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]

Potential G-quadruplexes and i-Motifs in the SARS-CoV-2

Quadruplex structures have been identified in a plethora of organisms where they play important functions in the regulation of molecular processes, and hence have been proposed as therapeutic targets for many diseases. In this paper we report the extensive bioinformatic analysis of the SARS-CoV-2 genome and related viruses using an upgraded version of the open-source algorithm G4-iM Grinder. This version improves the functionality of the software, including an easy way to determine the potential biological features affected by the candidates found. The quadruplex definitions of the algorithm were optimized for SARS-CoV-2. Using a lax quadruplex definition ruleset, which accepts amongst other parameters two residue G- and C-tracks, 512 potential quadruplex candidates were discovered. These sequences were evaluated by their in vitro formation probability, their position in the viral RNA, their uniqueness and their conservation rates (calculated in over seventeen thousand different COVID-19 clinical cases and sequenced at different times and locations during the ongoing pandemic). These results were then compared subsequently to other Coronaviridae members, other Group IV (+)ssRNA viruses and the entire viral realm. Sequences found in common with other viral species were further analyzed and characterized. Sequences with high scores unique to the SARS-CoV-2 were studied to investigate the variations amongst similar species. Quadruplex formation of the best candidates were then confirmed experimentally. Using NMR and CD spectroscopy, we found several highly stable RNA quadruplexes that may be suitable therapeutic targets for the SARS-CoV-2.

Nanomedicine: A Diagnostic and Therapeutic Approach to COVID-19

The SARS-CoV-2 virus is causing devastating morbidity and mortality worldwide. Nanomedicine approaches have a high potential to enhance conventional diagnostics, drugs and vaccines. In fact, lipid nanoparticle/mRNA vaccines are already widely used to protect from COVID-19. In this review, we present an overview of the taxonomy, structure, variants of concern, epidemiology, pathophysiology and detection methods of SARS-CoV-2. The efforts of repurposing, tailoring, and adapting pre-existing medications to battle COVID-19 and the state of vaccine developments are presented. Next, we discuss the broad concepts and limitations of how nanomedicine could address the COVID-19 threat. Nanomaterials are particles in the nanometer scale (10-100 nm) which possess unique properties related to their size, polarity, structural and chemical composition. Nanoparticles can be composed of precious metals (copper, silver, gold), inorganic materials (graphene, silicon), proteins, carbohydrates, lipids, RNA/DNA, or conjugates, combinations and polymers of all of the aforementioned. The advanced biochemical features of these nanoscale particles allow them to directly interact with virions and irreversibly disrupt their structure, which can render a virus incapable of replicating within the host. Virus-neutralizing coats and surfaces impregnated with nanomaterials can enhance personal protective equipment, hand sanitizers and air filter systems. Nanoparticles can enhance drug-based therapies by optimizing uptake, stability, target cell-specific delivery, and magnetic properties. In fact, recent studies have highlighted the potential of nanoparticles in different aspects of the fight against SARS-CoV-2, such as enhancing biosensors and diagnostic tests, drug therapies, designing new delivery mechanisms, and optimizing vaccines. This article summarizes the ongoing research on diagnostic strategies, treatments, and vaccines for COVID-19, while emphasizing the potential of nanoparticle-based pharmaceuticals and vaccines.

Development and validation of a new triplex real-time quantitative reverse Transcriptase-PCR assay for the clinical detection of SARS-CoV-2

To increase the repertoire of PCR based laboratory developed tests (LDTs) for the detection of SARS-CoV-2, we describe a new multiplex assay (SORP), targeting the SARS-CoV-2's, Spike and ORF8 genes. The widely used human RNaseP internal control was modified to specifically co-amplify the RNaseP mRNA. The SORP triplex assay was tested on a cohort (n = 372; POS = 144/NEG = 228) of nasopharyngeal flocked swab (NPFS) specimens, previously tested for the presence of SARS-CoV-2 using a PCR assay targeting E and RdRp genes. The overall sensitivity and specificity of the SORP assay was: 99.31% (95% CI: 96.22–99.98%), 100.0% (95% CI: 98.4–100%) respectively. The SORP assay could also detect a panel of variants of concern (VOC) from the B1.1.7 (UK) and B1.351 (SA) lineage. In summary, access to a repertoire of new SARS-CoV-2 LDT's would assist diagnostic laboratories in developing strategies to overcome some of the testing issues encountered during high-throughput SARS-CoV-2 testing.

Gamma irradiation-mediated inactivation of enveloped viruses with conservation of genome integrity: Potential application for SARS-CoV-2 inactivated vaccine development

Radiation inactivation of enveloped viruses occurs as the result of damages at the molecular level of their genome. The rapidly emerging and ongoing coronavirus disease 2019 (COVID-19) pneumonia pandemic prompted by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is now a global health crisis and an economic devastation. The readiness of an active and safe vaccine against the COVID-19 has become a race against time in this unqualified global panic caused by this pandemic. In this review, which we hope will be helpful in the current situation of COVID-19, we analyze the potential use of γ-irradiation to inactivate this virus by damaging at the molecular level its genetic material. This inactivation is a vital step towards the design and development of an urgently needed, effective vaccine against this disease.

Origin, Pathogenesis, Diagnosis and Treatment Options for SARS-CoV-2: A Review

Emerging viral infections are among the greatest challenges in the public health sector in the twenty-first century. Among these, most of the viruses jump from other species of animals to humans called zoonotic viruses. The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), by crossing species-barrier, has infected the human population for the third time in the current century and has caused the coronavirus disease-2019 (COVID-19) . Mutation and adaptation for years have greatly influenced the co-evolution and existence of coronaviruses and their possible hosts including humans. The appearance of SARS-CoV-2 in China thrust coronaviruses into the limelight and shocked the world. Presently, no coronavirus vaccines are clinically available to combat the virus's devastating effects. To counter the emergence of the COVID-19 pandemic, it is therefore important to understand the complex nature of coronaviruses and their clinical attributes. SARS and MERS outbreaks had ultimately led to socio-economic deprivation in the previous decades. In addressing the recent disastrous situation, the COVID-19 pandemic still needs some lessons from prior experience. In this review, we have highlighted the chronological order of coronavirus strains, their genomic features, the mechanism of action of SARS-CoV-2, and its disastrous repercussions on the world. We have also suggested some therapeutic options that could be effective against the COVID-19.

SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS-2 (SARS-COV-2) INFECTION: AN EPIDEMIOLOGICAL REVIEW

BACKGROUND

New strains of different organisms, three of which has been caused by betacorona viruses (SARS-CoV, MERS-CoV and SARSCoV- 2) have caused epidemics and pandemics. The COVID-19, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) started in China in December 2019 has spread globally. Understanding its pattern of spread and how it affects the populace helps to guide formulation of strategies at curbing its spread, managing the disease and allocation of limited resources in tackling the pandemic.

METHODOLOGY

This is a review article about the epidemiology of the coronavirus disease -2019 (COVID-19). Various search engines were used to accumulate literature on the topic; these include PubMed, Google scholar, Ajol.

RESULTS

As at October 29, 2020, SARS-CoV2 has spread to all continents except the Antarctica. Though a zoonotic disease, human to human transmission has resulted to this pandemic is via direct and indirect contact of droplets with mucosal surfaces. Most severe cases occur among the elderly, males, and people with co-morbid diseases. The average incubation period is 2-10 days. When compared with SARS-CoV (Ro: 2.3-3.7, mortality rate 11%) and MERS-CoV (Ro: 0.8-1.3, mortality rate: 34.3%), SARS-Cov-2 is a highly infective (Ro: as high as 6.5) with low mortality rates (average range mortality rates 1.83- 6.3%).

