreading around the globe since December 2019. There is an urgent need to develop sensitive and online methods for on-site diagnosing and monitoring of suspected COVID-19 patients. With the huge development of Internet of Things (IoT), the impact of Internet of Medical Things (IoMT) provides an impressive solution to this problem. In this paper, we proposed a 5G-enabled fluorescence sensor for quantitative detection of spike protein and nucleocapsid protein of SARS-CoV-2 by using mesoporous silica encapsulated up-conversion nanoparticles (UCNPs@mSiO₂) labeled lateral flow immunoassay (LFIA). The sensor can detect spike protein (SP) with a detection of limit (LOD) 1.6 ng/mL and nucleocapsid protein (NP) with an LOD of 2.2 ng/mL. The feasibility of the sensor in clinical use was further demonstrated by utilizing virus culture as real clinical samples. Moreover, the proposed fluorescence sensor is IoMT enabled, which is accessible to edge hardware devices (personal computers, 5G smartphones, IPTV, etc.) through Bluetooth. Medical data can be transmitted to the fog layer of the network and 5G cloud server with ultra-low latency and high reliably for edge computing and big data analysis. Furthermore, a COVID-19 monitoring module working with the proposed the system is developed on a smartphone application (App), which endows patients and their families to record their medical data and daily conditions remotely, releasing the burdens of going to central hospitals. We believe that the proposed system will be highly practical in the future treatment and prevention of COVID-19 and other mass infectious diseases.

Emerging paradigms of viral diseases and paramount role of natural resources as antiviral agents

In the current scenario, the increasing prevalence of diverse microbial infections as well as emergence and re-emergence of viral epidemics with high morbidity and mortality rates are major public health threat. Despite the persistent production of antiviral drugs and vaccines in the global market, viruses still remain as one of the leading causes of deadly human diseases. Effective control of viral diseases, particularly Zika virus disease, Nipah virus disease, Severe acute respiratory syndrome, Coronavirus disease, Herpes simplex virus infection, Acquired immunodeficiency syndrome, and Ebola virus disease remain promising goal amidst the mutating viral strains. Current trends in the development of antiviral drugs focus solely on testing novel drugs or repurposing drugs against potential targets of the viruses. Compared to synthetic drugs, medicines from natural resources offer less side-effect to humans and are often cost-effective in the productivity approaches. This review intends not only to emphasize on the major viral disease outbreaks in the past few decades and but also explores the potentialities of natural substances as antiviral traits to combat viral pathogens. Here, we spotlighted a comprehensive overview of antiviral components present in varied natural sources, including plants, fungi, and microorganisms in order to identify potent antiviral agents for developing alternative therapy in future.

Ethnobotany, Pharmacological activities and Bioavailability studies of "King of Bitter" (Kalmegh): A Review (2010-2020)

BACKGROUND

Andrographis paniculata, commonly known as "Kalmegh", is an annual herbaceous plant from family Acanthaceae. The whole plant of A. paniculata has explored for multiple pharmacological activities and is scientifically recognized by in-vivo and in-vitro studies. Various biotechnologically engineered techniques have been explored to enhance the bioavailability of this plant.

OBJECTIVE

In this review, we aim to present comprehensive recent advances in the ethnopharmacology, phytochemistry, specific pharmacology, safety and toxicology and bioavailability of A. paniculata and its pure compounds. Possible directions for future research are also outlined in brief, which will encourage advance investigations on this plant.

METHODS

Information on the recent updates of the present review is collected from different electronic scientific databases such as Science Direct, PubMed, Scopus, and Google Scholar. All the composed information is classified into different sections according to the objective of the paper.

RESULTS

More than hundred research and review papers have been studied and incorporated in the present manuscript. After vast literature search of A. paniculata, we present a noteworthy report of various phytoconstituents present in plant, which are accountable for potential therapeutic properties of the plant. Forty-five of studied articles give general information about introduction, ethnobotany and traditional uses of the plant. Twenty-two papers enclosed information about the phytoconstituents present in different parts of A. paniculata and seventy-two papers briefly outlined the pharmacological activities like antioxidant, anti-dengue, anti-ulcerogenic, antifungal, some miscellaneous activities like activity against SARS-CoV-2, antidiarrhoeal. Nineteen studies highlighted the research work conducted by various researchers to increased bioavailability of A. paniculata and two studies reported the safety and toxicology of the plant.

CONCLUSION

This review incorporated the scientifically validated research work encompassing the ethnobotanical description of the subjected plant, phytochemical profile, various pharmacological activities, and recent approaches to enhance the bioavailability of active metabolites.

Drosophila as a Model for Infectious Diseases

The fruit fly, Drosophila melanogaster, has been used to understand fundamental principles of genetics and biology for over a century. Drosophila is now also considered an essential tool to study mechanisms underlying numerous human genetic diseases. In this review, we will discuss how flies can be used to deepen our knowledge of infectious disease mechanisms in vivo. Flies make effective and applicable models for studying host-pathogen interactions thanks to their highly conserved innate immune systems and cellular processes commonly hijacked by pathogens. Drosophila researchers also possess the most powerful, rapid, and versatile tools for genetic manipulation in multicellular organisms. This allows for robust experiments in which specific pathogenic proteins can be expressed either one at a time or in conjunction with each other to dissect the molecular functions of each virulent factor in a cell-type-specific manner. Well documented phenotypes allow large genetic and pharmacological screens to be performed with relative ease using huge collections of mutant and transgenic strains that are publicly available. These factors combine to make Drosophila a powerful tool for dissecting out host-pathogen interactions as well as a tool to better understand how we can treat infectious diseases that pose risks to public health, including COVID-19, caused by SARS-CoV-2.

Recent advances in the discovery of potent RNA-dependent RNA-polymerase (RdRp) inhibitors targeting viruses

WHO has declared COVID-19 a pandemic, which has affected the whole world and has caused unprecedented social and economic disruption. Since the emergence of the disease, several druggable targets have been suggested including 3-chymotrypsin-like protease (3CLpro), spike, RNA-dependent RNA polymerase (RdRp), and the papain-like protease (PLpro) computational approach. From the beginning, viral replication has been the main focus for any antiviral drug development for viral diseases, including HCV, influenza virus, zika virus, norovirus, measles, dengue virus, and coronaviruses. This review lists the nucleoside, nucleotide, and non-nucleoside RdRp inhibitor analogues of various viral diseases that may be evaluated for drug development to treat COVID-19.

Advances in gene-based vaccine platforms to address the COVID-19 pandemic

The novel betacoronavirus, SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), has spread across the globe at an unprecedented rate since its first emergence in Wuhan City, China in December 2019. Scientific communities around the world have been rigorously working to develop a potent vaccine to combat COVID-19 (coronavirus disease 2019), employing conventional and novel vaccine strategies. Gene-based vaccine platforms based on viral vectors, DNA, and RNA, have shown promising results encompassing both humoral and cell-mediated immune responses in previous studies, supporting their implementation for COVID-19 vaccine development. In fact, the U.S. Food and Drug Administration (FDA) recently authorized the emergency use of two RNA-based COVID-19 vaccines. We review current gene-based vaccine candidates proceeding through clinical trials, including their antigenic targets, delivery vehicles, and route of administration. Important features of previous gene-based vaccine developments against other infectious diseases are discussed in guiding the design and development of effective vaccines against COVID-19 and future derivatives.

Management of Coronavirus Disease 2019 (COVID-19) Pandemic: From Diagnosis to Treatment Strategies

Following the emergence of severe acute respiratory syndrome (SARS) in 2002 and the Middle East respiratory syndrome (MERS) in 2012, the world is now combating a third large-scale outbreak caused by a coronavirus, the coronavirus disease 2019 (COVID-19). After the rapid spread of SARS-coronavirus (CoV)-2 (the virus causing COVID-19) from its origin in China, the World Health Organization (WHO) declared a Public Health Emergency of International Concern (PHEIC) on January 30, 2020. From the beginning of the COVID-19 pandemic, a significant number of studies have been conducted to better understand the biology and pathogenesis of the novel coronavirus, and to aid in developing effective treatment regimens, therapeutics, and vaccines. This review focuses on the recent advancements in the rapidly evolving areas of clinical care and management of COVID-19. The emerging strategies for the diagnosis and treatment of this disease are explored, and the development of effective vaccines is reviewed.