CONCLUSION

COVID-19 is a highly infective novel virus. Older persons and people with medical comorbidities are more susceptible to the severe form of the disease and mortality. As the second wave comes on, a sustainable measure of limiting the spread and consequences of COVID-19 should be more emphasized.

Biomedical Waste and Solid Waste Management in the Time of COVID-19: A Comprehensive Review of the National and International Scenario and Guidelines

Biomedical waste generated during the diagnosis, isolation, and treatment of coronavirus disease 2019 (COVID-19) patients can also be the source of new infections; hence, it needs special consideration. Previous guidelines for the management of biomedical waste need to be revisited as the majority of COVID-19 patients remain asymptomatic and reside in community. Personal protective equipment (PPE) like masks, hazmat suits, gloves, and visors are now being used by the public also. Thus, the general household waste and disposables now make an exponential increase in the waste that can be considered an environmental hazard. In this article, the authors have tried to present the problems arising from COVID-19 waste and the recommendations put forth by competent authorities both nationally and internationally on COVID-19 waste management. Furthermore, in all the guidelines, it is crucial that the COVID-19 waste management follows environmentally sound principles and practices of biomedical waste management, with safe work and infection-control practices. Segregation of COVID-19 waste at source, awareness, and precautions at all steps of the waste-cycle are the only way ahead in this crisis.

Eating habits and physical activity before and during the health emergency due to COVID-19 in Quito - Ecuador

COVID-19 has managed to paralyze the world for months, this paralysis has caused great changes in the habits, customs and routines of all people. Although science is directed to getting a vaccine to return to normality, these changes may remain in the population. For this reason, it is essential to identify them and observe what has improved or worsened. The IPAQ questionnaire (international physical activity questionnaire) was used to analyze physical activity and regarding food consumption a questionnaire on eating habits. These were applied in a representative sample of adults between 18 and 65 years old in the city of Quito (n: 1022) to collect information before and during the forced quarantine in the city. These data were analyzed and compared along with daily routines and demographic variables of age, education and income. Our working hypothesis was that enforced quarantine would have a significant impact on daily activities, including waking time, mealtimes, physical activity, and eating habits. Waking time went from 5 to 6 to 8-9 in the morning and the breakfast and lunch times changed. The physical activity of the entire population decreased while men proved to be more active than women before and during the health emergency. Our findings suggested that eating habits improved overall during the quarantine period; however, we found that a higher percentage of women reported very healthy eating habits compared to men. People from 18 to 41 years old, with a university education, regardless of their income, decreased their physical activity during quarantine, people with incomes of up to $ 400 per month changed their eating habits to unhealthy since the emergency began. The population in the city of Quito varied their daily routine of physical activity and their eating habits, this suggests that it should be analyzed what measures should be implemented to continue with what has been improved and change what has worsened, and thus avoid public health problems in the future.

Role of SARS-CoV-2 and ACE2 variations in COVID-19

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is one of the worst medical emergencies that has hit the world in almost a century. The virus has now spread to a large number of countries/territories and has caused over three million deaths. Evidently, the virus has been mutating and adapting during this period. Significant effort has been spent on identifying these variations and their impact on transmission, virulence and pathogenicity of SARS-CoV-2. Binding of the SARS-CoV-2 spike protein to the angiotensin converting enzyme 2 (ACE2) promotes cellular entry. Therefore, human ACE2 variations could also influence susceptibility or resistance to the virus. A deeper understanding of the evolution and genetic variations in SARS-CoV-2 as well as ACE2 could contribute to the development of effective treatment and preventive measures. Here, we review the literature on SARS-CoV-2 and ACE2 variations and their role in COVID-19.

Screening of natural compounds from Cyperus rotundus Linn against SARS-CoV-2 main protease (Mpro): An integrated computational approach

Coronavirus disease 2019 (COVID-19) is a viral respiratory disease that has been spreading across the globe. The World Health Organization (WHO) declared it as a public health emergency. The treatment of COVID-19 has been hampered due to the lack of effective therapeutic efforts. Main Protease (M^pro) is a key enzyme in the viral replication cycle and its non-specificity to human protease makes it a potential drug target. Cyperus rotundus Linn, which belongs to the Cyperaceae family, is a traditional herbal medicine that has been widely studied for its antiviral properties. In this study, a computational approach was used to screen natural compounds from C. rotundus Linn using BIOVIA Discovery Suite and novel potential molecules against M^pro of SARS-CoV-2 were predicted. Molecular docking was performed using LibDock protocol and selected ligands were further subjected to docking analysis by CDOCKER. The docking scores of the selected ligands were compared with standard antiretroviral drugs such as lopinavir and ritonavir to assess their binding potentials. Interaction pharmacophore analysis was then performed for the compounds exhibiting good binding scores to evaluate their protein–ligand interactions. The selected protein–ligand complexes were subjected to molecular dynamics simulation for 50 ns. Results of binding free energy analysis revealed that two compounds—β-amyrin and stigmasta-5,22-dien-3-ol—exhibited the best binding interactions and stability. Finally, absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies were performed to understand the pharmacokinetic properties and safety profile of the compounds. The overall results indicate that the phytochemicals from Cyperus rotundus Linn, namely β-amyrin and stigmasta-5,22-dien-3-ol, can be screened as potential inhibitors of SARS-CoV-2 M^pro.

Evolution of a Cohort of COVID-19 Infection Suspects Followed-Up from Primary Health Care

Diagnosis and home follow-up of patients affected by COVID-19 is being approached by primary health care professionals through telephone consultations. This modality of teleconsultation allows one to follow the evolution of patients and attend early to possible complications of the disease. The purpose of the study was to analyze the evolution of a cohort of patients with suspected SARS-CoV-2 disease followed by primary care professionals and to determine the factors that are associated with hospital admission. A prospective cohort study was carried out on 166 patients selected by consecutive sampling that showed symptoms compatible with COVID-19. The follow-up was approached via telephone for 14 days analyzing hospitalization and comorbidities of the patients. There were 75% of the hospitalized patients that were male (p = 0.002), and 70.8% presented comorbidities (p < 0.001). In patients with diabetes, the risk of hospitalization was 4.6-times larger, in hypertension patients it was 3.3-times, those suffering from renal insufficiency 3.8-times, and immunosuppressed patients 4.8-times (IC 95%: 1.9-11.7). In 86.7% of the cases, clinical deterioration was diagnosed in the first seven days of the infection, and 72% of healing was reached from day seven to fourteen. Monitoring from primary care of patients with COVID-19 allows early diagnosis of clinical deterioration and detection of comorbidities associated with the risk of poor evolution and hospital admission.

Possible Beneficial Actions of Caffeine in SARS-CoV-2

The COVID-19 pandemic has established an unparalleled necessity to rapidly find effective treatments for the illness; unfortunately, no specific treatment has been found yet. As this is a new emerging chaotic situation, already existing drugs have been suggested to ameliorate the infection of SARS-CoV-2. The consumption of caffeine has been suggested primarily because it improves exercise performance, reduces fatigue, and increases wakefulness and awareness. Caffeine has been proven to be an effective anti-inflammatory and immunomodulator. In airway smooth muscle, it has bronchodilator effects mainly due to its activity as a phosphodiesterase inhibitor and adenosine receptor antagonist. In addition, a recent published document has suggested the potential antiviral activity of this drug using in silico molecular dynamics and molecular docking; in this regard, caffeine might block the viral entrance into host cells by inhibiting the formation of a receptor-binding domain and the angiotensin-converting enzyme complex and, additionally, might reduce viral replication by the inhibition of the activity of 3-chymotrypsin-like proteases. Here, we discuss how caffeine through certain mechanisms of action could be beneficial in SARS-CoV-2. Nevertheless, further studies are required for validation through in vitro and in vivo models.