Nanomaterials-Based Biosensors for COVID-19 Detection-A Review

This review paper discusses the properties of nanomaterials, namely graphene, molybdenum disulfide, carbon nanotubes, and quantum dots for unique sensing applications. Based on the specific analyte to be detected and the functionalization techniques that are employed, some noteworthy sensors that have been developed are discussed. Further, biocompatible sensors fabricated from these materials capable of detecting specific chemical compounds are also highlighted for COVID-19 detection purposes, which can aid in efficient and reliable sensing as well as timely diagnosis.

COVID-19: Immunology, Immunopathogenesis and Potential Therapies

The Coronavirus Disease-2019 (COVID-19) imposed public health emergency and affected millions of people around the globe. As of January 2021, 100 million confirmed cases of COVID-19 along with more than 2 million deaths were reported worldwide. SARS-CoV-2 infection causes excessive production of pro-inflammatory cytokines thereby leading to the development of "Cytokine Storm Syndrome." This condition results in uncontrollable inflammation that further imposes multiple-organ-failure eventually leading to death. SARS-CoV-2 induces unrestrained innate immune response and impairs adaptive immune responses thereby causing tissue damage. Thus, understanding the foremost features and evolution of innate and adaptive immunity to SARS-CoV-2 is crucial in anticipating COVID-19 outcomes and in developing effective strategies to control the viral spread. In the present review, we exhaustively discuss the sequential key immunological events that occur during SARS-CoV-2 infection and are involved in the immunopathogenesis of COVID-19. In addition to this, we also highlight various therapeutic options already in use such as immunosuppressive drugs, plasma therapy and intravenous immunoglobulins along with various novel potent therapeutic options that should be considered in managing COVID-19 infection such as traditional medicines and probiotics.

Racial/Ethnic Heterogeneity and Rural-Urban Disparity of COVID-19 Case Fatality Ratio in the USA: a Negative Binomial and GIS-Based Analysis

The 2019 coronavirus disease (COVID-19) has exacerbated inequality in the United States of America (USA). Black, indigenous, and people of color (BIPOC) are disproportionately affected by the pandemic. This study examines determinants of COVID-19 case fatality ratio (CFR) based on publicly sourced data from January 1 to December 18, 2020, and sociodemographic and rural-urban continuum data from the US Census Bureau. Nonspatial negative binomial Poisson regression and geographically weighted Poisson regression were applied to estimate the global and local relationships between the CFR and predictors—rural-urban continuum, political inclination, and race/ethnicity in 2407 rural counties. The mean COVID-19 CFR among rural counties was 1.79 (standard deviation (SD) = 1.07; 95% CI 1.73-1.84) higher than the total US counties (M = 1.69, SD = 1.18; 95% CI: 1.65-1.73). Based on the global NB model, CFR was positively associated with counties classified as “completely rural” (incidence rate ratio (IRR) = 1.24; 95% CI: 1.12-1.39) and “mostly rural” (IRR = 1.26; 95% CI: 1.15-1.38) relative to “mostly urban” counties. Nonspatial regression indicates that COVID-19 CFR increases by a factor of 8.62, 5.87, 2.61, and 1.36 for one unit increase in county-level percent Blacks, Hispanics, American Indians, and Asian/Pacific Islanders, respectively. Local spatial regression shows CFR was significantly higher in rural counties with a higher share of BIPOC in the Northeast and Midwest regions, and political inclination predicted COVID-19 CFR in rural counties in the Midwest region. In conclusion, spatial and racial/ethnic disparities exist for COVID-19 CFR across the US rural counties, and findings from this study have implications for public health.

A Case Study: Analysis of Patents on Coronaviruses and Covid-19 for Technological Assessment and Future Research

BACKGROUND

Protecting intellectual property rights are important and particularly pertinent for inventions that are an outcome of rigorous research and development. While the grant of patents is subject to establishing novelty and inventive step, it further indicates the technological development and is helpful for researchers working in the same technical domain. The aim of the present research work is to map the existing work through an analysis of patent literature in the field of Coronaviruses (CoV), particularly COVID-19 (2019-nCoV). CoV is a large family of viruses known to cause illness in humans and animals, particularly known for causing respiratory infections, as evidenced in earlier times, such as in MERS i.e., Middle East Respiratory Syndrome; and SRS i.e., Severe Acute Respiratory Syndrome. A recently identified novel-coronavirus, known as COVID-19, has caused pandemic situations across the globe.

OBJECTIVE

To expand the analysis of patents related to CoV and 2019-nCoV, an evaluation has been conducted by patenting trends of particular strains of identified CoV diseases by present legal status, main concerned countries via the earliest priority years and its assignee types and inventors of identified relevant patents. The global patent documents were analyzed to check the scope of claims along with focuses and trends of the published patent documents for the entire CoV family, including 2019-nCoV through the present landscape.

METHODS

To extract the results, the Derwent Innovation database was used by a combination of different keystrings. Approximately 3800 patents were obtained and further scrutinized and analyzed. The present write-up also discusses the recent progress of patent applications in a period of the year 2010 to 2020 (present) along with the recent developments in India for the treatment options for CoV and 2019-nCoV.

RESULTS

Present analysis showed that key areas of the inventions were the vaccines and diagnostic kits apart from the composition for the treatment of CoV. It was also observed that no specific vaccine treatments are available for the treatment of 2019-nCov; however, developing novel chemical or biological drugs and kits for early diagnosis, prevention, and disease management is the primary governing topic among the patented inventions. The present study also indicates potential research opportunities for the future, particularly to combat 2019-nCoV.

CONCLUSION

The present paper analyzes the existing patents in the field of Coronaviruses and 2019-nCoV and suggests a way forward for the effective contribution in this upcoming research area. From the trend analysis, an increase in the filing of the overall trend of patent families was observed for a period of 2010 to the current year. This multifaceted analysis of identified patent literature provides an understanding of the focuses on present ongoing research and a grey area in terms of the trends of technological innovations in disease management in patients with CoV and 2019-nCoV. Furthermore, the findings and outcome of the present study offer insights for the proposed research and innovation opportunities and provide actionable information in order to facilitate policymakers, academia, research-driven institutes and also investors to make better decisions regarding programmed steps for research and development for the diagnosis, treatment and taking preventive measures for CoV and 2019-nCoV. The present article also emphasizes the need for future development and the role of academia and collaboration with industry for speedy research with a rationale.

Digestive system involvement of infections with SARS-CoV-2 and other coronaviruses: Clinical manifestations and potential mechanisms

Although coronavirus (CoV) infection is often characterized by respiratory symptoms, the virus can also result in extrapulmonary symptoms, especially the symptoms related to the digestive system. The outbreak of coronavirus disease 2019 (COVID-19) is currently the world’s most pressing public health threat and has a significant impact on civil societies and the global economy. The occurrence of digestive symptoms in patients with COVID-19 is closely related to the development and prognosis of the disease. Moreover, thus far, there are no specific antiviral drug or vaccine approved for the treatment or prevention of COVID-19. Therefore, we elaborate on the effects of CoVs on the digestive system and the potential underlying mechanisms.

Diversity lost: COVID-19 as a phenomenon of the total environment

If we want to learn how to deal with the COVID-19 pandemic, we have to embrace the complexity of this global phenomenon and capture interdependencies across scales and contexts. Yet, we still lack systematic approaches that we can use to deal holistically with the pandemic and its effects. In this Discussion, we first introduce a framework that highlights the systemic nature of the COVID-19 pandemic from the perspective of the total environment as a self-regulating and evolving system comprising of three spheres, the Geosphere, the Biosphere, and the Anthroposphere. Then, we use this framework to explore and organize information from the rapidly growing number of scientific papers, preprints, preliminary scientific reports, and journalistic pieces that give insights into the pandemic crisis. With this work, we point out that the pandemic should be understood as the result of preconditions that led to depletion of human, biological, and geochemical diversity as well as of feedback that differentially impacted the three spheres. We contend that protecting and promoting diversity, is necessary to contribute to more effective decision-making processes and policy interventions to face the current and future pandemics.

Nutritional perspectives for the prevention and mitigation of COVID-19

Worldwide, there is an array of clinical trials under way to evaluate treatment options against coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2. Concurrently, several nutritional therapies and alternative supportive treatments are also being used and tested to reduce the mortality associated with acute respiratory distress in patients with COVID-19. In the context of COVID-19, improved nutrition that includes micronutrient supplementation to augment the immune system has been recognized as a viable approach to both prevent and alleviate the severity of the infection. The potential role of micronutrients as immune-boosting agents is particularly relevant for low- and middle-income countries, which already have an existing high burden of undernutrition and micronutrient deficiencies. A systematic literature review was performed to identify nutritional interventions that might prevent or aid in the recovery from COVID-19. The PubMed, ScienceDirect, Cochrane, Scopus, Web of Science, and Google Scholar databases were searched electronically from February to April 2020. All abstracts and full-text articles were examined for their relevance to this review. The information gathered was collated under various categories. Deficiencies of micronutrients, especially vitamins A, B complex, C, and D, zinc, iron, and selenium, are common among vulnerable populations in general and among COVID-19 patients in particular and could plausibly increase the risk of mortality. Judicious use of need-based micronutrient supplementation, alongside existing micronutrient fortification programs, is warranted in the current global pandemic, especially in low- and middle-income economies.

Nutritional perspectives for the prevention and mitigation of COVID-19

Worldwide, there is an array of clinical trials under way to evaluate treatment options against coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2. Concurrently, several nutritional therapies and alternative supportive treatments are also being used and tested to reduce the mortality associated with acute respiratory distress in patients with COVID-19. In the context of COVID-19, improved nutrition that includes micronutrient supplementation to augment the immune system has been recognized as a viable approach to both prevent and alleviate the severity of the infection. The potential role of micronutrients as immune-boosting agents is particularly relevant for low- and middle-income countries, which already have an existing high burden of undernutrition and micronutrient deficiencies. A systematic literature review was performed to identify nutritional interventions that might prevent or aid in the recovery from COVID-19. The PubMed, ScienceDirect, Cochrane, Scopus, Web of Science, and Google Scholar databases were searched electronically from February to April 2020. All abstracts and full-text articles were examined for their relevance to this review. The information gathered was collated under various categories. Deficiencies of micronutrients, especially vitamins A, B complex, C, and D, zinc, iron, and selenium, are common among vulnerable populations in general and among COVID-19 patients in particular and could plausibly increase the risk of mortality. Judicious use of need-based micronutrient supplementation, alongside existing micronutrient fortification programs, is warranted in the current global pandemic, especially in low- and middle-income economies.

Molecular Evolution of Human Coronavirus 229E in Hong Kong and a Fatal COVID-19 Case Involving Coinfection with a Novel Human Coronavirus 229E Genogroup

Compared to other human coronaviruses, the genetic diversity and evolution of human coronavirus 229E (HCoV-229E) are relatively understudied. We report a fatal case of COVID-19 pneumonia coinfected with HCoV-229E in Hong Kong. Genome sequencing of SARS-CoV-2 and HCoV-229E from a nasopharyngeal sample of the patient showed that the SARS-CoV-2 strain HK13 was most closely related to SARS-CoV-2 type strain Wuhan-Hu-1 (99.99% nucleotide identity), compatible with his recent history of travel to Wuhan. The HCoV-229E strain HK20-42 was most closely related to HCoV-229E strain SC0865 from the United States (99.86% nucleotide identity). To investigate if it may represent a newly emerged HCoV-229E genotype in Hong Kong, we retrieved 41 archived respiratory samples that tested positive for HCoV-229E from 2004 to 2019. Pneumonia and exacerbations of chronic airway diseases were common among infected patients. Complete RdRp, S, and N gene sequencing of the 41 HCoV-229E strains revealed that our contemporary HCoV-229E strains have undergone significant genetic drift with clustering of strains in chronological order. Two novel genogroups were identified, in addition to previously described genogroups 1 to 4, with recent circulating strains including strain HK20-42 belonging to novel genogroup 6. Positive selection was detected in the spike protein and receptor-binding domain, which may be important for viral evolution at the receptor-binding interphase. Molecular dating analysis showed that HCoV-229E shared the most recent common ancestor with bat and camel/alpaca 229E-related viruses at ∼1884, while camel/alpaca viruses had a relatively recent common ancestor at ∼1999. Further studies are required to ascertain the evolutionary origin and path of HCoV-229E.IMPORTANCE Since its first appearance in the 1960s, the genetic diversity and evolution of human coronavirus 229E (HCoV-229E) have been relatively understudied. In this study, we report a fatal case of COVID-19 coinfected with HCoV-229E in Hong Kong. Genome sequencing revealed that our SARS-CoV-2 strain is highly identical to the SARS-CoV-2 strain from Wuhan, compatible with the patient's recent travel history, whereas our HCoV-229E strain in this study is highly identical to a recent strain in the United States. We also retrieved 41 archived HCoV-229E strains from 2004 to 2019 in Hong Kong for sequence analysis. Pneumonia and exacerbations of chronic airway diseases were common diagnoses among the 41 patients. The results showed that HCoV-229E was evolving in chronological order. Two novel genogroups were identified in addition to the four preexisting HCoV-229E genogroups, with recent circulating strains belonging to novel genogroup 6. Molecular clock analysis dated bat-to-human and bat-to-camelid transmission to as early as 1884.

The effects on European importers' food safety controls in the time of COVID-19

COVID-19 has highlighted the fragility of the global economic system. In just a few months, the consequences of the pandemic have left their mark on the affected countries at all levels and without exception. This article analyses the profile of food safety notifications reported by European countries in the first five months of 2020. The aim was to detect possible changes in food safety regulations imposed by control authorities that could aggravate the economic impacts of the pandemic. While COVID-19 does not appear to be a foodborne disease, some outbreaks have been linked to imported food, which might have affected the food control behaviour of importing countries. In this study, contingency tables and clustering were used to assess differences between years and notification characteristics and to detect homogeneous groups to help identify how the reported notifications might have changed. In the period considered in this study, the volume of notifications on most imported foodstuffs decreased considerably. This decrease was a direct consequence of the fall in international trade, which might have increased countries' reliance on domestic sources. The COVID-19 crisis has not caused a substantial change in the profile of European countries’ in terms of the characteristics of reported notifications (product category and risk decision). However, the worst affected countries have replaced border rejections with alerts, which may indicate greater reliance on intra-EU markets.

Targeting C-terminal Helical bundle of NCOVID19 Envelope (E) protein

One of the most crucial characteristic traits of Envelope (E) proteins in the severe acute respiratory syndrome SARS-CoV-1 and NCOVID19 viruses is their membrane-associated oligomerization led ion channel activity, virion assembly, and replication. NMR spectroscopic structural studies of envelope proteins from both the SARS CoV-1/2 reveal that this protein assembles into a homopentamer. Proof of concept studies via truncation mutants on either transmembrane (VFLLV), glycosylation motif (CACCN), hydrophobic helical bundle (PVYVY) as well as replacing C-terminal "DLLV" segments or point mutants such as S68, E69 residues with cysteine have significantly reduced viral titers of SARS-CoV-1. In this present study, we have first developed SARS-2 E protein homology model based on the pentamer coordinates of SARS-CoV-1 E protein (86.4% structural identity) with good stereochemical quality. Next, we focused on the glycosylation motif and hydrophobic helical bundle regions of E protein shown to be important for viral replication. A four feature (4F) model comprising of an acceptor targeting S60 hydroxyl group, a donor feature anchoring the C40 residue, and two hydrophobic features anchoring the V47 L28, L31, Y55, and P51 residues formed the protein based pharmacophore model targeting the glycosylation motif and helical bundle of E protein. Database screening with this 4F protein pharmacophore, ADMET property filtering on enamine small molecule discovery collection yielded a focused library of ~7000 hits. Further molecular docking and visual inspection of docked pose interactions at the above mention V47 L28, L31, Y55, P51, S60, C40 residues led to the identification of 10 best hits. Our STD NMR binding assay results demonstrate that the ligand 3, 2-(2-amino-2-oxo-ethoxy)-N-benzyl-benzamide, binds to NCOVID19 E protein with a binding affinity (K_D) of 141.7 ± 13.6 μM. Furthermore, the ligand 3 also showed binding to C-terminal peptide (NR25) as evidenced with the STD spectrums of wild type E protein would serve to confirm the involvement of C-terminal helical bundle as envisaged in this study.