Personalized Approach to Patient with MRI Brain Changes after SARS-CoV-2 Infection

From the beginning of SARS-CoV-2 virus pandemic, it was clear that respiratory symptoms are often accompanied with neurological symptoms. Neurological manifestations can occur even after mild forms of respiratory disease, and neurological symptoms are very often associated with worsening of the patient's condition. The aim of this study was to show abnormal brain neuroimaging findings evaluated by MRI in patients after SARS-CoV-2 infection and neurological symptoms. Methods: Sixteen patients after mild forms of SARS-CoV-2 infection, twenty-three patients after moderate forms of SARS-CoV-2 infection as well as sixteen healthy participants in the control group underwent MRI 3T brain scan. All subjects in the SARS-CoV-2 group had small, punctuate, strategically located and newly formed hyperintense lesions on T2 and FLAIR sequences. New lesions were formed more often in the bilateral frontal subcortical and bilateral periventricular, correlated with the severity of the clinical picture. These changes indicate an example of silent cerebrovascular disease related to SARS-CoV-2 and once again emphasize the neurotropism of the virus.

Meticulous assessment of natural compounds from NPASS database for identifying analogue of GRL0617, the only known inhibitor for SARS-CoV2 papain-like protease (PLpro) using rigorous computational workflow

The latest global outbreak of 2019 respiratory coronavirus disease (COVID-19) is triggered by the inception of novel coronavirus SARS-CoV2. If recent events are of any indicators of the epidemics of past, it is undeniable to state a fact that the SARS-CoV2 viral infection is highly transmissible with respect to its previously related SARS-CoV’s. Papain-like protease (PLpro) is an enzyme that is required by the virus itself for replicating into the host system; and it does so by processing its polyproteins into a functional replicase complex. PLpro is also known for downregulating the genes responsible for producing interferons, an essential family of molecules produced in response to viral infection, thus making this protein an indispensable drug target. In this study, PLpro inhibitors were identified through high throughput structure-based virtual screening approach from NPASS natural product library possessing ~ 35,000 compounds. Top five hits were scrutinised based on structural aromaticity and ability to interact with a key active site residue of PLpro, Tyr268. For second level of screening, the MM-GBSA End-Point Binding Free Energy Calculation of the docked complexes was performed, which identified Caesalpiniaphenol A as the best hit. Caesalpiniaphenol A not only possess a double ring aromatic moiety but also has lowest minimum binding energy, which is at par with the control GRL0617, the only known inhibitor of SARS-CoV2 PLpro. Details of the Molecular Dynamics (MD) simulation and ADMET analysis helped to conclusively determine Caesalpiniaphenol A as potentially an inhibitor of SARS-CoV2 PLpro.

Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations

Virus evolution and mutation analyses are crucial for tracing virus transmission, the potential variants, and other pathogenic determinants. Despite continuing circulation of the SARS-CoV-2, very limited studies have been conducted on genetic evolutionary analysis of the virus in Bangladesh. In this study, a total of 791 complete genome sequences of SARS-CoV-2 from Bangladesh deposited in the GISAID database during March 2020 to January 2021 were analyzed. Phylogenetic analysis revealed circulation of seven GISAID clades G, GH, GR, GRY, L, O, and S or five Nextstrain clades 20A, 20B, 20C, 19A, and 19B in the country during the study period. The GISAID clade GR or the Nextstrain clade 20B or lineage B.1.1.25 is predominant in Bangladesh and closely related to the sequences from India, USA, Canada, UK, and Italy. The GR clade or B.1.1.25 lineage is likely to be responsible for the widespread community transmission of SARS-CoV-2 in the country during the first wave of infection. Significant amino acid diversity was observed among Bangladeshi SARS-CoV-2 isolates, where a total of 1023 mutations were detected. In particular, the D614G mutation in the spike protein (S_D614G) was found in 97% of the sequences. However, the introduction of lineage B.1.1.7 (UK variant/S_N501Y) and S_E484K mutation in lineage B.1.1.25 in a few sequences reported in late December 2020 is of particular concern. The wide genomic diversity indicated multiple introductions of SARS-CoV-2 into Bangladesh through various routes. Therefore, a continuous and extensive genome sequence analysis would be necessary to understand the genomic epidemiology of SARS-CoV-2 in Bangladesh.

Drug repurposing approach to combating coronavirus: Potential drugs and drug targets

In the past two decades, three highly pathogenic human coronaviruses severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus, and, recently, SARS-CoV-2, have caused pandemics of severe acute respiratory diseases with alarming morbidity and mortality. Due to the lack of specific anti-CoV therapies, the ongoing pandemic of coronavirus disease 2019 (COVID-19) poses a great challenge to clinical management and highlights an urgent need for effective interventions. Drug repurposing is a rapid and feasible strategy to identify effective drugs for combating this deadly infection. In this review, we summarize the therapeutic CoV targets, focus on the existing small molecule drugs that have the potential to be repurposed for existing and emerging CoV infections of the future, and discuss the clinical progress of developing small molecule drugs for COVID-19.

Increased human-animal interface & emerging zoonotic diseases: An enigma requiring multi-sectoral efforts to address

Increased human-animal interfaces impose threats on human life by creating scope for the emergence and resurgence of many infectious diseases. Over the last two decades, emergence of novel viral diseases such as SARS, influenza A/H1N1(09) pdm; MERS; Nipah virus disease; Ebola haemorrhagic fever and the current COVID-19 has resulted in massive outbreaks, epidemics and pandemics thereby causing profound losses of human life, health and economy. The current COVID-19 pandemic has affected more than 200 countries, reporting a global case load of 167,878,000 with 2 per cent mortality as on May 26, 2021. This has highlighted the importance of reducing human- animal interfaces to prevent such zoonoses. Rapid deforestation, shrinking of boundaries between human and animal, crisis for natural habitation, increasing demands for wildlife products and threat of extinction compounded by biodiversity narrowing compel to increased human-animal conflict and contact. Large quantities of animal waste generated due to animal agriculture may also allow rapid selection, amplification, dissemination of zoonotic pathogens and facilitate zoonotic pathogen adaptation and hinder host evolution for resistance. Public health system faces challenges to contain such epidemics due to inadequate understanding, poor preparedness, lack of interdisciplinary approach in surveillance and control strategy and deficient political commitments. Because the management measures are beyond the purview of health system alone, policy-level adaptation in the transdisciplinary issues are required, emphasizing the engagement of multiple stakeholders towards wildlife protection, alternative land use, community empowerment for natural resource management and regulation on business of wildlife products to ensure comprehensive one health practice.

Therapeutic approaches to coronavirus infection according to "One Health" concept

Coronaviridae constantly infect human and animals causing respiratory, gastroenteric or systemic diseases. Over time, these viruses have shown a marked ability to mutate, jumping over the human-animal barrier, thus becoming from enzootic to zoonotic. In the last years, numerous therapeutic protocols have been developed, mainly for severe acute respiratory syndromes in humans. The aim of this review is to summarize drugs or other approaches used in coronavirus infections focusing on different roles of these molecules or bacterial products on viral adhesion and replication or in modulating the host's immune system. Within the "One Health" concept, the study of viral pathogenic role and possible therapeutic approaches in both humans and animals is essential to protect public health.

Characteristics and mortality determinants of COVID-19 patients undergoing hemodialysis

Background/aim

The COVID-19 infection, which started in Wuhan City, China, in December 2019, turned into a pandemic in a very short time, affecting mainly the elderly and those with serious chronic illnesses. COVID-19 infections have been observed to have a high mortality rate, especially in patients undergoing maintenance hemodialysis.