Tracing the origins of SARS-COV-2 in coronavirus phylogenies: a review

SARS-CoV-2 is a new human coronavirus (CoV), which emerged in China in late 2019 and is responsible for the global COVID-19 pandemic that caused more than 97 million infections and 2 million deaths in 12 months. Understanding the origin of this virus is an important issue, and it is necessary to determine the mechanisms of viral dissemination in order to contain future epidemics. Based on phylogenetic inferences, sequence analysis and structure-function relationships of coronavirus proteins, informed by the knowledge currently available on the virus, we discuss the different scenarios on the origin-natural or synthetic-of the virus. The data currently available are not sufficient to firmly assert whether SARS-CoV2 results from a zoonotic emergence or from an accidental escape of a laboratory strain. This question needs to be solved because it has important consequences on the risk/benefit balance of our interactions with ecosystems, on intensive breeding of wild and domestic animals, on some laboratory practices and on scientific policy and biosafety regulations. Regardless of COVID-19 origin, studying the evolution of the molecular mechanisms involved in the emergence of pandemic viruses is essential to develop therapeutic and vaccine strategies and to prevent future zoonoses. This article is a translation and update of a French article published in Médecine/Sciences, August/September 2020 (10.1051/medsci/2020123).

Supplementary Information

The online version of this article (10.1007/s10311-020-01151-1) contains supplementary material, which is available to authorized users.

Guidelines and Safety Considerations in the Laboratory Diagnosis of SARS-CoV-2 Infection: A Prerequisite Study for Health Professionals

Coronavirus disease 2019 (COVID-19) is an emerging challenging area for the researchers to buckle up against the spread and control of the virus. Since earlier times, the diagnosis has been an important procedure in estimating the fate of epidemics by indicating the extent to which disease has been spread and to the extent, further disease prognosis would occur. The absence of anti-viral therapies and vaccines for COVID-19 at present suggests early diagnosis and isolation of the patients as the only smart approach available as of now. Presently, the increasing death rates, faster rates of transmission, non-availability of vaccines, and treatment have over-pressurized the researchers, health professionals, and government officials to develop effective clinical strategies in diagnosis and to come up with guidelines to be followed during conduction of each diagnostic procedure for maintaining healthcare systems. Since the incubation period of this virus is 2-14 days, a patient can transmit the infection without showing symptoms. Therefore, early diagnosis and isolation of susceptible individuals are the only way to limit the spread of the virus. Significance of diagnosis and triaging, information on specimen collection, safety considerations while handling, transport, and storage of samples have been highlighted in this paper to make people more aware and develop better clinical strategies in the future.

Can Zn Be a Critical Element in COVID-19 Treatment?

The current COVID-19 pandemic caused by SARS-CoV-2 has prompted investigators worldwide to search for an effective anti-viral treatment. A number of anti-viral drugs such as ribavirin, remdesivir, lopinavir/ritonavir, antibiotics such as azithromycin and doxycycline, and anti-parasite such as ivermectin have been recommended for COVID-19 treatment. In addition, sufficient pre-clinical rationale and evidence have been presented to use chloroquine for the treatment of COVID-19. Furthermore, Zn has the ability to enhance innate and adaptive immunity in the course of a viral infection. Besides, Zn supplement can favour COVID-19 treatment using those suggested and/or recommended drugs. Again, the effectiveness of Zn can be enhanced by using chloroquine as an ionophore while Zn inside the infected cell can stop SARS-CoV-2 replication. Given those benefits, this perspective paper describes how and why Zn could be given due consideration as a complement to the prescribed treatment of COVID-19.

Profiling severe acute respiratory syndrome coronavirus 2 and its relevance to otolaryngologic examinations during the coronavirus disease 2019 pandemic

PURPOSE OF REVIEW

The WHO announced the coronavirus disease 2019 (COVID-19) outbreak as a pandemic in February 2020 with over 15 million confirmed cases of COVID-19 globally to date. Otolaryngologists are at a high risk of contracting COVID-19 during this pandemic if there is inadequate and improper personal protective equipment provision, as we are dealing with diseases of the upper-aerodigestive tract and routinely engaged in aerosol-generating procedures.

RECENT FINDINGS

This article discusses the background and transmission route for severe acute respiratory syndrome coronavirus 2, its viral load and temporal profile as well as precaution guidelines in outpatient and operative setting in otorhinolaryngology.

SUMMARY

As it is evident that COVID-19 can be transmitted at presymptomatic or asymptomatic period of infections, it is essential to practice ear, nose, and throat surgery with high vigilance in a safe and up-to-standard protection level during the pandemic. This article provides a summary for guidelines and recommendations in otorhinolaryngology.

Exploring human-animal host interactions and emergence of COVID-19: Evolutionary and ecological dynamics

The novel coronavirus disease (COVID-19) that emerged in December 2019 had caused substantial morbidity and mortality at the global level within few months. It affected economies, stopped travel, and isolated individuals and populations around the world. Wildlife, especially bats, serve as reservoirs of coronaviruses from which the variant Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) emerged that causes COVID-19. In this review, we describe the current knowledge on COVID-19 and the significance of wildlife hosts in its emergence. Mammalian and avian coronaviruses have diverse host ranges with distinct lineages of coronaviruses. Recombination and reassortments occur more frequently in mixed-animal markets where diverse viral genotypes intermingle. Human coronaviruses have evolved through gene gains and losses primarily in interfaces where wildlife and humans come in frequent contact. There is a gap in our understanding of bats as reservoirs of coronaviruses and there is a misconception that bats periodically transmit coronaviruses to humans. Future research should investigate bat viral diversity and loads at interfaces between humans and bats. Furthermore, there is an urgent need to evaluate viral strains circulating in mixed animal markets, where the coronaviruses circulated before becoming adapted to humans. We propose and discuss a management intervention plan for COVID-19 and raise questions on the suitability of current containment plans. We anticipate that more virulent coronaviruses could emerge unless proper measures are taken to limit interactions between diverse wildlife and humans in wild animal markets.

In silico docking analysis revealed the potential of phytochemicals present in Phyllanthus amarus and Andrographis paniculata, used in Ayurveda medicine in inhibiting SARS-CoV-2

The Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has resulted in outbreak of global pandemic, fatal pneumonia in human referred as Coronavirus Disease-2019 (Covid-19). Ayurveda, the age old practice of treating human ailments in India, can be considered against SARS-CoV-2. Attempt was made to provide preliminary evidences for interaction of 35 phytochemicals from two plants (Phyllanthus amarus and Andrographis paniculata used in Ayurveda) with SARS-CoV-2 proteins (open & closed state S protein, 3CLpro, PLpro and RdRp) through in silico docking analysis. The nucleotide analogue remdesivir, being used in treatment of SARS-CoV-2, was used as a positive control. The results revealed that 18 phytochemicals from P. amarus and 14 phytochemicals from A. paniculata shown binding energy affinity/dock score < - 6.0 kcal/mol, which is considered as minimum threshold for any compound to be used for drug development. Phytochemicals used for docking studies in the current study from P. amarus and A. paniculata showed binding affinity up to - 9.10 kcal/mol and - 10.60 kcal/mol, respectively. There was no significant difference in the binding affinities of these compounds with closed and open state S protein. Further, flavonoids (astragalin, kaempferol, quercetin, quercetin-3-O-glucoside and quercetin) and tannins (corilagin, furosin and geraniin) present in P. amarus have shown more binding affinity (up to - 10.60 kcal/mol) than remdesivir (up to - 9.50 kcal/mol). The pharmacokinetic predictions suggest that compounds from the two plants species studied in the current study are found to be non-carcinogenic, water soluble and biologically safe. The phytochemicals present in the extracts of P. amarus and A. paniculata might have synergistic effect with action on multiple target sites of SARS-CoV-2. The information generated here might serve as preliminary evidence for anti SARS-CoV-2 activity of phytochemicals present from P. amarus and A. paniculata and the potential of Ayurveda medicine in combating the virus.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-020-02578-7.

Vaccine formulations in clinical development for the prevention of severe acute respiratory syndrome coronavirus 2 infection

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to an unprecedented effort toward the development of an effective and safe vaccine. Aided by extensive research efforts into characterizing and developing countermeasures towards prior coronavirus epidemics, as well as recent developments of diverse vaccine platform technologies, hundreds of vaccine candidates using dozens of delivery vehicles and routes have been proposed and evaluated preclinically. A high demand coupled with massive effort from researchers has led to the advancement of at least 31 candidate vaccines in clinical trials, many using platforms that have never before been approved for use in humans. This review will address the approach and requirements for a successful vaccine against SARS-CoV-2, the background of the myriad of vaccine platforms currently in clinical trials for COVID-19 prevention, and a summary of the present results of those trials. It concludes with a perspective on formulation problems which remain to be addressed in COVID-19 vaccine development and antigens or adjuvants which may be worth further investigation.

Overview of antiviral drug candidates targeting coronaviral 3C-like main proteases

Coronaviruses (CoVs) are positive single-stranded RNA viruses that cause severe respiratory syndromes in humans, including severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). Coronavirus disease 2019 (COVID-19) caused by a novel severe acute respiratory syndrome CoV (SARS-CoV-2) at the end of 2019 became a global pandemic. The 3C-like cysteine protease (3CLpro) processes viral polyproteins to yield mature non-structural proteins, thus playing an important role in the CoV life cycle, and therefore is considered as a prominent target for antiviral drugs. To date, many 3CLpro inhibitors have been reported, and their molecular mechanisms have been illustrated. Here, we briefly introduce the structural features of 3CLpro of the human-related SARS-CoV, MERS-CoV and SARS-CoV-2, and explore the potency and mechanism of their cognate inhibitors. This information will shed light on the development and optimization of CoV 3CLpro inhibitors, which may benefit the further designation of therapeutic strategies for treating CoV diseases.

Symptom Profiles and Progression in Hospitalized and Nonhospitalized Patients with Coronavirus Disease, Colorado, USA, 2020

To improve recognition of coronavirus disease (COVID-19) and inform clinical and public health guidance, we randomly selected 600 COVID-19 case-patients in Colorado. A telephone questionnaire captured symptoms experienced, when symptoms occurred, and how long each lasted. Among 128 hospitalized patients, commonly reported symptoms included fever (84%), fatigue (83%), cough (73%), and dyspnea (72%). Among 236 nonhospitalized patients, commonly reported symptoms included fatigue (90%), fever (83%), cough (83%), and myalgia (74%). The most commonly reported initial symptoms were cough (21%-25%) and fever (20%-25%). In multivariable analysis, vomiting, dyspnea, altered mental status, dehydration, and wheezing were significantly associated with hospitalization, whereas rhinorrhea, headache, sore throat, and anosmia or ageusia were significantly associated with nonhospitalization. General symptoms and upper respiratory symptoms occurred earlier in disease, and anosmia, ageusia, lower respiratory symptoms, and gastrointestinal symptoms occurred later. Symptoms should be considered alongside other epidemiologic factors in clinical and public health decisions regarding potential COVID-19 cases.

Targeted Nanotherapeutics for Respiratory Diseases: Cancer, Fibrosis, and Coronavirus

Systemic delivery of therapeutics for treatment of lung diseases has several limitations including poor organ distribution of delivered payload with relatively low accumulation of active substances in the lungs and severe adverse side effects. In contrast, nanocarrier based therapeutics provide a broad range of opportunities due to their ability to encapsulate substances with different aqueous solubility, transport distinct types of cargo, target therapeutics specifically to the deceased organ, cell, or cellular organelle limiting adverse side effects and increasing the efficacy of therapy. Moreover, many nanotherapeutics can be delivered by inhalation locally to the lungs avoiding systemic circulation. In addition, nanoscale based delivery systems can be multifunctional, simultaneously carrying out several tasks including diagnostics, treatment and suppression of cellular resistance to the treatment. Nanoscale delivery systems improve the clinical efficacy of conventional therapeutics allowing new approaches for the treatment of respiratory diseases which are difficult to treat or possess intrinsic or acquired resistance to treatment. The present review summarizes recent advances in the development of nanocarrier based therapeutics for local and targeted delivery of drugs, nucleic acids and imaging agents for diagnostics and treatment of various diseases such as cancer, cystic fibrosis, and coronavirus.

Emerging infectious disease: An underappreciated area of strategic concern for food security

Emerging infectious diseases (EIDs) increasingly threaten global food security and public health. Despite technological breakthroughs, we are losing the battle with (re)emerging diseases as treatment costs and production losses rise. A horizon scan of diseases of crops, livestock, seafood and food-borne illness suggests these costs are unsustainable. The paradigm of coevolution between pathogens and particular hosts teaches that emerging diseases occur only when pathogens evolve specific capacities that allow them to move to new hosts. EIDs ought to be rare and unpredictable, so crisis response is the best we can do. Alternatively, the Stockholm Paradigm suggests that the world is full of susceptible but unexposed hosts that pathogens could infect, given the opportunity. Global climate change, globalized trade and travel, urbanization and land-use changes (often associated with biodiversity loss) increase those opportunities, making EID frequent. We can, however, anticipate their arrival in new locations and their behaviour once they have arrived. We can 'find them before they find us', mitigating their impacts. The DAMA (Document, Assess, Monitor, Act) protocol alters the current reactive stance and embodies proactive solutions to anticipate and mitigate the impacts of EID, extending human and material resources and buying time for development of new vaccinations, medications and control measures.

HTCC as a Polymeric Inhibitor of SARS-CoV-2 and MERS-CoV

Among seven coronaviruses that infect humans, three (severe acute respiratory syndrome coronavirus [SARS-CoV], Middle East respiratory syndrome coronavirus [MERS-CoV], and the newly identified severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) are associated with a severe, life-threatening respiratory infection and multiorgan failure. We previously proposed that the cationically modified chitosan N-(2-hydroxypropyl)-3-trimethylammonium chitosan chloride (HTCC) is a potent inhibitor of human coronavirus NL63 (HCoV-NL63). Next, we demonstrated the broad-spectrum antiviral activity of the compound, as it inhibited all low-pathogenicity human coronaviruses (HCoV-NL63, HCoV-229E, HCoV-OC43, and HCoV-HKU1). Here, using in vitro and ex vivo models of human airway epithelia, we show that HTCC effectively blocks MERS-CoV and SARS-CoV-2 infection. We also confirmed the mechanism of action for these two viruses, showing that the polymer blocks the virus entry into the host cell by interaction with the S protein.IMPORTANCE The beginning of 2020 brought us information about the novel coronavirus emerging in China. Rapid research resulted in the characterization of the pathogen, which appeared to be a member of the SARS-like cluster, commonly seen in bats. Despite the global and local efforts, the virus escaped the health care measures and rapidly spread in China and later globally, officially causing a pandemic and global crisis in March 2020. At present, different scenarios are being written to contain the virus, but the development of novel anticoronavirals for all highly pathogenic coronaviruses remains the major challenge. Here, we describe the antiviral activity of an HTCC compound, previously developed by us, which may be used as a potential inhibitor of currently circulating highly pathogenic coronaviruses-SARS-CoV-2 and MERS-CoV.