Materials and methods

Forty-two patients over 18 years of age who underwent a maintenance hemodialysis program at our unit, who tested positive for COVID-19 by PCR from nasopharyngeal swabs, and/or who were observed to have disease-related signs in their CTs were included in the study.

Results

In this study, 23 of 42 patients receiving hemodialysis support in our clinic were included. The median age was 67 years old (min: 35; max: 91 years), and all of our patients had primary hypertension and other comorbidities. Their clinical evaluation showed that dry cough (47.8%) and shortness of breath (47.8%) were the most common symptoms. Fever was less pronounced (30.4%). The median time from the onset of symptoms to hospitalization was 1 day (min: 0; max:), and the time from hospitalization to death was 18 days (min: 1; max: 22). Transfer from the inpatient ward to the ICU took a median of 7 days (min: 1; max: 13). Among the 23 patients, 3 died during follow-up, and 20 were discharged with full recovery. Baseline ferritin, procalcitonin levels, and CRP/albumin rates were higher, and neutrophil/lymphocyte levels were lower in patients who eventually died. In these patients, despite being nonsignificant, there were more diabetic patients, and the D-dimer levels were higher than 1000 ugFEU/L.

Conclusion

The COVID-19 infection is associated with increased mortality in chronic kidney diseases patients. Despite being nonsignificant, there was a trend towards increased mortality in patient with diabetes, D-dimer levels >1000 ugFEU/L, higher ferritin and prokalsitonin levels, an increased CRP/albumin ratio, and a lower neutrophil/lymphocyte ratio.

Clinical features of COVID-19 and SARS epidemics. A literature review

SARS-CoV-2, responsible for the current pandemic, is a novel strain of the Coronaviridae family, which has infected humans as a result of the leap to a new species. It causes an atypical pneumonia similar to that caused by SARS-CoV in 2003. SARS-CoV-2 has currently infected more than 9,200,000 people and caused almost 480,000 deaths worldwide. Although SARS-CoV-2 and SARS-CoV have similar phylogenetic and pathogenetic characteristics, they show important differences in clinical manifestations.

We have reviewed the recent literature comparing the characteristics of the two epidemics and highlight their peculiar aspects. An analysis of all signs and symptoms of 3,365 SARS patients and 23,280 COVID-19 patients as well as of the comorbidities has been carried out. A total of 17 and 75 studies regarding patients with SARS and COVID-19, respectively, were included in the analysis. The analysis revealed an overlap of some symptoms between the two infections. Unlike SARS patients, COVID-19 patients have developed respiratory, neurological and gastrointestinal symptoms, and, in a limited number of subjects, symptoms involving organs such as skin and subcutaneous tissue, kidneys, cardiovascular system, liver and eyes.

This analysis was conducted in order to direct towards an early identification of the infection, a suitable diagnostic procedure and the adoption of appropriate containment measures.

The Unfolded Protein Response and Autophagy on the Crossroads of Coronaviruses Infections

The ability to sense and adequately respond to variable environmental conditions is central for cellular and organismal homeostasis. Eukaryotic cells are equipped with highly conserved stress-response mechanisms that support cellular function when homeostasis is compromised, promoting survival. Two such mechanisms - the unfolded protein response (UPR) and autophagy - are involved in the cellular response to perturbations in the endoplasmic reticulum, in calcium homeostasis, in cellular energy or redox status. Each of them operates through conserved signaling pathways to promote cellular adaptations that include re-programming transcription of genes and translation of new proteins and degradation of cellular components. In addition to their specific functions, it is becoming increasingly clear that these pathways intersect in many ways in different contexts of cellular stress. Viral infections are a major cause of cellular stress as many cellular functions are coopted to support viral replication. Both UPR and autophagy are induced upon infection with many different viruses with varying outcomes - in some instances controlling infection while in others supporting viral replication and infection. The role of UPR and autophagy in response to coronavirus infection has been a matter of debate in the last decade. It has been suggested that CoV exploit components of autophagy machinery and UPR to generate double-membrane vesicles where it establishes its replicative niche and to control the balance between cell death and survival during infection. Even though the molecular mechanisms are not fully elucidated, it is clear that UPR and autophagy are intimately associated during CoV infections. The current SARS-CoV-2 pandemic has brought renewed interest to this topic as several drugs known to modulate autophagy - including chloroquine, niclosamide, valinomycin, and spermine - were proposed as therapeutic options. Their efficacy is still debatable, highlighting the need to better understand the molecular interactions between CoV, UPR and autophagy.

AC2: An Efficient Protein Sequence Compression Tool Using Artificial Neural Networks and Cache-Hash Models

Recently, the scientific community has witnessed a substantial increase in the generation of protein sequence data, triggering emergent challenges of increasing importance, namely efficient storage and improved data analysis. For both applications, data compression is a straightforward solution. However, in the literature, the number of specific protein sequence compressors is relatively low. Moreover, these specialized compressors marginally improve the compression ratio over the best general-purpose compressors. In this paper, we present AC2, a new lossless data compressor for protein (or amino acid) sequences. AC2 uses a neural network to mix experts with a stacked generalization approach and individual cache-hash memory models to the highest-context orders. Compared to the previous compressor (AC), we show gains of 2–9% and 6–7% in reference-free and reference-based modes, respectively. These gains come at the cost of three times slower computations. AC2 also improves memory usage against AC, with requirements about seven times lower, without being affected by the sequences’ input size. As an analysis application, we use AC2 to measure the similarity between each SARS-CoV-2 protein sequence with each viral protein sequence from the whole UniProt database. The results consistently show higher similarity to the pangolin coronavirus, followed by the bat and human coronaviruses, contributing with critical results to a current controversial subject. AC2 is available for free download under GPLv3 license.

Dyslipidemia in breast cancer patients increases the risk of SAR-CoV-2 infection

Breast cancer (BC) is the most diagnosed and second leading cause of death among women worldwide. Elevated levels of lipids have been reported in BC patients. On the other hand, lipids play an important role in coronavirus infections including the newly emerged disease caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and designated COVID-19 by WHO. Cancer patients including BC have been reported to be at higher risk of SARS-CoV-2 infection, which is mostly attributed to the chronic immunosuppressive status of cancer patients along with the use of cytotoxic drugs. Here in this review, we highlighted the role of dyslipidemia associated with BC patients in the incidence and severity of SARS-CoV-2 infection. Elevated levels of lipids namely phospholipids, cholesterol, sphingolipids, and eicosanoids in the serum of BC patients and their re-localization to the alveolar spaces can increase susceptibility and/or severity due to SARA-CoV-2 infection. Therefore, manipulation of dyslipidemia in BC patients should be recommended as prophylactic and therapy against SARS-CoV-2 infection.

Clinical efficacy of methylprednisolone and the combined use of lopinavir/ritonavir with arbidol in treatment of coronavirus disease 2019

This study aims to comparatively analyze the therapeutic efficacy upon multiple medication plans over lopinavir/ritonavir (LPV/r), arbidol (ARB), and methylprednisolone on patients with coronavirus disease 2019 (COVID‐19). Totally, 75 COVID‐19 patients admitted to The First Affiliated Hospital, Zhejiang University School of Medicine from January 22, 2020 to February 29, 2020 were recruited and grouped based on whether or not LPV/r and ARB were jointly used and whether or not methylprednisolone was used. Indexes including body temperature, time for nucleic acid negative conversion, hospital stays, and laboratory indexes were examined and compared. For all patients, there were no significant differences in the change of body temperature, the time for negative conversion, and hospital stays whether LPV/r and ARB were jointly used or not. While for severe and critically severe patients, methylprednisolone noticeably reduced the time for negative conversion. Meanwhile, the clinical efficacy was superior on patients receiving methylprednisolone within 3 days upon admission, and the duration of hospital stays was much shorter when methylprednisolone was given at a total dose of 0–400 mg than a higher dose of >400 mg if all patients received a similar dose per day. Nonetheless, no significant changes across hepatic, renal, and myocardial function indexes were observed. LPV/r combined with ARB produced no noticeably better effect on COVID‐19 patients relative to the single‐agent treatment. Additionally, methylprednisolone was efficient in severe and critically severe cases, and superior efficacy could be realized upon its early, appropriate, and short‐term application.