HTCC as a Polymeric Inhibitor of SARS-CoV-2 and MERS-CoV

Among seven coronaviruses that infect humans, three (severe acute respiratory syndrome coronavirus [SARS-CoV], Middle East respiratory syndrome coronavirus [MERS-CoV], and the newly identified severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) are associated with a severe, life-threatening respiratory infection and multiorgan failure. We previously proposed that the cationically modified chitosan N-(2-hydroxypropyl)-3-trimethylammonium chitosan chloride (HTCC) is a potent inhibitor of human coronavirus NL63 (HCoV-NL63). Next, we demonstrated the broad-spectrum antiviral activity of the compound, as it inhibited all low-pathogenicity human coronaviruses (HCoV-NL63, HCoV-229E, HCoV-OC43, and HCoV-HKU1). Here, using in vitro and ex vivo models of human airway epithelia, we show that HTCC effectively blocks MERS-CoV and SARS-CoV-2 infection. We also confirmed the mechanism of action for these two viruses, showing that the polymer blocks the virus entry into the host cell by interaction with the S protein.IMPORTANCE The beginning of 2020 brought us information about the novel coronavirus emerging in China. Rapid research resulted in the characterization of the pathogen, which appeared to be a member of the SARS-like cluster, commonly seen in bats. Despite the global and local efforts, the virus escaped the health care measures and rapidly spread in China and later globally, officially causing a pandemic and global crisis in March 2020. At present, different scenarios are being written to contain the virus, but the development of novel anticoronavirals for all highly pathogenic coronaviruses remains the major challenge. Here, we describe the antiviral activity of an HTCC compound, previously developed by us, which may be used as a potential inhibitor of currently circulating highly pathogenic coronaviruses-SARS-CoV-2 and MERS-CoV.

Natural and Nature-Derived Products Targeting Human Coronaviruses

The ongoing pandemic of severe acute respiratory syndrome (SARS), caused by the SARS-CoV-2 human coronavirus (HCoV), has brought the international scientific community before a state of emergency that needs to be addressed with intensive research for the discovery of pharmacological agents with antiviral activity. Potential antiviral natural products (NPs) have been discovered from plants of the global biodiversity, including extracts, compounds and categories of compounds with activity against several viruses of the respiratory tract such as HCoVs. However, the scarcity of natural products (NPs) and small-molecules (SMs) used as antiviral agents, especially for HCoVs, is notable. This is a review of 203 publications, which were selected using PubMed/MEDLINE, Web of Science, Scopus, and Google Scholar, evaluates the available literature since the discovery of the first human coronavirus in the 1960s; it summarizes important aspects of structure, function, and therapeutic targeting of HCoVs as well as NPs (19 total plant extracts and 204 isolated or semi-synthesized pure compounds) with anti-HCoV activity targeting viral and non-viral proteins, while focusing on the advances on the discovery of NPs with anti-SARS-CoV-2 activity, and providing a critical perspective.

Contact residue contributions to interaction energies between SARS-CoV-1 spike proteins and human ACE2 receptors

Several viruses of the corona family interact, via their spike (S) proteins, with human cellular receptors. Spike proteins of SARS-CoV-1 and SARS-CoV-2 virions, being structurally related but not identical, mediate attachment to the human angiotensin-converting enzyme 2 (hACE2) receptor in similar but non-identical ways. Molecular-level understanding of interactions between spike proteins and hACE2 can aid strategies for blocking attachment of SARS-CoV-1, a potentially reemerging health threat, to human cells. We have identified dominant molecular-level interactions, some attractive and some repulsive, between the receptor binding domain of SARS-CoV-1 spike proteins (S-RBD) and hACE2. We performed fragment-based quantum-biochemical calculations which directly relate biomolecular structure to the hACE2...S-RBD interaction energy. Consistent with X-ray crystallography and cryo-EM, the interaction energy between hACE2 and S-RBD (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\approx -$$\end{document}≈-26 kcal/mol) corresponds to a net intermolecular attraction which is significantly enhanced by inclusion of dispersion van der Waals forces. Protein fragments at the hACE2...S-RBD interface, that dominate host-virus attraction, have been identified together with their constituent amino acid residues. Two hACE2 fragments which include residues (GLU37, ASP38, TYR41, GLN42) and (GLU329, LYS353, GLY354), respectively, as well as three S-RBD fragments which include residues (TYR436), (ARG426) and (THR487, GLY488, TYR491), respectively, have been identified as primary attractors at the hACE2...S-RBD interface.

Host and viral determinants for efficient SARS-CoV-2 infection of the human lung

Understanding the factors that contribute to efficient SARS-CoV-2 infection of human cells may provide insights on SARS-CoV-2 transmissibility and pathogenesis, and reveal targets of intervention. Here, we analyze host and viral determinants essential for efficient SARS-CoV-2 infection in both human lung epithelial cells and ex vivo human lung tissues. We identify heparan sulfate as an important attachment factor for SARS-CoV-2 infection. Next, we show that sialic acids present on ACE2 prevent efficient spike/ACE2-interaction. While SARS-CoV infection is substantially limited by the sialic acid-mediated restriction in both human lung epithelial cells and ex vivo human lung tissues, infection by SARS-CoV-2 is limited to a lesser extent. We further demonstrate that the furin-like cleavage site in SARS-CoV-2 spike is required for efficient virus replication in human lung but not intestinal tissues. These findings provide insights on the efficient SARS-CoV-2 infection of human lungs.

COVID-19: What Should the General Practitioner Know?

BACKGROUND

SARS-CoV-2 infection is currently the most significant public health challenge. Its presentation ranges from mild to severe respiratory failure and septic shock. Rapid transmission of the virus is dangerous with a high possibility of life-threatening complications. Lack of treatment standards for SARS-CoV-2 is responsible for the current dilemma in clinical medicine.

METHODS

An electronic literature search was done using PubMed to gather information on the pathogenesis, transmission of infection, clinical symptoms, diagnosis, and therapeutic options for COVID-19. Search items included "SARS-CoV-2", "COVID-19" and "coronavirus infection".

RESULTS

In light of the current global crisis caused by SARS-CoV-2, the exchange of information within the scientific community should be quick and extremely transparent. Thus, this review presents the available information necessary for a general practitioner. Such presentation of data should allow the reader quick access to basic and crucial information related to epidemiology, viral transmission, clinical symptoms, diagnostics, treatment, and complications that may occur in the course of COVID-19.

CONCLUSION

Rapidly increasing amounts of information about the diagnosis and treatment of patients with SARS-CoV-2 allow a better understanding of the etiology and course of the infection. In the current epidemiological situation, readily accessible information helps minimize the time to acquire knowledge and focus on prevention methods, diagnostic and treatment options. Thus, this review highlights key issues related to SARS-CoV-2 infection and contains the most useful data for daily medical practice.

Identification of SARS-CoV-2 CTL epitopes for development of a multivalent subunit vaccine for COVID-19

An immunoinformatics-based approach was used to identify potential multivalent subunit CTL vaccine candidates for SARS-CoV-2. Criteria for computational screening included antigen processing, antigenicity, allergenicity, and toxicity. A total of 2604 epitopes were found to be strong binders to MHC class I molecules when analyzed using IEDB tools. Further testing for antigen processing yielded 826 peptides of which 451 were 9-mers that were analyzed for potential antigenicity. Antigenic properties were predicted for 102 of the 451 peptides. Further assessment for potential allergenicity and toxicity narrowed the number of candidate CTL epitopes to 50 peptide sequences, 45 of which were present in all strains of SARS-CoV-2 that were tested. The predicted CTL epitopes were then tested to eliminate those with MHC class II binding potential, a property that could induce hyperinflammatory responses mediated by T_H2 cells in immunized hosts. Eighteen of the 50 epitopes did not show class II binding potential. To our knowledge this is the first comprehensive analysis on the proteome of SARS-CoV-2 for prediction of CTL epitopes lacking binding properties that could stimulate unwanted T_H2 responses. Future studies will be needed to assess these epitopes as multivalent subunit vaccine candidates which stimulate protective CTL responses against SARS-COV-2.

The Treaty of Influenza and SARS-CoV-2: Titans Versus Olympians

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Recent Developments on Therapeutic and Diagnostic Approaches for COVID-19

The ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made a serious public health threat worldwide with millions of people at risk in a growing number of countries. Though there are no clinically approved antiviral drugs and vaccines for COVID-19, attempts are ongoing for clinical trials of several known antiviral drugs, their combination, as well as development of vaccines in patients with confirmed COVID-19. This review focuses on the latest approaches to diagnostics and therapy of COVID-19. We have summarized recent progress on the conventional therapeutics such as antiviral drugs, vaccines, anti-SARS-CoV-2 antibody treatments, and convalescent plasma therapy which are currently under extensive research and clinical trials for the treatment of COVID-19. The developments of nanoparticle-based therapeutic and diagnostic approaches have been also discussed for COVID-19. We have assessed recent literature data on this topic and made a summary of current development and future perspectives.

Lessons from the host defences of bats, a unique viral reservoir

There have been several major outbreaks of emerging viral diseases, including Hendra, Nipah, Marburg and Ebola virus diseases, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS)-as well as the current pandemic of coronavirus disease 2019 (COVID-19). Notably, all of these outbreaks have been linked to suspected zoonotic transmission of bat-borne viruses. Bats-the only flying mammal-display several additional features that are unique among mammals, such as a long lifespan relative to body size, a low rate of tumorigenesis and an exceptional ability to host viruses without presenting clinical disease. Here we discuss the mechanisms that underpin the host defence system and immune tolerance of bats, and their ramifications for human health and disease. Recent studies suggest that 64 million years of adaptive evolution have shaped the host defence system of bats to balance defence and tolerance, which has resulted in a unique ability to act as an ideal reservoir host for viruses. Lessons from the effective host defence of bats would help us to better understand viral evolution and to better predict, prevent and control future viral spillovers. Studying the mechanisms of immune tolerance in bats could lead to new approaches to improving human health. We strongly believe that it is time to focus on bats in research for the benefit of both bats and humankind.

Severe acute respiratory syndrome coronavirus 2 in cats: a systematic review

The epidemiological role of cats in the coronavirus disease pandemic remains unclear despite of several studies that have been conducted to understand it, in other words it is not yet known whether the cat would be able to transmit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to humans. Taking that into account, the objective of this study was to conduct a systematic review to identify what is known and not known on this topic. Our results revealed that cats can be infected through an airborne (perhaps oral, too) route and that the clinical development of the infection in cats is parallel to that in humans. The majority of infected cats remained asymptomatic, and more severe clinical cases described occurred only in animals with comorbidities. In addition to infection, cats achieved seroconversion with detectable titers. However, the epidemiological role of cats in relation to transmission routes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains unclear and needs to be studied further. We emphasize that, regardless of the conclusion regarding the epidemiological role of cats, this reinforces the concepts of ONE HEALTH to be incorporated into the studies and practices of epidemiological surveillance of infectious diseases, with multidisciplinary teams, to achieve an understanding of the transmission of diseases with zoonotic potential.

General Public Knowledge of Coronavirus Disease 2019 (COVID-19) at Early Stages of the Pandemic: A Random Online Survey in Saudi Arabia

BACKGROUND

A novel coronavirus was identified at the end of 2019 in Wuhan City, China. Later, it was named as coronavirus disease 2019 (COVID-19) and declared a pandemic in March 2020. Saudi and global health agencies have provided various COVID-19 knowledge tools and facts to the general public. Therefore, this study aims to assess COVID-19 knowledge among the general public in Saudi Arabia at the early stages of the pandemic.

PARTICIPANTS AND METHODS

A cross-sectional study was conducted in March 2020 in Saudi Arabia. The study included 1006 participants who responded to a random online COVID-19 public knowledge questionnaire that included five sections: demographic characteristics, general knowledge, prevention practices, home quarantine measures, and knowledge of governmental restrictions. Three levels of knowledge were established: excellent, intermediate, and poor. Differences in the percentages of participants with different knowledge levels by the demographic variables were analyzed using the chi-square test.

RESULTS

Regarding overall general knowledge of COVID-19, 75%, 24%, and 1% of the participants had excellent, intermediate, and poor knowledge levels, respectively. Knowledge levels were significantly different by nationality and age (P=0.027 and 0.008, respectively). Most participants (98.4%) reported excellent knowledge of prevention practices, with no statistically significant differences among groups (P>0.005). Older age groups reported higher knowledge of home quarantine measures (86.6% and 86.4% of the 51-60 and older than 60 age groups, respectively, P=0.001).

CONCLUSION AND RECOMMENDATIONS

High levels of knowledge about the virus, including prevention practices, are essential. The provision of COVID-19 facts and knowledge tools should be focused on younger generations to enhance compliance with the governmental restrictions required to stop the spread of COVID-19.

Genetic influences on viral-induced cytokine responses in the lung

Infection with respiratory viruses such as influenza, respiratory syncytial virus and coronavirus provides a difficult immunological challenge for the host, where a balance must be established between controlling viral replication and limiting damage to the delicate lung structure. Although the genetic architecture of host responses to respiratory viral infections is not yet understood, it is clear there is underlying heritability that influences pathogenesis. Immune control of virus replication is essential in respiratory infections, but overt activation can enhance inflammation and disease severity. Cytokines initiate antiviral immune responses but are implicated in viral pathogenesis. Here, we discuss how host genetic variation may influence cytokine responses to respiratory viral infections and, based on our current understanding of the role that cytokines play in viral pathogenesis, how this may influence disease severity. We also discuss how induced pluripotent stem cells may be utilised to probe the mechanistic implications of allelic variation in genes in virus-induced inflammatory responses. Ultimately, this could help to design better immune modulators, stratify high risk patients and tailor anti-inflammatory treatments, potentially expanding the ability to treat respiratory virus outbreaks in the future.

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.

Acute Arterial Thromboembolism in Patients with COVID-19 in the New York City Area

BACKGROUND

Coronavirus disease 2019 (COVID-19) predisposes to arterial and venous thromboembolic complications. We describe the clinical presentation, management, and outcomes of acute arterial ischemia and concomitant infection at the epicenter of cases in the United States.

METHODS

Patients with confirmed COVID-19 infection between March 1, 2020 and May 15, 2020 with an acute arterial thromboembolic event were reviewed. Data collected included demographics, anatomical location of the thromboembolism, treatments, and outcomes.

RESULTS

Over the 11-week period, the Northwell Health System cared for 12,630 hospitalized patients with COVID-19. A total of 49 patients with arterial thromboembolism and confirmed COVID-19 were identified. The median age was 67 years (58-75) and 37 (76%) were men. The most common preexisting conditions were hypertension (53%) and diabetes (35%). The median D-dimer level was 2,673 ng/mL (723-7,139). The distribution of thromboembolic events included upper 7 (14%) and lower 35 (71%) extremity ischemia, bowel ischemia 2 (4%), and cerebral ischemia 5 (10%). Six patients (12%) had thrombus in multiple locations. Concomitant deep vein thrombosis was found in 8 patients (16%). Twenty-two (45%) patients presented with signs of acute arterial ischemia and were subsequently diagnosed with COVID-19. The remaining 27 (55%) developed ischemia during hospitalization. Revascularization was performed in 13 (27%) patients, primary amputation in 5 (10%), administration of systemic tissue- plasminogen activator in 3 (6%), and 28 (57%) were treated with systemic anticoagulation only. The rate of limb loss was 18%. Twenty-one patients (46%) died in the hospital. Twenty-five (51%) were successfully discharged, and 3 patients are still in the hospital.

CONCLUSIONS

While the mechanism of thromboembolic events in patients with COVID-19 remains unclear, the occurrence of such complication is associated with acute arterial ischemia which results in a high limb loss and mortality.