A critical narrative of Ecuador's preparedness and response to the COVID-19 pandemic

Ecuador’s National Health System has been severely overwhelmed by the COVID-19 pandemic despite public health efforts. This was primarily due to limited health emergency planning responses. Ecuador’s COVID-19 mortality rate was 8.5% in early June 2020. The capital city (Quito) and Pichincha province, Guayaquil city and Guayas province, as well as Manabi, Azuay, the El Oro and Tungurahua provinces were the most severely impacted locations by the COVID-19 pandemic, resulting in thousands of positive cases. Using the World Health Organization (WHO) Operational Planning Guidelines to Support Country Strategic Preparedness and Response Plan for COVID-19 as a reference point, we highlight the urgent need to implement a proactive preparedness and response plan to address the COVID-19 pandemic, with the aim of improving Ecuador’s public health system. The mitigation of COVID-19 transmission and hazard reduction is crucial in protecting the most vulnerable at-risk populations in this nation.

Anti-SARS-CoV-2 Activity of Andrographis paniculata Extract and Its Major Component Andrographolide in Human Lung Epithelial Cells and Cytotoxicity Evaluation in Major Organ Cell Representatives

The coronaviruses disease 2019 (COVID-19) caused by a novel coronavirus (SARS-CoV-2) has become a major health problem, affecting more than 50 million people with over one million deaths globally. Effective antivirals are still lacking. Here, we optimized a high-content imaging platform and the plaque assay for viral output study using the legitimate model of human lung epithelial cells, Calu-3, to determine the anti-SARS-CoV-2 activity of Andrographis paniculata extract and its major component, andrographolide. SARS-CoV-2 at 25TCID50 was able to reach the maximal infectivity of 95% in Calu-3 cells. Postinfection treatment of A. paniculata and andrographolide in SARS-CoV-2-infected Calu-3 cells significantly inhibited the production of infectious virions with an IC50 of 0.036 μg/mL and 0.034 μM, respectively, as determined by the plaque assay. The cytotoxicity profile developed over the cell line representatives of major organs, including liver (HepG2 and imHC), kidney (HK-2), intestine (Caco-2), lung (Calu-3), and brain (SH-SY5Y), showed a CC50 of >100 μg/mL for A. paniculata extract and 13.2-81.5 μM for andrographolide, respectively, corresponding to a selectivity index of over 380. In conclusion, this study provided experimental evidence in favor of A. paniculata and andrographolide for further development as a monotherapy or in combination with other effective drugs against SARS-CoV-2 infection.

Diagnostic characteristics of serological tests for the detection of SARS-CoV-2 cases

To study the diagnostic characteristics of test systems for detecting antibodies to SARS-Cov-2. We studied the diagnostic characteristics of two test systems for detecting antibodies to SARS-Cov-2, registered in the Russian Federation. The first test system is a kit for detecting total antibodies to SARS-Cov-2 using immunochemiluminescence analysis on the «Cobas e 411» analyzer («Roche Diagnostics», Germany). The second test system is a kit for detecting IgM and IgG to SARS-Cov-2 («Core Technology Co., Ltd», China) by immunochromatographic analysis. The biological material for the study was blood serum. We assessed: diagnostic sensitivity, diagnostic specificity, and predictive value of positive and negative results. In the test system for detecting total antibodies to SARS-CoV-2, using an IHLA, the diagnostic sensitivity and specificity were 100%; the predictive value of positive and negative results was 100%. In the test system for the detection of IgM and IgG to Sars-CoV-2, using IHA, diagnostic sensitivity for IgM and IgG were 100%; diagnostic specificity for IgM - 60%, for IgG - 72%; predictive value of a positive result for IgM - 60%, IgG - 68,18%; predictive value of negative results for IgM and IgG - 100%. The best diagnostic characteristics were found in the test system for the detection of total antibodies to SARS-Cov-2, which must be taken into account when deciding whether to purchase test systems for the detection of antibodies to SARS-Cov-2.

Anti-SARS-CoV-2 Activity of Andrographis paniculata Extract and Its Major Component Andrographolide in Human Lung Epithelial Cells and Cytotoxicity Evaluation in Major Organ Cell Representatives

The coronaviruses disease 2019 (COVID-19) caused by a novel coronavirus (SARS-CoV-2) has become a major health problem, affecting more than 50 million people with over one million deaths globally. Effective antivirals are still lacking. Here, we optimized a high-content imaging platform and the plaque assay for viral output study using the legitimate model of human lung epithelial cells, Calu-3, to determine the anti-SARS-CoV-2 activity of Andrographis paniculata extract and its major component, andrographolide. SARS-CoV-2 at 25TCID₅₀ was able to reach the maximal infectivity of 95% in Calu-3 cells. Postinfection treatment of A. paniculata and andrographolide in SARS-CoV-2-infected Calu-3 cells significantly inhibited the production of infectious virions with an IC₅₀ of 0.036 μg/mL and 0.034 μM, respectively, as determined by the plaque assay. The cytotoxicity profile developed over the cell line representatives of major organs, including liver (HepG2 and imHC), kidney (HK-2), intestine (Caco-2), lung (Calu-3), and brain (SH-SY5Y), showed a CC₅₀ of >100 μg/mL for A. paniculata extract and 13.2-81.5 μM for andrographolide, respectively, corresponding to a selectivity index of over 380. In conclusion, this study provided experimental evidence in favor of A. paniculata and andrographolide for further development as a monotherapy or in combination with other effective drugs against SARS-CoV-2 infection.

RNA Coronaviruses' Outbreaks: Recent Progress on the SARS-CoV-2 Pandemic Diagnostic Tests, Vaccination and Therapeutics

Coronaviruses are RNA-infective viruses that could be considered principal players in universal high-profile outbreaks, namely the Severe Acute Respiratory Syndrome (SARS, 2002-2003), the Middle East Respiratory Syndrome (MERS, 2012) and the continuing novel coronavirus disease (COVID-19, 2019) pandemic. RNA coronaviruses infections raise public health concerns with infections' severity ranging from serious pandemics and highly contagious infections to common influenza episodes. With a wide consensus concerning the seminal role of early detection of the infectious agent on the clinical prognosis, recent technological endeavors have facilitated the rapid, sensitive and specific diagnosis of viral infections. Given that the burst of confirmed cases of the novel coronavirus disease 2019 (COVID-19) are climbing steeply, and we are amid this pandemic, this work will center at the respiratory RNA-viruses outbreaks, including the three coronaviruses-related pandemics, emphasizing on the approved diagnostic approaches, outlining therapeutic clinical trials as well as vaccine candidates. Based on the accumulated data and knowledge on the previous RNA-virus outbreaks, this review aspires to link the current intervention measures against SARS-CoV-2 infection with the previous interventions and to provide a roadmap for any possible future measures.

Facing coronavirus disease 2019: What do we know so far? (Review)

Although the World Health Organization declared the outbreak of coronavirus disease 2019 (COVID-19), which originated in China, as a public health emergency of international concern as early as January 30, 2020, the current COVID-19 epidemic is spreading rapidly. As of April 19, 2020, total of 2,392,165 confirmed cases had been reported in 211 countries and regions, with 614,421 (25.68%) cured cases and 164,391 (6.87%) deaths. Scientists and clinicians have made great efforts to learn much about COVID-19 so that it can be controlled as soon as possible. Herein, this review will discuss the epidemiology, pathology, clinical features, diagnosis and treatment of COVID-19 based on the current evidence.

Cytotoxic T-lymphocyte elicited vaccine against SARS-CoV-2 employing immunoinformatics framework

Development of effective counteragents against the novel coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains, requires clear insights and information for understanding the immune responses associated with it. This global pandemic has pushed the healthcare system and restricted the movement of people and succumbing of the available therapeutics utterly warrants the development of a potential vaccine to contest the deadly situation. In the present study, highly efficacious, immunodominant cytotoxic T-lymphocyte (CTL) epitopes were predicted by advanced immunoinformatics assays using the spike glycoprotein of SARS-CoV2, generating a robust and specific immune response with convincing immunological parameters (Antigenicity, TAP affinity, MHC binder) engendering an efficient viral vaccine. The molecular docking studies show strong binding of the CTL construct with MHC-1 and host membrane specific TLR2 receptors. The molecular dynamics simulation in an explicit system confirmed the stable and robust binding of CTL epitope with TLR2. Steep magnitude RMSD variation and compelling residual fluctuations existed in terminal residues and various loops of the β linker segments of TLR2-epitope (residues 105-156 and 239-254) to about 0.4 nm. The reduced R_g value (3.3 nm) and stagnant SASA analysis (275 nm/S²/N after 8 ns and 5 ns) for protein surface and its orientation in the exposed and buried regions suggests more compactness due to the strong binding interaction of the epitope. The CTL vaccine candidate establishes a high capability to elicit the critical immune regulators, like T-cells and memory cells as proven by the in silico immunization assays and can be further corroborated through in vitro and in vivo assays.

Rapid Detection of SARS-CoV-2 Virus Using Dual Reverse Transcriptional Colorimetric Loop-Mediated Isothermal Amplification

The outbreak and pandemic of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has developed into a public health emergency of international concern. The rapid and accurate detection of the virus is a critical means to prevent and control the disease. Herein, we provide a novel, rapid, and simple approach, named dual reverse transcriptional colorimetric loop-mediated isothermal amplification (dRT-cLAMP) assay, to accelerate the detection of the SARS-CoV-2 virus without using expensive equipment. The result of this assay is shown by color change and is easily detected by the naked eye. To improve the detection accuracy, we included two primer sets that specifically target the viral orf1ab and N genes in the same reaction mixture. Our assay can detect the synthesized SARS-CoV-2 N and orf1ab genes at a low level of 100 copies/μL. Sequence alignment analysis of the two synthesized genes and those of 9968 published SARS-CoV-2 genomes and 17 genomes of other pathogens from the same infection site or similar symptoms as COVID-19 revealed that the primers for the dRT-cLAMP assay are highly specific. Our assay of 27 clinical samples of SARS-CoV-2 virus and 27 standard-added environmental simulation samples demonstrated that compared to the commercial kits, the consistency of the positive, negative, and probable clinical samples was 100, 92.31, and 44.44%, respectively. Moreover, our results showed that the positive, but not negative, standard-added samples displayed a naked-eye-detectable color change. Together, our results demonstrate that the dRT-cLAMP assay is a feasible detection assay for SARS-CoV-2 virus and is of great significance since rapid onsite detection of the virus is urgently needed at the ports of entry, health care centers, and for internationally traded goods.

In silico approach to understand the epigenetic mechanism of SARS-CoV-2 and its impact on the environment

The novel coronavirus (2019-nCoV) has led to the apex pandemic in 2020, responsible for the recent sequential spread. The 2019-nCoV has been discerned to be a Beta-BAT-SARS-CoV-2 lineage. The gene ontology (GO) identifies the virus to be localized in the Golgi apparatus with a vital molecular function of binding and viral progression. The source organism is almost all bats, further suggesting that the host of this virus is bat rather than civets or snakes, and has motifs which are perfect matches to various human and mouse genomic motifs such as—zinc fingers, DNA-binding domains, and basic helix-loop-helix factors. It has basic clusters of orthologs (COGs)—Superfamily I DNA and RNA helicases and helicase subunits and Predicted phosphatase homologous to the C-terminal domain of histone macroH2A1 respectively hinting at the epigenetic alterations which could be the reason behind the “novelty” the virus. Our study discerns that the SARS-CoV-2 endorses the epigenetic mechanism essential for its replication and reproduction in the host organism. Furthermore, we identified six non-toxic disinfectants with higher pharmacokinetics and pharmacodynamics properties, namely Quaternary Ammonium, Octanoic acid, Citric acid, Phenolics, 1,2-Hexanediol, and Thymol, that bind to lyases, nuclear receptors, fatty acids binding family, enzymes, and family AG protein-coupled receptors indicating that they target the nucleocapsid (N) protein, envelope (E) protein, membranous proteins of the novel coronavirus, thus, killing it from the surfaces when sprayed and are not harmful to the biological environment.

COVID-19 outbreak: history, mechanism, transmission, structural studies and therapeutics

PURPOSE

The coronavirus outbreak emerged as a severe pandemic, claiming more than 0.8 million lives across the world and raised a major global health concern. We survey the history and mechanism of coronaviruses, and the structural characteristics of the spike protein and its key residues responsible for human transmissions.

METHODS

We have carried out a systematic review to summarize the origin, transmission and etiology of COVID-19. The structural analysis of the spike protein and its disordered residues explains the mechanism of the viral transmission. A meta-data analysis of the therapeutic compounds targeting the SARS-CoV-2 is also included.

RESULTS

Coronaviruses can cross the species barrier and infect humans with unexpected consequences for public health. The transmission rate of SARS-CoV-2 infection is higher compared to that of the closely related SARS-CoV infections. In SARS-CoV-2 infection, intrinsically disordered regions are observed at the interface of the spike protein and ACE2 receptor, providing a shape complementarity to the complex. The key residues of the spike protein have stronger binding affinity with ACE2. These can be probable reasons for the higher transmission rate of SARS-CoV-2. In addition, we have also discussed the therapeutic compounds and the vaccines to target SARS-CoV-2, which can help researchers to develop effective drugs/vaccines for COVID-19. The overall history and mechanism of entry of SARS-CoV-2 along with structural study of spike-ACE2 complex provide insights to understand disease pathogenesis and development of vaccines and drugs.

Perinatal COVID-19: review of current evidence and practical approach towards prevention and management

The clinical spectrum of the perinatal COVID-19 and prospective data on neonatal outcomes remains largely unexplored. Most of the existing literature is in the form of case series or single-centre experience. In this review, we aim to summarize available literature on the clinical spectrum of COVID-19 in neonates and mothers and suggest a practical approach towards management of clinical scenarios. This review explores the clinical characteristics and outcomes of COVID-19 in neonates born to mothers who were detected with the virus during the pregnancy. We conducted a comprehensive search of PubMed, Google Scholar and Cochrane Database of Systematic Review between November 2019 and June 2020 and screened articles related to perinatal COVID-19. This review included 786 mothers, among which 64% (504) were delivered by caesarian section. There were 3 still births and 107 (14%) were delivered preterm. Out of 793 neonates born, 629 neonates (79%) were tested after birth. The commonest symptom in neonates was respiratory distress. Respiratory support was needed in 60 neonates (7.6%), with 14 babies needing mechanical ventilation (1.8%), 25 needing non-invasive ventilation and 21 needing nasal oxygen. Only 35 of the 629 tested neonates (5.5%) were positive for COVID-19. Of the 35 positive neonates, 14 (40%) were symptomatic. The COVID-19 seems to have favourable neonatal outcomes. Majority of neonates are asymptomatic. Respiratory distress is the most common manifestation. What is known: •COVID-19 affects all ages. •Neonatal disease is usually mild. What is new: •Vertical transmission is a possible route of infection in neonates. •Breast milk and skin-to-skin contact are safe in COVID-19-infected mothers if performed with appropriate use of precautions such as hand and breast hygiene and masking.