Phytochemistry and pharmacological activity of the genus artemisia

Artemisia and its allied species have been employed for conventional medicine in the Northern temperate regions of North America, Europe, and Asia for the treatments of digestive problems, morning sickness, irregular menstrual cycle, typhoid, epilepsy, renal problems, bronchitis malaria, etc. The multidisciplinary use of artemisia species has various other health benefits that are related to its traditional and modern pharmaceutical perspectives. The main objective of this review is to evaluate the traditional, modern, biological as well as pharmacological use of the essential oil and herbal extracts of Artemisia nilagirica, Artemisia parviflora, and other allied species of Artemisia. It also discusses the botanical circulation and its phytochemical constituents viz disaccharides, polysaccharides, glycosides, saponins, terpenoids, flavonoids, and carotenoids. The plants have different biological importance like antiparasitic, antimalarial, antihyperlipidemic, antiasthmatic, antiepileptic, antitubercular, antihypertensive, antidiabetic, anxiolytic, antiemetic, antidepressant, anticancer, hepatoprotective, gastroprotective, insecticidal, antiviral activities, and also against COVID-19. Toxicological studies showed that the plants at a low dose and short duration are non or low-toxic. In contrast, a high dose at 3 g/kg and for a longer duration can cause toxicity like rapid respiration, neurotoxicity, reproductive toxicity, etc. However, further in-depth studies are needed to determine the medicinal uses, clinical efficacy and safety are crucial next steps.

Lessons learned and questions raised during and post-COVID-19 anthropopause period in relation to the environment and climate

In the first part, this work reports that during the global "anthropopause" period, that was imposed in March and April 2020 for limiting the spread of COVID-19, the concentrations of basic air pollutants over Europe were reduced by up to 70%. During May and June, the gradual lift of the stringent measures resulted in the recovery of these reductions with pollution concentrations approaching the levels before the lockdown by the end of June 2020. In the second part, this work examines the alleged correlations between the reported cases of COVID-19 and temperature, humidity and particulate matter for March and April 2020 in Europe. It was found that decreasing temperatures and relative humidity with increasing concentrations of particulate matter are correlated with an increase in the number of reported cases during these 2 months. However, when these calculations were repeated for May and June, we found a remarkable drop in the significance of the correlations which leads us to question the generally accepted inverse relation between pandemics and air temperature at least during the warmer months. Such a relationship could not be supported in our study for SARS-CoV-2 virus and the question remains open. In the third and last part of this work, we examine the question referring to the origin of pandemics. In this context we have examined the hypothesis that the observed climate warming in Siberia and the Arctic and the thawing of permafrost could result to the release of trapped in the permafrost pathogens in the atmosphere. We find that although such relations cannot be directly justified, they present a possible horrifying mechanism for the origin of viruses in the future during the developing global warming of our planet in the decades to come. Overall the findings of our study indicate that: (1) the reduction of anthropogenic emissions in Europe during the "anthropopause" period of March and April 2020 was significant, but when the lockdown measures were raised the concentrations of atmospheric pollutants quickly recovered to pre-pandemic levels and therefore any possible climatic feedbacks were negligible; (2) no robust relationship between atmospheric parameters and the spread of COVID-19 cases can be justified in the warmer part of the year and (3) more research needs to be done regarding the possible links between climate change and the release of new pathogens from thawing of permafrost areas.

Microfluidic devices for detection of RNA viruses

There is a long way to go before the coronavirus disease 2019 (Covid-19) outbreak comes under control. qRT-PCR is currently used for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of Covid-19, but it is expensive, time-consuming, and not as sensitive as it should be. Finding a rapid, easy-to-use, and cheap diagnostic method is necessary to help control the current outbreak. Microfluidic systems provide a platform for many diagnostic tests, including RT-PCR, RT-LAMP, nested-PCR, nucleic acid hybridization, ELISA, fluorescence-Based Assays, rolling circle amplification, aptamers, sample preparation multiplexer (SPM), Porous Silicon Nanowire Forest, silica sol-gel coating/bonding, and CRISPR. They promise faster, cheaper, and easy-to-use methods with higher sensitivity, so microfluidic devices have a high potential to be an alternative method for the detection of viral RNA. These devices have previously been used to detect RNA viruses such as H1N1, Zika, HAV, HIV, and norovirus, with acceptable results. This paper provides an overview of microfluidic systems as diagnostic methods for RNA viruses with a focus on SARS-CoV-2.

Zinc against COVID-19? Symptom surveillance and deficiency risk groups

A wide variety of symptoms is associated with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection, and these symptoms can overlap with other conditions and diseases. Knowing the distribution of symptoms across diseases and individuals can support clinical actions on timelines shorter than those for drug and vaccine development. Here, we focus on zinc deficiency symptoms, symptom overlap with other conditions, as well as zinc effects on immune health and mechanistic zinc deficiency risk groups. There are well-studied beneficial effects of zinc on the immune system including a decreased susceptibility to and improved clinical outcomes for infectious pathogens including multiple viruses. Zinc is also an anti-inflammatory and anti-oxidative stress agent, relevant to some severe Coronavirus Disease 2019 (COVID-19) symptoms. Unfortunately, zinc deficiency is common worldwide and not exclusive to the developing world. Lifestyle choices and preexisting conditions alone can result in zinc deficiency, and we compile zinc risk groups based on a review of the literature. It is also important to distinguish chronic zinc deficiency from deficiency acquired upon viral infection and immune response and their different supplementation strategies. Zinc is being considered as prophylactic or adjunct therapy for COVID-19, with 12 clinical trials underway, highlighting the relevance of this trace element for global pandemics. Using the example of zinc, we show that there is a critical need for a deeper understanding of essential trace elements in human health, and the resulting deficiency symptoms and their overlap with other conditions. This knowledge will directly support human immune health for decreasing susceptibility, shortening illness duration, and preventing progression to severe cases in the current and future pandemics.

Next-generation computational tools and resources for coronavirus research: From detection to vaccine discovery

The COVID-19 pandemic has affected 215 countries and territories around the world with 60,187,347 coronavirus cases and 17,125,719 currently infected patients confirmed as of the November 25, 2020. Currently, many countries are working on developing new vaccines and therapeutic drugs for this novel virus strain, and a few of them are in different phases of clinical trials. The advancement in high-throughput sequence technologies, along with the application of bioinformatics, offers invaluable knowledge on genomic characterization and molecular pathogenesis of coronaviruses. Recent multi-disciplinary studies using bioinformatics methods like sequence-similarity, phylogenomic, and computational structural biology have provided an in-depth understanding of the molecular and biochemical basis of infection, atomic-level recognition of the viral-host receptor interaction, functional annotation of important viral proteins, and evolutionary divergence across different strains. Additionally, various modern immunoinformatic approaches are also being used to target the most promiscuous antigenic epitopes from the SARS-CoV-2 proteome for accelerating the vaccine development process. In this review, we summarize various important computational tools and databases available for systematic sequence-structural study on coronaviruses. The features of these public resources have been comprehensively discussed, which may help experimental biologists with predictive insights useful for ongoing research efforts to find therapeutics against the infectious COVID-19 disease.

The Importance of Glycosylation in COVID-19 Infection

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is currently one of the major health problems worldwide. SARS-CoV-2 survival and virulence are shown to be impacted by glycans, covalently attached to proteins in a process of glycosylation, making glycans an area of interest in SARS-CoV-2 biology and COVID-19 infection. The SARS-CoV-2 uses its highly glycosylated spike (S) glycoproteins to bind to the cell surface receptor angiotensin-converting enzyme 2 (ACE2) glycoprotein and facilitate host cell entry. Viral glycosylation has wide-ranging roles in viral pathobiology, including mediating protein folding and stability, immune evasion, host receptor attachment, and cell entry. Modification of SARS-CoV-2 envelope membrane with glycans is important in host immune recognition and interaction between S and ACE2 glycoproteins. On the other hand, immunoglobulin G, a key molecule in immune response, shows a distinct glycosylation profile in COVID-19 infection and with increased disease severity. Hence, further studies on the role of glycosylation in SARS-CoV-2 infectivity and COVID-19 infection are needed for its successful prevention and treatment. This chapter focuses on recent findings on the importance of glycosylation in COVID-19 infection.