COVID-19 in Hong Kong - Public health, food safety, and animal vectors perspectives

The coronavirus disease 2019 (COVID-19) pandemic, caused by infection with a novel coronavirus (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2), has led to escalating morbidity and mortality in all nations and cities. SARS-CoV-2 lies within the same coronavirus family as SARS-CoV (2003) and MERS-CoV (2012), though there are genetic and epidemiological differences between the viruses, as well as different clinical presentations in the patients. Despite this, Hong Kong has so far managed to control the pandemic very successfully. Here we offer a Hong Kong perspective on different aspects of the pandemic virus (SARS-CoV-2) and the disease : public health (diagnosis and control), food safety (reducing transmission in the workplace) and animal vectors (controlling potential reservoirs of the virus and their movements).

Coagulation factors directly cleave SARS-CoV-2 spike and enhance viral entry

Coagulopathy is recognized as a significant aspect of morbidity in COVID-19 patients. The clotting cascade is propagated by a series of proteases, including factor Xa and thrombin. Other host proteases, including TMPRSS2, are recognized to be important for cleavage activation of SARS-CoV-2 spike to promote viral entry. Using biochemical and cell-based assays, we demonstrate that factor Xa and thrombin can also directly cleave SARS-CoV-2 spike, enhancing viral entry. A drug-repurposing screen identified a subset of protease inhibitors that promiscuously inhibited spike cleavage by both transmembrane serine proteases as well as coagulation factors. The mechanism of the protease inhibitors nafamostat and camostat extend beyond inhibition of TMPRSS2 to coagulation-induced spike cleavage. Anticoagulation is critical in the management of COVID-19, and early intervention could provide collateral benefit by suppressing SARS-CoV-2 viral entry. We propose a model of positive feedback whereby infection-induced hypercoagulation exacerbates SARS-CoV-2 infectivity.

A small molecule compound berberine as an orally active therapeutic candidate against COVID-19 and SARS: A computational and mechanistic study

The novel coronavirus disease, COVID-19, has grown into a global pandemic and a major public health threat since its breakout in December 2019. To date, no specific therapeutic drug or vaccine for treating COVID-19 and SARS has been FDA approved. Previous studies suggest that berberine, an isoquinoline alkaloid, has shown various biological activities that may help against COVID-19 and SARS, including antiviral, anti-allergy and inflammation, hepatoprotection against drug- and infection-induced liver injury, as well as reducing oxidative stress. In particular, berberine has a wide range of antiviral activities such as anti-influenza, anti-hepatitis C, anti-cytomegalovirus, and anti-alphavirus. As an ingredient recommended in guidelines issued by the China National Health Commission for COVID-19 to be combined with other therapy, berberine is a promising orally administered therapeutic candidate against SARS-CoV and SARS-CoV-2. The current study comprehensively evaluates the potential therapeutic mechanisms of berberine in preventing and treating COVID-19 and SARS using computational modeling, including target mining, gene ontology enrichment, pathway analyses, protein-protein interaction analysis, and in silico molecular docking. An orally available immunotherapeutic-berberine nanomedicine, named NIT-X, has been developed by our group and has shown significantly increased oral bioavailability of berberine, increased IFN-γ production by CD8+ T cells, and inhibition of mast cell histamine release in vivo, suggesting a protective immune response. We further validated the inhibition of replication of SARS-CoV-2 in lung epithelial cells line in vitro (Calu3 cells) by berberine. Moreover, the expression of targets including ACE2, TMPRSS2, IL-1α, IL-8, IL-6, and CCL-2 in SARS-CoV-2 infected Calu3 cells were significantly suppressed by NIT-X. By supporting protective immunity while inhibiting pro-inflammatory cytokines; inhibiting viral infection and replication; inducing apoptosis; and protecting against tissue damage, berberine is a promising candidate in preventing and treating COVID-19 and SARS. Given the high oral bioavailability and safety of berberine nanomedicine, the current study may lead to the development of berberine as an orally, active therapeutic against COVID-19 and SARS.

Nation-wide analysis of the impact of Covid-19 pandemic on daily urology practice in Turkey

OBJECTIVE

To present a nation-wide analysis of the workload of urology departments in Turkey week-by-week during Covid-19 pandemic.

METHODOLOGY

The centres participating in the study were divided into three groups as tertiary referral centres, state hospitals and private practice hospitals. The number of outpatients, inpatients, daily interventions and urological surgeries were recorded prospectively between 9-March-2020 and 31-May-2020. All these variables were recorded for the same time interval of 2019 as well. The weekly change of the workload of urology during pandemic period was evaluated, also the workload of urology and the distributions of certain urological surgeries were compared between the pandemic period and the same time interval of the year 2019.

RESULTS

A total of 51 centres participated in the study. The number of outpatients, inpatients, urological surgeries and daily interventions were found to be dramatically decreased by the 3rd week of pandemics in state hospitals and tertiary referral centres; however, the daily urological practice were similar in private practice hospitals throughout the pandemic period. When the workload of urology in pandemic period and the same time interval of the year 2019 were compared, a huge decrease was observed in all variables during pandemic period. However, temporary measures like ureteral stenting, nephrostomy placement and percutaneous cystostomy have been found to increase during Covid-19 pandemic compared with normal life.

CONCLUSIONS

Covid-19 pandemic significantly affected the routine daily urological practice likewise other subspecialties and priority was given to emergent and non-deferrable surgeries by urologists in concordance with published clinical guidelines.

In-silico analysis of the inhibition of the SARS-CoV-2 main protease by some active compounds from selected African plants

OBJECTIVES

Over the years, Azadirachta indica, Mangifera indica, and Moringa oleifera have been shown to possess some antiviral characteristics. This study applies molecular docking techniques to assess inhibitory effects of some bioactive compounds from the plants mentioned above against the main protease (Mpro), a key protein involved in SARS-CoV-2 replication. Furthermore, adsorption, distribution, metabolism, excretion, and toxicity (ADMET) profiles for screened compounds were predicted in silico.

METHODS

The crystal structure of Mpro was retrieved from the Protein Data Bank, while the plant bioactive compounds were retrieved from Pubchem. Drug-likeness of the selected compounds and a control drug (hydroxychloroquine) were assessed, and the compounds that satisfied the drug-likeness rule were docked against Mpro. The docked complexes were analyzed using LigPlot and the protein-ligand profiler server. The top five compound hits were subjected to ADMET screening using the ADMETSar server.

RESULTS

A total of 17 out of 22 screened compounds passed Lipinski's assessment. Additionally, the most active compounds from the investigated plants exhibited relative inhibitory potentials against Mpro compared with hydroxychloroquine, which alludes to their possible involvement in inhibiting the SARS-CoV-2 main protease replication process.

CONCLUSIONS

In our study, most of the active phytocomponents of the investigated plants exhibited relative inhibitory potentials against Mpro of SARS-CoV-2 and preferred pharmacological features when compared with hydroxychloroquine. These findings indicate these compounds are potentially antiviral candidates against SARS-CoV-2.

Autopsy Tool in Unknown Diseases: The Experience with Coronaviruses (SARS-CoV, MERS-CoV, SARS-CoV-2)

In the last two decades, three unknown pathogens have caused outbreaks, generating severe global health concerns. In 2003, after nucleic acid genotyping, a new virus was named severe acute respiratory syndrome coronavirus (SARS-CoV). After nine years, another coronavirus emerged in the middle east and was named MERS-CoV (Middle East Respiratory Syndrome-Coronavirus). Finally, in December 2019, a new unknown coronavirus was isolated from a cluster of patients and was named SARS-CoV-2 (COVID-19, coronavirus disease 2019). This review aims to propose a complete overview of autopsy in the three coronaviruses over the past two decades, showing its pivotal role in the management of unknown diseases. A total of 116 studies fulfilled the inclusion criteria: 14 studies were collected concerning SARS-CoV (87 autopsy reports, from Asian and American countries), 2 studies for MERS-CoV (2 autopsy reports, from Middle-East Asian countries), and 100 studies on SARS-CoV-2 (930 autopsy reports). Analyzing the data obtained on COVID-19, based on the country criterion, a large number of post-mortem investigation were performed in European countries (580 reports), followed by American countries (251 reports). It is interesting to note that no data were found from the Oceanic countries, maybe because of the minor involvement of the outbreak. In all cases, autopsy provided much information about each unknown coronavirus. Despite advanced technologies in the diagnostic fields, to date, autopsy remains the gold standard method to understand the biological features and the pathogenesis of unknown infections, especially when awareness of a pathogen is restricted and the impact on the healthcare system is substantial. The knowledge gained through this technique may positively influence therapeutic strategies, ultimately reducing mortality.

Pit latrines may be a potential risk in rural China and low-income countries when dealing with COVID-19

According to the latest reports, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which caused coronavirus disease 2019 (COVID-19), was successfully isolated from the excreta (stool and urine) of COVID-19 patients, suggesting SARS-CoV-2 could be transmitted through excreta contaminated water. As pit latrines and the use of untreated excreta as fertilizer were common in rural China, we surveyed 27 villages of Jiangxi and Hubei provinces and found that pit latrines could be a potential source of SARS-CoV-2 water pollution. Recently, bats have been widely recognized as the source of SARS-CoV-2. There were many possible intermediate hosts of SARS-CoV-2, including pangolin, snake, bird and fish, but which one was still not clear exactly. Here, we proposed a hypothesis to illustrate the mechanism that SARS-CoV-2 might spread from the excreta of infected humans in pit latrines to potential animal hosts, thus becoming a sustainable source of infection in rural China. Therefore, we believe that abolishing pit latrines and banning the use of untreated excreta as fertilizer can improve the local living environment and effectively prevent COVID-19 and other potential waterborne diseases that could emanate from the excreta of infected persons. Although this study focused on rural areas in China, the results could also be applied to low-income countries, especially in Africa.

Corona Viruses: A Review on SARS, MERS and COVID-19

After the outbreak of SARS and MERS, the world is now in the grip of another viral disease named COVID-19 caused by a beta Coronavirus - SARS COV-2 which appears to be the only one with a pandemic potential. The case of COVID-19 was reported in the Hubei province of Wuhan city in Central China at the end of December 2019 and it is suspected that the sea food market played a role in this outbreak which was closed abruptly. Subsequently, a Public Health Emergency of International Concern was declared on 30 January 2020 by the World Health Organization. Both SARS and MERS corona viruses had its reservoir in bats and were transferred to humans from palm civets and camels respectively. This virus can be transmitted through airborne droplets. Natural reservoir and intermediate host of COVID-19 is yet to be identified. This paper reviews the occurrences of viral diseases in the recent times including SARS and MERS. As an addition to this, the paper will contain a detailed examination of the COVID-19 Pandemic.

Structural analysis of viral ExoN domains reveals polyphyletic hijacking events

Nidoviruses and arenaviruses are the only known RNA viruses encoding a 3’-5’ exonuclease domain (ExoN). The proofreading activity of the ExoN domain has played a key role in the growth of nidoviral genomes, while in arenaviruses this domain partakes in the suppression of the host innate immune signaling. Sequence and structural homology analyses suggest that these proteins have been hijacked from cellular hosts many times. Analysis of the available nidoviral ExoN sequences reveals a high conservation level comparable to that of the viral RNA-dependent RNA polymerases (RdRp), which are the most conserved viral proteins. Two highly preserved zinc fingers are present in all nidoviral exonucleases, while in the arenaviral protein only one zinc finger can be identified. This is in sharp contrast with the reported lack of zinc fingers in cellular ExoNs, and opens the possibility of therapeutic strategies in the struggle against COVID-19.

COVID-19 pandemic: the implications of the natural history, challenges of diagnosis and management for care in sub-Saharan Africa

BACKGROUND

Coronavirus disease (COVID-19) is a severe acute respiratory infection which has afflicted virtually almost all nations of the earth. It is highly transmissible and represents one of the most serious pandemics in recent times, with the capacity to overwhelm any healthcare system and cause morbidity and fatality.

MAIN CONTENT

The diagnosis of this disease is daunting and challenging as it is dependent on emerging clinical symptomatology that continues to increase and change very rapidly. The definitive test is the very expensive and scarce polymerase chain reaction (PCR) viral identification technique. The management has remained largely supportive and empirical, as there are no officially approved therapeutic agents, vaccines or antiviral medications for the management of the disease. Severe cases often require intensive care facilities and personnel. Yet there is paucity of facilities including the personnel required for diagnosis and treatment of COVID-19 in sub-Saharan Africa (SSA). It is against this backdrop that a review of key published reports on the pandemic in SSA and globally is made, as understanding the natural history of a disease and the documented responses to diagnosis and management is usually a key public health strategy for designing and improving as appropriate, relevant interventions. Lead findings were that responses by most nations of SSA were adhoc, paucity of public health awareness strategies and absence of legislations that would help enforce preventive measures, as well as limited facilities (including personal protective equipment) and institutional capacities to deliver needed interventions.

CONCLUSION

COVID-19 is real and has overwhelmed global health care system especially low-income countries of the sub-Sahara such as Nigeria. Suggestions for improvement of healthcare policies and programs to contain the current pandemic and to respond more optimally in case of future pandemics are made herein.

In-Silico Pangenomics of SARS-CoV-2 Isolates Reveal Evidence for Subtle Adaptive Expression Strategies, Continued Clonal Evolution, and Sub-Clonal Emergences, Despite Genome Stability

The devastating SARS-CoV2 pandemic is worsening with relapsing surges, emerging mutants, and increasing mortalities. Despite enormous efforts, it is not clear how SARS-CoV2 adapts and evolves in a clonal background. Laboratory research is hindered by high biosafety demands. However, the rapid sequence availability opened doors for bioinformatics. Using different bioinformatics programs, we investigated 6305 sequences for clonality, expressions strategies, and evolutionary dynamics. Results showed high nucleotide identity of 99.9% among SARS-CoV2 indicating clonal evolution and genome. High sequence identity and phylogenetic tree concordance were obtained with isolates from different regions. In any given tree topology, ~50% of isolates in a country formed country-specific sub-clusters. However, abundances of subtle overexpression strategies were found including transversions, signature-sequences and slippery-structures. Five different short tracks dominated with identical location patterns in all genomes where Slippery-4 AAGAA was the most abundant. Interestingly, transversion and transition substitutions mostly affected the same amino acid residues implying compensatory changes. To ensure these strategies were independent of sequence clonality, we simultaneously examined sequence homology indicators; tandem-repeats, restriction-site, and 3′UTR, 5′ UTR-caps and stem-loop locations in addition to stringent alignment parameters for 100% identity which all confirmed stability. Nevertheless, two rare events; a rearrangement in two SARS-CoV2 isolates against betacoronavirus ancestor and a polymorphism in S gene, were detected. Thus, we report on abundance of transversions, slippery sequences, and ON/OFF molecular structures, implying adaptive expressions had occurred, despite clonal evolution and genome stability. Furthermore, functional validation of the point mutations would provide insights into mechanisms of SARS-CoV2 virulence and adaptation.

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.